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

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> source("/xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/Correlate_Clinical_Cnvsarms_onlysig.11.3769/CNV2ClinicalAnalysis_nozzle_onlysig.R")
> result <- main("/xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/Correlate_Clinical_Cnvsarms_onlysig.11.3769/", "-nF=/xchip/tcga/Tools/Nozzle/v1.current", "-iD=/xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/159067/broad_values_by_arm.mutsig.cluster.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPickerPipeline/STAD/1669740/1.GDAC_clinicalDataPicker.Finished/STAD.clin.merged.picked.txt", "-fF=ALL", "-fC=3", "-fH=5", "-fW=9", "-fP=OUT", "-cP=1", "-cQ=0.25", "-MF=ONLYSIG", "-oT=STAD", "-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=STAD"
[1] "opt"        "-OP=MUTSIG"
[1] "tl"   "-iT="
[1] "dx"   "-iX="
[1] "opt"    "MUTSIG"
[1] "dx" ""  

nPatients in clinical file=159, in cluster file=161, common to both=158
[1] "Reduce the number of clustering variables from 80 to 73."
[1]  73 158
[1] "1p gain mutation analysis"
[1] 3
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
                3               155 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
                3               155 
[1] "1q gain mutation analysis"
[1] 3
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               19               139 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               19               139 
[1] "2p gain mutation analysis"
[1] 3
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               12               146 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               12               146 
[1] "2q gain mutation analysis"
[1] 3
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               12               146 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               12               146 
[1] "3p gain mutation analysis"
[1] 3
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
                3               155 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
                3               155 
[1] "3q gain mutation analysis"
[1] 3
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               14               144 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               14               144 
[1] "5p gain mutation analysis"
[1] 3
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               26               132 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               26               132 
[1] "5q gain mutation analysis"
[1] 3
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
                5               153 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
                5               153 
[1] "6p gain mutation analysis"
[1] 3
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               13               145 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               13               145 
[1] "6q gain mutation analysis"
[1] 3
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               12               146 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               12               146 
[1] "7p gain mutation analysis"
[1] 3
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               51               107 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               51               107 
[1] "7q gain mutation analysis"
[1] 3
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               45               113 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               45               113 
[1] "8p gain mutation analysis"
[1] 3
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               53               105 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               53               105 
[1] "8q gain mutation analysis"
[1] 3
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               72                86 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               72                86 
[1] "9p gain mutation analysis"
[1] 3
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               11               147 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               11               147 
[1] "9q gain mutation analysis"
[1] 3
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               15               143 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               15               143 
[1] "10p gain mutation analysis"
[1] 3
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                24                134 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                24                134 
[1] "10q gain mutation analysis"
[1] 3
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                10                148 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                10                148 
[1] "11p gain mutation analysis"
[1] 3
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 5                153 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 5                153 
[1] "11q gain mutation analysis"
[1] 3
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 8                150 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 8                150 
[1] "12p gain mutation analysis"
[1] 3
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                17                141 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                17                141 
[1] "12q gain mutation analysis"
[1] 3
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                11                147 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                11                147 
[1] "13q gain mutation analysis"
[1] 3
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                35                123 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                35                123 
[1] "14q gain mutation analysis"
[1] 3
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                 4                154 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                 4                154 
[1] "15q gain mutation analysis"
[1] 3
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                 7                151 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                 7                151 
[1] "16p gain mutation analysis"
[1] 3
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                12                146 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                12                146 
[1] "16q gain mutation analysis"
[1] 3
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                 7                151 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                 7                151 
[1] "17p gain mutation analysis"
[1] 3
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                 5                153 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                 5                153 
[1] "17q gain mutation analysis"
[1] 3
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                10                148 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                10                148 
[1] "18p gain mutation analysis"
[1] 3
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                18                140 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                18                140 
[1] "18q gain mutation analysis"
[1] 3
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 8                150 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 8                150 
[1] "19p gain mutation analysis"
[1] 3
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                10                148 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                10                148 
[1] "19q gain mutation analysis"
[1] 3
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                17                141 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                17                141 
[1] "20p gain mutation analysis"
[1] 3
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                65                 93 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                65                 93 
[1] "20q gain mutation analysis"
[1] 3
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                82                 76 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                82                 76 
[1] "22q gain mutation analysis"
[1] 3
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                 4                154 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                 4                154 
[1] "1p loss mutation analysis"
[1] 3
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
                8               150 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
                8               150 
[1] "1q loss mutation analysis"
[1] 3
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
                4               154 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
                4               154 
[1] "3p loss mutation analysis"
[1] 3
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               11               147 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               11               147 
[1] "3q loss mutation analysis"
[1] 3
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
                7               151 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
                7               151 
[1] "4p loss mutation analysis"
[1] 3
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               23               135 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               23               135 
[1] "4q loss mutation analysis"
[1] 3
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               22               136 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               22               136 
[1] "5p loss mutation analysis"
[1] 3
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
                8               150 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
                8               150 
[1] "5q loss mutation analysis"
[1] 3
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               18               140 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               18               140 
[1] "6p loss mutation analysis"
[1] 3
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
                8               150 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
                8               150 
[1] "6q loss mutation analysis"
[1] 3
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               12               146 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               12               146 
[1] "7p loss mutation analysis"
[1] 3
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
                3               155 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
                3               155 
[1] "7q loss mutation analysis"
[1] 3
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
                5               153 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
                5               153 
[1] "8p loss mutation analysis"
[1] 3
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               13               145 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               13               145 
[1] "8q loss mutation analysis"
[1] 3
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                4               154 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                4               154 
[1] "9p loss mutation analysis"
[1] 3
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               28               130 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               28               130 
[1] "9q loss mutation analysis"
[1] 3
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               12               146 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               12               146 
[1] "10p loss mutation analysis"
[1] 3
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                12                146 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                12                146 
[1] "10q loss mutation analysis"
[1] 3
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                11                147 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                11                147 
[1] "11p loss mutation analysis"
[1] 3
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                13                145 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                13                145 
[1] "11q loss mutation analysis"
[1] 3
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                10                148 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                10                148 
[1] "12p loss mutation analysis"
[1] 3
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                12                146 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                12                146 
[1] "12q loss mutation analysis"
[1] 3
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                 8                150 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                 8                150 
[1] "13q loss mutation analysis"
[1] 3
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                 5                153 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                 5                153 
[1] "14q loss mutation analysis"
[1] 3
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                10                148 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                10                148 
[1] "15q loss mutation analysis"
[1] 3
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                11                147 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                11                147 
[1] "16p loss mutation analysis"
[1] 3
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                10                148 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                10                148 
[1] "16q loss mutation analysis"
[1] 3
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                14                144 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                14                144 
[1] "17p loss mutation analysis"
[1] 3
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                35                123 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                35                123 
[1] "17q loss mutation analysis"
[1] 3
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                 8                150 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                 8                150 
[1] "18p loss mutation analysis"
[1] 3
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                15                143 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                15                143 
[1] "18q loss mutation analysis"
[1] 3
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                29                129 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                29                129 
[1] "19p loss mutation analysis"
[1] 3
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                16                142 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                16                142 
[1] "19q loss mutation analysis"
[1] 3
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                12                146 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                12                146 
[1] "20p loss mutation analysis"
[1] 3
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                 4                154 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                 4                154 
[1] "21q loss mutation analysis"
[1] 3
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                31                127 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                31                127 
[1] "22q loss mutation analysis"
[1] 3
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                24                134 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                24                134 
[1] "Xq loss mutation analysis"
[1] 3
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
                7               151 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
                7               151 
[1] "data2feature, selection=ALL"
 [1] "YEARSTOBIRTH"                          
 [2] "DAYSTODEATH"                           
 [3] "DAYSTOLASTFOLLOWUP"                    
 [4] "VITALSTATUS"                           
 [5] "DCCUPLOADDATE"                         
 [6] "PRIMARYSITEOFDESEASE"                  
 [7] "GENDER"                                
 [8] "DATEOFINITIALPATHOLOGICDIAGNOSIS"      
 [9] "HISTOLOGICALTYPE"                      
[10] "PATHOLOGICSPREAD(PT)"                  
[11] "PATHOLOGICSPREAD(PN)"                  
[12] "PATHOLOGICSPREAD(M)"                   
[13] "TUMORSTAGE"                            
[14] "RADIATIONS.RADIATION.REGIMENINDICATION"
[15] "NEOADJUVANTTHERAPY"                    
[16] "BATCHNUMBER"                           

Input Data has 16 rows and 158 columns.

[1] "Batch" "16"   
[1] "Last Follow UP"
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
         171            3           NA           NA           NA           NA 
TCGA-BR-4190 TCGA-BR-4191 TCGA-BR-4194 TCGA-BR-4195 TCGA-BR-4199 TCGA-BR-4200 
          NA           NA           NA           NA           NA           NA 
TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4259 
          NA           NA           NA           NA           NA           NA 
TCGA-BR-4261 TCGA-BR-4265 TCGA-BR-4267 TCGA-BR-4277 TCGA-BR-4278 TCGA-BR-4279 
          NA           NA           NA           NA           NA           NA 
TCGA-BR-4280 TCGA-BR-4281 TCGA-BR-4284 TCGA-BR-4291 TCGA-BR-4292 TCGA-BR-4294 
          NA           NA           NA           NA           NA           NA 
TCGA-BR-4298 TCGA-BR-4357 TCGA-BR-4361 TCGA-BR-4362 TCGA-BR-4363 TCGA-BR-4366 
          NA           NA           NA           NA           NA           NA 
TCGA-BR-4367 TCGA-BR-4368 TCGA-BR-4369 TCGA-BR-4370 TCGA-BR-4371 TCGA-BR-4375 
          NA           NA           NA           NA           NA           NA 
TCGA-BR-4376 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6454 TCGA-BR-6455 TCGA-BR-6456 
          NA           29           NA           NA           43           NA 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 
          41           41           26           25           19           19 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 
          52           66           30           37           20           34 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
          23           20            8           37           45           14 
TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
          38            4           32           25           21            5 
TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-CD-5798 TCGA-CD-5799 
         138           30           29           21           25           21 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CG-4300 
          11           15            9            2           NA          609 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
          92          822          485           31         1611          245 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4442 TCGA-CG-4443 TCGA-CG-4444 
        1644          122          426           NA          912         1431 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4460 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
         580          366          669           31          273          576 
TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4474 TCGA-CG-4475 TCGA-CG-4476 TCGA-CG-4477 
         215          365           31           NA           NA           31 
TCGA-CG-5716 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
          31          211           31           31           30          182 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5727 
          29         2131          366          457          881          944 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
        1980          122         1674          641          243          263 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
         109          138          298          476          293          249 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
         210           21          181          201          126           51 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-EQ-5647 
         111          143          123           89          130           19 
TCGA-F1-6177 TCGA-F1-6874 TCGA-F1-6875 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7998 
         199           61           NA           12            6          109 
TCGA-HF-7131 TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-7136 TCGA-IN-7806 
          NA           NA           NA           NA           NA          209 
TCGA-IN-7808 TCGA-IP-7968 
         108           77 
Variable 1:'AGE':	nDistinctValues=45,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'DAYSTODEATH':	nDistinctValues=15,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 3:'DAYSTOLASTFOLLOWUP':	nDistinctValues=81,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 5:'DCCUPLOADDAY':	nDistinctValues=3,	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=10,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 9:'HISTOLOGICAL.TYPE':	nDistinctValues=6,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'PATHOLOGY.T':	nDistinctValues=11,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 11:'PATHOLOGY.N':	nDistinctValues=6,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 12:'PATHOLOGICSPREAD(M)':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 13:'TUMOR.STAGE':	nDistinctValues=11,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 14:'RADIATIONS.RADIATION.REGIMENINDICATION':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 15:'NEOADJUVANT.THERAPY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 16:'BATCH.NUMBER':	nDistinctValues=7,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
[1] "AGE"                                   
[2] "GENDER"                                
[3] "HISTOLOGICAL.TYPE"                     
[4] "PATHOLOGY.T"                           
[5] "PATHOLOGY.N"                           
[6] "PATHOLOGICSPREAD(M)"                   
[7] "TUMOR.STAGE"                           
[8] "RADIATIONS.RADIATION.REGIMENINDICATION"
[9] "NEOADJUVANT.THERAPY"                   
[1] "TUMOR.?STAGE" "7"           
[1] "stage2"
vv
 1  2  3  4 
24 37 43 26 
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T" "4"          
[1] "PATHOLOGY.N" "5"          
Output Data has 158 columns, 1 survival variables, and 9 non-survival variables.
AGE, nv=45, binary=FALSE, numeric=TRUE
GENDER, nv=2, binary=FALSE, numeric=FALSE
HISTOLOGICAL.TYPE, nv=6, binary=FALSE, numeric=FALSE
PATHOLOGY.T, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.T',vnm)"
vv
T1 T2 T3 T4 
 6 52 61 18 
[1] "table(vv)"
vv
T1 T2 T3 T4 
 6 52 61 18 
$ClinVariableName
[1] "PATHOLOGY.T"

$Table
vv
T1 T2 T3 T4 
 6 52 61 18 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


T1 T2 T3 T4 
 6 52 61 18 
PATHOLOGY.N, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.N',vnm)"
vv
N0 N1 N2 N3 
44 57 24 15 
[1] "table(vv)"
vv
N0 N1 N2 N3 
44 57 24 15 
$ClinVariableName
[1] "PATHOLOGY.N"

$Table
vv
N0 N1 N2 N3 
44 57 24 15 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


N0 N1 N2 N3 
44 57 24 15 
PATHOLOGICSPREAD(M), nv=3, binary=FALSE, numeric=FALSE
TUMOR.STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('TUMOR.?STAGE',vnm)"
vv
  I  II III  IV 
 24  37  43  26 
[1] "table(vv)"
vv
  I  II III  IV 
 24  37  43  26 
$ClinVariableName
[1] "TUMOR.STAGE"

$Table
vv
  I  II III  IV 
 24  37  43  26 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


  I  II III  IV 
 24  37  43  26 
RADIATIONS.RADIATION.REGIMENINDICATION, nv=2, binary=FALSE, numeric=FALSE
NEOADJUVANT.THERAPY, nv=2, binary=FALSE, numeric=FALSE

Clustering(1) Variable = 1p gain mutation analysis
D1V1, survival
                   sevent
clus2                0  1
  1P GAIN WILD-TYPE 90 15
1P GAIN WILD-TYPE 
              105 
[1] 15
$`1P GAIN WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-6452 TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6458 
        5.62         0.10         0.95         1.41         1.35         1.35 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
        0.85         0.82         0.62         0.62         1.71         2.17 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
        0.99         1.22         0.66         1.12         0.76         0.66 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
        0.26         1.22         1.48         0.46         1.25         0.13 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 
        1.05         0.82         0.69         0.16         4.54         0.99 
TCGA-BR-7901 TCGA-BR-7957 TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
        0.95         0.69         0.82         0.69         0.36         0.49 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
        0.30         0.07        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02        52.96         8.05        54.05         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4460 TCGA-CG-4462 
       29.98        47.05        19.07        12.03        21.99         1.02 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4474 TCGA-CG-4477 
        8.98        18.94         7.07        12.00         1.02         1.02 
TCGA-CG-5716 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
        1.02         6.94         1.02         1.02         0.99         5.98 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5727 
        0.95        70.06        12.03        15.02        28.96        31.04 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        55.04        21.07         7.99         8.65 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
        3.58         4.54         9.80        15.65         9.63         8.19 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
        6.90         0.69         5.95         6.61         4.14         1.68 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-EQ-5647 
        3.65         4.70         4.04         2.93         4.27         0.62 
TCGA-F1-6177 TCGA-F1-6874 TCGA-F1-6875 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7998 
        6.54         2.01        72.23         0.39         0.20         3.58 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IP-7968 
        6.87         3.55         2.53 

1P GAIN WILD-TYPE 
             0.07 
1P GAIN WILD-TYPE 
            72.23 
1P GAIN WILD-TYPE 
             2.93 
[1] "0.1 - 72.2 (2.9)"
       TCGA-B7-5816        TCGA-B7-5818        TCGA-BR-6452        TCGA-BR-6455 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-BR-6457        TCGA-BR-6458        TCGA-BR-6563        TCGA-BR-6564 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-BR-6565        TCGA-BR-6566        TCGA-BR-6705        TCGA-BR-6706 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-BR-6707        TCGA-BR-6709        TCGA-BR-6710        TCGA-BR-6801 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-BR-6802        TCGA-BR-6803        TCGA-BR-6852        TCGA-BR-7196 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-BR-7197        TCGA-BR-7703        TCGA-BR-7704        TCGA-BR-7707 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-BR-7715        TCGA-BR-7716        TCGA-BR-7717        TCGA-BR-7722 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-BR-7723        TCGA-BR-7851        TCGA-BR-7901        TCGA-BR-7957 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CD-5798        TCGA-CD-5799        TCGA-CD-5800        TCGA-CD-5801 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CD-5802        TCGA-CD-5803        TCGA-CG-4300        TCGA-CG-4301 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CG-4304        TCGA-CG-4305        TCGA-CG-4306        TCGA-CG-4436 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CG-4437        TCGA-CG-4438        TCGA-CG-4440        TCGA-CG-4441 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CG-4443        TCGA-CG-4444        TCGA-CG-4449        TCGA-CG-4455 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CG-4460        TCGA-CG-4462        TCGA-CG-4465        TCGA-CG-4466 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CG-4469        TCGA-CG-4472        TCGA-CG-4474        TCGA-CG-4477 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CG-5716        TCGA-CG-5717        TCGA-CG-5718        TCGA-CG-5719 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CG-5720        TCGA-CG-5721        TCGA-CG-5722        TCGA-CG-5723 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CG-5724        TCGA-CG-5725        TCGA-CG-5726        TCGA-CG-5727 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CG-5728        TCGA-CG-5730        TCGA-CG-5732        TCGA-CG-5733 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CG-5734        TCGA-D7-5577        TCGA-D7-5578        TCGA-D7-5579 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-D7-6518        TCGA-D7-6519        TCGA-D7-6520        TCGA-D7-6521 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-D7-6522        TCGA-D7-6524        TCGA-D7-6525        TCGA-D7-6526 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-D7-6527        TCGA-D7-6528        TCGA-D7-6815        TCGA-D7-6817 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-D7-6818        TCGA-D7-6820        TCGA-D7-6822        TCGA-EQ-5647 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875        TCGA-FP-7735 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-FP-7829        TCGA-FP-7998        TCGA-IN-7806        TCGA-IN-7808 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-IP-7968 
"1P GAIN WILD-TYPE" 
       TCGA-B7-5816        TCGA-B7-5818        TCGA-BR-6452        TCGA-BR-6455 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-BR-6457        TCGA-BR-6458        TCGA-BR-6563        TCGA-BR-6564 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-BR-6565        TCGA-BR-6566        TCGA-BR-6705        TCGA-BR-6706 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-BR-6707        TCGA-BR-6709        TCGA-BR-6710        TCGA-BR-6801 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-BR-6802        TCGA-BR-6803        TCGA-BR-6852        TCGA-BR-7196 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-BR-7197        TCGA-BR-7703        TCGA-BR-7704        TCGA-BR-7707 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-BR-7715        TCGA-BR-7716        TCGA-BR-7717        TCGA-BR-7722 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-BR-7723        TCGA-BR-7851        TCGA-BR-7901        TCGA-BR-7957 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CD-5798        TCGA-CD-5799        TCGA-CD-5800        TCGA-CD-5801 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CD-5802        TCGA-CD-5803        TCGA-CG-4300        TCGA-CG-4301 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CG-4304        TCGA-CG-4305        TCGA-CG-4306        TCGA-CG-4436 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CG-4437        TCGA-CG-4438        TCGA-CG-4440        TCGA-CG-4441 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CG-4443        TCGA-CG-4444        TCGA-CG-4449        TCGA-CG-4455 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CG-4460        TCGA-CG-4462        TCGA-CG-4465        TCGA-CG-4466 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CG-4469        TCGA-CG-4472        TCGA-CG-4474        TCGA-CG-4477 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CG-5716        TCGA-CG-5717        TCGA-CG-5718        TCGA-CG-5719 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CG-5720        TCGA-CG-5721        TCGA-CG-5722        TCGA-CG-5723 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CG-5724        TCGA-CG-5725        TCGA-CG-5726        TCGA-CG-5727 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CG-5728        TCGA-CG-5730        TCGA-CG-5732        TCGA-CG-5733 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CG-5734        TCGA-D7-5577        TCGA-D7-5578        TCGA-D7-5579 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-D7-6518        TCGA-D7-6519        TCGA-D7-6520        TCGA-D7-6521 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-D7-6522        TCGA-D7-6524        TCGA-D7-6525        TCGA-D7-6526 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-D7-6527        TCGA-D7-6528        TCGA-D7-6815        TCGA-D7-6817 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-D7-6818        TCGA-D7-6820        TCGA-D7-6822        TCGA-EQ-5647 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875        TCGA-FP-7735 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-FP-7829        TCGA-FP-7998        TCGA-IN-7806        TCGA-IN-7808 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-IP-7968 
"1P GAIN WILD-TYPE" 
       TCGA-B7-5816        TCGA-B7-5818        TCGA-BR-6452        TCGA-BR-6455 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-BR-6457        TCGA-BR-6458        TCGA-BR-6563        TCGA-BR-6564 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-BR-6565        TCGA-BR-6566        TCGA-BR-6705        TCGA-BR-6706 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-BR-6707        TCGA-BR-6709        TCGA-BR-6710        TCGA-BR-6801 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-BR-6802        TCGA-BR-6803        TCGA-BR-6852        TCGA-BR-7196 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-BR-7197        TCGA-BR-7703        TCGA-BR-7704        TCGA-BR-7707 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-BR-7715        TCGA-BR-7716        TCGA-BR-7717        TCGA-BR-7722 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-BR-7723        TCGA-BR-7851        TCGA-BR-7901        TCGA-BR-7957 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CD-5798        TCGA-CD-5799        TCGA-CD-5800        TCGA-CD-5801 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CD-5802        TCGA-CD-5803        TCGA-CG-4300        TCGA-CG-4301 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CG-4304        TCGA-CG-4305        TCGA-CG-4306        TCGA-CG-4436 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CG-4437        TCGA-CG-4438        TCGA-CG-4440        TCGA-CG-4441 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CG-4443        TCGA-CG-4444        TCGA-CG-4449        TCGA-CG-4455 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CG-4460        TCGA-CG-4462        TCGA-CG-4465        TCGA-CG-4466 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CG-4469        TCGA-CG-4472        TCGA-CG-4474        TCGA-CG-4477 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CG-5716        TCGA-CG-5717        TCGA-CG-5718        TCGA-CG-5719 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CG-5720        TCGA-CG-5721        TCGA-CG-5722        TCGA-CG-5723 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CG-5724        TCGA-CG-5725        TCGA-CG-5726        TCGA-CG-5727 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CG-5728        TCGA-CG-5730        TCGA-CG-5732        TCGA-CG-5733 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CG-5734        TCGA-D7-5577        TCGA-D7-5578        TCGA-D7-5579 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-D7-6518        TCGA-D7-6519        TCGA-D7-6520        TCGA-D7-6521 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-D7-6522        TCGA-D7-6524        TCGA-D7-6525        TCGA-D7-6526 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-D7-6527        TCGA-D7-6528        TCGA-D7-6815        TCGA-D7-6817 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-D7-6818        TCGA-D7-6820        TCGA-D7-6822        TCGA-EQ-5647 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875        TCGA-FP-7735 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-FP-7829        TCGA-FP-7998        TCGA-IN-7806        TCGA-IN-7808 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-IP-7968 
"1P GAIN WILD-TYPE" 
D1V2, continuous
D1V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED      1    2
  1P GAIN WILD-TYPE   59   96
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  FEMALE               1                59
  MALE                 2                96
D1V4, multiclass
D1V5, multiclass
[1] "Remove cluster labels:" "1P GAIN MUTATED"       
clus
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
                2               135 
       TCGA-B7-5816        TCGA-B7-5818        TCGA-BR-4183        TCGA-BR-4184 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-BR-4190        TCGA-BR-4201        TCGA-BR-4253        TCGA-BR-4255 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-BR-4277        TCGA-BR-4278        TCGA-BR-4279        TCGA-BR-4280 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-BR-4292        TCGA-BR-4294        TCGA-BR-4298        TCGA-BR-4361 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-BR-4363        TCGA-BR-4368        TCGA-BR-4371        TCGA-BR-4376 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-BR-6452        TCGA-BR-6453        TCGA-BR-6454        TCGA-BR-6455 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-BR-6456        TCGA-BR-6457        TCGA-BR-6458        TCGA-BR-6563 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-BR-6564        TCGA-BR-6565        TCGA-BR-6566        TCGA-BR-6705 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-BR-6706        TCGA-BR-6707        TCGA-BR-6709        TCGA-BR-6710 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-BR-6801        TCGA-BR-6802        TCGA-BR-6803        TCGA-BR-6852 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-BR-7196        TCGA-BR-7197        TCGA-BR-7703        TCGA-BR-7704 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-BR-7707        TCGA-BR-7715        TCGA-BR-7716        TCGA-BR-7717 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-BR-7722        TCGA-BR-7723        TCGA-BR-7851        TCGA-BR-7901 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-BR-7957        TCGA-CD-5798        TCGA-CD-5799        TCGA-CD-5800 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CD-5801        TCGA-CD-5802        TCGA-CD-5803        TCGA-CD-5804 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CG-4300        TCGA-CG-4301        TCGA-CG-4304        TCGA-CG-4305 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CG-4306        TCGA-CG-4436        TCGA-CG-4437        TCGA-CG-4438 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CG-4440        TCGA-CG-4441        TCGA-CG-4442        TCGA-CG-4443 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CG-4444        TCGA-CG-4449        TCGA-CG-4455        TCGA-CG-4460 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CG-4462        TCGA-CG-4465        TCGA-CG-4466        TCGA-CG-4469 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CG-4472        TCGA-CG-4474        TCGA-CG-4475        TCGA-CG-4476 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CG-4477        TCGA-CG-5716        TCGA-CG-5717        TCGA-CG-5718 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CG-5719        TCGA-CG-5720        TCGA-CG-5721        TCGA-CG-5722 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CG-5723        TCGA-CG-5724        TCGA-CG-5725        TCGA-CG-5726 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CG-5727        TCGA-CG-5728        TCGA-CG-5730        TCGA-CG-5732 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CG-5733        TCGA-CG-5734        TCGA-D7-5577        TCGA-D7-5578 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-D7-5579        TCGA-D7-6518        TCGA-D7-6519        TCGA-D7-6520 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-D7-6521        TCGA-D7-6522        TCGA-D7-6524        TCGA-D7-6525 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-D7-6526        TCGA-D7-6527        TCGA-D7-6528        TCGA-D7-6815 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-D7-6817        TCGA-D7-6818        TCGA-D7-6820        TCGA-D7-6822 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-EQ-5647        TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-FP-7735        TCGA-FP-7829        TCGA-FP-7998        TCGA-HF-7131 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-HF-7132        TCGA-HF-7133        TCGA-HF-7134        TCGA-HF-7136 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-IN-7806        TCGA-IN-7808        TCGA-IP-7968 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
D1V6, multiclass
[1] "Remove cluster labels:" "1P GAIN MUTATED"       
clus
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
                1               139 
       TCGA-B7-5816        TCGA-B7-5818        TCGA-BR-4183        TCGA-BR-4184 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-BR-4188        TCGA-BR-4190        TCGA-BR-4191        TCGA-BR-4195 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-BR-4199        TCGA-BR-4200        TCGA-BR-4253        TCGA-BR-4255 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-BR-4256        TCGA-BR-4261        TCGA-BR-4278        TCGA-BR-4279 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-BR-4280        TCGA-BR-4281        TCGA-BR-4298        TCGA-BR-4361 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-BR-4362        TCGA-BR-4367        TCGA-BR-4368        TCGA-BR-4376 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-BR-6452        TCGA-BR-6453        TCGA-BR-6454        TCGA-BR-6455 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-BR-6456        TCGA-BR-6457        TCGA-BR-6458        TCGA-BR-6563 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-BR-6564        TCGA-BR-6565        TCGA-BR-6566        TCGA-BR-6705 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-BR-6706        TCGA-BR-6707        TCGA-BR-6709        TCGA-BR-6710 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-BR-6801        TCGA-BR-6802        TCGA-BR-6803        TCGA-BR-6852 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-BR-7196        TCGA-BR-7197        TCGA-BR-7703        TCGA-BR-7704 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-BR-7707        TCGA-BR-7715        TCGA-BR-7716        TCGA-BR-7717 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-BR-7722        TCGA-BR-7723        TCGA-BR-7851        TCGA-BR-7901 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-BR-7957        TCGA-CD-5798        TCGA-CD-5799        TCGA-CD-5800 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CD-5801        TCGA-CD-5802        TCGA-CD-5803        TCGA-CD-5804 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CG-4300        TCGA-CG-4301        TCGA-CG-4304        TCGA-CG-4305 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CG-4306        TCGA-CG-4436        TCGA-CG-4437        TCGA-CG-4438 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CG-4440        TCGA-CG-4441        TCGA-CG-4442        TCGA-CG-4443 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CG-4444        TCGA-CG-4449        TCGA-CG-4455        TCGA-CG-4460 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CG-4462        TCGA-CG-4465        TCGA-CG-4466        TCGA-CG-4469 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CG-4472        TCGA-CG-4474        TCGA-CG-4475        TCGA-CG-4476 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CG-4477        TCGA-CG-5716        TCGA-CG-5717        TCGA-CG-5718 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CG-5719        TCGA-CG-5720        TCGA-CG-5721        TCGA-CG-5722 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CG-5723        TCGA-CG-5724        TCGA-CG-5725        TCGA-CG-5726 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CG-5727        TCGA-CG-5728        TCGA-CG-5730        TCGA-CG-5732 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CG-5733        TCGA-CG-5734        TCGA-D7-5577        TCGA-D7-5578 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-D7-5579        TCGA-D7-6518        TCGA-D7-6519        TCGA-D7-6520 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-D7-6521        TCGA-D7-6522        TCGA-D7-6524        TCGA-D7-6525 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-D7-6526        TCGA-D7-6527        TCGA-D7-6528        TCGA-D7-6815 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-D7-6817        TCGA-D7-6818        TCGA-D7-6820        TCGA-D7-6822 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-EQ-5647        TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-FP-7735        TCGA-FP-7829        TCGA-FP-7998        TCGA-HF-7131 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-HF-7132        TCGA-HF-7133        TCGA-HF-7134        TCGA-HF-7136 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-IN-7806        TCGA-IN-7808        TCGA-IP-7968 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
D1V7, multiclass
    clus
vv   1P GAIN MUTATED 1P GAIN WILD-TYPE
  M0               2               132
  M1               0                16
  MX               1                 7
D1V8, multiclass
[1] "Remove cluster labels:" "1P GAIN MUTATED"       
clus
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
                1               129 
       TCGA-B7-5816        TCGA-B7-5818        TCGA-BR-4183        TCGA-BR-4184 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-BR-4190        TCGA-BR-4253        TCGA-BR-4255        TCGA-BR-4278 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-BR-4279        TCGA-BR-4280        TCGA-BR-4298        TCGA-BR-4361 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-BR-4368        TCGA-BR-4376        TCGA-BR-6452        TCGA-BR-6453 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-BR-6454        TCGA-BR-6455        TCGA-BR-6456        TCGA-BR-6457 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-BR-6458        TCGA-BR-6563        TCGA-BR-6564        TCGA-BR-6565 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-BR-6566        TCGA-BR-6705        TCGA-BR-6706        TCGA-BR-6707 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-BR-6709        TCGA-BR-6710        TCGA-BR-6801        TCGA-BR-6802 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-BR-6803        TCGA-BR-6852        TCGA-BR-7196        TCGA-BR-7197 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-BR-7703        TCGA-BR-7704        TCGA-BR-7707        TCGA-BR-7715 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-BR-7716        TCGA-BR-7717        TCGA-BR-7722        TCGA-BR-7723 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-BR-7851        TCGA-BR-7901        TCGA-BR-7957        TCGA-CD-5798 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CD-5799        TCGA-CD-5800        TCGA-CD-5801        TCGA-CD-5802 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CD-5803        TCGA-CD-5804        TCGA-CG-4300        TCGA-CG-4301 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CG-4304        TCGA-CG-4305        TCGA-CG-4306        TCGA-CG-4436 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CG-4437        TCGA-CG-4438        TCGA-CG-4440        TCGA-CG-4441 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CG-4442        TCGA-CG-4443        TCGA-CG-4444        TCGA-CG-4449 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CG-4455        TCGA-CG-4460        TCGA-CG-4462        TCGA-CG-4465 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CG-4466        TCGA-CG-4469        TCGA-CG-4472        TCGA-CG-4474 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CG-4475        TCGA-CG-4476        TCGA-CG-4477        TCGA-CG-5716 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CG-5717        TCGA-CG-5718        TCGA-CG-5719        TCGA-CG-5720 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CG-5721        TCGA-CG-5722        TCGA-CG-5723        TCGA-CG-5724 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CG-5725        TCGA-CG-5726        TCGA-CG-5727        TCGA-CG-5728 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CG-5730        TCGA-CG-5732        TCGA-CG-5733        TCGA-CG-5734 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-D7-5577        TCGA-D7-5578        TCGA-D7-5579        TCGA-D7-6518 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-D7-6519        TCGA-D7-6520        TCGA-D7-6521        TCGA-D7-6522 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-D7-6524        TCGA-D7-6525        TCGA-D7-6526        TCGA-D7-6527 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-D7-6528        TCGA-D7-6815        TCGA-D7-6817        TCGA-D7-6818 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-D7-6820        TCGA-D7-6822        TCGA-EQ-5647        TCGA-F1-6177 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-F1-6874        TCGA-F1-6875        TCGA-FP-7735        TCGA-FP-7829 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-FP-7998        TCGA-HF-7131        TCGA-HF-7132        TCGA-HF-7133 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-HF-7134        TCGA-HF-7136        TCGA-IN-7806        TCGA-IN-7808 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-IP-7968 
"1P GAIN WILD-TYPE" 
D1V9, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED      0    3
  1P GAIN WILD-TYPE    5  150
     clus
vv    1P GAIN MUTATED 1P GAIN WILD-TYPE
  NO                0                 5
  YES               3               150
D1V10, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED      0    3
  1P GAIN WILD-TYPE   10  145
     clus
vv    1P GAIN MUTATED 1P GAIN WILD-TYPE
  NO                0                10
  YES               3               145

Clustering(2) Variable = 1q gain mutation analysis
D2V1, survival
                   sevent
clus2                0  1
  1Q GAIN MUTATED    9  3
  1Q GAIN WILD-TYPE 81 12
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               12                93 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
                3                12 
$`1Q GAIN MUTATED`
TCGA-BR-7717 TCGA-BR-7723 TCGA-CG-4460 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6817 
        0.69         4.54        21.99         6.61         4.14         4.70 
TCGA-D7-6818 TCGA-D7-6822 TCGA-EQ-5647 TCGA-F1-6875 TCGA-FP-7735 TCGA-IN-7808 
        4.04         4.27         0.62        72.23         0.39         3.55 

$`1Q GAIN WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-6452 TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6458 
        5.62         0.10         0.95         1.41         1.35         1.35 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
        0.85         0.82         0.62         0.62         1.71         2.17 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
        0.99         1.22         0.66         1.12         0.76         0.66 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
        0.26         1.22         1.48         0.46         1.25         0.13 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7722 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 
        1.05         0.82         0.16         0.99         0.95         0.69 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
        0.82         0.69         0.36         0.49         0.30         0.07 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02        52.96 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 
        8.05        54.05         4.01        14.01        29.98        47.05 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         1.02         8.98        18.94         7.07 
TCGA-CG-4472 TCGA-CG-4474 TCGA-CG-4477 TCGA-CG-5716 TCGA-CG-5717 TCGA-CG-5718 
       12.00         1.02         1.02         1.02         6.94         1.02 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
        1.02         0.99         5.98         0.95        70.06        12.03 
TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       15.02        28.96        31.04        65.10         4.01        55.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99         8.65         3.58         4.54         9.80 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       15.65         9.63         8.19         6.90         0.69         5.95 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6820 TCGA-F1-6177 TCGA-F1-6874 TCGA-FP-7829 
        1.68         3.65         2.93         6.54         2.01         0.20 
TCGA-FP-7998 TCGA-IN-7806 TCGA-IP-7968 
        3.58         6.87         2.53 

  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
             0.39              0.07 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
            72.23             70.06 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
            4.205             2.010 
[1] "0.4 - 72.2 (4.2)" "0.1 - 70.1 (2.0)"
       TCGA-B7-5816        TCGA-B7-5818        TCGA-BR-6452        TCGA-BR-6455 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-BR-6457        TCGA-BR-6458        TCGA-BR-6563        TCGA-BR-6564 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-BR-6565        TCGA-BR-6566        TCGA-BR-6705        TCGA-BR-6706 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-BR-6707        TCGA-BR-6709        TCGA-BR-6710        TCGA-BR-6801 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-BR-6802        TCGA-BR-6803        TCGA-BR-6852        TCGA-BR-7196 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-BR-7197        TCGA-BR-7703        TCGA-BR-7704        TCGA-BR-7707 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-BR-7715        TCGA-BR-7716        TCGA-BR-7717        TCGA-BR-7722 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" 
       TCGA-BR-7723        TCGA-BR-7851        TCGA-BR-7901        TCGA-BR-7957 
  "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-CD-5798        TCGA-CD-5799        TCGA-CD-5800        TCGA-CD-5801 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-CD-5802        TCGA-CD-5803        TCGA-CG-4300        TCGA-CG-4301 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-CG-4304        TCGA-CG-4305        TCGA-CG-4306        TCGA-CG-4436 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-CG-4437        TCGA-CG-4438        TCGA-CG-4440        TCGA-CG-4441 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-CG-4443        TCGA-CG-4444        TCGA-CG-4449        TCGA-CG-4455 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-CG-4460        TCGA-CG-4462        TCGA-CG-4465        TCGA-CG-4466 
  "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-CG-4469        TCGA-CG-4472        TCGA-CG-4474        TCGA-CG-4477 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-CG-5716        TCGA-CG-5717        TCGA-CG-5718        TCGA-CG-5719 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-CG-5720        TCGA-CG-5721        TCGA-CG-5722        TCGA-CG-5723 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-CG-5724        TCGA-CG-5725        TCGA-CG-5726        TCGA-CG-5727 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-CG-5728        TCGA-CG-5730        TCGA-CG-5732        TCGA-CG-5733 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-CG-5734        TCGA-D7-5577        TCGA-D7-5578        TCGA-D7-5579 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-D7-6518        TCGA-D7-6519        TCGA-D7-6520        TCGA-D7-6521 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-D7-6522        TCGA-D7-6524        TCGA-D7-6525        TCGA-D7-6526 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" 
       TCGA-D7-6527        TCGA-D7-6528        TCGA-D7-6815        TCGA-D7-6817 
  "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" 
       TCGA-D7-6818        TCGA-D7-6820        TCGA-D7-6822        TCGA-EQ-5647 
  "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED" 
       TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875        TCGA-FP-7735 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED" 
       TCGA-FP-7829        TCGA-FP-7998        TCGA-IN-7806        TCGA-IN-7808 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" 
       TCGA-IP-7968 
"1Q GAIN WILD-TYPE" 
       TCGA-B7-5816        TCGA-B7-5818        TCGA-BR-6452        TCGA-BR-6455 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-BR-6457        TCGA-BR-6458        TCGA-BR-6563        TCGA-BR-6564 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-BR-6565        TCGA-BR-6566        TCGA-BR-6705        TCGA-BR-6706 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-BR-6707        TCGA-BR-6709        TCGA-BR-6710        TCGA-BR-6801 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-BR-6802        TCGA-BR-6803        TCGA-BR-6852        TCGA-BR-7196 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-BR-7197        TCGA-BR-7703        TCGA-BR-7704        TCGA-BR-7707 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-BR-7715        TCGA-BR-7716        TCGA-BR-7717        TCGA-BR-7722 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" 
       TCGA-BR-7723        TCGA-BR-7851        TCGA-BR-7901        TCGA-BR-7957 
  "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-CD-5798        TCGA-CD-5799        TCGA-CD-5800        TCGA-CD-5801 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-CD-5802        TCGA-CD-5803        TCGA-CG-4300        TCGA-CG-4301 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-CG-4304        TCGA-CG-4305        TCGA-CG-4306        TCGA-CG-4436 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-CG-4437        TCGA-CG-4438        TCGA-CG-4440        TCGA-CG-4441 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-CG-4443        TCGA-CG-4444        TCGA-CG-4449        TCGA-CG-4455 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-CG-4460        TCGA-CG-4462        TCGA-CG-4465        TCGA-CG-4466 
  "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-CG-4469        TCGA-CG-4472        TCGA-CG-4474        TCGA-CG-4477 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-CG-5716        TCGA-CG-5717        TCGA-CG-5718        TCGA-CG-5719 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-CG-5720        TCGA-CG-5721        TCGA-CG-5722        TCGA-CG-5723 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-CG-5724        TCGA-CG-5725        TCGA-CG-5726        TCGA-CG-5727 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-CG-5728        TCGA-CG-5730        TCGA-CG-5732        TCGA-CG-5733 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-CG-5734        TCGA-D7-5577        TCGA-D7-5578        TCGA-D7-5579 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-D7-6518        TCGA-D7-6519        TCGA-D7-6520        TCGA-D7-6521 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-D7-6522        TCGA-D7-6524        TCGA-D7-6525        TCGA-D7-6526 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" 
       TCGA-D7-6527        TCGA-D7-6528        TCGA-D7-6815        TCGA-D7-6817 
  "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" 
       TCGA-D7-6818        TCGA-D7-6820        TCGA-D7-6822        TCGA-EQ-5647 
  "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED" 
       TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875        TCGA-FP-7735 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED" 
       TCGA-FP-7829        TCGA-FP-7998        TCGA-IN-7806        TCGA-IN-7808 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" 
       TCGA-IP-7968 
"1Q GAIN WILD-TYPE" 
       TCGA-B7-5816        TCGA-B7-5818        TCGA-BR-6452        TCGA-BR-6455 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-BR-6457        TCGA-BR-6458        TCGA-BR-6563        TCGA-BR-6564 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-BR-6565        TCGA-BR-6566        TCGA-BR-6705        TCGA-BR-6706 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-BR-6707        TCGA-BR-6709        TCGA-BR-6710        TCGA-BR-6801 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-BR-6802        TCGA-BR-6803        TCGA-BR-6852        TCGA-BR-7196 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-BR-7197        TCGA-BR-7703        TCGA-BR-7704        TCGA-BR-7707 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-BR-7715        TCGA-BR-7716        TCGA-BR-7717        TCGA-BR-7722 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" 
       TCGA-BR-7723        TCGA-BR-7851        TCGA-BR-7901        TCGA-BR-7957 
  "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-CD-5798        TCGA-CD-5799        TCGA-CD-5800        TCGA-CD-5801 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-CD-5802        TCGA-CD-5803        TCGA-CG-4300        TCGA-CG-4301 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-CG-4304        TCGA-CG-4305        TCGA-CG-4306        TCGA-CG-4436 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-CG-4437        TCGA-CG-4438        TCGA-CG-4440        TCGA-CG-4441 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-CG-4443        TCGA-CG-4444        TCGA-CG-4449        TCGA-CG-4455 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-CG-4460        TCGA-CG-4462        TCGA-CG-4465        TCGA-CG-4466 
  "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-CG-4469        TCGA-CG-4472        TCGA-CG-4474        TCGA-CG-4477 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-CG-5716        TCGA-CG-5717        TCGA-CG-5718        TCGA-CG-5719 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-CG-5720        TCGA-CG-5721        TCGA-CG-5722        TCGA-CG-5723 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-CG-5724        TCGA-CG-5725        TCGA-CG-5726        TCGA-CG-5727 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-CG-5728        TCGA-CG-5730        TCGA-CG-5732        TCGA-CG-5733 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-CG-5734        TCGA-D7-5577        TCGA-D7-5578        TCGA-D7-5579 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-D7-6518        TCGA-D7-6519        TCGA-D7-6520        TCGA-D7-6521 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-D7-6522        TCGA-D7-6524        TCGA-D7-6525        TCGA-D7-6526 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" 
       TCGA-D7-6527        TCGA-D7-6528        TCGA-D7-6815        TCGA-D7-6817 
  "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" 
       TCGA-D7-6818        TCGA-D7-6820        TCGA-D7-6822        TCGA-EQ-5647 
  "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED" 
       TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875        TCGA-FP-7735 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED" 
       TCGA-FP-7829        TCGA-FP-7998        TCGA-IN-7806        TCGA-IN-7808 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" 
       TCGA-IP-7968 
"1Q GAIN WILD-TYPE" 
[1] "hr=" "1.4"
D2V2, continuous
D2V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED      6   13
  1Q GAIN WILD-TYPE   54   85
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  FEMALE               6                54
  MALE                13                85
D2V4, multiclass
D2V5, multiclass
    clus
vv   1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  T1               1                 5
  T2               8                44
  T3               5                56
  T4               3                15
D2V6, multiclass
    clus
vv   1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  N0               6                38
  N1               3                54
  N2               2                22
  N3               4                11
D2V7, multiclass
    clus
vv   1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  M0              14               120
  M1               3                13
  MX               2                 6
D2V8, multiclass
     clus
vv    1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  I                 5                19
  II                3                34
  III               3                40
  IV                4                22
D2V9, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED      2   17
  1Q GAIN WILD-TYPE    3  136
     clus
vv    1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  NO                2                 3
  YES              17               136
D2V10, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED      3   16
  1Q GAIN WILD-TYPE    7  132
     clus
vv    1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  NO                3                 7
  YES              16               132

Clustering(3) Variable = 2p gain mutation analysis
D3V1, survival
                   sevent
clus2                0  1
  2P GAIN MUTATED    9  1
  2P GAIN WILD-TYPE 81 14
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               10                95 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
                1                14 
$`2P GAIN MUTATED`
TCGA-BR-7197 TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7717 TCGA-CD-5801 TCGA-CD-5802 
        1.48         1.25         1.05         0.69         0.49         0.30 
TCGA-CG-4460 TCGA-CG-4472 TCGA-CG-5718 TCGA-CG-5727 
       21.99        12.00         1.02        31.04 

$`2P GAIN WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-6452 TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6458 
        5.62         0.10         0.95         1.41         1.35         1.35 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
        0.85         0.82         0.62         0.62         1.71         2.17 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
        0.99         1.22         0.66         1.12         0.76         0.66 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7716 TCGA-BR-7722 
        0.26         1.22         0.46         0.13         0.82         0.16 
TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-CD-5798 TCGA-CD-5799 
        4.54         0.99         0.95         0.69         0.82         0.69 
TCGA-CD-5800 TCGA-CD-5803 TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
        0.36         0.07        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02        52.96         8.05        54.05         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       29.98        47.05        19.07        12.03         1.02         8.98 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4474 TCGA-CG-4477 TCGA-CG-5716 TCGA-CG-5717 
       18.94         7.07         1.02         1.02         1.02         6.94 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
        1.02         0.99         5.98         0.95        70.06        12.03 
TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       15.02        28.96        65.10         4.01        55.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99         8.65         3.58         4.54         9.80        15.65 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
        9.63         8.19         6.90         0.69         5.95         6.61 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
        4.14         1.68         3.65         4.70         4.04         2.93 
TCGA-D7-6822 TCGA-EQ-5647 TCGA-F1-6177 TCGA-F1-6874 TCGA-F1-6875 TCGA-FP-7735 
        4.27         0.62         6.54         2.01        72.23         0.39 
TCGA-FP-7829 TCGA-FP-7998 TCGA-IN-7806 TCGA-IN-7808 TCGA-IP-7968 
        0.20         3.58         6.87         3.55         2.53 

  2P GAIN MUTATED 2P GAIN WILD-TYPE 
             0.30              0.07 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
            31.04             72.23 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
             1.15              3.55 
[1] "0.3 - 31.0 (1.1)" "0.1 - 72.2 (3.5)"
       TCGA-B7-5816        TCGA-B7-5818        TCGA-BR-6452        TCGA-BR-6455 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-BR-6457        TCGA-BR-6458        TCGA-BR-6563        TCGA-BR-6564 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-BR-6565        TCGA-BR-6566        TCGA-BR-6705        TCGA-BR-6706 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-BR-6707        TCGA-BR-6709        TCGA-BR-6710        TCGA-BR-6801 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-BR-6802        TCGA-BR-6803        TCGA-BR-6852        TCGA-BR-7196 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-BR-7197        TCGA-BR-7703        TCGA-BR-7704        TCGA-BR-7707 
  "2P GAIN MUTATED" "2P GAIN WILD-TYPE"   "2P GAIN MUTATED" "2P GAIN WILD-TYPE" 
       TCGA-BR-7715        TCGA-BR-7716        TCGA-BR-7717        TCGA-BR-7722 
  "2P GAIN MUTATED" "2P GAIN WILD-TYPE"   "2P GAIN MUTATED" "2P GAIN WILD-TYPE" 
       TCGA-BR-7723        TCGA-BR-7851        TCGA-BR-7901        TCGA-BR-7957 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-CD-5798        TCGA-CD-5799        TCGA-CD-5800        TCGA-CD-5801 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE"   "2P GAIN MUTATED" 
       TCGA-CD-5802        TCGA-CD-5803        TCGA-CG-4300        TCGA-CG-4301 
  "2P GAIN MUTATED" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-CG-4304        TCGA-CG-4305        TCGA-CG-4306        TCGA-CG-4436 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-CG-4437        TCGA-CG-4438        TCGA-CG-4440        TCGA-CG-4441 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-CG-4443        TCGA-CG-4444        TCGA-CG-4449        TCGA-CG-4455 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-CG-4460        TCGA-CG-4462        TCGA-CG-4465        TCGA-CG-4466 
  "2P GAIN MUTATED" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-CG-4469        TCGA-CG-4472        TCGA-CG-4474        TCGA-CG-4477 
"2P GAIN WILD-TYPE"   "2P GAIN MUTATED" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-CG-5716        TCGA-CG-5717        TCGA-CG-5718        TCGA-CG-5719 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE"   "2P GAIN MUTATED" "2P GAIN WILD-TYPE" 
       TCGA-CG-5720        TCGA-CG-5721        TCGA-CG-5722        TCGA-CG-5723 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-CG-5724        TCGA-CG-5725        TCGA-CG-5726        TCGA-CG-5727 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE"   "2P GAIN MUTATED" 
       TCGA-CG-5728        TCGA-CG-5730        TCGA-CG-5732        TCGA-CG-5733 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-CG-5734        TCGA-D7-5577        TCGA-D7-5578        TCGA-D7-5579 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-D7-6518        TCGA-D7-6519        TCGA-D7-6520        TCGA-D7-6521 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-D7-6522        TCGA-D7-6524        TCGA-D7-6525        TCGA-D7-6526 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-D7-6527        TCGA-D7-6528        TCGA-D7-6815        TCGA-D7-6817 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-D7-6818        TCGA-D7-6820        TCGA-D7-6822        TCGA-EQ-5647 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875        TCGA-FP-7735 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-FP-7829        TCGA-FP-7998        TCGA-IN-7806        TCGA-IN-7808 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-IP-7968 
"2P GAIN WILD-TYPE" 
       TCGA-B7-5816        TCGA-B7-5818        TCGA-BR-6452        TCGA-BR-6455 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-BR-6457        TCGA-BR-6458        TCGA-BR-6563        TCGA-BR-6564 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-BR-6565        TCGA-BR-6566        TCGA-BR-6705        TCGA-BR-6706 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-BR-6707        TCGA-BR-6709        TCGA-BR-6710        TCGA-BR-6801 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-BR-6802        TCGA-BR-6803        TCGA-BR-6852        TCGA-BR-7196 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-BR-7197        TCGA-BR-7703        TCGA-BR-7704        TCGA-BR-7707 
  "2P GAIN MUTATED" "2P GAIN WILD-TYPE"   "2P GAIN MUTATED" "2P GAIN WILD-TYPE" 
       TCGA-BR-7715        TCGA-BR-7716        TCGA-BR-7717        TCGA-BR-7722 
  "2P GAIN MUTATED" "2P GAIN WILD-TYPE"   "2P GAIN MUTATED" "2P GAIN WILD-TYPE" 
       TCGA-BR-7723        TCGA-BR-7851        TCGA-BR-7901        TCGA-BR-7957 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-CD-5798        TCGA-CD-5799        TCGA-CD-5800        TCGA-CD-5801 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE"   "2P GAIN MUTATED" 
       TCGA-CD-5802        TCGA-CD-5803        TCGA-CG-4300        TCGA-CG-4301 
  "2P GAIN MUTATED" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-CG-4304        TCGA-CG-4305        TCGA-CG-4306        TCGA-CG-4436 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-CG-4437        TCGA-CG-4438        TCGA-CG-4440        TCGA-CG-4441 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-CG-4443        TCGA-CG-4444        TCGA-CG-4449        TCGA-CG-4455 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-CG-4460        TCGA-CG-4462        TCGA-CG-4465        TCGA-CG-4466 
  "2P GAIN MUTATED" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-CG-4469        TCGA-CG-4472        TCGA-CG-4474        TCGA-CG-4477 
"2P GAIN WILD-TYPE"   "2P GAIN MUTATED" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-CG-5716        TCGA-CG-5717        TCGA-CG-5718        TCGA-CG-5719 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE"   "2P GAIN MUTATED" "2P GAIN WILD-TYPE" 
       TCGA-CG-5720        TCGA-CG-5721        TCGA-CG-5722        TCGA-CG-5723 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-CG-5724        TCGA-CG-5725        TCGA-CG-5726        TCGA-CG-5727 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE"   "2P GAIN MUTATED" 
       TCGA-CG-5728        TCGA-CG-5730        TCGA-CG-5732        TCGA-CG-5733 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-CG-5734        TCGA-D7-5577        TCGA-D7-5578        TCGA-D7-5579 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-D7-6518        TCGA-D7-6519        TCGA-D7-6520        TCGA-D7-6521 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-D7-6522        TCGA-D7-6524        TCGA-D7-6525        TCGA-D7-6526 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-D7-6527        TCGA-D7-6528        TCGA-D7-6815        TCGA-D7-6817 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-D7-6818        TCGA-D7-6820        TCGA-D7-6822        TCGA-EQ-5647 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875        TCGA-FP-7735 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-FP-7829        TCGA-FP-7998        TCGA-IN-7806        TCGA-IN-7808 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-IP-7968 
"2P GAIN WILD-TYPE" 
       TCGA-B7-5816        TCGA-B7-5818        TCGA-BR-6452        TCGA-BR-6455 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-BR-6457        TCGA-BR-6458        TCGA-BR-6563        TCGA-BR-6564 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-BR-6565        TCGA-BR-6566        TCGA-BR-6705        TCGA-BR-6706 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-BR-6707        TCGA-BR-6709        TCGA-BR-6710        TCGA-BR-6801 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-BR-6802        TCGA-BR-6803        TCGA-BR-6852        TCGA-BR-7196 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-BR-7197        TCGA-BR-7703        TCGA-BR-7704        TCGA-BR-7707 
  "2P GAIN MUTATED" "2P GAIN WILD-TYPE"   "2P GAIN MUTATED" "2P GAIN WILD-TYPE" 
       TCGA-BR-7715        TCGA-BR-7716        TCGA-BR-7717        TCGA-BR-7722 
  "2P GAIN MUTATED" "2P GAIN WILD-TYPE"   "2P GAIN MUTATED" "2P GAIN WILD-TYPE" 
       TCGA-BR-7723        TCGA-BR-7851        TCGA-BR-7901        TCGA-BR-7957 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-CD-5798        TCGA-CD-5799        TCGA-CD-5800        TCGA-CD-5801 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE"   "2P GAIN MUTATED" 
       TCGA-CD-5802        TCGA-CD-5803        TCGA-CG-4300        TCGA-CG-4301 
  "2P GAIN MUTATED" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-CG-4304        TCGA-CG-4305        TCGA-CG-4306        TCGA-CG-4436 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-CG-4437        TCGA-CG-4438        TCGA-CG-4440        TCGA-CG-4441 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-CG-4443        TCGA-CG-4444        TCGA-CG-4449        TCGA-CG-4455 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-CG-4460        TCGA-CG-4462        TCGA-CG-4465        TCGA-CG-4466 
  "2P GAIN MUTATED" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-CG-4469        TCGA-CG-4472        TCGA-CG-4474        TCGA-CG-4477 
"2P GAIN WILD-TYPE"   "2P GAIN MUTATED" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-CG-5716        TCGA-CG-5717        TCGA-CG-5718        TCGA-CG-5719 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE"   "2P GAIN MUTATED" "2P GAIN WILD-TYPE" 
       TCGA-CG-5720        TCGA-CG-5721        TCGA-CG-5722        TCGA-CG-5723 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-CG-5724        TCGA-CG-5725        TCGA-CG-5726        TCGA-CG-5727 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE"   "2P GAIN MUTATED" 
       TCGA-CG-5728        TCGA-CG-5730        TCGA-CG-5732        TCGA-CG-5733 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-CG-5734        TCGA-D7-5577        TCGA-D7-5578        TCGA-D7-5579 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-D7-6518        TCGA-D7-6519        TCGA-D7-6520        TCGA-D7-6521 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-D7-6522        TCGA-D7-6524        TCGA-D7-6525        TCGA-D7-6526 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-D7-6527        TCGA-D7-6528        TCGA-D7-6815        TCGA-D7-6817 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-D7-6818        TCGA-D7-6820        TCGA-D7-6822        TCGA-EQ-5647 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875        TCGA-FP-7735 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-FP-7829        TCGA-FP-7998        TCGA-IN-7806        TCGA-IN-7808 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-IP-7968 
"2P GAIN WILD-TYPE" 
[1] "hr=" "1.5"
D3V2, continuous
D3V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED      4    8
  2P GAIN WILD-TYPE   56   90
        clus
vv       2P GAIN MUTATED 2P GAIN WILD-TYPE
  FEMALE               4                56
  MALE                 8                90
D3V4, multiclass
D3V5, multiclass
    clus
vv   2P GAIN MUTATED 2P GAIN WILD-TYPE
  T1               0                 6
  T2               1                51
  T3               6                55
  T4               3                15
D3V6, multiclass
    clus
vv   2P GAIN MUTATED 2P GAIN WILD-TYPE
  N0               5                39
  N1               5                52
  N2               0                24
  N3               0                15
D3V7, multiclass
    clus
vv   2P GAIN MUTATED 2P GAIN WILD-TYPE
  M0              11               123
  M1               1                15
  MX               0                 8
D3V8, multiclass
     clus
vv    2P GAIN MUTATED 2P GAIN WILD-TYPE
  I                 0                24
  II                6                31
  III               1                42
  IV                3                23
D3V9, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED      0   12
  2P GAIN WILD-TYPE    5  141
     clus
vv    2P GAIN MUTATED 2P GAIN WILD-TYPE
  NO                0                 5
  YES              12               141
D3V10, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED      0   12
  2P GAIN WILD-TYPE   10  136
     clus
vv    2P GAIN MUTATED 2P GAIN WILD-TYPE
  NO                0                10
  YES              12               136

Clustering(4) Variable = 2q gain mutation analysis
D4V1, survival
                   sevent
clus2                0  1
  2Q GAIN MUTATED    8  2
  2Q GAIN WILD-TYPE 82 13
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               10                95 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
                2                13 
$`2Q GAIN MUTATED`
TCGA-BR-7197 TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7717 TCGA-CD-5801 TCGA-CG-4460 
        1.48         1.25         1.05         0.69         0.49        21.99 
TCGA-CG-4472 TCGA-CG-5718 TCGA-CG-5727 TCGA-F1-6875 
       12.00         1.02        31.04        72.23 

$`2Q GAIN WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-6452 TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6458 
        5.62         0.10         0.95         1.41         1.35         1.35 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
        0.85         0.82         0.62         0.62         1.71         2.17 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
        0.99         1.22         0.66         1.12         0.76         0.66 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7716 TCGA-BR-7722 
        0.26         1.22         0.46         0.13         0.82         0.16 
TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-CD-5798 TCGA-CD-5799 
        4.54         0.99         0.95         0.69         0.82         0.69 
TCGA-CD-5800 TCGA-CD-5802 TCGA-CD-5803 TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
        0.36         0.30         0.07        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02        52.96         8.05        54.05         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
       14.01        29.98        47.05        19.07        12.03         1.02 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4474 TCGA-CG-4477 TCGA-CG-5716 
        8.98        18.94         7.07         1.02         1.02         1.02 
TCGA-CG-5717 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
        6.94         1.02         0.99         5.98         0.95        70.06 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        15.02        28.96        65.10         4.01        55.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99         8.65         3.58         4.54         9.80 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       15.65         9.63         8.19         6.90         0.69         5.95 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
        6.61         4.14         1.68         3.65         4.70         4.04 
TCGA-D7-6820 TCGA-D7-6822 TCGA-EQ-5647 TCGA-F1-6177 TCGA-F1-6874 TCGA-FP-7735 
        2.93         4.27         0.62         6.54         2.01         0.39 
TCGA-FP-7829 TCGA-FP-7998 TCGA-IN-7806 TCGA-IN-7808 TCGA-IP-7968 
        0.20         3.58         6.87         3.55         2.53 

  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
             0.49              0.07 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
            72.23             70.06 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
            1.365             3.020 
[1] "0.5 - 72.2 (1.4)" "0.1 - 70.1 (3.0)"
       TCGA-B7-5816        TCGA-B7-5818        TCGA-BR-6452        TCGA-BR-6455 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-BR-6457        TCGA-BR-6458        TCGA-BR-6563        TCGA-BR-6564 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-BR-6565        TCGA-BR-6566        TCGA-BR-6705        TCGA-BR-6706 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-BR-6707        TCGA-BR-6709        TCGA-BR-6710        TCGA-BR-6801 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-BR-6802        TCGA-BR-6803        TCGA-BR-6852        TCGA-BR-7196 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-BR-7197        TCGA-BR-7703        TCGA-BR-7704        TCGA-BR-7707 
  "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" 
       TCGA-BR-7715        TCGA-BR-7716        TCGA-BR-7717        TCGA-BR-7722 
  "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" 
       TCGA-BR-7723        TCGA-BR-7851        TCGA-BR-7901        TCGA-BR-7957 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-CD-5798        TCGA-CD-5799        TCGA-CD-5800        TCGA-CD-5801 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" 
       TCGA-CD-5802        TCGA-CD-5803        TCGA-CG-4300        TCGA-CG-4301 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-CG-4304        TCGA-CG-4305        TCGA-CG-4306        TCGA-CG-4436 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-CG-4437        TCGA-CG-4438        TCGA-CG-4440        TCGA-CG-4441 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-CG-4443        TCGA-CG-4444        TCGA-CG-4449        TCGA-CG-4455 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-CG-4460        TCGA-CG-4462        TCGA-CG-4465        TCGA-CG-4466 
  "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-CG-4469        TCGA-CG-4472        TCGA-CG-4474        TCGA-CG-4477 
"2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-CG-5716        TCGA-CG-5717        TCGA-CG-5718        TCGA-CG-5719 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" 
       TCGA-CG-5720        TCGA-CG-5721        TCGA-CG-5722        TCGA-CG-5723 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-CG-5724        TCGA-CG-5725        TCGA-CG-5726        TCGA-CG-5727 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" 
       TCGA-CG-5728        TCGA-CG-5730        TCGA-CG-5732        TCGA-CG-5733 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-CG-5734        TCGA-D7-5577        TCGA-D7-5578        TCGA-D7-5579 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-D7-6518        TCGA-D7-6519        TCGA-D7-6520        TCGA-D7-6521 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-D7-6522        TCGA-D7-6524        TCGA-D7-6525        TCGA-D7-6526 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-D7-6527        TCGA-D7-6528        TCGA-D7-6815        TCGA-D7-6817 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-D7-6818        TCGA-D7-6820        TCGA-D7-6822        TCGA-EQ-5647 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875        TCGA-FP-7735 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" 
       TCGA-FP-7829        TCGA-FP-7998        TCGA-IN-7806        TCGA-IN-7808 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-IP-7968 
"2Q GAIN WILD-TYPE" 
       TCGA-B7-5816        TCGA-B7-5818        TCGA-BR-6452        TCGA-BR-6455 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-BR-6457        TCGA-BR-6458        TCGA-BR-6563        TCGA-BR-6564 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-BR-6565        TCGA-BR-6566        TCGA-BR-6705        TCGA-BR-6706 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-BR-6707        TCGA-BR-6709        TCGA-BR-6710        TCGA-BR-6801 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-BR-6802        TCGA-BR-6803        TCGA-BR-6852        TCGA-BR-7196 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-BR-7197        TCGA-BR-7703        TCGA-BR-7704        TCGA-BR-7707 
  "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" 
       TCGA-BR-7715        TCGA-BR-7716        TCGA-BR-7717        TCGA-BR-7722 
  "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" 
       TCGA-BR-7723        TCGA-BR-7851        TCGA-BR-7901        TCGA-BR-7957 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-CD-5798        TCGA-CD-5799        TCGA-CD-5800        TCGA-CD-5801 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" 
       TCGA-CD-5802        TCGA-CD-5803        TCGA-CG-4300        TCGA-CG-4301 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-CG-4304        TCGA-CG-4305        TCGA-CG-4306        TCGA-CG-4436 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-CG-4437        TCGA-CG-4438        TCGA-CG-4440        TCGA-CG-4441 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-CG-4443        TCGA-CG-4444        TCGA-CG-4449        TCGA-CG-4455 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-CG-4460        TCGA-CG-4462        TCGA-CG-4465        TCGA-CG-4466 
  "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-CG-4469        TCGA-CG-4472        TCGA-CG-4474        TCGA-CG-4477 
"2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-CG-5716        TCGA-CG-5717        TCGA-CG-5718        TCGA-CG-5719 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" 
       TCGA-CG-5720        TCGA-CG-5721        TCGA-CG-5722        TCGA-CG-5723 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-CG-5724        TCGA-CG-5725        TCGA-CG-5726        TCGA-CG-5727 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" 
       TCGA-CG-5728        TCGA-CG-5730        TCGA-CG-5732        TCGA-CG-5733 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-CG-5734        TCGA-D7-5577        TCGA-D7-5578        TCGA-D7-5579 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-D7-6518        TCGA-D7-6519        TCGA-D7-6520        TCGA-D7-6521 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-D7-6522        TCGA-D7-6524        TCGA-D7-6525        TCGA-D7-6526 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-D7-6527        TCGA-D7-6528        TCGA-D7-6815        TCGA-D7-6817 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-D7-6818        TCGA-D7-6820        TCGA-D7-6822        TCGA-EQ-5647 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875        TCGA-FP-7735 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" 
       TCGA-FP-7829        TCGA-FP-7998        TCGA-IN-7806        TCGA-IN-7808 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-IP-7968 
"2Q GAIN WILD-TYPE" 
       TCGA-B7-5816        TCGA-B7-5818        TCGA-BR-6452        TCGA-BR-6455 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-BR-6457        TCGA-BR-6458        TCGA-BR-6563        TCGA-BR-6564 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-BR-6565        TCGA-BR-6566        TCGA-BR-6705        TCGA-BR-6706 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-BR-6707        TCGA-BR-6709        TCGA-BR-6710        TCGA-BR-6801 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-BR-6802        TCGA-BR-6803        TCGA-BR-6852        TCGA-BR-7196 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-BR-7197        TCGA-BR-7703        TCGA-BR-7704        TCGA-BR-7707 
  "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" 
       TCGA-BR-7715        TCGA-BR-7716        TCGA-BR-7717        TCGA-BR-7722 
  "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" 
       TCGA-BR-7723        TCGA-BR-7851        TCGA-BR-7901        TCGA-BR-7957 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-CD-5798        TCGA-CD-5799        TCGA-CD-5800        TCGA-CD-5801 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" 
       TCGA-CD-5802        TCGA-CD-5803        TCGA-CG-4300        TCGA-CG-4301 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-CG-4304        TCGA-CG-4305        TCGA-CG-4306        TCGA-CG-4436 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-CG-4437        TCGA-CG-4438        TCGA-CG-4440        TCGA-CG-4441 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-CG-4443        TCGA-CG-4444        TCGA-CG-4449        TCGA-CG-4455 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-CG-4460        TCGA-CG-4462        TCGA-CG-4465        TCGA-CG-4466 
  "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-CG-4469        TCGA-CG-4472        TCGA-CG-4474        TCGA-CG-4477 
"2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-CG-5716        TCGA-CG-5717        TCGA-CG-5718        TCGA-CG-5719 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" 
       TCGA-CG-5720        TCGA-CG-5721        TCGA-CG-5722        TCGA-CG-5723 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-CG-5724        TCGA-CG-5725        TCGA-CG-5726        TCGA-CG-5727 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" 
       TCGA-CG-5728        TCGA-CG-5730        TCGA-CG-5732        TCGA-CG-5733 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-CG-5734        TCGA-D7-5577        TCGA-D7-5578        TCGA-D7-5579 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-D7-6518        TCGA-D7-6519        TCGA-D7-6520        TCGA-D7-6521 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-D7-6522        TCGA-D7-6524        TCGA-D7-6525        TCGA-D7-6526 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-D7-6527        TCGA-D7-6528        TCGA-D7-6815        TCGA-D7-6817 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-D7-6818        TCGA-D7-6820        TCGA-D7-6822        TCGA-EQ-5647 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875        TCGA-FP-7735 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" 
       TCGA-FP-7829        TCGA-FP-7998        TCGA-IN-7806        TCGA-IN-7808 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-IP-7968 
"2Q GAIN WILD-TYPE" 
[1] "hr=" "2.3"
D4V2, continuous
D4V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED      3    9
  2Q GAIN WILD-TYPE   57   89
        clus
vv       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  FEMALE               3                57
  MALE                 9                89
D4V4, multiclass
D4V5, multiclass
    clus
vv   2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  T1               0                 6
  T2               2                50
  T3               6                55
  T4               3                15
D4V6, multiclass
    clus
vv   2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  N0               5                39
  N1               5                52
  N2               0                24
  N3               0                15
D4V7, multiclass
    clus
vv   2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  M0              10               124
  M1               1                15
  MX               1                 7
D4V8, multiclass
     clus
vv    2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  I                 1                23
  II                5                32
  III               1                42
  IV                3                23
D4V9, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED      0   12
  2Q GAIN WILD-TYPE    5  141
     clus
vv    2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  NO                0                 5
  YES              12               141
D4V10, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED      0   12
  2Q GAIN WILD-TYPE   10  136
     clus
vv    2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  NO                0                10
  YES              12               136

Clustering(5) Variable = 3p gain mutation analysis
D5V1, survival
                   sevent
clus2                0  1
  3P GAIN MUTATED    1  0
  3P GAIN WILD-TYPE 89 15
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
                1               104 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
                0                15 
$`3P GAIN MUTATED`
TCGA-BR-7722 
        0.16 

$`3P GAIN WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-6452 TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6458 
        5.62         0.10         0.95         1.41         1.35         1.35 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
        0.85         0.82         0.62         0.62         1.71         2.17 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
        0.99         1.22         0.66         1.12         0.76         0.66 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
        0.26         1.22         1.48         0.46         1.25         0.13 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 
        1.05         0.82         0.69         4.54         0.99         0.95 
TCGA-BR-7957 TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        0.69         0.82         0.69         0.36         0.49         0.30 
TCGA-CD-5803 TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
        0.07        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
       52.96         8.05        54.05         4.01        14.01        29.98 
TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4460 TCGA-CG-4462 TCGA-CG-4465 
       47.05        19.07        12.03        21.99         1.02         8.98 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4474 TCGA-CG-4477 TCGA-CG-5716 
       18.94         7.07        12.00         1.02         1.02         1.02 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.94         1.02         1.02         0.99         5.98         0.95 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 
       70.06        12.03        15.02        28.96        31.04        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        55.04        21.07         7.99         8.65         3.58 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
        4.54         9.80        15.65         9.63         8.19         6.90 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
        0.69         5.95         6.61         4.14         1.68         3.65 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-EQ-5647 TCGA-F1-6177 
        4.70         4.04         2.93         4.27         0.62         6.54 
TCGA-F1-6874 TCGA-F1-6875 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7998 TCGA-IN-7806 
        2.01        72.23         0.39         0.20         3.58         6.87 
TCGA-IN-7808 TCGA-IP-7968 
        3.55         2.53 

  3P GAIN MUTATED 3P GAIN WILD-TYPE 
             0.16              0.07 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
             0.16             72.23 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
            0.160             2.975 
[1] "0.2 - 0.2 (0.2)"  "0.1 - 72.2 (3.0)"
       TCGA-B7-5816        TCGA-B7-5818        TCGA-BR-6452        TCGA-BR-6455 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BR-6457        TCGA-BR-6458        TCGA-BR-6563        TCGA-BR-6564 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BR-6565        TCGA-BR-6566        TCGA-BR-6705        TCGA-BR-6706 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BR-6707        TCGA-BR-6709        TCGA-BR-6710        TCGA-BR-6801 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BR-6802        TCGA-BR-6803        TCGA-BR-6852        TCGA-BR-7196 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BR-7197        TCGA-BR-7703        TCGA-BR-7704        TCGA-BR-7707 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BR-7715        TCGA-BR-7716        TCGA-BR-7717        TCGA-BR-7722 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"   "3P GAIN MUTATED" 
       TCGA-BR-7723        TCGA-BR-7851        TCGA-BR-7901        TCGA-BR-7957 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-CD-5798        TCGA-CD-5799        TCGA-CD-5800        TCGA-CD-5801 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-CD-5802        TCGA-CD-5803        TCGA-CG-4300        TCGA-CG-4301 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-CG-4304        TCGA-CG-4305        TCGA-CG-4306        TCGA-CG-4436 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-CG-4437        TCGA-CG-4438        TCGA-CG-4440        TCGA-CG-4441 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-CG-4443        TCGA-CG-4444        TCGA-CG-4449        TCGA-CG-4455 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-CG-4460        TCGA-CG-4462        TCGA-CG-4465        TCGA-CG-4466 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-CG-4469        TCGA-CG-4472        TCGA-CG-4474        TCGA-CG-4477 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-CG-5716        TCGA-CG-5717        TCGA-CG-5718        TCGA-CG-5719 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-CG-5720        TCGA-CG-5721        TCGA-CG-5722        TCGA-CG-5723 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-CG-5724        TCGA-CG-5725        TCGA-CG-5726        TCGA-CG-5727 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-CG-5728        TCGA-CG-5730        TCGA-CG-5732        TCGA-CG-5733 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-CG-5734        TCGA-D7-5577        TCGA-D7-5578        TCGA-D7-5579 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-D7-6518        TCGA-D7-6519        TCGA-D7-6520        TCGA-D7-6521 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-D7-6522        TCGA-D7-6524        TCGA-D7-6525        TCGA-D7-6526 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-D7-6527        TCGA-D7-6528        TCGA-D7-6815        TCGA-D7-6817 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-D7-6818        TCGA-D7-6820        TCGA-D7-6822        TCGA-EQ-5647 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875        TCGA-FP-7735 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-FP-7829        TCGA-FP-7998        TCGA-IN-7806        TCGA-IN-7808 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-IP-7968 
"3P GAIN WILD-TYPE" 
       TCGA-B7-5816        TCGA-B7-5818        TCGA-BR-6452        TCGA-BR-6455 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BR-6457        TCGA-BR-6458        TCGA-BR-6563        TCGA-BR-6564 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BR-6565        TCGA-BR-6566        TCGA-BR-6705        TCGA-BR-6706 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BR-6707        TCGA-BR-6709        TCGA-BR-6710        TCGA-BR-6801 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BR-6802        TCGA-BR-6803        TCGA-BR-6852        TCGA-BR-7196 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BR-7197        TCGA-BR-7703        TCGA-BR-7704        TCGA-BR-7707 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BR-7715        TCGA-BR-7716        TCGA-BR-7717        TCGA-BR-7722 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"   "3P GAIN MUTATED" 
       TCGA-BR-7723        TCGA-BR-7851        TCGA-BR-7901        TCGA-BR-7957 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-CD-5798        TCGA-CD-5799        TCGA-CD-5800        TCGA-CD-5801 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-CD-5802        TCGA-CD-5803        TCGA-CG-4300        TCGA-CG-4301 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-CG-4304        TCGA-CG-4305        TCGA-CG-4306        TCGA-CG-4436 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-CG-4437        TCGA-CG-4438        TCGA-CG-4440        TCGA-CG-4441 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-CG-4443        TCGA-CG-4444        TCGA-CG-4449        TCGA-CG-4455 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-CG-4460        TCGA-CG-4462        TCGA-CG-4465        TCGA-CG-4466 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-CG-4469        TCGA-CG-4472        TCGA-CG-4474        TCGA-CG-4477 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-CG-5716        TCGA-CG-5717        TCGA-CG-5718        TCGA-CG-5719 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-CG-5720        TCGA-CG-5721        TCGA-CG-5722        TCGA-CG-5723 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-CG-5724        TCGA-CG-5725        TCGA-CG-5726        TCGA-CG-5727 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-CG-5728        TCGA-CG-5730        TCGA-CG-5732        TCGA-CG-5733 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-CG-5734        TCGA-D7-5577        TCGA-D7-5578        TCGA-D7-5579 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-D7-6518        TCGA-D7-6519        TCGA-D7-6520        TCGA-D7-6521 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-D7-6522        TCGA-D7-6524        TCGA-D7-6525        TCGA-D7-6526 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-D7-6527        TCGA-D7-6528        TCGA-D7-6815        TCGA-D7-6817 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-D7-6818        TCGA-D7-6820        TCGA-D7-6822        TCGA-EQ-5647 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875        TCGA-FP-7735 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-FP-7829        TCGA-FP-7998        TCGA-IN-7806        TCGA-IN-7808 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-IP-7968 
"3P GAIN WILD-TYPE" 
       TCGA-B7-5816        TCGA-B7-5818        TCGA-BR-6452        TCGA-BR-6455 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BR-6457        TCGA-BR-6458        TCGA-BR-6563        TCGA-BR-6564 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BR-6565        TCGA-BR-6566        TCGA-BR-6705        TCGA-BR-6706 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BR-6707        TCGA-BR-6709        TCGA-BR-6710        TCGA-BR-6801 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BR-6802        TCGA-BR-6803        TCGA-BR-6852        TCGA-BR-7196 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BR-7197        TCGA-BR-7703        TCGA-BR-7704        TCGA-BR-7707 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BR-7715        TCGA-BR-7716        TCGA-BR-7717        TCGA-BR-7722 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"   "3P GAIN MUTATED" 
       TCGA-BR-7723        TCGA-BR-7851        TCGA-BR-7901        TCGA-BR-7957 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-CD-5798        TCGA-CD-5799        TCGA-CD-5800        TCGA-CD-5801 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-CD-5802        TCGA-CD-5803        TCGA-CG-4300        TCGA-CG-4301 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-CG-4304        TCGA-CG-4305        TCGA-CG-4306        TCGA-CG-4436 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-CG-4437        TCGA-CG-4438        TCGA-CG-4440        TCGA-CG-4441 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-CG-4443        TCGA-CG-4444        TCGA-CG-4449        TCGA-CG-4455 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-CG-4460        TCGA-CG-4462        TCGA-CG-4465        TCGA-CG-4466 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-CG-4469        TCGA-CG-4472        TCGA-CG-4474        TCGA-CG-4477 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-CG-5716        TCGA-CG-5717        TCGA-CG-5718        TCGA-CG-5719 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-CG-5720        TCGA-CG-5721        TCGA-CG-5722        TCGA-CG-5723 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-CG-5724        TCGA-CG-5725        TCGA-CG-5726        TCGA-CG-5727 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-CG-5728        TCGA-CG-5730        TCGA-CG-5732        TCGA-CG-5733 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-CG-5734        TCGA-D7-5577        TCGA-D7-5578        TCGA-D7-5579 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-D7-6518        TCGA-D7-6519        TCGA-D7-6520        TCGA-D7-6521 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-D7-6522        TCGA-D7-6524        TCGA-D7-6525        TCGA-D7-6526 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-D7-6527        TCGA-D7-6528        TCGA-D7-6815        TCGA-D7-6817 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-D7-6818        TCGA-D7-6820        TCGA-D7-6822        TCGA-EQ-5647 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875        TCGA-FP-7735 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-FP-7829        TCGA-FP-7998        TCGA-IN-7806        TCGA-IN-7808 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-IP-7968 
"3P GAIN WILD-TYPE" 
[1] "Remove cluster labels:" "3P GAIN MUTATED"       
clus
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
                1               104 
       TCGA-B7-5816        TCGA-B7-5818        TCGA-BR-6452        TCGA-BR-6455 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BR-6457        TCGA-BR-6458        TCGA-BR-6563        TCGA-BR-6564 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BR-6565        TCGA-BR-6566        TCGA-BR-6705        TCGA-BR-6706 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BR-6707        TCGA-BR-6709        TCGA-BR-6710        TCGA-BR-6801 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BR-6802        TCGA-BR-6803        TCGA-BR-6852        TCGA-BR-7196 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BR-7197        TCGA-BR-7703        TCGA-BR-7704        TCGA-BR-7707 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BR-7715        TCGA-BR-7716        TCGA-BR-7717        TCGA-BR-7723 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BR-7851        TCGA-BR-7901        TCGA-BR-7957        TCGA-CD-5798 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-CD-5799        TCGA-CD-5800        TCGA-CD-5801        TCGA-CD-5802 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-CD-5803        TCGA-CG-4300        TCGA-CG-4301        TCGA-CG-4304 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-CG-4305        TCGA-CG-4306        TCGA-CG-4436        TCGA-CG-4437 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-CG-4438        TCGA-CG-4440        TCGA-CG-4441        TCGA-CG-4443 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-CG-4444        TCGA-CG-4449        TCGA-CG-4455        TCGA-CG-4460 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-CG-4462        TCGA-CG-4465        TCGA-CG-4466        TCGA-CG-4469 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-CG-4472        TCGA-CG-4474        TCGA-CG-4477        TCGA-CG-5716 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-CG-5717        TCGA-CG-5718        TCGA-CG-5719        TCGA-CG-5720 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-CG-5721        TCGA-CG-5722        TCGA-CG-5723        TCGA-CG-5724 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-CG-5725        TCGA-CG-5726        TCGA-CG-5727        TCGA-CG-5728 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-CG-5730        TCGA-CG-5732        TCGA-CG-5733        TCGA-CG-5734 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-D7-5577        TCGA-D7-5578        TCGA-D7-5579        TCGA-D7-6518 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-D7-6519        TCGA-D7-6520        TCGA-D7-6521        TCGA-D7-6522 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-D7-6524        TCGA-D7-6525        TCGA-D7-6526        TCGA-D7-6527 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-D7-6528        TCGA-D7-6815        TCGA-D7-6817        TCGA-D7-6818 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-D7-6820        TCGA-D7-6822        TCGA-EQ-5647        TCGA-F1-6177 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-F1-6874        TCGA-F1-6875        TCGA-FP-7735        TCGA-FP-7829 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-FP-7998        TCGA-IN-7806        TCGA-IN-7808        TCGA-IP-7968 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
D5V2, continuous
D5V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED      1    2
  3P GAIN WILD-TYPE   59   96
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  FEMALE               1                59
  MALE                 2                96
D5V4, multiclass
D5V5, multiclass
    clus
vv   3P GAIN MUTATED 3P GAIN WILD-TYPE
  T1               0                 6
  T2               1                51
  T3               1                60
  T4               1                17
D5V6, multiclass
    clus
vv   3P GAIN MUTATED 3P GAIN WILD-TYPE
  N0               1                43
  N1               1                56
  N2               1                23
  N3               0                15
D5V7, multiclass
    clus
vv   3P GAIN MUTATED 3P GAIN WILD-TYPE
  M0               3               131
  M1               0                16
  MX               0                 8
D5V8, multiclass
     clus
vv    3P GAIN MUTATED 3P GAIN WILD-TYPE
  I                 1                23
  II                0                37
  III               1                42
  IV                1                25
D5V9, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED      0    3
  3P GAIN WILD-TYPE    5  150
     clus
vv    3P GAIN MUTATED 3P GAIN WILD-TYPE
  NO                0                 5
  YES               3               150
D5V10, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED      0    3
  3P GAIN WILD-TYPE   10  145
     clus
vv    3P GAIN MUTATED 3P GAIN WILD-TYPE
  NO                0                10
  YES               3               145

Clustering(6) Variable = 3q gain mutation analysis
D6V1, survival
                   sevent
clus2                0  1
  3Q GAIN MUTATED    9  0
  3Q GAIN WILD-TYPE 81 15
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
                9                96 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
                0                15 
$`3Q GAIN MUTATED`
TCGA-B7-5818 TCGA-BR-6565 TCGA-BR-7722 TCGA-BR-7723 TCGA-CD-5799 TCGA-CD-5801 
        0.10         0.62         0.16         4.54         0.69         0.49 
TCGA-CG-4305 TCGA-CG-4472 TCGA-D7-6521 
       15.95        12.00         8.19 

$`3Q GAIN WILD-TYPE`
TCGA-B7-5816 TCGA-BR-6452 TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
        5.62         0.95         1.41         1.35         1.35         0.85 
TCGA-BR-6564 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
        0.82         0.62         1.71         2.17         0.99         1.22 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        0.66         1.12         0.76         0.66         0.26         1.22 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 
        1.48         0.46         1.25         0.13         1.05         0.82 
TCGA-BR-7717 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-CD-5798 TCGA-CD-5800 
        0.69         0.99         0.95         0.69         0.82         0.36 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4306 
        0.30         0.07        20.02         3.02        27.02         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
       52.96         8.05        54.05         4.01        14.01        29.98 
TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4460 TCGA-CG-4462 TCGA-CG-4465 
       47.05        19.07        12.03        21.99         1.02         8.98 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4474 TCGA-CG-4477 TCGA-CG-5716 TCGA-CG-5717 
       18.94         7.07         1.02         1.02         1.02         6.94 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
        1.02         1.02         0.99         5.98         0.95        70.06 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 
       12.03        15.02        28.96        31.04        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       55.04        21.07         7.99         8.65         3.58         4.54 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
        9.80        15.65         9.63         6.90         0.69         5.95 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
        6.61         4.14         1.68         3.65         4.70         4.04 
TCGA-D7-6820 TCGA-D7-6822 TCGA-EQ-5647 TCGA-F1-6177 TCGA-F1-6874 TCGA-F1-6875 
        2.93         4.27         0.62         6.54         2.01        72.23 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7998 TCGA-IN-7806 TCGA-IN-7808 TCGA-IP-7968 
        0.39         0.20         3.58         6.87         3.55         2.53 

  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
             0.10              0.07 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
            15.95             72.23 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
            0.690             2.975 
[1] "0.1 - 15.9 (0.7)" "0.1 - 72.2 (3.0)"
       TCGA-B7-5816        TCGA-B7-5818        TCGA-BR-6452        TCGA-BR-6455 
"3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-BR-6457        TCGA-BR-6458        TCGA-BR-6563        TCGA-BR-6564 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-BR-6565        TCGA-BR-6566        TCGA-BR-6705        TCGA-BR-6706 
  "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-BR-6707        TCGA-BR-6709        TCGA-BR-6710        TCGA-BR-6801 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-BR-6802        TCGA-BR-6803        TCGA-BR-6852        TCGA-BR-7196 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-BR-7197        TCGA-BR-7703        TCGA-BR-7704        TCGA-BR-7707 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-BR-7715        TCGA-BR-7716        TCGA-BR-7717        TCGA-BR-7722 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" 
       TCGA-BR-7723        TCGA-BR-7851        TCGA-BR-7901        TCGA-BR-7957 
  "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-CD-5798        TCGA-CD-5799        TCGA-CD-5800        TCGA-CD-5801 
"3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" 
       TCGA-CD-5802        TCGA-CD-5803        TCGA-CG-4300        TCGA-CG-4301 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-CG-4304        TCGA-CG-4305        TCGA-CG-4306        TCGA-CG-4436 
"3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-CG-4437        TCGA-CG-4438        TCGA-CG-4440        TCGA-CG-4441 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-CG-4443        TCGA-CG-4444        TCGA-CG-4449        TCGA-CG-4455 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-CG-4460        TCGA-CG-4462        TCGA-CG-4465        TCGA-CG-4466 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-CG-4469        TCGA-CG-4472        TCGA-CG-4474        TCGA-CG-4477 
"3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-CG-5716        TCGA-CG-5717        TCGA-CG-5718        TCGA-CG-5719 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-CG-5720        TCGA-CG-5721        TCGA-CG-5722        TCGA-CG-5723 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-CG-5724        TCGA-CG-5725        TCGA-CG-5726        TCGA-CG-5727 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-CG-5728        TCGA-CG-5730        TCGA-CG-5732        TCGA-CG-5733 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-CG-5734        TCGA-D7-5577        TCGA-D7-5578        TCGA-D7-5579 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-D7-6518        TCGA-D7-6519        TCGA-D7-6520        TCGA-D7-6521 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" 
       TCGA-D7-6522        TCGA-D7-6524        TCGA-D7-6525        TCGA-D7-6526 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-D7-6527        TCGA-D7-6528        TCGA-D7-6815        TCGA-D7-6817 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-D7-6818        TCGA-D7-6820        TCGA-D7-6822        TCGA-EQ-5647 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875        TCGA-FP-7735 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-FP-7829        TCGA-FP-7998        TCGA-IN-7806        TCGA-IN-7808 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-IP-7968 
"3Q GAIN WILD-TYPE" 
       TCGA-B7-5816        TCGA-B7-5818        TCGA-BR-6452        TCGA-BR-6455 
"3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-BR-6457        TCGA-BR-6458        TCGA-BR-6563        TCGA-BR-6564 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-BR-6565        TCGA-BR-6566        TCGA-BR-6705        TCGA-BR-6706 
  "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-BR-6707        TCGA-BR-6709        TCGA-BR-6710        TCGA-BR-6801 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-BR-6802        TCGA-BR-6803        TCGA-BR-6852        TCGA-BR-7196 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-BR-7197        TCGA-BR-7703        TCGA-BR-7704        TCGA-BR-7707 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-BR-7715        TCGA-BR-7716        TCGA-BR-7717        TCGA-BR-7722 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" 
       TCGA-BR-7723        TCGA-BR-7851        TCGA-BR-7901        TCGA-BR-7957 
  "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-CD-5798        TCGA-CD-5799        TCGA-CD-5800        TCGA-CD-5801 
"3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" 
       TCGA-CD-5802        TCGA-CD-5803        TCGA-CG-4300        TCGA-CG-4301 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-CG-4304        TCGA-CG-4305        TCGA-CG-4306        TCGA-CG-4436 
"3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-CG-4437        TCGA-CG-4438        TCGA-CG-4440        TCGA-CG-4441 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-CG-4443        TCGA-CG-4444        TCGA-CG-4449        TCGA-CG-4455 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-CG-4460        TCGA-CG-4462        TCGA-CG-4465        TCGA-CG-4466 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-CG-4469        TCGA-CG-4472        TCGA-CG-4474        TCGA-CG-4477 
"3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-CG-5716        TCGA-CG-5717        TCGA-CG-5718        TCGA-CG-5719 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-CG-5720        TCGA-CG-5721        TCGA-CG-5722        TCGA-CG-5723 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-CG-5724        TCGA-CG-5725        TCGA-CG-5726        TCGA-CG-5727 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-CG-5728        TCGA-CG-5730        TCGA-CG-5732        TCGA-CG-5733 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-CG-5734        TCGA-D7-5577        TCGA-D7-5578        TCGA-D7-5579 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-D7-6518        TCGA-D7-6519        TCGA-D7-6520        TCGA-D7-6521 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" 
       TCGA-D7-6522        TCGA-D7-6524        TCGA-D7-6525        TCGA-D7-6526 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-D7-6527        TCGA-D7-6528        TCGA-D7-6815        TCGA-D7-6817 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-D7-6818        TCGA-D7-6820        TCGA-D7-6822        TCGA-EQ-5647 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875        TCGA-FP-7735 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-FP-7829        TCGA-FP-7998        TCGA-IN-7806        TCGA-IN-7808 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-IP-7968 
"3Q GAIN WILD-TYPE" 
       TCGA-B7-5816        TCGA-B7-5818        TCGA-BR-6452        TCGA-BR-6455 
"3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-BR-6457        TCGA-BR-6458        TCGA-BR-6563        TCGA-BR-6564 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-BR-6565        TCGA-BR-6566        TCGA-BR-6705        TCGA-BR-6706 
  "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-BR-6707        TCGA-BR-6709        TCGA-BR-6710        TCGA-BR-6801 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-BR-6802        TCGA-BR-6803        TCGA-BR-6852        TCGA-BR-7196 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-BR-7197        TCGA-BR-7703        TCGA-BR-7704        TCGA-BR-7707 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-BR-7715        TCGA-BR-7716        TCGA-BR-7717        TCGA-BR-7722 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" 
       TCGA-BR-7723        TCGA-BR-7851        TCGA-BR-7901        TCGA-BR-7957 
  "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-CD-5798        TCGA-CD-5799        TCGA-CD-5800        TCGA-CD-5801 
"3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" 
       TCGA-CD-5802        TCGA-CD-5803        TCGA-CG-4300        TCGA-CG-4301 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-CG-4304        TCGA-CG-4305        TCGA-CG-4306        TCGA-CG-4436 
"3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-CG-4437        TCGA-CG-4438        TCGA-CG-4440        TCGA-CG-4441 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-CG-4443        TCGA-CG-4444        TCGA-CG-4449        TCGA-CG-4455 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-CG-4460        TCGA-CG-4462        TCGA-CG-4465        TCGA-CG-4466 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-CG-4469        TCGA-CG-4472        TCGA-CG-4474        TCGA-CG-4477 
"3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-CG-5716        TCGA-CG-5717        TCGA-CG-5718        TCGA-CG-5719 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-CG-5720        TCGA-CG-5721        TCGA-CG-5722        TCGA-CG-5723 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-CG-5724        TCGA-CG-5725        TCGA-CG-5726        TCGA-CG-5727 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-CG-5728        TCGA-CG-5730        TCGA-CG-5732        TCGA-CG-5733 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-CG-5734        TCGA-D7-5577        TCGA-D7-5578        TCGA-D7-5579 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-D7-6518        TCGA-D7-6519        TCGA-D7-6520        TCGA-D7-6521 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" 
       TCGA-D7-6522        TCGA-D7-6524        TCGA-D7-6525        TCGA-D7-6526 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-D7-6527        TCGA-D7-6528        TCGA-D7-6815        TCGA-D7-6817 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-D7-6818        TCGA-D7-6820        TCGA-D7-6822        TCGA-EQ-5647 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875        TCGA-FP-7735 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-FP-7829        TCGA-FP-7998        TCGA-IN-7806        TCGA-IN-7808 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-IP-7968 
"3Q GAIN WILD-TYPE" 
[1] "hr="     "7.4e+07"
D6V2, continuous
D6V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED      2   12
  3Q GAIN WILD-TYPE   58   86
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  FEMALE               2                58
  MALE                12                86
D6V4, multiclass
D6V5, multiclass
    clus
vv   3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  T1               0                 6
  T2               5                47
  T3               5                56
  T4               2                16
D6V6, multiclass
    clus
vv   3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  N0               3                41
  N1               6                51
  N2               3                21
  N3               0                15
D6V7, multiclass
    clus
vv   3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  M0              13               121
  M1               0                16
  MX               1                 7
D6V8, multiclass
     clus
vv    3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  I                 2                22
  II                4                33
  III               3                40
  IV                2                24
D6V9, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED      0   14
  3Q GAIN WILD-TYPE    5  139
     clus
vv    3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  NO                0                 5
  YES              14               139
D6V10, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED      1   13
  3Q GAIN WILD-TYPE    9  135
     clus
vv    3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  NO                1                 9
  YES              13               135

Clustering(7) Variable = 5p gain mutation analysis
D7V1, survival
                   sevent
clus2                0  1
  5P GAIN MUTATED   17  4
  5P GAIN WILD-TYPE 73 11
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               21                84 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
                4                11 
$`5P GAIN MUTATED`
TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-CD-5801 TCGA-CG-4436 
        1.25         1.05         0.82         0.69         0.49        52.96 
TCGA-CG-4438 TCGA-CG-4444 TCGA-CG-4455 TCGA-CG-4460 TCGA-CG-4466 TCGA-CG-4472 
       54.05        47.05        12.03        21.99        18.94        12.00 
TCGA-CG-5718 TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5725 TCGA-D7-5579 TCGA-D7-6818 
        1.02         0.95        12.03        15.02         4.54         4.04 
TCGA-D7-6820 TCGA-EQ-5647 TCGA-FP-7829 
        2.93         0.62         0.20 

$`5P GAIN WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-6452 TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6458 
        5.62         0.10         0.95         1.41         1.35         1.35 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
        0.85         0.82         0.62         0.62         1.71         2.17 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
        0.99         1.22         0.66         1.12         0.76         0.66 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7722 
        0.26         1.22         1.48         0.46         0.13         0.16 
TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-CD-5798 TCGA-CD-5799 
        4.54         0.99         0.95         0.69         0.82         0.69 
TCGA-CD-5800 TCGA-CD-5802 TCGA-CD-5803 TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
        0.36         0.30         0.07        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4437 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
       15.95         1.02         8.05         4.01        14.01        29.98 
TCGA-CG-4449 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4469 TCGA-CG-4474 TCGA-CG-4477 
       19.07         1.02         8.98         7.07         1.02         1.02 
TCGA-CG-5716 TCGA-CG-5717 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5723 
        1.02         6.94         1.02         0.99         5.98        70.06 
TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       28.96        31.04        65.10         4.01        55.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
        7.99         8.65         3.58         9.80        15.65         9.63 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
        8.19         6.90         0.69         5.95         6.61         4.14 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6822 TCGA-F1-6177 TCGA-F1-6874 
        1.68         3.65         4.70         4.27         6.54         2.01 
TCGA-F1-6875 TCGA-FP-7735 TCGA-FP-7998 TCGA-IN-7806 TCGA-IN-7808 TCGA-IP-7968 
       72.23         0.39         3.58         6.87         3.55         2.53 

  5P GAIN MUTATED 5P GAIN WILD-TYPE 
             0.20              0.07 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
            54.05             72.23 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
             4.04              2.35 
[1] "0.2 - 54.0 (4.0)" "0.1 - 72.2 (2.3)"
       TCGA-B7-5816        TCGA-B7-5818        TCGA-BR-6452        TCGA-BR-6455 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-BR-6457        TCGA-BR-6458        TCGA-BR-6563        TCGA-BR-6564 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-BR-6565        TCGA-BR-6566        TCGA-BR-6705        TCGA-BR-6706 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-BR-6707        TCGA-BR-6709        TCGA-BR-6710        TCGA-BR-6801 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-BR-6802        TCGA-BR-6803        TCGA-BR-6852        TCGA-BR-7196 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-BR-7197        TCGA-BR-7703        TCGA-BR-7704        TCGA-BR-7707 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" 
       TCGA-BR-7715        TCGA-BR-7716        TCGA-BR-7717        TCGA-BR-7722 
  "5P GAIN MUTATED"   "5P GAIN MUTATED"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" 
       TCGA-BR-7723        TCGA-BR-7851        TCGA-BR-7901        TCGA-BR-7957 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-CD-5798        TCGA-CD-5799        TCGA-CD-5800        TCGA-CD-5801 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" 
       TCGA-CD-5802        TCGA-CD-5803        TCGA-CG-4300        TCGA-CG-4301 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-CG-4304        TCGA-CG-4305        TCGA-CG-4306        TCGA-CG-4436 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" 
       TCGA-CG-4437        TCGA-CG-4438        TCGA-CG-4440        TCGA-CG-4441 
"5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-CG-4443        TCGA-CG-4444        TCGA-CG-4449        TCGA-CG-4455 
"5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" 
       TCGA-CG-4460        TCGA-CG-4462        TCGA-CG-4465        TCGA-CG-4466 
  "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" 
       TCGA-CG-4469        TCGA-CG-4472        TCGA-CG-4474        TCGA-CG-4477 
"5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-CG-5716        TCGA-CG-5717        TCGA-CG-5718        TCGA-CG-5719 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" 
       TCGA-CG-5720        TCGA-CG-5721        TCGA-CG-5722        TCGA-CG-5723 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" 
       TCGA-CG-5724        TCGA-CG-5725        TCGA-CG-5726        TCGA-CG-5727 
  "5P GAIN MUTATED"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-CG-5728        TCGA-CG-5730        TCGA-CG-5732        TCGA-CG-5733 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-CG-5734        TCGA-D7-5577        TCGA-D7-5578        TCGA-D7-5579 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" 
       TCGA-D7-6518        TCGA-D7-6519        TCGA-D7-6520        TCGA-D7-6521 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-D7-6522        TCGA-D7-6524        TCGA-D7-6525        TCGA-D7-6526 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-D7-6527        TCGA-D7-6528        TCGA-D7-6815        TCGA-D7-6817 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-D7-6818        TCGA-D7-6820        TCGA-D7-6822        TCGA-EQ-5647 
  "5P GAIN MUTATED"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" 
       TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875        TCGA-FP-7735 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-FP-7829        TCGA-FP-7998        TCGA-IN-7806        TCGA-IN-7808 
  "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-IP-7968 
"5P GAIN WILD-TYPE" 
       TCGA-B7-5816        TCGA-B7-5818        TCGA-BR-6452        TCGA-BR-6455 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-BR-6457        TCGA-BR-6458        TCGA-BR-6563        TCGA-BR-6564 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-BR-6565        TCGA-BR-6566        TCGA-BR-6705        TCGA-BR-6706 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-BR-6707        TCGA-BR-6709        TCGA-BR-6710        TCGA-BR-6801 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-BR-6802        TCGA-BR-6803        TCGA-BR-6852        TCGA-BR-7196 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-BR-7197        TCGA-BR-7703        TCGA-BR-7704        TCGA-BR-7707 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" 
       TCGA-BR-7715        TCGA-BR-7716        TCGA-BR-7717        TCGA-BR-7722 
  "5P GAIN MUTATED"   "5P GAIN MUTATED"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" 
       TCGA-BR-7723        TCGA-BR-7851        TCGA-BR-7901        TCGA-BR-7957 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-CD-5798        TCGA-CD-5799        TCGA-CD-5800        TCGA-CD-5801 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" 
       TCGA-CD-5802        TCGA-CD-5803        TCGA-CG-4300        TCGA-CG-4301 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-CG-4304        TCGA-CG-4305        TCGA-CG-4306        TCGA-CG-4436 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" 
       TCGA-CG-4437        TCGA-CG-4438        TCGA-CG-4440        TCGA-CG-4441 
"5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-CG-4443        TCGA-CG-4444        TCGA-CG-4449        TCGA-CG-4455 
"5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" 
       TCGA-CG-4460        TCGA-CG-4462        TCGA-CG-4465        TCGA-CG-4466 
  "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" 
       TCGA-CG-4469        TCGA-CG-4472        TCGA-CG-4474        TCGA-CG-4477 
"5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-CG-5716        TCGA-CG-5717        TCGA-CG-5718        TCGA-CG-5719 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" 
       TCGA-CG-5720        TCGA-CG-5721        TCGA-CG-5722        TCGA-CG-5723 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" 
       TCGA-CG-5724        TCGA-CG-5725        TCGA-CG-5726        TCGA-CG-5727 
  "5P GAIN MUTATED"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-CG-5728        TCGA-CG-5730        TCGA-CG-5732        TCGA-CG-5733 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-CG-5734        TCGA-D7-5577        TCGA-D7-5578        TCGA-D7-5579 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" 
       TCGA-D7-6518        TCGA-D7-6519        TCGA-D7-6520        TCGA-D7-6521 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-D7-6522        TCGA-D7-6524        TCGA-D7-6525        TCGA-D7-6526 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-D7-6527        TCGA-D7-6528        TCGA-D7-6815        TCGA-D7-6817 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-D7-6818        TCGA-D7-6820        TCGA-D7-6822        TCGA-EQ-5647 
  "5P GAIN MUTATED"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" 
       TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875        TCGA-FP-7735 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-FP-7829        TCGA-FP-7998        TCGA-IN-7806        TCGA-IN-7808 
  "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-IP-7968 
"5P GAIN WILD-TYPE" 
       TCGA-B7-5816        TCGA-B7-5818        TCGA-BR-6452        TCGA-BR-6455 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-BR-6457        TCGA-BR-6458        TCGA-BR-6563        TCGA-BR-6564 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-BR-6565        TCGA-BR-6566        TCGA-BR-6705        TCGA-BR-6706 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-BR-6707        TCGA-BR-6709        TCGA-BR-6710        TCGA-BR-6801 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-BR-6802        TCGA-BR-6803        TCGA-BR-6852        TCGA-BR-7196 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-BR-7197        TCGA-BR-7703        TCGA-BR-7704        TCGA-BR-7707 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" 
       TCGA-BR-7715        TCGA-BR-7716        TCGA-BR-7717        TCGA-BR-7722 
  "5P GAIN MUTATED"   "5P GAIN MUTATED"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" 
       TCGA-BR-7723        TCGA-BR-7851        TCGA-BR-7901        TCGA-BR-7957 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-CD-5798        TCGA-CD-5799        TCGA-CD-5800        TCGA-CD-5801 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" 
       TCGA-CD-5802        TCGA-CD-5803        TCGA-CG-4300        TCGA-CG-4301 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-CG-4304        TCGA-CG-4305        TCGA-CG-4306        TCGA-CG-4436 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" 
       TCGA-CG-4437        TCGA-CG-4438        TCGA-CG-4440        TCGA-CG-4441 
"5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-CG-4443        TCGA-CG-4444        TCGA-CG-4449        TCGA-CG-4455 
"5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" 
       TCGA-CG-4460        TCGA-CG-4462        TCGA-CG-4465        TCGA-CG-4466 
  "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" 
       TCGA-CG-4469        TCGA-CG-4472        TCGA-CG-4474        TCGA-CG-4477 
"5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-CG-5716        TCGA-CG-5717        TCGA-CG-5718        TCGA-CG-5719 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" 
       TCGA-CG-5720        TCGA-CG-5721        TCGA-CG-5722        TCGA-CG-5723 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" 
       TCGA-CG-5724        TCGA-CG-5725        TCGA-CG-5726        TCGA-CG-5727 
  "5P GAIN MUTATED"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-CG-5728        TCGA-CG-5730        TCGA-CG-5732        TCGA-CG-5733 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-CG-5734        TCGA-D7-5577        TCGA-D7-5578        TCGA-D7-5579 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" 
       TCGA-D7-6518        TCGA-D7-6519        TCGA-D7-6520        TCGA-D7-6521 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-D7-6522        TCGA-D7-6524        TCGA-D7-6525        TCGA-D7-6526 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-D7-6527        TCGA-D7-6528        TCGA-D7-6815        TCGA-D7-6817 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-D7-6818        TCGA-D7-6820        TCGA-D7-6822        TCGA-EQ-5647 
  "5P GAIN MUTATED"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" 
       TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875        TCGA-FP-7735 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-FP-7829        TCGA-FP-7998        TCGA-IN-7806        TCGA-IN-7808 
  "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-IP-7968 
"5P GAIN WILD-TYPE" 
[1] "hr=" "1"  
D7V2, continuous
D7V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED      8   18
  5P GAIN WILD-TYPE   52   80
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  FEMALE               8                52
  MALE                18                80
D7V4, multiclass
D7V5, multiclass
    clus
vv   5P GAIN MUTATED 5P GAIN WILD-TYPE
  T1               0                 6
  T2               8                44
  T3               9                52
  T4               6                12
D7V6, multiclass
    clus
vv   5P GAIN MUTATED 5P GAIN WILD-TYPE
  N0               6                38
  N1              12                45
  N2               4                20
  N3               3                12
D7V7, multiclass
    clus
vv   5P GAIN MUTATED 5P GAIN WILD-TYPE
  M0              22               112
  M1               4                12
  MX               0                 8
D7V8, multiclass
     clus
vv    5P GAIN MUTATED 5P GAIN WILD-TYPE
  I                 3                21
  II                8                29
  III               3                40
  IV                9                17
D7V9, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED      1   25
  5P GAIN WILD-TYPE    4  128
     clus
vv    5P GAIN MUTATED 5P GAIN WILD-TYPE
  NO                1                 4
  YES              25               128
D7V10, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED      2   24
  5P GAIN WILD-TYPE    8  124
     clus
vv    5P GAIN MUTATED 5P GAIN WILD-TYPE
  NO                2                 8
  YES              24               124

Clustering(8) Variable = 5q gain mutation analysis
D8V1, survival
                   sevent
clus2                0  1
  5Q GAIN MUTATED    5  0
  5Q GAIN WILD-TYPE 85 15
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
                5               100 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
                0                15 
$`5Q GAIN MUTATED`
TCGA-BR-7715 TCGA-CG-4436 TCGA-CG-4455 TCGA-CG-4466 TCGA-FP-7829 
        1.05        52.96        12.03        18.94         0.20 

$`5Q GAIN WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-6452 TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6458 
        5.62         0.10         0.95         1.41         1.35         1.35 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
        0.85         0.82         0.62         0.62         1.71         2.17 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
        0.99         1.22         0.66         1.12         0.76         0.66 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
        0.26         1.22         1.48         0.46         1.25         0.13 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 
        0.82         0.69         0.16         4.54         0.99         0.95 
TCGA-BR-7957 TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        0.69         0.82         0.69         0.36         0.49         0.30 
TCGA-CD-5803 TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
        0.07        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 
        8.05        54.05         4.01        14.01        29.98        47.05 
TCGA-CG-4449 TCGA-CG-4460 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4469 TCGA-CG-4472 
       19.07        21.99         1.02         8.98         7.07        12.00 
TCGA-CG-4474 TCGA-CG-4477 TCGA-CG-5716 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
        1.02         1.02         1.02         6.94         1.02         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 
        0.99         5.98         0.95        70.06        12.03        15.02 
TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       28.96        31.04        65.10         4.01        55.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99         8.65         3.58         4.54         9.80        15.65 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
        9.63         8.19         6.90         0.69         5.95         6.61 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
        4.14         1.68         3.65         4.70         4.04         2.93 
TCGA-D7-6822 TCGA-EQ-5647 TCGA-F1-6177 TCGA-F1-6874 TCGA-F1-6875 TCGA-FP-7735 
        4.27         0.62         6.54         2.01        72.23         0.39 
TCGA-FP-7998 TCGA-IN-7806 TCGA-IN-7808 TCGA-IP-7968 
        3.58         6.87         3.55         2.53 

  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
             0.20              0.07 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
            52.96             72.23 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
            12.03              2.73 
[1] "0.2 - 53.0 (12.0)" "0.1 - 72.2 (2.7)" 
       TCGA-B7-5816        TCGA-B7-5818        TCGA-BR-6452        TCGA-BR-6455 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-BR-6457        TCGA-BR-6458        TCGA-BR-6563        TCGA-BR-6564 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-BR-6565        TCGA-BR-6566        TCGA-BR-6705        TCGA-BR-6706 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-BR-6707        TCGA-BR-6709        TCGA-BR-6710        TCGA-BR-6801 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-BR-6802        TCGA-BR-6803        TCGA-BR-6852        TCGA-BR-7196 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-BR-7197        TCGA-BR-7703        TCGA-BR-7704        TCGA-BR-7707 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-BR-7715        TCGA-BR-7716        TCGA-BR-7717        TCGA-BR-7722 
  "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-BR-7723        TCGA-BR-7851        TCGA-BR-7901        TCGA-BR-7957 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-CD-5798        TCGA-CD-5799        TCGA-CD-5800        TCGA-CD-5801 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-CD-5802        TCGA-CD-5803        TCGA-CG-4300        TCGA-CG-4301 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-CG-4304        TCGA-CG-4305        TCGA-CG-4306        TCGA-CG-4436 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED" 
       TCGA-CG-4437        TCGA-CG-4438        TCGA-CG-4440        TCGA-CG-4441 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-CG-4443        TCGA-CG-4444        TCGA-CG-4449        TCGA-CG-4455 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED" 
       TCGA-CG-4460        TCGA-CG-4462        TCGA-CG-4465        TCGA-CG-4466 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED" 
       TCGA-CG-4469        TCGA-CG-4472        TCGA-CG-4474        TCGA-CG-4477 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-CG-5716        TCGA-CG-5717        TCGA-CG-5718        TCGA-CG-5719 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-CG-5720        TCGA-CG-5721        TCGA-CG-5722        TCGA-CG-5723 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-CG-5724        TCGA-CG-5725        TCGA-CG-5726        TCGA-CG-5727 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-CG-5728        TCGA-CG-5730        TCGA-CG-5732        TCGA-CG-5733 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-CG-5734        TCGA-D7-5577        TCGA-D7-5578        TCGA-D7-5579 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-D7-6518        TCGA-D7-6519        TCGA-D7-6520        TCGA-D7-6521 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-D7-6522        TCGA-D7-6524        TCGA-D7-6525        TCGA-D7-6526 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-D7-6527        TCGA-D7-6528        TCGA-D7-6815        TCGA-D7-6817 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-D7-6818        TCGA-D7-6820        TCGA-D7-6822        TCGA-EQ-5647 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875        TCGA-FP-7735 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-FP-7829        TCGA-FP-7998        TCGA-IN-7806        TCGA-IN-7808 
  "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-IP-7968 
"5Q GAIN WILD-TYPE" 
       TCGA-B7-5816        TCGA-B7-5818        TCGA-BR-6452        TCGA-BR-6455 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-BR-6457        TCGA-BR-6458        TCGA-BR-6563        TCGA-BR-6564 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-BR-6565        TCGA-BR-6566        TCGA-BR-6705        TCGA-BR-6706 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-BR-6707        TCGA-BR-6709        TCGA-BR-6710        TCGA-BR-6801 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-BR-6802        TCGA-BR-6803        TCGA-BR-6852        TCGA-BR-7196 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-BR-7197        TCGA-BR-7703        TCGA-BR-7704        TCGA-BR-7707 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-BR-7715        TCGA-BR-7716        TCGA-BR-7717        TCGA-BR-7722 
  "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-BR-7723        TCGA-BR-7851        TCGA-BR-7901        TCGA-BR-7957 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-CD-5798        TCGA-CD-5799        TCGA-CD-5800        TCGA-CD-5801 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-CD-5802        TCGA-CD-5803        TCGA-CG-4300        TCGA-CG-4301 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-CG-4304        TCGA-CG-4305        TCGA-CG-4306        TCGA-CG-4436 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED" 
       TCGA-CG-4437        TCGA-CG-4438        TCGA-CG-4440        TCGA-CG-4441 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-CG-4443        TCGA-CG-4444        TCGA-CG-4449        TCGA-CG-4455 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED" 
       TCGA-CG-4460        TCGA-CG-4462        TCGA-CG-4465        TCGA-CG-4466 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED" 
       TCGA-CG-4469        TCGA-CG-4472        TCGA-CG-4474        TCGA-CG-4477 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-CG-5716        TCGA-CG-5717        TCGA-CG-5718        TCGA-CG-5719 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-CG-5720        TCGA-CG-5721        TCGA-CG-5722        TCGA-CG-5723 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-CG-5724        TCGA-CG-5725        TCGA-CG-5726        TCGA-CG-5727 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-CG-5728        TCGA-CG-5730        TCGA-CG-5732        TCGA-CG-5733 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-CG-5734        TCGA-D7-5577        TCGA-D7-5578        TCGA-D7-5579 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-D7-6518        TCGA-D7-6519        TCGA-D7-6520        TCGA-D7-6521 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-D7-6522        TCGA-D7-6524        TCGA-D7-6525        TCGA-D7-6526 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-D7-6527        TCGA-D7-6528        TCGA-D7-6815        TCGA-D7-6817 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-D7-6818        TCGA-D7-6820        TCGA-D7-6822        TCGA-EQ-5647 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875        TCGA-FP-7735 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-FP-7829        TCGA-FP-7998        TCGA-IN-7806        TCGA-IN-7808 
  "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-IP-7968 
"5Q GAIN WILD-TYPE" 
       TCGA-B7-5816        TCGA-B7-5818        TCGA-BR-6452        TCGA-BR-6455 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-BR-6457        TCGA-BR-6458        TCGA-BR-6563        TCGA-BR-6564 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-BR-6565        TCGA-BR-6566        TCGA-BR-6705        TCGA-BR-6706 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-BR-6707        TCGA-BR-6709        TCGA-BR-6710        TCGA-BR-6801 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-BR-6802        TCGA-BR-6803        TCGA-BR-6852        TCGA-BR-7196 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-BR-7197        TCGA-BR-7703        TCGA-BR-7704        TCGA-BR-7707 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-BR-7715        TCGA-BR-7716        TCGA-BR-7717        TCGA-BR-7722 
  "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-BR-7723        TCGA-BR-7851        TCGA-BR-7901        TCGA-BR-7957 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-CD-5798        TCGA-CD-5799        TCGA-CD-5800        TCGA-CD-5801 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-CD-5802        TCGA-CD-5803        TCGA-CG-4300        TCGA-CG-4301 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-CG-4304        TCGA-CG-4305        TCGA-CG-4306        TCGA-CG-4436 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED" 
       TCGA-CG-4437        TCGA-CG-4438        TCGA-CG-4440        TCGA-CG-4441 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-CG-4443        TCGA-CG-4444        TCGA-CG-4449        TCGA-CG-4455 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED" 
       TCGA-CG-4460        TCGA-CG-4462        TCGA-CG-4465        TCGA-CG-4466 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED" 
       TCGA-CG-4469        TCGA-CG-4472        TCGA-CG-4474        TCGA-CG-4477 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-CG-5716        TCGA-CG-5717        TCGA-CG-5718        TCGA-CG-5719 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-CG-5720        TCGA-CG-5721        TCGA-CG-5722        TCGA-CG-5723 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-CG-5724        TCGA-CG-5725        TCGA-CG-5726        TCGA-CG-5727 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-CG-5728        TCGA-CG-5730        TCGA-CG-5732        TCGA-CG-5733 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-CG-5734        TCGA-D7-5577        TCGA-D7-5578        TCGA-D7-5579 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-D7-6518        TCGA-D7-6519        TCGA-D7-6520        TCGA-D7-6521 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-D7-6522        TCGA-D7-6524        TCGA-D7-6525        TCGA-D7-6526 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-D7-6527        TCGA-D7-6528        TCGA-D7-6815        TCGA-D7-6817 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-D7-6818        TCGA-D7-6820        TCGA-D7-6822        TCGA-EQ-5647 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875        TCGA-FP-7735 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-FP-7829        TCGA-FP-7998        TCGA-IN-7806        TCGA-IN-7808 
  "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-IP-7968 
"5Q GAIN WILD-TYPE" 
[1] "hr="     "7.7e+07"
D8V2, continuous
D8V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED      1    4
  5Q GAIN WILD-TYPE   59   94
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  FEMALE               1                59
  MALE                 4                94
D8V4, multiclass
D8V5, multiclass
    clus
vv   5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  T1               0                 6
  T2               3                49
  T3               2                59
  T4               0                18
D8V6, multiclass
    clus
vv   5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  N0               3                41
  N1               2                55
  N2               0                24
  N3               0                15
D8V7, multiclass
    clus
vv   5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  M0               5               129
  M1               0                16
  MX               0                 8
D8V8, multiclass
     clus
vv    5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  I                 2                22
  II                2                35
  III               1                42
  IV                0                26
D8V9, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED      0    5
  5Q GAIN WILD-TYPE    5  148
     clus
vv    5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  NO                0                 5
  YES               5               148
D8V10, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED      0    5
  5Q GAIN WILD-TYPE   10  143
     clus
vv    5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  NO                0                10
  YES               5               143

Clustering(9) Variable = 6p gain mutation analysis
D9V1, survival
                   sevent
clus2                0  1
  6P GAIN MUTATED    6  1
  6P GAIN WILD-TYPE 84 14
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
                7                98 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
                1                14 
$`6P GAIN MUTATED`
TCGA-BR-7197 TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7717 TCGA-CG-4438 TCGA-CG-4460 
        1.48         1.25         1.05         0.69        54.05        21.99 
TCGA-D7-6822 
        4.27 

$`6P GAIN WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-6452 TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6458 
        5.62         0.10         0.95         1.41         1.35         1.35 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
        0.85         0.82         0.62         0.62         1.71         2.17 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
        0.99         1.22         0.66         1.12         0.76         0.66 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7716 TCGA-BR-7722 
        0.26         1.22         0.46         0.13         0.82         0.16 
TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-CD-5798 TCGA-CD-5799 
        4.54         0.99         0.95         0.69         0.82         0.69 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CG-4300 TCGA-CG-4301 
        0.36         0.49         0.30         0.07        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4440 
       27.02        15.95         1.02        52.96         8.05         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
       14.01        29.98        47.05        19.07        12.03         1.02 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4474 TCGA-CG-4477 
        8.98        18.94         7.07        12.00         1.02         1.02 
TCGA-CG-5716 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
        1.02         6.94         1.02         1.02         0.99         5.98 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5727 
        0.95        70.06        12.03        15.02        28.96        31.04 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        55.04        21.07         7.99         8.65 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
        3.58         4.54         9.80        15.65         9.63         8.19 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
        6.90         0.69         5.95         6.61         4.14         1.68 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-EQ-5647 TCGA-F1-6177 
        3.65         4.70         4.04         2.93         0.62         6.54 
TCGA-F1-6874 TCGA-F1-6875 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7998 TCGA-IN-7806 
        2.01        72.23         0.39         0.20         3.58         6.87 
TCGA-IN-7808 TCGA-IP-7968 
        3.55         2.53 

  6P GAIN MUTATED 6P GAIN WILD-TYPE 
             0.69              0.07 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
            54.05             72.23 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
            1.480             2.975 
[1] "0.7 - 54.0 (1.5)" "0.1 - 72.2 (3.0)"
       TCGA-B7-5816        TCGA-B7-5818        TCGA-BR-6452        TCGA-BR-6455 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-BR-6457        TCGA-BR-6458        TCGA-BR-6563        TCGA-BR-6564 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-BR-6565        TCGA-BR-6566        TCGA-BR-6705        TCGA-BR-6706 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-BR-6707        TCGA-BR-6709        TCGA-BR-6710        TCGA-BR-6801 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-BR-6802        TCGA-BR-6803        TCGA-BR-6852        TCGA-BR-7196 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-BR-7197        TCGA-BR-7703        TCGA-BR-7704        TCGA-BR-7707 
  "6P GAIN MUTATED" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" 
       TCGA-BR-7715        TCGA-BR-7716        TCGA-BR-7717        TCGA-BR-7722 
  "6P GAIN MUTATED" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" 
       TCGA-BR-7723        TCGA-BR-7851        TCGA-BR-7901        TCGA-BR-7957 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-CD-5798        TCGA-CD-5799        TCGA-CD-5800        TCGA-CD-5801 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-CD-5802        TCGA-CD-5803        TCGA-CG-4300        TCGA-CG-4301 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-CG-4304        TCGA-CG-4305        TCGA-CG-4306        TCGA-CG-4436 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-CG-4437        TCGA-CG-4438        TCGA-CG-4440        TCGA-CG-4441 
"6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-CG-4443        TCGA-CG-4444        TCGA-CG-4449        TCGA-CG-4455 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-CG-4460        TCGA-CG-4462        TCGA-CG-4465        TCGA-CG-4466 
  "6P GAIN MUTATED" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-CG-4469        TCGA-CG-4472        TCGA-CG-4474        TCGA-CG-4477 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-CG-5716        TCGA-CG-5717        TCGA-CG-5718        TCGA-CG-5719 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-CG-5720        TCGA-CG-5721        TCGA-CG-5722        TCGA-CG-5723 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-CG-5724        TCGA-CG-5725        TCGA-CG-5726        TCGA-CG-5727 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-CG-5728        TCGA-CG-5730        TCGA-CG-5732        TCGA-CG-5733 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-CG-5734        TCGA-D7-5577        TCGA-D7-5578        TCGA-D7-5579 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-D7-6518        TCGA-D7-6519        TCGA-D7-6520        TCGA-D7-6521 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-D7-6522        TCGA-D7-6524        TCGA-D7-6525        TCGA-D7-6526 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-D7-6527        TCGA-D7-6528        TCGA-D7-6815        TCGA-D7-6817 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-D7-6818        TCGA-D7-6820        TCGA-D7-6822        TCGA-EQ-5647 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" 
       TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875        TCGA-FP-7735 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-FP-7829        TCGA-FP-7998        TCGA-IN-7806        TCGA-IN-7808 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-IP-7968 
"6P GAIN WILD-TYPE" 
       TCGA-B7-5816        TCGA-B7-5818        TCGA-BR-6452        TCGA-BR-6455 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-BR-6457        TCGA-BR-6458        TCGA-BR-6563        TCGA-BR-6564 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-BR-6565        TCGA-BR-6566        TCGA-BR-6705        TCGA-BR-6706 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-BR-6707        TCGA-BR-6709        TCGA-BR-6710        TCGA-BR-6801 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-BR-6802        TCGA-BR-6803        TCGA-BR-6852        TCGA-BR-7196 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-BR-7197        TCGA-BR-7703        TCGA-BR-7704        TCGA-BR-7707 
  "6P GAIN MUTATED" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" 
       TCGA-BR-7715        TCGA-BR-7716        TCGA-BR-7717        TCGA-BR-7722 
  "6P GAIN MUTATED" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" 
       TCGA-BR-7723        TCGA-BR-7851        TCGA-BR-7901        TCGA-BR-7957 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-CD-5798        TCGA-CD-5799        TCGA-CD-5800        TCGA-CD-5801 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-CD-5802        TCGA-CD-5803        TCGA-CG-4300        TCGA-CG-4301 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-CG-4304        TCGA-CG-4305        TCGA-CG-4306        TCGA-CG-4436 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-CG-4437        TCGA-CG-4438        TCGA-CG-4440        TCGA-CG-4441 
"6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-CG-4443        TCGA-CG-4444        TCGA-CG-4449        TCGA-CG-4455 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-CG-4460        TCGA-CG-4462        TCGA-CG-4465        TCGA-CG-4466 
  "6P GAIN MUTATED" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-CG-4469        TCGA-CG-4472        TCGA-CG-4474        TCGA-CG-4477 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-CG-5716        TCGA-CG-5717        TCGA-CG-5718        TCGA-CG-5719 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-CG-5720        TCGA-CG-5721        TCGA-CG-5722        TCGA-CG-5723 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-CG-5724        TCGA-CG-5725        TCGA-CG-5726        TCGA-CG-5727 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-CG-5728        TCGA-CG-5730        TCGA-CG-5732        TCGA-CG-5733 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-CG-5734        TCGA-D7-5577        TCGA-D7-5578        TCGA-D7-5579 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-D7-6518        TCGA-D7-6519        TCGA-D7-6520        TCGA-D7-6521 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-D7-6522        TCGA-D7-6524        TCGA-D7-6525        TCGA-D7-6526 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-D7-6527        TCGA-D7-6528        TCGA-D7-6815        TCGA-D7-6817 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-D7-6818        TCGA-D7-6820        TCGA-D7-6822        TCGA-EQ-5647 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" 
       TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875        TCGA-FP-7735 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-FP-7829        TCGA-FP-7998        TCGA-IN-7806        TCGA-IN-7808 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-IP-7968 
"6P GAIN WILD-TYPE" 
       TCGA-B7-5816        TCGA-B7-5818        TCGA-BR-6452        TCGA-BR-6455 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-BR-6457        TCGA-BR-6458        TCGA-BR-6563        TCGA-BR-6564 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-BR-6565        TCGA-BR-6566        TCGA-BR-6705        TCGA-BR-6706 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-BR-6707        TCGA-BR-6709        TCGA-BR-6710        TCGA-BR-6801 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-BR-6802        TCGA-BR-6803        TCGA-BR-6852        TCGA-BR-7196 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-BR-7197        TCGA-BR-7703        TCGA-BR-7704        TCGA-BR-7707 
  "6P GAIN MUTATED" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" 
       TCGA-BR-7715        TCGA-BR-7716        TCGA-BR-7717        TCGA-BR-7722 
  "6P GAIN MUTATED" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" 
       TCGA-BR-7723        TCGA-BR-7851        TCGA-BR-7901        TCGA-BR-7957 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-CD-5798        TCGA-CD-5799        TCGA-CD-5800        TCGA-CD-5801 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-CD-5802        TCGA-CD-5803        TCGA-CG-4300        TCGA-CG-4301 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-CG-4304        TCGA-CG-4305        TCGA-CG-4306        TCGA-CG-4436 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-CG-4437        TCGA-CG-4438        TCGA-CG-4440        TCGA-CG-4441 
"6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-CG-4443        TCGA-CG-4444        TCGA-CG-4449        TCGA-CG-4455 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-CG-4460        TCGA-CG-4462        TCGA-CG-4465        TCGA-CG-4466 
  "6P GAIN MUTATED" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-CG-4469        TCGA-CG-4472        TCGA-CG-4474        TCGA-CG-4477 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-CG-5716        TCGA-CG-5717        TCGA-CG-5718        TCGA-CG-5719 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-CG-5720        TCGA-CG-5721        TCGA-CG-5722        TCGA-CG-5723 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-CG-5724        TCGA-CG-5725        TCGA-CG-5726        TCGA-CG-5727 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-CG-5728        TCGA-CG-5730        TCGA-CG-5732        TCGA-CG-5733 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-CG-5734        TCGA-D7-5577        TCGA-D7-5578        TCGA-D7-5579 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-D7-6518        TCGA-D7-6519        TCGA-D7-6520        TCGA-D7-6521 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-D7-6522        TCGA-D7-6524        TCGA-D7-6525        TCGA-D7-6526 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-D7-6527        TCGA-D7-6528        TCGA-D7-6815        TCGA-D7-6817 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-D7-6818        TCGA-D7-6820        TCGA-D7-6822        TCGA-EQ-5647 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" 
       TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875        TCGA-FP-7735 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-FP-7829        TCGA-FP-7998        TCGA-IN-7806        TCGA-IN-7808 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-IP-7968 
"6P GAIN WILD-TYPE" 
[1] "hr=" "1.3"
D9V2, continuous
D9V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED      7    6
  6P GAIN WILD-TYPE   53   92
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  FEMALE               7                53
  MALE                 6                92
D9V4, multiclass
D9V5, multiclass
    clus
vv   6P GAIN MUTATED 6P GAIN WILD-TYPE
  T1               0                 6
  T2               2                50
  T3               5                56
  T4               4                14
D9V6, multiclass
    clus
vv   6P GAIN MUTATED 6P GAIN WILD-TYPE
  N0               5                39
  N1               5                52
  N2               2                22
  N3               0                15
D9V7, multiclass
    clus
vv   6P GAIN MUTATED 6P GAIN WILD-TYPE
  M0              11               123
  M1               1                15
  MX               1                 7
D9V8, multiclass
     clus
vv    6P GAIN MUTATED 6P GAIN WILD-TYPE
  I                 2                22
  II                3                34
  III               2                41
  IV                4                22
D9V9, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED      1   12
  6P GAIN WILD-TYPE    4  141
     clus
vv    6P GAIN MUTATED 6P GAIN WILD-TYPE
  NO                1                 4
  YES              12               141
D9V10, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED      1   12
  6P GAIN WILD-TYPE    9  136
     clus
vv    6P GAIN MUTATED 6P GAIN WILD-TYPE
  NO                1                 9
  YES              12               136

Clustering(10) Variable = 6q gain mutation analysis
D10V1, survival
                   sevent
clus2                0  1
  6Q GAIN MUTATED    6  0
  6Q GAIN WILD-TYPE 84 15
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
                6                99 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
                0                15 
$`6Q GAIN MUTATED`
TCGA-BR-7197 TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7717 TCGA-CG-4438 TCGA-D7-6822 
        1.48         1.25         1.05         0.69        54.05         4.27 

$`6Q GAIN WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-6452 TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6458 
        5.62         0.10         0.95         1.41         1.35         1.35 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
        0.85         0.82         0.62         0.62         1.71         2.17 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
        0.99         1.22         0.66         1.12         0.76         0.66 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7716 TCGA-BR-7722 
        0.26         1.22         0.46         0.13         0.82         0.16 
TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-CD-5798 TCGA-CD-5799 
        4.54         0.99         0.95         0.69         0.82         0.69 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CG-4300 TCGA-CG-4301 
        0.36         0.49         0.30         0.07        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4440 
       27.02        15.95         1.02        52.96         8.05         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4460 
       14.01        29.98        47.05        19.07        12.03        21.99 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4474 
        1.02         8.98        18.94         7.07        12.00         1.02 
TCGA-CG-4477 TCGA-CG-5716 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
        1.02         1.02         6.94         1.02         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 
        5.98         0.95        70.06        12.03        15.02        28.96 
TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       31.04        65.10         4.01        55.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
        8.65         3.58         4.54         9.80        15.65         9.63 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
        8.19         6.90         0.69         5.95         6.61         4.14 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-EQ-5647 
        1.68         3.65         4.70         4.04         2.93         0.62 
TCGA-F1-6177 TCGA-F1-6874 TCGA-F1-6875 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7998 
        6.54         2.01        72.23         0.39         0.20         3.58 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IP-7968 
        6.87         3.55         2.53 

  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
             0.69              0.07 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
            54.05             72.23 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
            1.365             3.020 
[1] "0.7 - 54.0 (1.4)" "0.1 - 72.2 (3.0)"
       TCGA-B7-5816        TCGA-B7-5818        TCGA-BR-6452        TCGA-BR-6455 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-BR-6457        TCGA-BR-6458        TCGA-BR-6563        TCGA-BR-6564 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-BR-6565        TCGA-BR-6566        TCGA-BR-6705        TCGA-BR-6706 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-BR-6707        TCGA-BR-6709        TCGA-BR-6710        TCGA-BR-6801 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-BR-6802        TCGA-BR-6803        TCGA-BR-6852        TCGA-BR-7196 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-BR-7197        TCGA-BR-7703        TCGA-BR-7704        TCGA-BR-7707 
  "6Q GAIN MUTATED" "6Q GAIN WILD-TYPE"   "6Q GAIN MUTATED" "6Q GAIN WILD-TYPE" 
       TCGA-BR-7715        TCGA-BR-7716        TCGA-BR-7717        TCGA-BR-7722 
  "6Q GAIN MUTATED" "6Q GAIN WILD-TYPE"   "6Q GAIN MUTATED" "6Q GAIN WILD-TYPE" 
       TCGA-BR-7723        TCGA-BR-7851        TCGA-BR-7901        TCGA-BR-7957 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-CD-5798        TCGA-CD-5799        TCGA-CD-5800        TCGA-CD-5801 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-CD-5802        TCGA-CD-5803        TCGA-CG-4300        TCGA-CG-4301 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-CG-4304        TCGA-CG-4305        TCGA-CG-4306        TCGA-CG-4436 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-CG-4437        TCGA-CG-4438        TCGA-CG-4440        TCGA-CG-4441 
"6Q GAIN WILD-TYPE"   "6Q GAIN MUTATED" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-CG-4443        TCGA-CG-4444        TCGA-CG-4449        TCGA-CG-4455 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-CG-4460        TCGA-CG-4462        TCGA-CG-4465        TCGA-CG-4466 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-CG-4469        TCGA-CG-4472        TCGA-CG-4474        TCGA-CG-4477 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-CG-5716        TCGA-CG-5717        TCGA-CG-5718        TCGA-CG-5719 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-CG-5720        TCGA-CG-5721        TCGA-CG-5722        TCGA-CG-5723 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-CG-5724        TCGA-CG-5725        TCGA-CG-5726        TCGA-CG-5727 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-CG-5728        TCGA-CG-5730        TCGA-CG-5732        TCGA-CG-5733 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-CG-5734        TCGA-D7-5577        TCGA-D7-5578        TCGA-D7-5579 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-D7-6518        TCGA-D7-6519        TCGA-D7-6520        TCGA-D7-6521 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-D7-6522        TCGA-D7-6524        TCGA-D7-6525        TCGA-D7-6526 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-D7-6527        TCGA-D7-6528        TCGA-D7-6815        TCGA-D7-6817 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-D7-6818        TCGA-D7-6820        TCGA-D7-6822        TCGA-EQ-5647 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE"   "6Q GAIN MUTATED" "6Q GAIN WILD-TYPE" 
       TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875        TCGA-FP-7735 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-FP-7829        TCGA-FP-7998        TCGA-IN-7806        TCGA-IN-7808 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-IP-7968 
"6Q GAIN WILD-TYPE" 
       TCGA-B7-5816        TCGA-B7-5818        TCGA-BR-6452        TCGA-BR-6455 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-BR-6457        TCGA-BR-6458        TCGA-BR-6563        TCGA-BR-6564 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-BR-6565        TCGA-BR-6566        TCGA-BR-6705        TCGA-BR-6706 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-BR-6707        TCGA-BR-6709        TCGA-BR-6710        TCGA-BR-6801 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-BR-6802        TCGA-BR-6803        TCGA-BR-6852        TCGA-BR-7196 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-BR-7197        TCGA-BR-7703        TCGA-BR-7704        TCGA-BR-7707 
  "6Q GAIN MUTATED" "6Q GAIN WILD-TYPE"   "6Q GAIN MUTATED" "6Q GAIN WILD-TYPE" 
       TCGA-BR-7715        TCGA-BR-7716        TCGA-BR-7717        TCGA-BR-7722 
  "6Q GAIN MUTATED" "6Q GAIN WILD-TYPE"   "6Q GAIN MUTATED" "6Q GAIN WILD-TYPE" 
       TCGA-BR-7723        TCGA-BR-7851        TCGA-BR-7901        TCGA-BR-7957 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-CD-5798        TCGA-CD-5799        TCGA-CD-5800        TCGA-CD-5801 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-CD-5802        TCGA-CD-5803        TCGA-CG-4300        TCGA-CG-4301 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-CG-4304        TCGA-CG-4305        TCGA-CG-4306        TCGA-CG-4436 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-CG-4437        TCGA-CG-4438        TCGA-CG-4440        TCGA-CG-4441 
"6Q GAIN WILD-TYPE"   "6Q GAIN MUTATED" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-CG-4443        TCGA-CG-4444        TCGA-CG-4449        TCGA-CG-4455 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-CG-4460        TCGA-CG-4462        TCGA-CG-4465        TCGA-CG-4466 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-CG-4469        TCGA-CG-4472        TCGA-CG-4474        TCGA-CG-4477 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-CG-5716        TCGA-CG-5717        TCGA-CG-5718        TCGA-CG-5719 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-CG-5720        TCGA-CG-5721        TCGA-CG-5722        TCGA-CG-5723 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-CG-5724        TCGA-CG-5725        TCGA-CG-5726        TCGA-CG-5727 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-CG-5728        TCGA-CG-5730        TCGA-CG-5732        TCGA-CG-5733 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-CG-5734        TCGA-D7-5577        TCGA-D7-5578        TCGA-D7-5579 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-D7-6518        TCGA-D7-6519        TCGA-D7-6520        TCGA-D7-6521 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-D7-6522        TCGA-D7-6524        TCGA-D7-6525        TCGA-D7-6526 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-D7-6527        TCGA-D7-6528        TCGA-D7-6815        TCGA-D7-6817 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-D7-6818        TCGA-D7-6820        TCGA-D7-6822        TCGA-EQ-5647 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE"   "6Q GAIN MUTATED" "6Q GAIN WILD-TYPE" 
       TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875        TCGA-FP-7735 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-FP-7829        TCGA-FP-7998        TCGA-IN-7806        TCGA-IN-7808 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-IP-7968 
"6Q GAIN WILD-TYPE" 
       TCGA-B7-5816        TCGA-B7-5818        TCGA-BR-6452        TCGA-BR-6455 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-BR-6457        TCGA-BR-6458        TCGA-BR-6563        TCGA-BR-6564 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-BR-6565        TCGA-BR-6566        TCGA-BR-6705        TCGA-BR-6706 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-BR-6707        TCGA-BR-6709        TCGA-BR-6710        TCGA-BR-6801 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-BR-6802        TCGA-BR-6803        TCGA-BR-6852        TCGA-BR-7196 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-BR-7197        TCGA-BR-7703        TCGA-BR-7704        TCGA-BR-7707 
  "6Q GAIN MUTATED" "6Q GAIN WILD-TYPE"   "6Q GAIN MUTATED" "6Q GAIN WILD-TYPE" 
       TCGA-BR-7715        TCGA-BR-7716        TCGA-BR-7717        TCGA-BR-7722 
  "6Q GAIN MUTATED" "6Q GAIN WILD-TYPE"   "6Q GAIN MUTATED" "6Q GAIN WILD-TYPE" 
       TCGA-BR-7723        TCGA-BR-7851        TCGA-BR-7901        TCGA-BR-7957 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-CD-5798        TCGA-CD-5799        TCGA-CD-5800        TCGA-CD-5801 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-CD-5802        TCGA-CD-5803        TCGA-CG-4300        TCGA-CG-4301 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-CG-4304        TCGA-CG-4305        TCGA-CG-4306        TCGA-CG-4436 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-CG-4437        TCGA-CG-4438        TCGA-CG-4440        TCGA-CG-4441 
"6Q GAIN WILD-TYPE"   "6Q GAIN MUTATED" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-CG-4443        TCGA-CG-4444        TCGA-CG-4449        TCGA-CG-4455 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-CG-4460        TCGA-CG-4462        TCGA-CG-4465        TCGA-CG-4466 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-CG-4469        TCGA-CG-4472        TCGA-CG-4474        TCGA-CG-4477 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-CG-5716        TCGA-CG-5717        TCGA-CG-5718        TCGA-CG-5719 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-CG-5720        TCGA-CG-5721        TCGA-CG-5722        TCGA-CG-5723 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-CG-5724        TCGA-CG-5725        TCGA-CG-5726        TCGA-CG-5727 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-CG-5728        TCGA-CG-5730        TCGA-CG-5732        TCGA-CG-5733 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-CG-5734        TCGA-D7-5577        TCGA-D7-5578        TCGA-D7-5579 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-D7-6518        TCGA-D7-6519        TCGA-D7-6520        TCGA-D7-6521 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-D7-6522        TCGA-D7-6524        TCGA-D7-6525        TCGA-D7-6526 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-D7-6527        TCGA-D7-6528        TCGA-D7-6815        TCGA-D7-6817 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-D7-6818        TCGA-D7-6820        TCGA-D7-6822        TCGA-EQ-5647 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE"   "6Q GAIN MUTATED" "6Q GAIN WILD-TYPE" 
       TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875        TCGA-FP-7735 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-FP-7829        TCGA-FP-7998        TCGA-IN-7806        TCGA-IN-7808 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-IP-7968 
"6Q GAIN WILD-TYPE" 
[1] "hr="     "7.3e+07"
D10V2, continuous
D10V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED      6    6
  6Q GAIN WILD-TYPE   54   92
        clus
vv       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  FEMALE               6                54
  MALE                 6                92
D10V4, multiclass
D10V5, multiclass
    clus
vv   6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  T1               0                 6
  T2               2                50
  T3               5                56
  T4               3                15
D10V6, multiclass
    clus
vv   6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  N0               5                39
  N1               4                53
  N2               2                22
  N3               0                15
D10V7, multiclass
    clus
vv   6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  M0              11               123
  M1               0                16
  MX               1                 7
D10V8, multiclass
     clus
vv    6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  I                 2                22
  II                3                34
  III               2                41
  IV                3                23
D10V9, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED      1   11
  6Q GAIN WILD-TYPE    4  142
     clus
vv    6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  NO                1                 4
  YES              11               142
D10V10, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED      1   11
  6Q GAIN WILD-TYPE    9  137
     clus
vv    6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  NO                1                 9
  YES              11               137

Clustering(11) Variable = 7p gain mutation analysis
D11V1, survival
                   sevent
clus2                0  1
  7P GAIN MUTATED   28  6
  7P GAIN WILD-TYPE 62  9
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               34                71 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
                6                 9 
$`7P GAIN MUTATED`
TCGA-B7-5818 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6801 TCGA-BR-7197 TCGA-BR-7704 
        0.10         0.62         0.62         1.12         1.48         1.25 
TCGA-BR-7715 TCGA-BR-7717 TCGA-BR-7901 TCGA-CD-5801 TCGA-CG-4300 TCGA-CG-4304 
        1.05         0.69         0.95         0.49        20.02        27.02 
TCGA-CG-4305 TCGA-CG-4436 TCGA-CG-4460 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4474 
       15.95        52.96        21.99         7.07        12.00         1.02 
TCGA-CG-5718 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5733 TCGA-D7-6518 
        1.02        12.03        28.96        31.04        21.07         9.80 
TCGA-D7-6521 TCGA-D7-6526 TCGA-D7-6528 TCGA-D7-6818 TCGA-D7-6822 TCGA-F1-6177 
        8.19         6.61         1.68         4.04         4.27         6.54 
TCGA-F1-6874 TCGA-F1-6875 TCGA-FP-7735 TCGA-IN-7808 
        2.01        72.23         0.39         3.55 

$`7P GAIN WILD-TYPE`
TCGA-B7-5816 TCGA-BR-6452 TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
        5.62         0.95         1.41         1.35         1.35         0.85 
TCGA-BR-6564 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 
        0.82         1.71         2.17         0.99         1.22         0.66 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7703 TCGA-BR-7707 
        0.76         0.66         0.26         1.22         0.46         0.13 
TCGA-BR-7716 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7957 TCGA-CD-5798 
        0.82         0.16         4.54         0.99         0.69         0.82 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5802 TCGA-CD-5803 TCGA-CG-4301 TCGA-CG-4306 
        0.69         0.36         0.30         0.07         3.02         1.02 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 
        8.05        54.05         4.01        14.01        29.98        47.05 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4477 
       19.07        12.03         1.02         8.98        18.94         1.02 
TCGA-CG-5716 TCGA-CG-5717 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        1.02         6.94         1.02         0.99         5.98         0.95 
TCGA-CG-5723 TCGA-CG-5725 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5734 
       70.06        15.02        65.10         4.01        55.04         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6522 
        8.65         3.58         4.54        15.65         9.63         6.90 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6527 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6820 
        0.69         5.95         4.14         3.65         4.70         2.93 
TCGA-EQ-5647 TCGA-FP-7829 TCGA-FP-7998 TCGA-IN-7806 TCGA-IP-7968 
        0.62         0.20         3.58         6.87         2.53 

  7P GAIN MUTATED 7P GAIN WILD-TYPE 
             0.10              0.07 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
            72.23             70.06 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
            4.155             2.170 
[1] "0.1 - 72.2 (4.2)" "0.1 - 70.1 (2.2)"
       TCGA-B7-5816        TCGA-B7-5818        TCGA-BR-6452        TCGA-BR-6455 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-BR-6457        TCGA-BR-6458        TCGA-BR-6563        TCGA-BR-6564 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-BR-6565        TCGA-BR-6566        TCGA-BR-6705        TCGA-BR-6706 
  "7P GAIN MUTATED"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-BR-6707        TCGA-BR-6709        TCGA-BR-6710        TCGA-BR-6801 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       TCGA-BR-6802        TCGA-BR-6803        TCGA-BR-6852        TCGA-BR-7196 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-BR-7197        TCGA-BR-7703        TCGA-BR-7704        TCGA-BR-7707 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-BR-7715        TCGA-BR-7716        TCGA-BR-7717        TCGA-BR-7722 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-BR-7723        TCGA-BR-7851        TCGA-BR-7901        TCGA-BR-7957 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-CD-5798        TCGA-CD-5799        TCGA-CD-5800        TCGA-CD-5801 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       TCGA-CD-5802        TCGA-CD-5803        TCGA-CG-4300        TCGA-CG-4301 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-CG-4304        TCGA-CG-4305        TCGA-CG-4306        TCGA-CG-4436 
  "7P GAIN MUTATED"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       TCGA-CG-4437        TCGA-CG-4438        TCGA-CG-4440        TCGA-CG-4441 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-CG-4443        TCGA-CG-4444        TCGA-CG-4449        TCGA-CG-4455 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-CG-4460        TCGA-CG-4462        TCGA-CG-4465        TCGA-CG-4466 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-CG-4469        TCGA-CG-4472        TCGA-CG-4474        TCGA-CG-4477 
  "7P GAIN MUTATED"   "7P GAIN MUTATED"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-CG-5716        TCGA-CG-5717        TCGA-CG-5718        TCGA-CG-5719 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-CG-5720        TCGA-CG-5721        TCGA-CG-5722        TCGA-CG-5723 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-CG-5724        TCGA-CG-5725        TCGA-CG-5726        TCGA-CG-5727 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-CG-5728        TCGA-CG-5730        TCGA-CG-5732        TCGA-CG-5733 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       TCGA-CG-5734        TCGA-D7-5577        TCGA-D7-5578        TCGA-D7-5579 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-D7-6518        TCGA-D7-6519        TCGA-D7-6520        TCGA-D7-6521 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       TCGA-D7-6522        TCGA-D7-6524        TCGA-D7-6525        TCGA-D7-6526 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       TCGA-D7-6527        TCGA-D7-6528        TCGA-D7-6815        TCGA-D7-6817 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-D7-6818        TCGA-D7-6820        TCGA-D7-6822        TCGA-EQ-5647 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875        TCGA-FP-7735 
  "7P GAIN MUTATED"   "7P GAIN MUTATED"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-FP-7829        TCGA-FP-7998        TCGA-IN-7806        TCGA-IN-7808 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       TCGA-IP-7968 
"7P GAIN WILD-TYPE" 
       TCGA-B7-5816        TCGA-B7-5818        TCGA-BR-6452        TCGA-BR-6455 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-BR-6457        TCGA-BR-6458        TCGA-BR-6563        TCGA-BR-6564 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-BR-6565        TCGA-BR-6566        TCGA-BR-6705        TCGA-BR-6706 
  "7P GAIN MUTATED"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-BR-6707        TCGA-BR-6709        TCGA-BR-6710        TCGA-BR-6801 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       TCGA-BR-6802        TCGA-BR-6803        TCGA-BR-6852        TCGA-BR-7196 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-BR-7197        TCGA-BR-7703        TCGA-BR-7704        TCGA-BR-7707 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-BR-7715        TCGA-BR-7716        TCGA-BR-7717        TCGA-BR-7722 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-BR-7723        TCGA-BR-7851        TCGA-BR-7901        TCGA-BR-7957 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-CD-5798        TCGA-CD-5799        TCGA-CD-5800        TCGA-CD-5801 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       TCGA-CD-5802        TCGA-CD-5803        TCGA-CG-4300        TCGA-CG-4301 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-CG-4304        TCGA-CG-4305        TCGA-CG-4306        TCGA-CG-4436 
  "7P GAIN MUTATED"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       TCGA-CG-4437        TCGA-CG-4438        TCGA-CG-4440        TCGA-CG-4441 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-CG-4443        TCGA-CG-4444        TCGA-CG-4449        TCGA-CG-4455 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-CG-4460        TCGA-CG-4462        TCGA-CG-4465        TCGA-CG-4466 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-CG-4469        TCGA-CG-4472        TCGA-CG-4474        TCGA-CG-4477 
  "7P GAIN MUTATED"   "7P GAIN MUTATED"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-CG-5716        TCGA-CG-5717        TCGA-CG-5718        TCGA-CG-5719 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-CG-5720        TCGA-CG-5721        TCGA-CG-5722        TCGA-CG-5723 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-CG-5724        TCGA-CG-5725        TCGA-CG-5726        TCGA-CG-5727 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-CG-5728        TCGA-CG-5730        TCGA-CG-5732        TCGA-CG-5733 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       TCGA-CG-5734        TCGA-D7-5577        TCGA-D7-5578        TCGA-D7-5579 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-D7-6518        TCGA-D7-6519        TCGA-D7-6520        TCGA-D7-6521 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       TCGA-D7-6522        TCGA-D7-6524        TCGA-D7-6525        TCGA-D7-6526 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       TCGA-D7-6527        TCGA-D7-6528        TCGA-D7-6815        TCGA-D7-6817 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-D7-6818        TCGA-D7-6820        TCGA-D7-6822        TCGA-EQ-5647 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875        TCGA-FP-7735 
  "7P GAIN MUTATED"   "7P GAIN MUTATED"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-FP-7829        TCGA-FP-7998        TCGA-IN-7806        TCGA-IN-7808 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       TCGA-IP-7968 
"7P GAIN WILD-TYPE" 
       TCGA-B7-5816        TCGA-B7-5818        TCGA-BR-6452        TCGA-BR-6455 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-BR-6457        TCGA-BR-6458        TCGA-BR-6563        TCGA-BR-6564 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-BR-6565        TCGA-BR-6566        TCGA-BR-6705        TCGA-BR-6706 
  "7P GAIN MUTATED"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-BR-6707        TCGA-BR-6709        TCGA-BR-6710        TCGA-BR-6801 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       TCGA-BR-6802        TCGA-BR-6803        TCGA-BR-6852        TCGA-BR-7196 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-BR-7197        TCGA-BR-7703        TCGA-BR-7704        TCGA-BR-7707 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-BR-7715        TCGA-BR-7716        TCGA-BR-7717        TCGA-BR-7722 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-BR-7723        TCGA-BR-7851        TCGA-BR-7901        TCGA-BR-7957 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-CD-5798        TCGA-CD-5799        TCGA-CD-5800        TCGA-CD-5801 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       TCGA-CD-5802        TCGA-CD-5803        TCGA-CG-4300        TCGA-CG-4301 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-CG-4304        TCGA-CG-4305        TCGA-CG-4306        TCGA-CG-4436 
  "7P GAIN MUTATED"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       TCGA-CG-4437        TCGA-CG-4438        TCGA-CG-4440        TCGA-CG-4441 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-CG-4443        TCGA-CG-4444        TCGA-CG-4449        TCGA-CG-4455 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-CG-4460        TCGA-CG-4462        TCGA-CG-4465        TCGA-CG-4466 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-CG-4469        TCGA-CG-4472        TCGA-CG-4474        TCGA-CG-4477 
  "7P GAIN MUTATED"   "7P GAIN MUTATED"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-CG-5716        TCGA-CG-5717        TCGA-CG-5718        TCGA-CG-5719 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-CG-5720        TCGA-CG-5721        TCGA-CG-5722        TCGA-CG-5723 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-CG-5724        TCGA-CG-5725        TCGA-CG-5726        TCGA-CG-5727 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-CG-5728        TCGA-CG-5730        TCGA-CG-5732        TCGA-CG-5733 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       TCGA-CG-5734        TCGA-D7-5577        TCGA-D7-5578        TCGA-D7-5579 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-D7-6518        TCGA-D7-6519        TCGA-D7-6520        TCGA-D7-6521 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       TCGA-D7-6522        TCGA-D7-6524        TCGA-D7-6525        TCGA-D7-6526 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       TCGA-D7-6527        TCGA-D7-6528        TCGA-D7-6815        TCGA-D7-6817 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-D7-6818        TCGA-D7-6820        TCGA-D7-6822        TCGA-EQ-5647 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875        TCGA-FP-7735 
  "7P GAIN MUTATED"   "7P GAIN MUTATED"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-FP-7829        TCGA-FP-7998        TCGA-IN-7806        TCGA-IN-7808 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       TCGA-IP-7968 
"7P GAIN WILD-TYPE" 
[1] "hr=" "1.4"
D11V2, continuous
D11V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED     16   35
  7P GAIN WILD-TYPE   44   63
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  FEMALE              16                44
  MALE                35                63
D11V4, multiclass
D11V5, multiclass
    clus
vv   7P GAIN MUTATED 7P GAIN WILD-TYPE
  T1               3                 3
  T2              16                36
  T3              18                43
  T4               7                11
D11V6, multiclass
    clus
vv   7P GAIN MUTATED 7P GAIN WILD-TYPE
  N0              19                25
  N1              14                43
  N2               6                18
  N3               6                 9
D11V7, multiclass
    clus
vv   7P GAIN MUTATED 7P GAIN WILD-TYPE
  M0              44                90
  M1               4                12
  MX               3                 5
D11V8, multiclass
     clus
vv    7P GAIN MUTATED 7P GAIN WILD-TYPE
  I                12                12
  II               11                26
  III              11                32
  IV                9                17
D11V9, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED      2   49
  7P GAIN WILD-TYPE    3  104
     clus
vv    7P GAIN MUTATED 7P GAIN WILD-TYPE
  NO                2                 3
  YES              49               104
D11V10, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED      4   47
  7P GAIN WILD-TYPE    6  101
     clus
vv    7P GAIN MUTATED 7P GAIN WILD-TYPE
  NO                4                 6
  YES              47               101

Clustering(12) Variable = 7q gain mutation analysis
D12V1, survival
                   sevent
clus2                0  1
  7Q GAIN MUTATED   23  6
  7Q GAIN WILD-TYPE 67  9
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               29                76 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
                6                 9 
$`7Q GAIN MUTATED`
TCGA-B7-5818 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6801 TCGA-BR-7197 TCGA-BR-7704 
        0.10         0.62         0.62         1.12         1.48         1.25 
TCGA-BR-7715 TCGA-CD-5801 TCGA-CG-4300 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4436 
        1.05         0.49        20.02        27.02        15.95        52.96 
TCGA-CG-4440 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4474 TCGA-CG-5718 TCGA-CG-5724 
        4.01         7.07        12.00         1.02         1.02        12.03 
TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5733 TCGA-D7-6518 TCGA-D7-6521 TCGA-D7-6526 
       28.96        31.04        21.07         9.80         8.19         6.61 
TCGA-D7-6528 TCGA-F1-6177 TCGA-F1-6874 TCGA-F1-6875 TCGA-FP-7735 
        1.68         6.54         2.01        72.23         0.39 

$`7Q GAIN WILD-TYPE`
TCGA-B7-5816 TCGA-BR-6452 TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
        5.62         0.95         1.41         1.35         1.35         0.85 
TCGA-BR-6564 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 
        0.82         1.71         2.17         0.99         1.22         0.66 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7703 TCGA-BR-7707 
        0.76         0.66         0.26         1.22         0.46         0.13 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 
        0.82         0.69         0.16         4.54         0.99         0.95 
TCGA-BR-7957 TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5802 TCGA-CD-5803 
        0.69         0.82         0.69         0.36         0.30         0.07 
TCGA-CG-4301 TCGA-CG-4306 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4441 TCGA-CG-4443 
        3.02         1.02         8.05        54.05        14.01        29.98 
TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4460 TCGA-CG-4462 TCGA-CG-4465 
       47.05        19.07        12.03        21.99         1.02         8.98 
TCGA-CG-4466 TCGA-CG-4477 TCGA-CG-5716 TCGA-CG-5717 TCGA-CG-5719 TCGA-CG-5720 
       18.94         1.02         1.02         6.94         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5725 TCGA-CG-5728 TCGA-CG-5730 
        5.98         0.95        70.06        15.02        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6519 
       55.04         7.99         8.65         3.58         4.54        15.65 
TCGA-D7-6520 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6527 TCGA-D7-6815 
        9.63         6.90         0.69         5.95         4.14         3.65 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-EQ-5647 TCGA-FP-7829 
        4.70         4.04         2.93         4.27         0.62         0.20 
TCGA-FP-7998 TCGA-IN-7806 TCGA-IN-7808 TCGA-IP-7968 
        3.58         6.87         3.55         2.53 

  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
             0.10              0.07 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
            72.23             70.06 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
             6.54              2.35 
[1] "0.1 - 72.2 (6.5)" "0.1 - 70.1 (2.3)"
       TCGA-B7-5816        TCGA-B7-5818        TCGA-BR-6452        TCGA-BR-6455 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-BR-6457        TCGA-BR-6458        TCGA-BR-6563        TCGA-BR-6564 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-BR-6565        TCGA-BR-6566        TCGA-BR-6705        TCGA-BR-6706 
  "7Q GAIN MUTATED"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-BR-6707        TCGA-BR-6709        TCGA-BR-6710        TCGA-BR-6801 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-BR-6802        TCGA-BR-6803        TCGA-BR-6852        TCGA-BR-7196 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-BR-7197        TCGA-BR-7703        TCGA-BR-7704        TCGA-BR-7707 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-BR-7715        TCGA-BR-7716        TCGA-BR-7717        TCGA-BR-7722 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-BR-7723        TCGA-BR-7851        TCGA-BR-7901        TCGA-BR-7957 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-CD-5798        TCGA-CD-5799        TCGA-CD-5800        TCGA-CD-5801 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-CD-5802        TCGA-CD-5803        TCGA-CG-4300        TCGA-CG-4301 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-CG-4304        TCGA-CG-4305        TCGA-CG-4306        TCGA-CG-4436 
  "7Q GAIN MUTATED"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-CG-4437        TCGA-CG-4438        TCGA-CG-4440        TCGA-CG-4441 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-CG-4443        TCGA-CG-4444        TCGA-CG-4449        TCGA-CG-4455 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-CG-4460        TCGA-CG-4462        TCGA-CG-4465        TCGA-CG-4466 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-CG-4469        TCGA-CG-4472        TCGA-CG-4474        TCGA-CG-4477 
  "7Q GAIN MUTATED"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-CG-5716        TCGA-CG-5717        TCGA-CG-5718        TCGA-CG-5719 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-CG-5720        TCGA-CG-5721        TCGA-CG-5722        TCGA-CG-5723 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-CG-5724        TCGA-CG-5725        TCGA-CG-5726        TCGA-CG-5727 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" 
       TCGA-CG-5728        TCGA-CG-5730        TCGA-CG-5732        TCGA-CG-5733 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-CG-5734        TCGA-D7-5577        TCGA-D7-5578        TCGA-D7-5579 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-D7-6518        TCGA-D7-6519        TCGA-D7-6520        TCGA-D7-6521 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-D7-6522        TCGA-D7-6524        TCGA-D7-6525        TCGA-D7-6526 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-D7-6527        TCGA-D7-6528        TCGA-D7-6815        TCGA-D7-6817 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-D7-6818        TCGA-D7-6820        TCGA-D7-6822        TCGA-EQ-5647 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875        TCGA-FP-7735 
  "7Q GAIN MUTATED"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" 
       TCGA-FP-7829        TCGA-FP-7998        TCGA-IN-7806        TCGA-IN-7808 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-IP-7968 
"7Q GAIN WILD-TYPE" 
       TCGA-B7-5816        TCGA-B7-5818        TCGA-BR-6452        TCGA-BR-6455 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-BR-6457        TCGA-BR-6458        TCGA-BR-6563        TCGA-BR-6564 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-BR-6565        TCGA-BR-6566        TCGA-BR-6705        TCGA-BR-6706 
  "7Q GAIN MUTATED"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-BR-6707        TCGA-BR-6709        TCGA-BR-6710        TCGA-BR-6801 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-BR-6802        TCGA-BR-6803        TCGA-BR-6852        TCGA-BR-7196 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-BR-7197        TCGA-BR-7703        TCGA-BR-7704        TCGA-BR-7707 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-BR-7715        TCGA-BR-7716        TCGA-BR-7717        TCGA-BR-7722 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-BR-7723        TCGA-BR-7851        TCGA-BR-7901        TCGA-BR-7957 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-CD-5798        TCGA-CD-5799        TCGA-CD-5800        TCGA-CD-5801 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-CD-5802        TCGA-CD-5803        TCGA-CG-4300        TCGA-CG-4301 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-CG-4304        TCGA-CG-4305        TCGA-CG-4306        TCGA-CG-4436 
  "7Q GAIN MUTATED"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-CG-4437        TCGA-CG-4438        TCGA-CG-4440        TCGA-CG-4441 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-CG-4443        TCGA-CG-4444        TCGA-CG-4449        TCGA-CG-4455 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-CG-4460        TCGA-CG-4462        TCGA-CG-4465        TCGA-CG-4466 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-CG-4469        TCGA-CG-4472        TCGA-CG-4474        TCGA-CG-4477 
  "7Q GAIN MUTATED"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-CG-5716        TCGA-CG-5717        TCGA-CG-5718        TCGA-CG-5719 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-CG-5720        TCGA-CG-5721        TCGA-CG-5722        TCGA-CG-5723 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-CG-5724        TCGA-CG-5725        TCGA-CG-5726        TCGA-CG-5727 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" 
       TCGA-CG-5728        TCGA-CG-5730        TCGA-CG-5732        TCGA-CG-5733 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-CG-5734        TCGA-D7-5577        TCGA-D7-5578        TCGA-D7-5579 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-D7-6518        TCGA-D7-6519        TCGA-D7-6520        TCGA-D7-6521 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-D7-6522        TCGA-D7-6524        TCGA-D7-6525        TCGA-D7-6526 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-D7-6527        TCGA-D7-6528        TCGA-D7-6815        TCGA-D7-6817 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-D7-6818        TCGA-D7-6820        TCGA-D7-6822        TCGA-EQ-5647 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875        TCGA-FP-7735 
  "7Q GAIN MUTATED"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" 
       TCGA-FP-7829        TCGA-FP-7998        TCGA-IN-7806        TCGA-IN-7808 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-IP-7968 
"7Q GAIN WILD-TYPE" 
       TCGA-B7-5816        TCGA-B7-5818        TCGA-BR-6452        TCGA-BR-6455 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-BR-6457        TCGA-BR-6458        TCGA-BR-6563        TCGA-BR-6564 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-BR-6565        TCGA-BR-6566        TCGA-BR-6705        TCGA-BR-6706 
  "7Q GAIN MUTATED"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-BR-6707        TCGA-BR-6709        TCGA-BR-6710        TCGA-BR-6801 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-BR-6802        TCGA-BR-6803        TCGA-BR-6852        TCGA-BR-7196 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-BR-7197        TCGA-BR-7703        TCGA-BR-7704        TCGA-BR-7707 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-BR-7715        TCGA-BR-7716        TCGA-BR-7717        TCGA-BR-7722 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-BR-7723        TCGA-BR-7851        TCGA-BR-7901        TCGA-BR-7957 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-CD-5798        TCGA-CD-5799        TCGA-CD-5800        TCGA-CD-5801 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-CD-5802        TCGA-CD-5803        TCGA-CG-4300        TCGA-CG-4301 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-CG-4304        TCGA-CG-4305        TCGA-CG-4306        TCGA-CG-4436 
  "7Q GAIN MUTATED"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-CG-4437        TCGA-CG-4438        TCGA-CG-4440        TCGA-CG-4441 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-CG-4443        TCGA-CG-4444        TCGA-CG-4449        TCGA-CG-4455 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-CG-4460        TCGA-CG-4462        TCGA-CG-4465        TCGA-CG-4466 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-CG-4469        TCGA-CG-4472        TCGA-CG-4474        TCGA-CG-4477 
  "7Q GAIN MUTATED"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-CG-5716        TCGA-CG-5717        TCGA-CG-5718        TCGA-CG-5719 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-CG-5720        TCGA-CG-5721        TCGA-CG-5722        TCGA-CG-5723 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-CG-5724        TCGA-CG-5725        TCGA-CG-5726        TCGA-CG-5727 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" 
       TCGA-CG-5728        TCGA-CG-5730        TCGA-CG-5732        TCGA-CG-5733 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-CG-5734        TCGA-D7-5577        TCGA-D7-5578        TCGA-D7-5579 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-D7-6518        TCGA-D7-6519        TCGA-D7-6520        TCGA-D7-6521 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-D7-6522        TCGA-D7-6524        TCGA-D7-6525        TCGA-D7-6526 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-D7-6527        TCGA-D7-6528        TCGA-D7-6815        TCGA-D7-6817 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-D7-6818        TCGA-D7-6820        TCGA-D7-6822        TCGA-EQ-5647 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875        TCGA-FP-7735 
  "7Q GAIN MUTATED"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" 
       TCGA-FP-7829        TCGA-FP-7998        TCGA-IN-7806        TCGA-IN-7808 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-IP-7968 
"7Q GAIN WILD-TYPE" 
[1] "hr=" "1.1"
D12V2, continuous
D12V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED     15   30
  7Q GAIN WILD-TYPE   45   68
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  FEMALE              15                45
  MALE                30                68
D12V4, multiclass
D12V5, multiclass
    clus
vv   7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  T1               3                 3
  T2              14                38
  T3              17                44
  T4               5                13
D12V6, multiclass
    clus
vv   7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  N0              17                27
  N1              12                45
  N2               6                18
  N3               5                10
D12V7, multiclass
    clus
vv   7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  M0              38                96
  M1               3                13
  MX               4                 4
D12V8, multiclass
     clus
vv    7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  I                11                13
  II               10                27
  III               9                34
  IV                7                19
D12V9, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED      1   44
  7Q GAIN WILD-TYPE    4  109
     clus
vv    7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  NO                1                 4
  YES              44               109
D12V10, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED      3   42
  7Q GAIN WILD-TYPE    7  106
     clus
vv    7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  NO                3                 7
  YES              42               106

Clustering(13) Variable = 8p gain mutation analysis
D13V1, survival
                   sevent
clus2                0  1
  8P GAIN MUTATED   26  7
  8P GAIN WILD-TYPE 64  8
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               33                72 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
                7                 8 
$`8P GAIN MUTATED`
TCGA-B7-5816 TCGA-BR-6452 TCGA-BR-6455 TCGA-BR-6707 TCGA-BR-6852 TCGA-BR-7704 
        5.62         0.95         1.41         0.99         0.26         1.25 
TCGA-BR-7707 TCGA-BR-7715 TCGA-CG-4305 TCGA-CG-4441 TCGA-CG-4455 TCGA-CG-4460 
        0.13         1.05        15.95        14.01        12.03        21.99 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-5718 TCGA-CG-5725 TCGA-CG-5726 
       18.94         7.07        12.00         1.02        15.02        28.96 
TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5733 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6520 
       31.04        65.10        21.07         3.58         4.54         9.63 
TCGA-D7-6524 TCGA-D7-6526 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
        0.69         6.61         4.70         4.04         2.93         4.27 
TCGA-EQ-5647 TCGA-FP-7829 TCGA-IN-7808 
        0.62         0.20         3.55 

$`8P GAIN WILD-TYPE`
TCGA-B7-5818 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
        0.10         1.35         1.35         0.85         0.82         0.62 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 
        0.62         1.71         2.17         1.22         0.66         1.12 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7716 
        0.76         0.66         1.22         1.48         0.46         0.82 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 
        0.69         0.16         4.54         0.99         0.95         0.69 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
        0.82         0.69         0.36         0.49         0.30         0.07 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
       20.02         3.02        27.02         1.02        52.96         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4462 
       54.05         4.01        29.98        47.05        19.07         1.02 
TCGA-CG-4465 TCGA-CG-4474 TCGA-CG-4477 TCGA-CG-5716 TCGA-CG-5717 TCGA-CG-5719 
        8.98         1.02         1.02         1.02         6.94         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5730 
        0.99         5.98         0.95        70.06        12.03         4.01 
TCGA-CG-5732 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6521 
       55.04         7.99         8.65         9.80        15.65         8.19 
TCGA-D7-6522 TCGA-D7-6525 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-F1-6177 
        6.90         5.95         4.14         1.68         3.65         6.54 
TCGA-F1-6874 TCGA-F1-6875 TCGA-FP-7735 TCGA-FP-7998 TCGA-IN-7806 TCGA-IP-7968 
        2.01        72.23         0.39         3.58         6.87         2.53 

  8P GAIN MUTATED 8P GAIN WILD-TYPE 
             0.13              0.07 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
            65.10             72.23 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
             4.54              1.58 
[1] "0.1 - 65.1 (4.5)" "0.1 - 72.2 (1.6)"
       TCGA-B7-5816        TCGA-B7-5818        TCGA-BR-6452        TCGA-BR-6455 
  "8P GAIN MUTATED" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED"   "8P GAIN MUTATED" 
       TCGA-BR-6457        TCGA-BR-6458        TCGA-BR-6563        TCGA-BR-6564 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-BR-6565        TCGA-BR-6566        TCGA-BR-6705        TCGA-BR-6706 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-BR-6707        TCGA-BR-6709        TCGA-BR-6710        TCGA-BR-6801 
  "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-BR-6802        TCGA-BR-6803        TCGA-BR-6852        TCGA-BR-7196 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" 
       TCGA-BR-7197        TCGA-BR-7703        TCGA-BR-7704        TCGA-BR-7707 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED"   "8P GAIN MUTATED" 
       TCGA-BR-7715        TCGA-BR-7716        TCGA-BR-7717        TCGA-BR-7722 
  "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-BR-7723        TCGA-BR-7851        TCGA-BR-7901        TCGA-BR-7957 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-CD-5798        TCGA-CD-5799        TCGA-CD-5800        TCGA-CD-5801 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-CD-5802        TCGA-CD-5803        TCGA-CG-4300        TCGA-CG-4301 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-CG-4304        TCGA-CG-4305        TCGA-CG-4306        TCGA-CG-4436 
"8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-CG-4437        TCGA-CG-4438        TCGA-CG-4440        TCGA-CG-4441 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" 
       TCGA-CG-4443        TCGA-CG-4444        TCGA-CG-4449        TCGA-CG-4455 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" 
       TCGA-CG-4460        TCGA-CG-4462        TCGA-CG-4465        TCGA-CG-4466 
  "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" 
       TCGA-CG-4469        TCGA-CG-4472        TCGA-CG-4474        TCGA-CG-4477 
  "8P GAIN MUTATED"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-CG-5716        TCGA-CG-5717        TCGA-CG-5718        TCGA-CG-5719 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" 
       TCGA-CG-5720        TCGA-CG-5721        TCGA-CG-5722        TCGA-CG-5723 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-CG-5724        TCGA-CG-5725        TCGA-CG-5726        TCGA-CG-5727 
"8P GAIN WILD-TYPE"   "8P GAIN MUTATED"   "8P GAIN MUTATED"   "8P GAIN MUTATED" 
       TCGA-CG-5728        TCGA-CG-5730        TCGA-CG-5732        TCGA-CG-5733 
  "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" 
       TCGA-CG-5734        TCGA-D7-5577        TCGA-D7-5578        TCGA-D7-5579 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED"   "8P GAIN MUTATED" 
       TCGA-D7-6518        TCGA-D7-6519        TCGA-D7-6520        TCGA-D7-6521 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" 
       TCGA-D7-6522        TCGA-D7-6524        TCGA-D7-6525        TCGA-D7-6526 
"8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" 
       TCGA-D7-6527        TCGA-D7-6528        TCGA-D7-6815        TCGA-D7-6817 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" 
       TCGA-D7-6818        TCGA-D7-6820        TCGA-D7-6822        TCGA-EQ-5647 
  "8P GAIN MUTATED"   "8P GAIN MUTATED"   "8P GAIN MUTATED"   "8P GAIN MUTATED" 
       TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875        TCGA-FP-7735 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-FP-7829        TCGA-FP-7998        TCGA-IN-7806        TCGA-IN-7808 
  "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" 
       TCGA-IP-7968 
"8P GAIN WILD-TYPE" 
       TCGA-B7-5816        TCGA-B7-5818        TCGA-BR-6452        TCGA-BR-6455 
  "8P GAIN MUTATED" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED"   "8P GAIN MUTATED" 
       TCGA-BR-6457        TCGA-BR-6458        TCGA-BR-6563        TCGA-BR-6564 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-BR-6565        TCGA-BR-6566        TCGA-BR-6705        TCGA-BR-6706 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-BR-6707        TCGA-BR-6709        TCGA-BR-6710        TCGA-BR-6801 
  "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-BR-6802        TCGA-BR-6803        TCGA-BR-6852        TCGA-BR-7196 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" 
       TCGA-BR-7197        TCGA-BR-7703        TCGA-BR-7704        TCGA-BR-7707 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED"   "8P GAIN MUTATED" 
       TCGA-BR-7715        TCGA-BR-7716        TCGA-BR-7717        TCGA-BR-7722 
  "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-BR-7723        TCGA-BR-7851        TCGA-BR-7901        TCGA-BR-7957 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-CD-5798        TCGA-CD-5799        TCGA-CD-5800        TCGA-CD-5801 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-CD-5802        TCGA-CD-5803        TCGA-CG-4300        TCGA-CG-4301 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-CG-4304        TCGA-CG-4305        TCGA-CG-4306        TCGA-CG-4436 
"8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-CG-4437        TCGA-CG-4438        TCGA-CG-4440        TCGA-CG-4441 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" 
       TCGA-CG-4443        TCGA-CG-4444        TCGA-CG-4449        TCGA-CG-4455 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" 
       TCGA-CG-4460        TCGA-CG-4462        TCGA-CG-4465        TCGA-CG-4466 
  "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" 
       TCGA-CG-4469        TCGA-CG-4472        TCGA-CG-4474        TCGA-CG-4477 
  "8P GAIN MUTATED"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-CG-5716        TCGA-CG-5717        TCGA-CG-5718        TCGA-CG-5719 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" 
       TCGA-CG-5720        TCGA-CG-5721        TCGA-CG-5722        TCGA-CG-5723 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-CG-5724        TCGA-CG-5725        TCGA-CG-5726        TCGA-CG-5727 
"8P GAIN WILD-TYPE"   "8P GAIN MUTATED"   "8P GAIN MUTATED"   "8P GAIN MUTATED" 
       TCGA-CG-5728        TCGA-CG-5730        TCGA-CG-5732        TCGA-CG-5733 
  "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" 
       TCGA-CG-5734        TCGA-D7-5577        TCGA-D7-5578        TCGA-D7-5579 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED"   "8P GAIN MUTATED" 
       TCGA-D7-6518        TCGA-D7-6519        TCGA-D7-6520        TCGA-D7-6521 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" 
       TCGA-D7-6522        TCGA-D7-6524        TCGA-D7-6525        TCGA-D7-6526 
"8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" 
       TCGA-D7-6527        TCGA-D7-6528        TCGA-D7-6815        TCGA-D7-6817 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" 
       TCGA-D7-6818        TCGA-D7-6820        TCGA-D7-6822        TCGA-EQ-5647 
  "8P GAIN MUTATED"   "8P GAIN MUTATED"   "8P GAIN MUTATED"   "8P GAIN MUTATED" 
       TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875        TCGA-FP-7735 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-FP-7829        TCGA-FP-7998        TCGA-IN-7806        TCGA-IN-7808 
  "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" 
       TCGA-IP-7968 
"8P GAIN WILD-TYPE" 
       TCGA-B7-5816        TCGA-B7-5818        TCGA-BR-6452        TCGA-BR-6455 
  "8P GAIN MUTATED" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED"   "8P GAIN MUTATED" 
       TCGA-BR-6457        TCGA-BR-6458        TCGA-BR-6563        TCGA-BR-6564 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-BR-6565        TCGA-BR-6566        TCGA-BR-6705        TCGA-BR-6706 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-BR-6707        TCGA-BR-6709        TCGA-BR-6710        TCGA-BR-6801 
  "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-BR-6802        TCGA-BR-6803        TCGA-BR-6852        TCGA-BR-7196 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" 
       TCGA-BR-7197        TCGA-BR-7703        TCGA-BR-7704        TCGA-BR-7707 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED"   "8P GAIN MUTATED" 
       TCGA-BR-7715        TCGA-BR-7716        TCGA-BR-7717        TCGA-BR-7722 
  "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-BR-7723        TCGA-BR-7851        TCGA-BR-7901        TCGA-BR-7957 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-CD-5798        TCGA-CD-5799        TCGA-CD-5800        TCGA-CD-5801 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-CD-5802        TCGA-CD-5803        TCGA-CG-4300        TCGA-CG-4301 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-CG-4304        TCGA-CG-4305        TCGA-CG-4306        TCGA-CG-4436 
"8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-CG-4437        TCGA-CG-4438        TCGA-CG-4440        TCGA-CG-4441 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" 
       TCGA-CG-4443        TCGA-CG-4444        TCGA-CG-4449        TCGA-CG-4455 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" 
       TCGA-CG-4460        TCGA-CG-4462        TCGA-CG-4465        TCGA-CG-4466 
  "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" 
       TCGA-CG-4469        TCGA-CG-4472        TCGA-CG-4474        TCGA-CG-4477 
  "8P GAIN MUTATED"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-CG-5716        TCGA-CG-5717        TCGA-CG-5718        TCGA-CG-5719 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" 
       TCGA-CG-5720        TCGA-CG-5721        TCGA-CG-5722        TCGA-CG-5723 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-CG-5724        TCGA-CG-5725        TCGA-CG-5726        TCGA-CG-5727 
"8P GAIN WILD-TYPE"   "8P GAIN MUTATED"   "8P GAIN MUTATED"   "8P GAIN MUTATED" 
       TCGA-CG-5728        TCGA-CG-5730        TCGA-CG-5732        TCGA-CG-5733 
  "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" 
       TCGA-CG-5734        TCGA-D7-5577        TCGA-D7-5578        TCGA-D7-5579 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED"   "8P GAIN MUTATED" 
       TCGA-D7-6518        TCGA-D7-6519        TCGA-D7-6520        TCGA-D7-6521 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" 
       TCGA-D7-6522        TCGA-D7-6524        TCGA-D7-6525        TCGA-D7-6526 
"8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" 
       TCGA-D7-6527        TCGA-D7-6528        TCGA-D7-6815        TCGA-D7-6817 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" 
       TCGA-D7-6818        TCGA-D7-6820        TCGA-D7-6822        TCGA-EQ-5647 
  "8P GAIN MUTATED"   "8P GAIN MUTATED"   "8P GAIN MUTATED"   "8P GAIN MUTATED" 
       TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875        TCGA-FP-7735 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-FP-7829        TCGA-FP-7998        TCGA-IN-7806        TCGA-IN-7808 
  "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" 
       TCGA-IP-7968 
"8P GAIN WILD-TYPE" 
[1] "hr=" "1.6"
D13V2, continuous
D13V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED     25   28
  8P GAIN WILD-TYPE   35   70
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  FEMALE              25                35
  MALE                28                70
D13V4, multiclass
D13V5, multiclass
    clus
vv   8P GAIN MUTATED 8P GAIN WILD-TYPE
  T1               3                 3
  T2              21                31
  T3              16                45
  T4               6                12
D13V6, multiclass
    clus
vv   8P GAIN MUTATED 8P GAIN WILD-TYPE
  N0              17                27
  N1              16                41
  N2               8                16
  N3               5                10
D13V7, multiclass
    clus
vv   8P GAIN MUTATED 8P GAIN WILD-TYPE
  M0              49                85
  M1               3                13
  MX               1                 7
D13V8, multiclass
     clus
vv    8P GAIN MUTATED 8P GAIN WILD-TYPE
  I                 9                15
  II               15                22
  III              13                30
  IV                6                20
D13V9, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED      3   50
  8P GAIN WILD-TYPE    2  103
     clus
vv    8P GAIN MUTATED 8P GAIN WILD-TYPE
  NO                3                 2
  YES              50               103
D13V10, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED      5   48
  8P GAIN WILD-TYPE    5  100
     clus
vv    8P GAIN MUTATED 8P GAIN WILD-TYPE
  NO                5                 5
  YES              48               100

Clustering(14) Variable = 8q gain mutation analysis
D14V1, survival
                   sevent
clus2                0  1
  8Q GAIN MUTATED   39  8
  8Q GAIN WILD-TYPE 51  7
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               47                58 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
                8                 7 
$`8Q GAIN MUTATED`
TCGA-B7-5816 TCGA-BR-6452 TCGA-BR-6455 TCGA-BR-6565 TCGA-BR-6707 TCGA-BR-6709 
        5.62         0.95         1.41         0.62         0.99         1.22 
TCGA-BR-6852 TCGA-BR-7197 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 
        0.26         1.48         1.25         0.13         1.05         0.82 
TCGA-CD-5800 TCGA-CG-4305 TCGA-CG-4436 TCGA-CG-4438 TCGA-CG-4441 TCGA-CG-4443 
        0.36        15.95        52.96        54.05        14.01        29.98 
TCGA-CG-4455 TCGA-CG-4460 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-5718 
       12.03        21.99        18.94         7.07        12.00         1.02 
TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5733 
       15.02        28.96        31.04        65.10         4.01        21.07 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6520 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
        3.58         4.54         9.63         0.69         5.95         6.61 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-EQ-5647 
        3.65         4.70         4.04         2.93         4.27         0.62 
TCGA-F1-6177 TCGA-F1-6875 TCGA-FP-7735 TCGA-FP-7829 TCGA-IN-7808 
        6.54        72.23         0.39         0.20         3.55 

$`8Q GAIN WILD-TYPE`
TCGA-B7-5818 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6566 
        0.10         1.35         1.35         0.85         0.82         0.62 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
        1.71         2.17         0.66         1.12         0.76         0.66 
TCGA-BR-7196 TCGA-BR-7703 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 
        1.22         0.46         0.69         0.16         4.54         0.99 
TCGA-BR-7901 TCGA-BR-7957 TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5801 TCGA-CD-5802 
        0.95         0.69         0.82         0.69         0.49         0.30 
TCGA-CD-5803 TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4306 TCGA-CG-4437 
        0.07        20.02         3.02        27.02         1.02         8.05 
TCGA-CG-4440 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4474 
        4.01        47.05        19.07         1.02         8.98         1.02 
TCGA-CG-4477 TCGA-CG-5716 TCGA-CG-5717 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
        1.02         1.02         6.94         1.02         0.99         5.98 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5732 TCGA-CG-5734 TCGA-D7-5577 
        0.95        70.06        12.03        55.04         7.99         8.65 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6527 TCGA-D7-6528 
        9.80        15.65         8.19         6.90         4.14         1.68 
TCGA-F1-6874 TCGA-FP-7998 TCGA-IN-7806 TCGA-IP-7968 
        2.01         3.58         6.87         2.53 

  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
             0.13              0.07 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
            72.23             70.06 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
             4.27              1.35 
[1] "0.1 - 72.2 (4.3)" "0.1 - 70.1 (1.4)"
       TCGA-B7-5816        TCGA-B7-5818        TCGA-BR-6452        TCGA-BR-6455 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" 
       TCGA-BR-6457        TCGA-BR-6458        TCGA-BR-6563        TCGA-BR-6564 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-BR-6565        TCGA-BR-6566        TCGA-BR-6705        TCGA-BR-6706 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-BR-6707        TCGA-BR-6709        TCGA-BR-6710        TCGA-BR-6801 
  "8Q GAIN MUTATED"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-BR-6802        TCGA-BR-6803        TCGA-BR-6852        TCGA-BR-7196 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-BR-7197        TCGA-BR-7703        TCGA-BR-7704        TCGA-BR-7707 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" 
       TCGA-BR-7715        TCGA-BR-7716        TCGA-BR-7717        TCGA-BR-7722 
  "8Q GAIN MUTATED"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-BR-7723        TCGA-BR-7851        TCGA-BR-7901        TCGA-BR-7957 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-CD-5798        TCGA-CD-5799        TCGA-CD-5800        TCGA-CD-5801 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-CD-5802        TCGA-CD-5803        TCGA-CG-4300        TCGA-CG-4301 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-CG-4304        TCGA-CG-4305        TCGA-CG-4306        TCGA-CG-4436 
"8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
       TCGA-CG-4437        TCGA-CG-4438        TCGA-CG-4440        TCGA-CG-4441 
"8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
       TCGA-CG-4443        TCGA-CG-4444        TCGA-CG-4449        TCGA-CG-4455 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
       TCGA-CG-4460        TCGA-CG-4462        TCGA-CG-4465        TCGA-CG-4466 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
       TCGA-CG-4469        TCGA-CG-4472        TCGA-CG-4474        TCGA-CG-4477 
  "8Q GAIN MUTATED"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-CG-5716        TCGA-CG-5717        TCGA-CG-5718        TCGA-CG-5719 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-CG-5720        TCGA-CG-5721        TCGA-CG-5722        TCGA-CG-5723 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-CG-5724        TCGA-CG-5725        TCGA-CG-5726        TCGA-CG-5727 
"8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" 
       TCGA-CG-5728        TCGA-CG-5730        TCGA-CG-5732        TCGA-CG-5733 
  "8Q GAIN MUTATED"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
       TCGA-CG-5734        TCGA-D7-5577        TCGA-D7-5578        TCGA-D7-5579 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" 
       TCGA-D7-6518        TCGA-D7-6519        TCGA-D7-6520        TCGA-D7-6521 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-D7-6522        TCGA-D7-6524        TCGA-D7-6525        TCGA-D7-6526 
"8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" 
       TCGA-D7-6527        TCGA-D7-6528        TCGA-D7-6815        TCGA-D7-6817 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" 
       TCGA-D7-6818        TCGA-D7-6820        TCGA-D7-6822        TCGA-EQ-5647 
  "8Q GAIN MUTATED"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" 
       TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875        TCGA-FP-7735 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" 
       TCGA-FP-7829        TCGA-FP-7998        TCGA-IN-7806        TCGA-IN-7808 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
       TCGA-IP-7968 
"8Q GAIN WILD-TYPE" 
       TCGA-B7-5816        TCGA-B7-5818        TCGA-BR-6452        TCGA-BR-6455 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" 
       TCGA-BR-6457        TCGA-BR-6458        TCGA-BR-6563        TCGA-BR-6564 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-BR-6565        TCGA-BR-6566        TCGA-BR-6705        TCGA-BR-6706 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-BR-6707        TCGA-BR-6709        TCGA-BR-6710        TCGA-BR-6801 
  "8Q GAIN MUTATED"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-BR-6802        TCGA-BR-6803        TCGA-BR-6852        TCGA-BR-7196 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-BR-7197        TCGA-BR-7703        TCGA-BR-7704        TCGA-BR-7707 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" 
       TCGA-BR-7715        TCGA-BR-7716        TCGA-BR-7717        TCGA-BR-7722 
  "8Q GAIN MUTATED"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-BR-7723        TCGA-BR-7851        TCGA-BR-7901        TCGA-BR-7957 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-CD-5798        TCGA-CD-5799        TCGA-CD-5800        TCGA-CD-5801 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-CD-5802        TCGA-CD-5803        TCGA-CG-4300        TCGA-CG-4301 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-CG-4304        TCGA-CG-4305        TCGA-CG-4306        TCGA-CG-4436 
"8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
       TCGA-CG-4437        TCGA-CG-4438        TCGA-CG-4440        TCGA-CG-4441 
"8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
       TCGA-CG-4443        TCGA-CG-4444        TCGA-CG-4449        TCGA-CG-4455 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
       TCGA-CG-4460        TCGA-CG-4462        TCGA-CG-4465        TCGA-CG-4466 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
       TCGA-CG-4469        TCGA-CG-4472        TCGA-CG-4474        TCGA-CG-4477 
  "8Q GAIN MUTATED"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-CG-5716        TCGA-CG-5717        TCGA-CG-5718        TCGA-CG-5719 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-CG-5720        TCGA-CG-5721        TCGA-CG-5722        TCGA-CG-5723 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-CG-5724        TCGA-CG-5725        TCGA-CG-5726        TCGA-CG-5727 
"8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" 
       TCGA-CG-5728        TCGA-CG-5730        TCGA-CG-5732        TCGA-CG-5733 
  "8Q GAIN MUTATED"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
       TCGA-CG-5734        TCGA-D7-5577        TCGA-D7-5578        TCGA-D7-5579 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" 
       TCGA-D7-6518        TCGA-D7-6519        TCGA-D7-6520        TCGA-D7-6521 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-D7-6522        TCGA-D7-6524        TCGA-D7-6525        TCGA-D7-6526 
"8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" 
       TCGA-D7-6527        TCGA-D7-6528        TCGA-D7-6815        TCGA-D7-6817 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" 
       TCGA-D7-6818        TCGA-D7-6820        TCGA-D7-6822        TCGA-EQ-5647 
  "8Q GAIN MUTATED"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" 
       TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875        TCGA-FP-7735 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" 
       TCGA-FP-7829        TCGA-FP-7998        TCGA-IN-7806        TCGA-IN-7808 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
       TCGA-IP-7968 
"8Q GAIN WILD-TYPE" 
       TCGA-B7-5816        TCGA-B7-5818        TCGA-BR-6452        TCGA-BR-6455 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" 
       TCGA-BR-6457        TCGA-BR-6458        TCGA-BR-6563        TCGA-BR-6564 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-BR-6565        TCGA-BR-6566        TCGA-BR-6705        TCGA-BR-6706 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-BR-6707        TCGA-BR-6709        TCGA-BR-6710        TCGA-BR-6801 
  "8Q GAIN MUTATED"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-BR-6802        TCGA-BR-6803        TCGA-BR-6852        TCGA-BR-7196 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-BR-7197        TCGA-BR-7703        TCGA-BR-7704        TCGA-BR-7707 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" 
       TCGA-BR-7715        TCGA-BR-7716        TCGA-BR-7717        TCGA-BR-7722 
  "8Q GAIN MUTATED"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-BR-7723        TCGA-BR-7851        TCGA-BR-7901        TCGA-BR-7957 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-CD-5798        TCGA-CD-5799        TCGA-CD-5800        TCGA-CD-5801 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-CD-5802        TCGA-CD-5803        TCGA-CG-4300        TCGA-CG-4301 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-CG-4304        TCGA-CG-4305        TCGA-CG-4306        TCGA-CG-4436 
"8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
       TCGA-CG-4437        TCGA-CG-4438        TCGA-CG-4440        TCGA-CG-4441 
"8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
       TCGA-CG-4443        TCGA-CG-4444        TCGA-CG-4449        TCGA-CG-4455 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
       TCGA-CG-4460        TCGA-CG-4462        TCGA-CG-4465        TCGA-CG-4466 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
       TCGA-CG-4469        TCGA-CG-4472        TCGA-CG-4474        TCGA-CG-4477 
  "8Q GAIN MUTATED"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-CG-5716        TCGA-CG-5717        TCGA-CG-5718        TCGA-CG-5719 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-CG-5720        TCGA-CG-5721        TCGA-CG-5722        TCGA-CG-5723 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-CG-5724        TCGA-CG-5725        TCGA-CG-5726        TCGA-CG-5727 
"8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" 
       TCGA-CG-5728        TCGA-CG-5730        TCGA-CG-5732        TCGA-CG-5733 
  "8Q GAIN MUTATED"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
       TCGA-CG-5734        TCGA-D7-5577        TCGA-D7-5578        TCGA-D7-5579 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" 
       TCGA-D7-6518        TCGA-D7-6519        TCGA-D7-6520        TCGA-D7-6521 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-D7-6522        TCGA-D7-6524        TCGA-D7-6525        TCGA-D7-6526 
"8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" 
       TCGA-D7-6527        TCGA-D7-6528        TCGA-D7-6815        TCGA-D7-6817 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" 
       TCGA-D7-6818        TCGA-D7-6820        TCGA-D7-6822        TCGA-EQ-5647 
  "8Q GAIN MUTATED"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" 
       TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875        TCGA-FP-7735 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" 
       TCGA-FP-7829        TCGA-FP-7998        TCGA-IN-7806        TCGA-IN-7808 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
       TCGA-IP-7968 
"8Q GAIN WILD-TYPE" 
[1] "hr=" "1.4"
D14V2, continuous
D14V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED     33   39
  8Q GAIN WILD-TYPE   27   59
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  FEMALE              33                27
  MALE                39                59
D14V4, multiclass
D14V5, multiclass
    clus
vv   8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  T1               5                 1
  T2              27                25
  T3              23                38
  T4               8                10
D14V6, multiclass
    clus
vv   8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  N0              24                20
  N1              22                35
  N2              12                12
  N3               5                10
D14V7, multiclass
    clus
vv   8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  M0              64                70
  M1               4                12
  MX               4                 4
D14V8, multiclass
     clus
vv    8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  I                14                10
  II               19                18
  III              17                26
  IV                9                17
D14V9, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED      3   69
  8Q GAIN WILD-TYPE    2   84
     clus
vv    8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  NO                3                 2
  YES              69                84
D14V10, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED      6   66
  8Q GAIN WILD-TYPE    4   82
     clus
vv    8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  NO                6                 4
  YES              66                82

Clustering(15) Variable = 9p gain mutation analysis
D15V1, survival
                   sevent
clus2                0  1
  9P GAIN MUTATED    6  1
  9P GAIN WILD-TYPE 84 14
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
                7                98 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
                1                14 
$`9P GAIN MUTATED`
TCGA-BR-6707 TCGA-BR-7707 TCGA-CG-4436 TCGA-D7-6528 TCGA-D7-6818 TCGA-D7-6822 
        0.99         0.13        52.96         1.68         4.04         4.27 
TCGA-EQ-5647 
        0.62 

$`9P GAIN WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-6452 TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6458 
        5.62         0.10         0.95         1.41         1.35         1.35 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
        0.85         0.82         0.62         0.62         1.71         2.17 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
        1.22         0.66         1.12         0.76         0.66         0.26 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7716 
        1.22         1.48         0.46         1.25         1.05         0.82 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 
        0.69         0.16         4.54         0.99         0.95         0.69 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
        0.82         0.69         0.36         0.49         0.30         0.07 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4437 
       20.02         3.02        27.02        15.95         1.02         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 
       54.05         4.01        14.01        29.98        47.05        19.07 
TCGA-CG-4455 TCGA-CG-4460 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       12.03        21.99         1.02         8.98        18.94         7.07 
TCGA-CG-4472 TCGA-CG-4474 TCGA-CG-4477 TCGA-CG-5716 TCGA-CG-5717 TCGA-CG-5718 
       12.00         1.02         1.02         1.02         6.94         1.02 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
        1.02         0.99         5.98         0.95        70.06        12.03 
TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       15.02        28.96        31.04        65.10         4.01        55.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99         8.65         3.58         4.54         9.80 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       15.65         9.63         8.19         6.90         0.69         5.95 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6820 TCGA-F1-6177 
        6.61         4.14         3.65         4.70         2.93         6.54 
TCGA-F1-6874 TCGA-F1-6875 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7998 TCGA-IN-7806 
        2.01        72.23         0.39         0.20         3.58         6.87 
TCGA-IN-7808 TCGA-IP-7968 
        3.55         2.53 

  9P GAIN MUTATED 9P GAIN WILD-TYPE 
             0.13              0.07 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
            52.96             72.23 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
            1.680             2.975 
[1] "0.1 - 53.0 (1.7)" "0.1 - 72.2 (3.0)"
       TCGA-B7-5816        TCGA-B7-5818        TCGA-BR-6452        TCGA-BR-6455 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-BR-6457        TCGA-BR-6458        TCGA-BR-6563        TCGA-BR-6564 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-BR-6565        TCGA-BR-6566        TCGA-BR-6705        TCGA-BR-6706 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-BR-6707        TCGA-BR-6709        TCGA-BR-6710        TCGA-BR-6801 
  "9P GAIN MUTATED" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-BR-6802        TCGA-BR-6803        TCGA-BR-6852        TCGA-BR-7196 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-BR-7197        TCGA-BR-7703        TCGA-BR-7704        TCGA-BR-7707 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE"   "9P GAIN MUTATED" 
       TCGA-BR-7715        TCGA-BR-7716        TCGA-BR-7717        TCGA-BR-7722 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-BR-7723        TCGA-BR-7851        TCGA-BR-7901        TCGA-BR-7957 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-CD-5798        TCGA-CD-5799        TCGA-CD-5800        TCGA-CD-5801 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-CD-5802        TCGA-CD-5803        TCGA-CG-4300        TCGA-CG-4301 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-CG-4304        TCGA-CG-4305        TCGA-CG-4306        TCGA-CG-4436 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE"   "9P GAIN MUTATED" 
       TCGA-CG-4437        TCGA-CG-4438        TCGA-CG-4440        TCGA-CG-4441 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-CG-4443        TCGA-CG-4444        TCGA-CG-4449        TCGA-CG-4455 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-CG-4460        TCGA-CG-4462        TCGA-CG-4465        TCGA-CG-4466 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-CG-4469        TCGA-CG-4472        TCGA-CG-4474        TCGA-CG-4477 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-CG-5716        TCGA-CG-5717        TCGA-CG-5718        TCGA-CG-5719 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-CG-5720        TCGA-CG-5721        TCGA-CG-5722        TCGA-CG-5723 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-CG-5724        TCGA-CG-5725        TCGA-CG-5726        TCGA-CG-5727 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-CG-5728        TCGA-CG-5730        TCGA-CG-5732        TCGA-CG-5733 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-CG-5734        TCGA-D7-5577        TCGA-D7-5578        TCGA-D7-5579 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-D7-6518        TCGA-D7-6519        TCGA-D7-6520        TCGA-D7-6521 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-D7-6522        TCGA-D7-6524        TCGA-D7-6525        TCGA-D7-6526 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-D7-6527        TCGA-D7-6528        TCGA-D7-6815        TCGA-D7-6817 
"9P GAIN WILD-TYPE"   "9P GAIN MUTATED" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-D7-6818        TCGA-D7-6820        TCGA-D7-6822        TCGA-EQ-5647 
  "9P GAIN MUTATED" "9P GAIN WILD-TYPE"   "9P GAIN MUTATED"   "9P GAIN MUTATED" 
       TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875        TCGA-FP-7735 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-FP-7829        TCGA-FP-7998        TCGA-IN-7806        TCGA-IN-7808 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-IP-7968 
"9P GAIN WILD-TYPE" 
       TCGA-B7-5816        TCGA-B7-5818        TCGA-BR-6452        TCGA-BR-6455 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-BR-6457        TCGA-BR-6458        TCGA-BR-6563        TCGA-BR-6564 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-BR-6565        TCGA-BR-6566        TCGA-BR-6705        TCGA-BR-6706 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-BR-6707        TCGA-BR-6709        TCGA-BR-6710        TCGA-BR-6801 
  "9P GAIN MUTATED" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-BR-6802        TCGA-BR-6803        TCGA-BR-6852        TCGA-BR-7196 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-BR-7197        TCGA-BR-7703        TCGA-BR-7704        TCGA-BR-7707 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE"   "9P GAIN MUTATED" 
       TCGA-BR-7715        TCGA-BR-7716        TCGA-BR-7717        TCGA-BR-7722 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-BR-7723        TCGA-BR-7851        TCGA-BR-7901        TCGA-BR-7957 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-CD-5798        TCGA-CD-5799        TCGA-CD-5800        TCGA-CD-5801 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-CD-5802        TCGA-CD-5803        TCGA-CG-4300        TCGA-CG-4301 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-CG-4304        TCGA-CG-4305        TCGA-CG-4306        TCGA-CG-4436 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE"   "9P GAIN MUTATED" 
       TCGA-CG-4437        TCGA-CG-4438        TCGA-CG-4440        TCGA-CG-4441 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-CG-4443        TCGA-CG-4444        TCGA-CG-4449        TCGA-CG-4455 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-CG-4460        TCGA-CG-4462        TCGA-CG-4465        TCGA-CG-4466 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-CG-4469        TCGA-CG-4472        TCGA-CG-4474        TCGA-CG-4477 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-CG-5716        TCGA-CG-5717        TCGA-CG-5718        TCGA-CG-5719 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-CG-5720        TCGA-CG-5721        TCGA-CG-5722        TCGA-CG-5723 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-CG-5724        TCGA-CG-5725        TCGA-CG-5726        TCGA-CG-5727 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-CG-5728        TCGA-CG-5730        TCGA-CG-5732        TCGA-CG-5733 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-CG-5734        TCGA-D7-5577        TCGA-D7-5578        TCGA-D7-5579 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-D7-6518        TCGA-D7-6519        TCGA-D7-6520        TCGA-D7-6521 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-D7-6522        TCGA-D7-6524        TCGA-D7-6525        TCGA-D7-6526 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-D7-6527        TCGA-D7-6528        TCGA-D7-6815        TCGA-D7-6817 
"9P GAIN WILD-TYPE"   "9P GAIN MUTATED" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-D7-6818        TCGA-D7-6820        TCGA-D7-6822        TCGA-EQ-5647 
  "9P GAIN MUTATED" "9P GAIN WILD-TYPE"   "9P GAIN MUTATED"   "9P GAIN MUTATED" 
       TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875        TCGA-FP-7735 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-FP-7829        TCGA-FP-7998        TCGA-IN-7806        TCGA-IN-7808 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-IP-7968 
"9P GAIN WILD-TYPE" 
       TCGA-B7-5816        TCGA-B7-5818        TCGA-BR-6452        TCGA-BR-6455 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-BR-6457        TCGA-BR-6458        TCGA-BR-6563        TCGA-BR-6564 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-BR-6565        TCGA-BR-6566        TCGA-BR-6705        TCGA-BR-6706 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-BR-6707        TCGA-BR-6709        TCGA-BR-6710        TCGA-BR-6801 
  "9P GAIN MUTATED" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-BR-6802        TCGA-BR-6803        TCGA-BR-6852        TCGA-BR-7196 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-BR-7197        TCGA-BR-7703        TCGA-BR-7704        TCGA-BR-7707 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE"   "9P GAIN MUTATED" 
       TCGA-BR-7715        TCGA-BR-7716        TCGA-BR-7717        TCGA-BR-7722 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-BR-7723        TCGA-BR-7851        TCGA-BR-7901        TCGA-BR-7957 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-CD-5798        TCGA-CD-5799        TCGA-CD-5800        TCGA-CD-5801 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-CD-5802        TCGA-CD-5803        TCGA-CG-4300        TCGA-CG-4301 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-CG-4304        TCGA-CG-4305        TCGA-CG-4306        TCGA-CG-4436 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE"   "9P GAIN MUTATED" 
       TCGA-CG-4437        TCGA-CG-4438        TCGA-CG-4440        TCGA-CG-4441 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-CG-4443        TCGA-CG-4444        TCGA-CG-4449        TCGA-CG-4455 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-CG-4460        TCGA-CG-4462        TCGA-CG-4465        TCGA-CG-4466 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-CG-4469        TCGA-CG-4472        TCGA-CG-4474        TCGA-CG-4477 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-CG-5716        TCGA-CG-5717        TCGA-CG-5718        TCGA-CG-5719 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-CG-5720        TCGA-CG-5721        TCGA-CG-5722        TCGA-CG-5723 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-CG-5724        TCGA-CG-5725        TCGA-CG-5726        TCGA-CG-5727 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-CG-5728        TCGA-CG-5730        TCGA-CG-5732        TCGA-CG-5733 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-CG-5734        TCGA-D7-5577        TCGA-D7-5578        TCGA-D7-5579 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-D7-6518        TCGA-D7-6519        TCGA-D7-6520        TCGA-D7-6521 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-D7-6522        TCGA-D7-6524        TCGA-D7-6525        TCGA-D7-6526 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-D7-6527        TCGA-D7-6528        TCGA-D7-6815        TCGA-D7-6817 
"9P GAIN WILD-TYPE"   "9P GAIN MUTATED" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-D7-6818        TCGA-D7-6820        TCGA-D7-6822        TCGA-EQ-5647 
  "9P GAIN MUTATED" "9P GAIN WILD-TYPE"   "9P GAIN MUTATED"   "9P GAIN MUTATED" 
       TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875        TCGA-FP-7735 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-FP-7829        TCGA-FP-7998        TCGA-IN-7806        TCGA-IN-7808 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-IP-7968 
"9P GAIN WILD-TYPE" 
[1] "hr=" "1.3"
D15V2, continuous
D15V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED      6    5
  9P GAIN WILD-TYPE   54   93
        clus
vv       9P GAIN MUTATED 9P GAIN WILD-TYPE
  FEMALE               6                54
  MALE                 5                93
D15V4, multiclass
D15V5, multiclass
    clus
vv   9P GAIN MUTATED 9P GAIN WILD-TYPE
  T1               2                 4
  T2               5                47
  T3               2                59
  T4               1                17
D15V6, multiclass
    clus
vv   9P GAIN MUTATED 9P GAIN WILD-TYPE
  N0               6                38
  N1               2                55
  N2               0                24
  N3               2                13
D15V7, multiclass
    clus
vv   9P GAIN MUTATED 9P GAIN WILD-TYPE
  M0              10               124
  M1               1                15
  MX               0                 8
D15V8, multiclass
     clus
vv    9P GAIN MUTATED 9P GAIN WILD-TYPE
  I                 5                19
  II                2                35
  III               0                43
  IV                2                24
D15V9, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED      1   10
  9P GAIN WILD-TYPE    4  143
     clus
vv    9P GAIN MUTATED 9P GAIN WILD-TYPE
  NO                1                 4
  YES              10               143
D15V10, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED      1   10
  9P GAIN WILD-TYPE    9  138
     clus
vv    9P GAIN MUTATED 9P GAIN WILD-TYPE
  NO                1                 9
  YES              10               138

Clustering(16) Variable = 9q gain mutation analysis
D16V1, survival
                   sevent
clus2                0  1
  9Q GAIN MUTATED    8  1
  9Q GAIN WILD-TYPE 82 14
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
                9                96 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
                1                14 
$`9Q GAIN MUTATED`
TCGA-BR-6707 TCGA-BR-7704 TCGA-BR-7707 TCGA-CG-4436 TCGA-D7-6528 TCGA-D7-6818 
        0.99         1.25         0.13        52.96         1.68         4.04 
TCGA-EQ-5647 TCGA-FP-7735 TCGA-IN-7808 
        0.62         0.39         3.55 

$`9Q GAIN WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-6452 TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6458 
        5.62         0.10         0.95         1.41         1.35         1.35 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
        0.85         0.82         0.62         0.62         1.71         2.17 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
        1.22         0.66         1.12         0.76         0.66         0.26 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
        1.22         1.48         0.46         1.05         0.82         0.69 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-CD-5798 
        0.16         4.54         0.99         0.95         0.69         0.82 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CG-4300 
        0.69         0.36         0.49         0.30         0.07        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4437 TCGA-CG-4438 
        3.02        27.02        15.95         1.02         8.05        54.05 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 
        4.01        14.01        29.98        47.05        19.07        12.03 
TCGA-CG-4460 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 
       21.99         1.02         8.98        18.94         7.07        12.00 
TCGA-CG-4474 TCGA-CG-4477 TCGA-CG-5716 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
        1.02         1.02         1.02         6.94         1.02         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 
        0.99         5.98         0.95        70.06        12.03        15.02 
TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       28.96        31.04        65.10         4.01        55.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99         8.65         3.58         4.54         9.80        15.65 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
        9.63         8.19         6.90         0.69         5.95         6.61 
TCGA-D7-6527 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6820 TCGA-D7-6822 TCGA-F1-6177 
        4.14         3.65         4.70         2.93         4.27         6.54 
TCGA-F1-6874 TCGA-F1-6875 TCGA-FP-7829 TCGA-FP-7998 TCGA-IN-7806 TCGA-IP-7968 
        2.01        72.23         0.20         3.58         6.87         2.53 

  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
             0.13              0.07 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
            52.96             72.23 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
             1.25              3.30 
[1] "0.1 - 53.0 (1.2)" "0.1 - 72.2 (3.3)"
       TCGA-B7-5816        TCGA-B7-5818        TCGA-BR-6452        TCGA-BR-6455 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-BR-6457        TCGA-BR-6458        TCGA-BR-6563        TCGA-BR-6564 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-BR-6565        TCGA-BR-6566        TCGA-BR-6705        TCGA-BR-6706 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-BR-6707        TCGA-BR-6709        TCGA-BR-6710        TCGA-BR-6801 
  "9Q GAIN MUTATED" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-BR-6802        TCGA-BR-6803        TCGA-BR-6852        TCGA-BR-7196 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-BR-7197        TCGA-BR-7703        TCGA-BR-7704        TCGA-BR-7707 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE"   "9Q GAIN MUTATED"   "9Q GAIN MUTATED" 
       TCGA-BR-7715        TCGA-BR-7716        TCGA-BR-7717        TCGA-BR-7722 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-BR-7723        TCGA-BR-7851        TCGA-BR-7901        TCGA-BR-7957 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-CD-5798        TCGA-CD-5799        TCGA-CD-5800        TCGA-CD-5801 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-CD-5802        TCGA-CD-5803        TCGA-CG-4300        TCGA-CG-4301 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-CG-4304        TCGA-CG-4305        TCGA-CG-4306        TCGA-CG-4436 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE"   "9Q GAIN MUTATED" 
       TCGA-CG-4437        TCGA-CG-4438        TCGA-CG-4440        TCGA-CG-4441 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-CG-4443        TCGA-CG-4444        TCGA-CG-4449        TCGA-CG-4455 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-CG-4460        TCGA-CG-4462        TCGA-CG-4465        TCGA-CG-4466 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-CG-4469        TCGA-CG-4472        TCGA-CG-4474        TCGA-CG-4477 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-CG-5716        TCGA-CG-5717        TCGA-CG-5718        TCGA-CG-5719 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-CG-5720        TCGA-CG-5721        TCGA-CG-5722        TCGA-CG-5723 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-CG-5724        TCGA-CG-5725        TCGA-CG-5726        TCGA-CG-5727 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-CG-5728        TCGA-CG-5730        TCGA-CG-5732        TCGA-CG-5733 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-CG-5734        TCGA-D7-5577        TCGA-D7-5578        TCGA-D7-5579 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-D7-6518        TCGA-D7-6519        TCGA-D7-6520        TCGA-D7-6521 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-D7-6522        TCGA-D7-6524        TCGA-D7-6525        TCGA-D7-6526 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-D7-6527        TCGA-D7-6528        TCGA-D7-6815        TCGA-D7-6817 
"9Q GAIN WILD-TYPE"   "9Q GAIN MUTATED" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-D7-6818        TCGA-D7-6820        TCGA-D7-6822        TCGA-EQ-5647 
  "9Q GAIN MUTATED" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE"   "9Q GAIN MUTATED" 
       TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875        TCGA-FP-7735 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE"   "9Q GAIN MUTATED" 
       TCGA-FP-7829        TCGA-FP-7998        TCGA-IN-7806        TCGA-IN-7808 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE"   "9Q GAIN MUTATED" 
       TCGA-IP-7968 
"9Q GAIN WILD-TYPE" 
       TCGA-B7-5816        TCGA-B7-5818        TCGA-BR-6452        TCGA-BR-6455 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-BR-6457        TCGA-BR-6458        TCGA-BR-6563        TCGA-BR-6564 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-BR-6565        TCGA-BR-6566        TCGA-BR-6705        TCGA-BR-6706 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-BR-6707        TCGA-BR-6709        TCGA-BR-6710        TCGA-BR-6801 
  "9Q GAIN MUTATED" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-BR-6802        TCGA-BR-6803        TCGA-BR-6852        TCGA-BR-7196 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-BR-7197        TCGA-BR-7703        TCGA-BR-7704        TCGA-BR-7707 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE"   "9Q GAIN MUTATED"   "9Q GAIN MUTATED" 
       TCGA-BR-7715        TCGA-BR-7716        TCGA-BR-7717        TCGA-BR-7722 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-BR-7723        TCGA-BR-7851        TCGA-BR-7901        TCGA-BR-7957 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-CD-5798        TCGA-CD-5799        TCGA-CD-5800        TCGA-CD-5801 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-CD-5802        TCGA-CD-5803        TCGA-CG-4300        TCGA-CG-4301 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-CG-4304        TCGA-CG-4305        TCGA-CG-4306        TCGA-CG-4436 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE"   "9Q GAIN MUTATED" 
       TCGA-CG-4437        TCGA-CG-4438        TCGA-CG-4440        TCGA-CG-4441 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-CG-4443        TCGA-CG-4444        TCGA-CG-4449        TCGA-CG-4455 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-CG-4460        TCGA-CG-4462        TCGA-CG-4465        TCGA-CG-4466 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-CG-4469        TCGA-CG-4472        TCGA-CG-4474        TCGA-CG-4477 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-CG-5716        TCGA-CG-5717        TCGA-CG-5718        TCGA-CG-5719 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-CG-5720        TCGA-CG-5721        TCGA-CG-5722        TCGA-CG-5723 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-CG-5724        TCGA-CG-5725        TCGA-CG-5726        TCGA-CG-5727 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-CG-5728        TCGA-CG-5730        TCGA-CG-5732        TCGA-CG-5733 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-CG-5734        TCGA-D7-5577        TCGA-D7-5578        TCGA-D7-5579 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-D7-6518        TCGA-D7-6519        TCGA-D7-6520        TCGA-D7-6521 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-D7-6522        TCGA-D7-6524        TCGA-D7-6525        TCGA-D7-6526 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-D7-6527        TCGA-D7-6528        TCGA-D7-6815        TCGA-D7-6817 
"9Q GAIN WILD-TYPE"   "9Q GAIN MUTATED" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-D7-6818        TCGA-D7-6820        TCGA-D7-6822        TCGA-EQ-5647 
  "9Q GAIN MUTATED" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE"   "9Q GAIN MUTATED" 
       TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875        TCGA-FP-7735 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE"   "9Q GAIN MUTATED" 
       TCGA-FP-7829        TCGA-FP-7998        TCGA-IN-7806        TCGA-IN-7808 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE"   "9Q GAIN MUTATED" 
       TCGA-IP-7968 
"9Q GAIN WILD-TYPE" 
       TCGA-B7-5816        TCGA-B7-5818        TCGA-BR-6452        TCGA-BR-6455 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-BR-6457        TCGA-BR-6458        TCGA-BR-6563        TCGA-BR-6564 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-BR-6565        TCGA-BR-6566        TCGA-BR-6705        TCGA-BR-6706 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-BR-6707        TCGA-BR-6709        TCGA-BR-6710        TCGA-BR-6801 
  "9Q GAIN MUTATED" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-BR-6802        TCGA-BR-6803        TCGA-BR-6852        TCGA-BR-7196 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-BR-7197        TCGA-BR-7703        TCGA-BR-7704        TCGA-BR-7707 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE"   "9Q GAIN MUTATED"   "9Q GAIN MUTATED" 
       TCGA-BR-7715        TCGA-BR-7716        TCGA-BR-7717        TCGA-BR-7722 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-BR-7723        TCGA-BR-7851        TCGA-BR-7901        TCGA-BR-7957 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-CD-5798        TCGA-CD-5799        TCGA-CD-5800        TCGA-CD-5801 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-CD-5802        TCGA-CD-5803        TCGA-CG-4300        TCGA-CG-4301 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-CG-4304        TCGA-CG-4305        TCGA-CG-4306        TCGA-CG-4436 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE"   "9Q GAIN MUTATED" 
       TCGA-CG-4437        TCGA-CG-4438        TCGA-CG-4440        TCGA-CG-4441 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-CG-4443        TCGA-CG-4444        TCGA-CG-4449        TCGA-CG-4455 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-CG-4460        TCGA-CG-4462        TCGA-CG-4465        TCGA-CG-4466 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-CG-4469        TCGA-CG-4472        TCGA-CG-4474        TCGA-CG-4477 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-CG-5716        TCGA-CG-5717        TCGA-CG-5718        TCGA-CG-5719 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-CG-5720        TCGA-CG-5721        TCGA-CG-5722        TCGA-CG-5723 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-CG-5724        TCGA-CG-5725        TCGA-CG-5726        TCGA-CG-5727 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-CG-5728        TCGA-CG-5730        TCGA-CG-5732        TCGA-CG-5733 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-CG-5734        TCGA-D7-5577        TCGA-D7-5578        TCGA-D7-5579 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-D7-6518        TCGA-D7-6519        TCGA-D7-6520        TCGA-D7-6521 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-D7-6522        TCGA-D7-6524        TCGA-D7-6525        TCGA-D7-6526 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-D7-6527        TCGA-D7-6528        TCGA-D7-6815        TCGA-D7-6817 
"9Q GAIN WILD-TYPE"   "9Q GAIN MUTATED" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-D7-6818        TCGA-D7-6820        TCGA-D7-6822        TCGA-EQ-5647 
  "9Q GAIN MUTATED" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE"   "9Q GAIN MUTATED" 
       TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875        TCGA-FP-7735 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE"   "9Q GAIN MUTATED" 
       TCGA-FP-7829        TCGA-FP-7998        TCGA-IN-7806        TCGA-IN-7808 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE"   "9Q GAIN MUTATED" 
       TCGA-IP-7968 
"9Q GAIN WILD-TYPE" 
[1] "hr=" "1.3"
D16V2, continuous
D16V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED      7    8
  9Q GAIN WILD-TYPE   53   90
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  FEMALE               7                53
  MALE                 8                90
D16V4, multiclass
D16V5, multiclass
    clus
vv   9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  T1               2                 4
  T2               5                47
  T3               5                56
  T4               1                17
D16V6, multiclass
    clus
vv   9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  N0               7                37
  N1               4                53
  N2               0                24
  N3               3                12
D16V7, multiclass
    clus
vv   9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  M0              12               122
  M1               2                14
  MX               1                 7
D16V8, multiclass
     clus
vv    9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  I                 5                19
  II                3                34
  III               2                41
  IV                2                24
D16V9, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED      1   14
  9Q GAIN WILD-TYPE    4  139
     clus
vv    9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  NO                1                 4
  YES              14               139
D16V10, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED      1   14
  9Q GAIN WILD-TYPE    9  134
     clus
vv    9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  NO                1                 9
  YES              14               134

Clustering(17) Variable = 10p gain mutation analysis
D17V1, survival
                    sevent
clus2                 0  1
  10P GAIN MUTATED   14  4
  10P GAIN WILD-TYPE 76 11
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                18                 87 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                 4                 11 
$`10P GAIN MUTATED`
TCGA-BR-6565 TCGA-BR-6801 TCGA-BR-7197 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
        0.62         1.12         1.48         1.05         0.82         0.69 
TCGA-BR-7723 TCGA-CD-5801 TCGA-CG-4300 TCGA-CG-4440 TCGA-CG-4444 TCGA-CG-4460 
        4.54         0.49        20.02         4.01        47.05        21.99 
TCGA-CG-4472 TCGA-CG-5730 TCGA-D7-6518 TCGA-D7-6520 TCGA-EQ-5647 TCGA-F1-6875 
       12.00         4.01         9.80         9.63         0.62        72.23 

$`10P GAIN WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-6452 TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6458 
        5.62         0.10         0.95         1.41         1.35         1.35 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
        0.85         0.82         0.62         1.71         2.17         0.99 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        1.22         0.66         0.76         0.66         0.26         1.22 
TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7722 TCGA-BR-7851 TCGA-BR-7901 
        0.46         1.25         0.13         0.16         0.99         0.95 
TCGA-BR-7957 TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5802 TCGA-CD-5803 
        0.69         0.82         0.69         0.36         0.30         0.07 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02        52.96         8.05 
TCGA-CG-4438 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
       54.05        14.01        29.98        19.07        12.03         1.02 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4474 TCGA-CG-4477 TCGA-CG-5716 
        8.98        18.94         7.07         1.02         1.02         1.02 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.94         1.02         1.02         0.99         5.98         0.95 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 
       70.06        12.03        15.02        28.96        31.04        65.10 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       55.04        21.07         7.99         8.65         3.58         4.54 
TCGA-D7-6519 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       15.65         8.19         6.90         0.69         5.95         6.61 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
        4.14         1.68         3.65         4.70         4.04         2.93 
TCGA-D7-6822 TCGA-F1-6177 TCGA-F1-6874 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7998 
        4.27         6.54         2.01         0.39         0.20         3.58 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IP-7968 
        6.87         3.55         2.53 

  10P GAIN MUTATED 10P GAIN WILD-TYPE 
              0.49               0.07 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
             72.23              70.06 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
              4.01               2.53 
[1] "0.5 - 72.2 (4.0)" "0.1 - 70.1 (2.5)"
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE"   "10P GAIN MUTATED" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
  "10P GAIN MUTATED" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE"   "10P GAIN MUTATED" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
  "10P GAIN MUTATED"   "10P GAIN MUTATED"   "10P GAIN MUTATED" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"10P GAIN WILD-TYPE"   "10P GAIN MUTATED" "10P GAIN WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-CD-5798 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-CD-5799         TCGA-CD-5800         TCGA-CD-5801 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE"   "10P GAIN MUTATED" 
        TCGA-CD-5802         TCGA-CD-5803         TCGA-CG-4300 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE"   "10P GAIN MUTATED" 
        TCGA-CG-4301         TCGA-CG-4304         TCGA-CG-4305 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-CG-4306         TCGA-CG-4436         TCGA-CG-4437 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-CG-4438         TCGA-CG-4440         TCGA-CG-4441 
"10P GAIN WILD-TYPE"   "10P GAIN MUTATED" "10P GAIN WILD-TYPE" 
        TCGA-CG-4443         TCGA-CG-4444         TCGA-CG-4449 
"10P GAIN WILD-TYPE"   "10P GAIN MUTATED" "10P GAIN WILD-TYPE" 
        TCGA-CG-4455         TCGA-CG-4460         TCGA-CG-4462 
"10P GAIN WILD-TYPE"   "10P GAIN MUTATED" "10P GAIN WILD-TYPE" 
        TCGA-CG-4465         TCGA-CG-4466         TCGA-CG-4469 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-CG-4472         TCGA-CG-4474         TCGA-CG-4477 
  "10P GAIN MUTATED" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-CG-5716         TCGA-CG-5717         TCGA-CG-5718 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-CG-5719         TCGA-CG-5720         TCGA-CG-5721 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-CG-5722         TCGA-CG-5723         TCGA-CG-5724 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-CG-5725         TCGA-CG-5726         TCGA-CG-5727 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-CG-5728         TCGA-CG-5730         TCGA-CG-5732 
"10P GAIN WILD-TYPE"   "10P GAIN MUTATED" "10P GAIN WILD-TYPE" 
        TCGA-CG-5733         TCGA-CG-5734         TCGA-D7-5577 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-D7-5578         TCGA-D7-5579         TCGA-D7-6518 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE"   "10P GAIN MUTATED" 
        TCGA-D7-6519         TCGA-D7-6520         TCGA-D7-6521 
"10P GAIN WILD-TYPE"   "10P GAIN MUTATED" "10P GAIN WILD-TYPE" 
        TCGA-D7-6522         TCGA-D7-6524         TCGA-D7-6525 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-D7-6526         TCGA-D7-6527         TCGA-D7-6528 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-D7-6815         TCGA-D7-6817         TCGA-D7-6818 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-D7-6820         TCGA-D7-6822         TCGA-EQ-5647 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE"   "10P GAIN MUTATED" 
        TCGA-F1-6177         TCGA-F1-6874         TCGA-F1-6875 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE"   "10P GAIN MUTATED" 
        TCGA-FP-7735         TCGA-FP-7829         TCGA-FP-7998 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-IN-7806         TCGA-IN-7808         TCGA-IP-7968 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE"   "10P GAIN MUTATED" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
  "10P GAIN MUTATED" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE"   "10P GAIN MUTATED" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
  "10P GAIN MUTATED"   "10P GAIN MUTATED"   "10P GAIN MUTATED" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"10P GAIN WILD-TYPE"   "10P GAIN MUTATED" "10P GAIN WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-CD-5798 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-CD-5799         TCGA-CD-5800         TCGA-CD-5801 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE"   "10P GAIN MUTATED" 
        TCGA-CD-5802         TCGA-CD-5803         TCGA-CG-4300 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE"   "10P GAIN MUTATED" 
        TCGA-CG-4301         TCGA-CG-4304         TCGA-CG-4305 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-CG-4306         TCGA-CG-4436         TCGA-CG-4437 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-CG-4438         TCGA-CG-4440         TCGA-CG-4441 
"10P GAIN WILD-TYPE"   "10P GAIN MUTATED" "10P GAIN WILD-TYPE" 
        TCGA-CG-4443         TCGA-CG-4444         TCGA-CG-4449 
"10P GAIN WILD-TYPE"   "10P GAIN MUTATED" "10P GAIN WILD-TYPE" 
        TCGA-CG-4455         TCGA-CG-4460         TCGA-CG-4462 
"10P GAIN WILD-TYPE"   "10P GAIN MUTATED" "10P GAIN WILD-TYPE" 
        TCGA-CG-4465         TCGA-CG-4466         TCGA-CG-4469 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-CG-4472         TCGA-CG-4474         TCGA-CG-4477 
  "10P GAIN MUTATED" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-CG-5716         TCGA-CG-5717         TCGA-CG-5718 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-CG-5719         TCGA-CG-5720         TCGA-CG-5721 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-CG-5722         TCGA-CG-5723         TCGA-CG-5724 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-CG-5725         TCGA-CG-5726         TCGA-CG-5727 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-CG-5728         TCGA-CG-5730         TCGA-CG-5732 
"10P GAIN WILD-TYPE"   "10P GAIN MUTATED" "10P GAIN WILD-TYPE" 
        TCGA-CG-5733         TCGA-CG-5734         TCGA-D7-5577 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-D7-5578         TCGA-D7-5579         TCGA-D7-6518 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE"   "10P GAIN MUTATED" 
        TCGA-D7-6519         TCGA-D7-6520         TCGA-D7-6521 
"10P GAIN WILD-TYPE"   "10P GAIN MUTATED" "10P GAIN WILD-TYPE" 
        TCGA-D7-6522         TCGA-D7-6524         TCGA-D7-6525 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-D7-6526         TCGA-D7-6527         TCGA-D7-6528 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-D7-6815         TCGA-D7-6817         TCGA-D7-6818 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-D7-6820         TCGA-D7-6822         TCGA-EQ-5647 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE"   "10P GAIN MUTATED" 
        TCGA-F1-6177         TCGA-F1-6874         TCGA-F1-6875 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE"   "10P GAIN MUTATED" 
        TCGA-FP-7735         TCGA-FP-7829         TCGA-FP-7998 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-IN-7806         TCGA-IN-7808         TCGA-IP-7968 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE"   "10P GAIN MUTATED" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
  "10P GAIN MUTATED" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE"   "10P GAIN MUTATED" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
  "10P GAIN MUTATED"   "10P GAIN MUTATED"   "10P GAIN MUTATED" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"10P GAIN WILD-TYPE"   "10P GAIN MUTATED" "10P GAIN WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-CD-5798 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-CD-5799         TCGA-CD-5800         TCGA-CD-5801 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE"   "10P GAIN MUTATED" 
        TCGA-CD-5802         TCGA-CD-5803         TCGA-CG-4300 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE"   "10P GAIN MUTATED" 
        TCGA-CG-4301         TCGA-CG-4304         TCGA-CG-4305 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-CG-4306         TCGA-CG-4436         TCGA-CG-4437 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-CG-4438         TCGA-CG-4440         TCGA-CG-4441 
"10P GAIN WILD-TYPE"   "10P GAIN MUTATED" "10P GAIN WILD-TYPE" 
        TCGA-CG-4443         TCGA-CG-4444         TCGA-CG-4449 
"10P GAIN WILD-TYPE"   "10P GAIN MUTATED" "10P GAIN WILD-TYPE" 
        TCGA-CG-4455         TCGA-CG-4460         TCGA-CG-4462 
"10P GAIN WILD-TYPE"   "10P GAIN MUTATED" "10P GAIN WILD-TYPE" 
        TCGA-CG-4465         TCGA-CG-4466         TCGA-CG-4469 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-CG-4472         TCGA-CG-4474         TCGA-CG-4477 
  "10P GAIN MUTATED" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-CG-5716         TCGA-CG-5717         TCGA-CG-5718 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-CG-5719         TCGA-CG-5720         TCGA-CG-5721 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-CG-5722         TCGA-CG-5723         TCGA-CG-5724 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-CG-5725         TCGA-CG-5726         TCGA-CG-5727 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-CG-5728         TCGA-CG-5730         TCGA-CG-5732 
"10P GAIN WILD-TYPE"   "10P GAIN MUTATED" "10P GAIN WILD-TYPE" 
        TCGA-CG-5733         TCGA-CG-5734         TCGA-D7-5577 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-D7-5578         TCGA-D7-5579         TCGA-D7-6518 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE"   "10P GAIN MUTATED" 
        TCGA-D7-6519         TCGA-D7-6520         TCGA-D7-6521 
"10P GAIN WILD-TYPE"   "10P GAIN MUTATED" "10P GAIN WILD-TYPE" 
        TCGA-D7-6522         TCGA-D7-6524         TCGA-D7-6525 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-D7-6526         TCGA-D7-6527         TCGA-D7-6528 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-D7-6815         TCGA-D7-6817         TCGA-D7-6818 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-D7-6820         TCGA-D7-6822         TCGA-EQ-5647 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE"   "10P GAIN MUTATED" 
        TCGA-F1-6177         TCGA-F1-6874         TCGA-F1-6875 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE"   "10P GAIN MUTATED" 
        TCGA-FP-7735         TCGA-FP-7829         TCGA-FP-7998 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-IN-7806         TCGA-IN-7808         TCGA-IP-7968 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
[1] "hr=" "1"  
D17V2, continuous
D17V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED      9   15
  10P GAIN WILD-TYPE   51   83
        clus
vv       10P GAIN MUTATED 10P GAIN WILD-TYPE
  FEMALE                9                 51
  MALE                 15                 83
D17V4, multiclass
D17V5, multiclass
    clus
vv   10P GAIN MUTATED 10P GAIN WILD-TYPE
  T1                0                  6
  T2                5                 47
  T3               10                 51
  T4                7                 11
D17V6, multiclass
    clus
vv   10P GAIN MUTATED 10P GAIN WILD-TYPE
  N0                5                 39
  N1                9                 48
  N2                5                 19
  N3                3                 12
D17V7, multiclass
    clus
vv   10P GAIN MUTATED 10P GAIN WILD-TYPE
  M0               19                115
  M1                4                 12
  MX                1                  7
D17V8, multiclass
     clus
vv    10P GAIN MUTATED 10P GAIN WILD-TYPE
  I                  1                 23
  II                 5                 32
  III                6                 37
  IV                 9                 17
D17V9, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED      0   24
  10P GAIN WILD-TYPE    5  129
     clus
vv    10P GAIN MUTATED 10P GAIN WILD-TYPE
  NO                 0                  5
  YES               24                129
D17V10, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED      0   24
  10P GAIN WILD-TYPE   10  124
     clus
vv    10P GAIN MUTATED 10P GAIN WILD-TYPE
  NO                 0                 10
  YES               24                124

Clustering(18) Variable = 10q gain mutation analysis
D18V1, survival
                    sevent
clus2                 0  1
  10Q GAIN MUTATED    6  3
  10Q GAIN WILD-TYPE 84 12
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                 9                 96 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                 3                 12 
$`10Q GAIN MUTATED`
TCGA-BR-7197 TCGA-BR-7715 TCGA-CD-5801 TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4472 
        1.48         1.05         0.49        47.05        21.99        12.00 
TCGA-D7-6520 TCGA-EQ-5647 TCGA-F1-6875 
        9.63         0.62        72.23 

$`10Q GAIN WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-6452 TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6458 
        5.62         0.10         0.95         1.41         1.35         1.35 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
        0.85         0.82         0.62         0.62         1.71         2.17 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
        0.99         1.22         0.66         1.12         0.76         0.66 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7716 
        0.26         1.22         0.46         1.25         0.13         0.82 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 
        0.69         0.16         4.54         0.99         0.95         0.69 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5802 TCGA-CD-5803 TCGA-CG-4300 
        0.82         0.69         0.36         0.30         0.07        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02        52.96         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 
       54.05         4.01        14.01        29.98        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4474 TCGA-CG-4477 
        1.02         8.98        18.94         7.07         1.02         1.02 
TCGA-CG-5716 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
        1.02         6.94         1.02         1.02         0.99         5.98 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5727 
        0.95        70.06        12.03        15.02        28.96        31.04 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        55.04        21.07         7.99         8.65 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6521 TCGA-D7-6522 
        3.58         4.54         9.80        15.65         8.19         6.90 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
        0.69         5.95         6.61         4.14         1.68         3.65 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-F1-6177 TCGA-F1-6874 
        4.70         4.04         2.93         4.27         6.54         2.01 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7998 TCGA-IN-7806 TCGA-IN-7808 TCGA-IP-7968 
        0.39         0.20         3.58         6.87         3.55         2.53 

  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
              0.49               0.07 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
             72.23              70.06 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
              9.63               2.73 
[1] "0.5 - 72.2 (9.6)" "0.1 - 70.1 (2.7)"
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE"   "10Q GAIN MUTATED" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
  "10Q GAIN MUTATED" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-CD-5798 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CD-5799         TCGA-CD-5800         TCGA-CD-5801 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE"   "10Q GAIN MUTATED" 
        TCGA-CD-5802         TCGA-CD-5803         TCGA-CG-4300 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CG-4301         TCGA-CG-4304         TCGA-CG-4305 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CG-4306         TCGA-CG-4436         TCGA-CG-4437 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CG-4438         TCGA-CG-4440         TCGA-CG-4441 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CG-4443         TCGA-CG-4444         TCGA-CG-4449 
"10Q GAIN WILD-TYPE"   "10Q GAIN MUTATED" "10Q GAIN WILD-TYPE" 
        TCGA-CG-4455         TCGA-CG-4460         TCGA-CG-4462 
"10Q GAIN WILD-TYPE"   "10Q GAIN MUTATED" "10Q GAIN WILD-TYPE" 
        TCGA-CG-4465         TCGA-CG-4466         TCGA-CG-4469 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CG-4472         TCGA-CG-4474         TCGA-CG-4477 
  "10Q GAIN MUTATED" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CG-5716         TCGA-CG-5717         TCGA-CG-5718 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CG-5719         TCGA-CG-5720         TCGA-CG-5721 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CG-5722         TCGA-CG-5723         TCGA-CG-5724 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CG-5725         TCGA-CG-5726         TCGA-CG-5727 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CG-5728         TCGA-CG-5730         TCGA-CG-5732 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CG-5733         TCGA-CG-5734         TCGA-D7-5577 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-D7-5578         TCGA-D7-5579         TCGA-D7-6518 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-D7-6519         TCGA-D7-6520         TCGA-D7-6521 
"10Q GAIN WILD-TYPE"   "10Q GAIN MUTATED" "10Q GAIN WILD-TYPE" 
        TCGA-D7-6522         TCGA-D7-6524         TCGA-D7-6525 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-D7-6526         TCGA-D7-6527         TCGA-D7-6528 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-D7-6815         TCGA-D7-6817         TCGA-D7-6818 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-D7-6820         TCGA-D7-6822         TCGA-EQ-5647 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE"   "10Q GAIN MUTATED" 
        TCGA-F1-6177         TCGA-F1-6874         TCGA-F1-6875 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE"   "10Q GAIN MUTATED" 
        TCGA-FP-7735         TCGA-FP-7829         TCGA-FP-7998 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-IN-7806         TCGA-IN-7808         TCGA-IP-7968 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE"   "10Q GAIN MUTATED" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
  "10Q GAIN MUTATED" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-CD-5798 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CD-5799         TCGA-CD-5800         TCGA-CD-5801 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE"   "10Q GAIN MUTATED" 
        TCGA-CD-5802         TCGA-CD-5803         TCGA-CG-4300 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CG-4301         TCGA-CG-4304         TCGA-CG-4305 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CG-4306         TCGA-CG-4436         TCGA-CG-4437 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CG-4438         TCGA-CG-4440         TCGA-CG-4441 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CG-4443         TCGA-CG-4444         TCGA-CG-4449 
"10Q GAIN WILD-TYPE"   "10Q GAIN MUTATED" "10Q GAIN WILD-TYPE" 
        TCGA-CG-4455         TCGA-CG-4460         TCGA-CG-4462 
"10Q GAIN WILD-TYPE"   "10Q GAIN MUTATED" "10Q GAIN WILD-TYPE" 
        TCGA-CG-4465         TCGA-CG-4466         TCGA-CG-4469 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CG-4472         TCGA-CG-4474         TCGA-CG-4477 
  "10Q GAIN MUTATED" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CG-5716         TCGA-CG-5717         TCGA-CG-5718 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CG-5719         TCGA-CG-5720         TCGA-CG-5721 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CG-5722         TCGA-CG-5723         TCGA-CG-5724 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CG-5725         TCGA-CG-5726         TCGA-CG-5727 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CG-5728         TCGA-CG-5730         TCGA-CG-5732 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CG-5733         TCGA-CG-5734         TCGA-D7-5577 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-D7-5578         TCGA-D7-5579         TCGA-D7-6518 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-D7-6519         TCGA-D7-6520         TCGA-D7-6521 
"10Q GAIN WILD-TYPE"   "10Q GAIN MUTATED" "10Q GAIN WILD-TYPE" 
        TCGA-D7-6522         TCGA-D7-6524         TCGA-D7-6525 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-D7-6526         TCGA-D7-6527         TCGA-D7-6528 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-D7-6815         TCGA-D7-6817         TCGA-D7-6818 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-D7-6820         TCGA-D7-6822         TCGA-EQ-5647 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE"   "10Q GAIN MUTATED" 
        TCGA-F1-6177         TCGA-F1-6874         TCGA-F1-6875 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE"   "10Q GAIN MUTATED" 
        TCGA-FP-7735         TCGA-FP-7829         TCGA-FP-7998 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-IN-7806         TCGA-IN-7808         TCGA-IP-7968 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE"   "10Q GAIN MUTATED" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
  "10Q GAIN MUTATED" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-CD-5798 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CD-5799         TCGA-CD-5800         TCGA-CD-5801 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE"   "10Q GAIN MUTATED" 
        TCGA-CD-5802         TCGA-CD-5803         TCGA-CG-4300 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CG-4301         TCGA-CG-4304         TCGA-CG-4305 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CG-4306         TCGA-CG-4436         TCGA-CG-4437 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CG-4438         TCGA-CG-4440         TCGA-CG-4441 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CG-4443         TCGA-CG-4444         TCGA-CG-4449 
"10Q GAIN WILD-TYPE"   "10Q GAIN MUTATED" "10Q GAIN WILD-TYPE" 
        TCGA-CG-4455         TCGA-CG-4460         TCGA-CG-4462 
"10Q GAIN WILD-TYPE"   "10Q GAIN MUTATED" "10Q GAIN WILD-TYPE" 
        TCGA-CG-4465         TCGA-CG-4466         TCGA-CG-4469 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CG-4472         TCGA-CG-4474         TCGA-CG-4477 
  "10Q GAIN MUTATED" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CG-5716         TCGA-CG-5717         TCGA-CG-5718 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CG-5719         TCGA-CG-5720         TCGA-CG-5721 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CG-5722         TCGA-CG-5723         TCGA-CG-5724 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CG-5725         TCGA-CG-5726         TCGA-CG-5727 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CG-5728         TCGA-CG-5730         TCGA-CG-5732 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CG-5733         TCGA-CG-5734         TCGA-D7-5577 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-D7-5578         TCGA-D7-5579         TCGA-D7-6518 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-D7-6519         TCGA-D7-6520         TCGA-D7-6521 
"10Q GAIN WILD-TYPE"   "10Q GAIN MUTATED" "10Q GAIN WILD-TYPE" 
        TCGA-D7-6522         TCGA-D7-6524         TCGA-D7-6525 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-D7-6526         TCGA-D7-6527         TCGA-D7-6528 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-D7-6815         TCGA-D7-6817         TCGA-D7-6818 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-D7-6820         TCGA-D7-6822         TCGA-EQ-5647 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE"   "10Q GAIN MUTATED" 
        TCGA-F1-6177         TCGA-F1-6874         TCGA-F1-6875 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE"   "10Q GAIN MUTATED" 
        TCGA-FP-7735         TCGA-FP-7829         TCGA-FP-7998 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-IN-7806         TCGA-IN-7808         TCGA-IP-7968 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
[1] "hr=" "1.1"
D18V2, continuous
D18V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED      3    7
  10Q GAIN WILD-TYPE   57   91
        clus
vv       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  FEMALE                3                 57
  MALE                  7                 91
D18V4, multiclass
D18V5, multiclass
    clus
vv   10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  T1                0                  6
  T2                3                 49
  T3                3                 58
  T4                4                 14
D18V6, multiclass
    clus
vv   10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  N0                3                 41
  N1                3                 54
  N2                3                 21
  N3                1                 14
D18V7, multiclass
    clus
vv   10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  M0                8                126
  M1                2                 14
  MX                0                  8
D18V8, multiclass
     clus
vv    10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  I                  1                 23
  II                 2                 35
  III                3                 40
  IV                 4                 22
D18V9, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED      0   10
  10Q GAIN WILD-TYPE    5  143
     clus
vv    10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  NO                 0                  5
  YES               10                143
D18V10, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED      0   10
  10Q GAIN WILD-TYPE   10  138
     clus
vv    10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  NO                 0                 10
  YES               10                138

Clustering(19) Variable = 11p gain mutation analysis
D19V1, survival
                    sevent
clus2                 0  1
  11P GAIN MUTATED    2  0
  11P GAIN WILD-TYPE 88 15
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 2                103 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 0                 15 
$`11P GAIN MUTATED`
TCGA-BR-6455 TCGA-CG-4300 
        1.41        20.02 

$`11P GAIN WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-6452 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
        5.62         0.10         0.95         1.35         1.35         0.85 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
        0.82         0.62         0.62         1.71         2.17         0.99 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
        1.22         0.66         1.12         0.76         0.66         0.26 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
        1.22         1.48         0.46         1.25         0.13         1.05 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 
        0.82         0.69         0.16         4.54         0.99         0.95 
TCGA-BR-7957 TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        0.69         0.82         0.69         0.36         0.49         0.30 
TCGA-CD-5803 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
        0.07         3.02        27.02        15.95         1.02        52.96 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 
        8.05        54.05         4.01        14.01        29.98        47.05 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4460 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       19.07        12.03        21.99         1.02         8.98        18.94 
TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4474 TCGA-CG-4477 TCGA-CG-5716 TCGA-CG-5717 
        7.07        12.00         1.02         1.02         1.02         6.94 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
        1.02         1.02         0.99         5.98         0.95        70.06 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 
       12.03        15.02        28.96        31.04        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       55.04        21.07         7.99         8.65         3.58         4.54 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
        9.80        15.65         9.63         8.19         6.90         0.69 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
        5.95         6.61         4.14         1.68         3.65         4.70 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-EQ-5647 TCGA-F1-6177 TCGA-F1-6874 
        4.04         2.93         4.27         0.62         6.54         2.01 
TCGA-F1-6875 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7998 TCGA-IN-7806 TCGA-IN-7808 
       72.23         0.39         0.20         3.58         6.87         3.55 
TCGA-IP-7968 
        2.53 

  11P GAIN MUTATED 11P GAIN WILD-TYPE 
              1.41               0.07 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
             20.02              72.23 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
            10.715              2.930 
[1] "1.4 - 20.0 (10.7)" "0.1 - 72.2 (2.9)" 
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
  "11P GAIN MUTATED" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-CD-5798 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-CD-5799         TCGA-CD-5800         TCGA-CD-5801 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-CD-5802         TCGA-CD-5803         TCGA-CG-4300 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE"   "11P GAIN MUTATED" 
        TCGA-CG-4301         TCGA-CG-4304         TCGA-CG-4305 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-CG-4306         TCGA-CG-4436         TCGA-CG-4437 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-CG-4438         TCGA-CG-4440         TCGA-CG-4441 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-CG-4443         TCGA-CG-4444         TCGA-CG-4449 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-CG-4455         TCGA-CG-4460         TCGA-CG-4462 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-CG-4465         TCGA-CG-4466         TCGA-CG-4469 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-CG-4472         TCGA-CG-4474         TCGA-CG-4477 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-CG-5716         TCGA-CG-5717         TCGA-CG-5718 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-CG-5719         TCGA-CG-5720         TCGA-CG-5721 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-CG-5722         TCGA-CG-5723         TCGA-CG-5724 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-CG-5725         TCGA-CG-5726         TCGA-CG-5727 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-CG-5728         TCGA-CG-5730         TCGA-CG-5732 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-CG-5733         TCGA-CG-5734         TCGA-D7-5577 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-D7-5578         TCGA-D7-5579         TCGA-D7-6518 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-D7-6519         TCGA-D7-6520         TCGA-D7-6521 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-D7-6522         TCGA-D7-6524         TCGA-D7-6525 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-D7-6526         TCGA-D7-6527         TCGA-D7-6528 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-D7-6815         TCGA-D7-6817         TCGA-D7-6818 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-D7-6820         TCGA-D7-6822         TCGA-EQ-5647 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-F1-6177         TCGA-F1-6874         TCGA-F1-6875 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-FP-7735         TCGA-FP-7829         TCGA-FP-7998 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-IN-7806         TCGA-IN-7808         TCGA-IP-7968 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
  "11P GAIN MUTATED" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-CD-5798 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-CD-5799         TCGA-CD-5800         TCGA-CD-5801 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-CD-5802         TCGA-CD-5803         TCGA-CG-4300 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE"   "11P GAIN MUTATED" 
        TCGA-CG-4301         TCGA-CG-4304         TCGA-CG-4305 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-CG-4306         TCGA-CG-4436         TCGA-CG-4437 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-CG-4438         TCGA-CG-4440         TCGA-CG-4441 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-CG-4443         TCGA-CG-4444         TCGA-CG-4449 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-CG-4455         TCGA-CG-4460         TCGA-CG-4462 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-CG-4465         TCGA-CG-4466         TCGA-CG-4469 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-CG-4472         TCGA-CG-4474         TCGA-CG-4477 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-CG-5716         TCGA-CG-5717         TCGA-CG-5718 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-CG-5719         TCGA-CG-5720         TCGA-CG-5721 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-CG-5722         TCGA-CG-5723         TCGA-CG-5724 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-CG-5725         TCGA-CG-5726         TCGA-CG-5727 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-CG-5728         TCGA-CG-5730         TCGA-CG-5732 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-CG-5733         TCGA-CG-5734         TCGA-D7-5577 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-D7-5578         TCGA-D7-5579         TCGA-D7-6518 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-D7-6519         TCGA-D7-6520         TCGA-D7-6521 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-D7-6522         TCGA-D7-6524         TCGA-D7-6525 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-D7-6526         TCGA-D7-6527         TCGA-D7-6528 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-D7-6815         TCGA-D7-6817         TCGA-D7-6818 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-D7-6820         TCGA-D7-6822         TCGA-EQ-5647 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-F1-6177         TCGA-F1-6874         TCGA-F1-6875 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-FP-7735         TCGA-FP-7829         TCGA-FP-7998 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-IN-7806         TCGA-IN-7808         TCGA-IP-7968 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
  "11P GAIN MUTATED" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-CD-5798 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-CD-5799         TCGA-CD-5800         TCGA-CD-5801 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-CD-5802         TCGA-CD-5803         TCGA-CG-4300 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE"   "11P GAIN MUTATED" 
        TCGA-CG-4301         TCGA-CG-4304         TCGA-CG-4305 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-CG-4306         TCGA-CG-4436         TCGA-CG-4437 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-CG-4438         TCGA-CG-4440         TCGA-CG-4441 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-CG-4443         TCGA-CG-4444         TCGA-CG-4449 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-CG-4455         TCGA-CG-4460         TCGA-CG-4462 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-CG-4465         TCGA-CG-4466         TCGA-CG-4469 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-CG-4472         TCGA-CG-4474         TCGA-CG-4477 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-CG-5716         TCGA-CG-5717         TCGA-CG-5718 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-CG-5719         TCGA-CG-5720         TCGA-CG-5721 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-CG-5722         TCGA-CG-5723         TCGA-CG-5724 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-CG-5725         TCGA-CG-5726         TCGA-CG-5727 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-CG-5728         TCGA-CG-5730         TCGA-CG-5732 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-CG-5733         TCGA-CG-5734         TCGA-D7-5577 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-D7-5578         TCGA-D7-5579         TCGA-D7-6518 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-D7-6519         TCGA-D7-6520         TCGA-D7-6521 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-D7-6522         TCGA-D7-6524         TCGA-D7-6525 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-D7-6526         TCGA-D7-6527         TCGA-D7-6528 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-D7-6815         TCGA-D7-6817         TCGA-D7-6818 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-D7-6820         TCGA-D7-6822         TCGA-EQ-5647 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-F1-6177         TCGA-F1-6874         TCGA-F1-6875 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-FP-7735         TCGA-FP-7829         TCGA-FP-7998 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-IN-7806         TCGA-IN-7808         TCGA-IP-7968 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
[1] "Remove cluster labels:" "11P GAIN MUTATED"      
clus
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 2                103 
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-BR-6457         TCGA-BR-6458         TCGA-BR-6563 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-BR-6564         TCGA-BR-6565         TCGA-BR-6566 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-BR-6705         TCGA-BR-6706         TCGA-BR-6707 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-BR-6709         TCGA-BR-6710         TCGA-BR-6801 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-BR-6802         TCGA-BR-6803         TCGA-BR-6852 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-BR-7196         TCGA-BR-7197         TCGA-BR-7703 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-BR-7704         TCGA-BR-7707         TCGA-BR-7715 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-BR-7716         TCGA-BR-7717         TCGA-BR-7722 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-BR-7723         TCGA-BR-7851         TCGA-BR-7901 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-BR-7957         TCGA-CD-5798         TCGA-CD-5799 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-CD-5800         TCGA-CD-5801         TCGA-CD-5802 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-CD-5803         TCGA-CG-4301         TCGA-CG-4304 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-CG-4305         TCGA-CG-4306         TCGA-CG-4436 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-CG-4437         TCGA-CG-4438         TCGA-CG-4440 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-CG-4441         TCGA-CG-4443         TCGA-CG-4444 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-CG-4449         TCGA-CG-4455         TCGA-CG-4460 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-CG-4462         TCGA-CG-4465         TCGA-CG-4466 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-CG-4469         TCGA-CG-4472         TCGA-CG-4474 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-CG-4477         TCGA-CG-5716         TCGA-CG-5717 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-CG-5718         TCGA-CG-5719         TCGA-CG-5720 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-CG-5721         TCGA-CG-5722         TCGA-CG-5723 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-CG-5724         TCGA-CG-5725         TCGA-CG-5726 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-CG-5727         TCGA-CG-5728         TCGA-CG-5730 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-CG-5732         TCGA-CG-5733         TCGA-CG-5734 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-D7-5577         TCGA-D7-5578         TCGA-D7-5579 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-D7-6518         TCGA-D7-6519         TCGA-D7-6520 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-D7-6521         TCGA-D7-6522         TCGA-D7-6524 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-D7-6525         TCGA-D7-6526         TCGA-D7-6527 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-D7-6528         TCGA-D7-6815         TCGA-D7-6817 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-D7-6818         TCGA-D7-6820         TCGA-D7-6822 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-EQ-5647         TCGA-F1-6177         TCGA-F1-6874 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-F1-6875         TCGA-FP-7735         TCGA-FP-7829 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-FP-7998         TCGA-IN-7806         TCGA-IN-7808 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-IP-7968 
"11P GAIN WILD-TYPE" 
D19V2, continuous
D19V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED      2    3
  11P GAIN WILD-TYPE   58   95
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  FEMALE                2                 58
  MALE                  3                 95
D19V4, multiclass
D19V5, multiclass
    clus
vv   11P GAIN MUTATED 11P GAIN WILD-TYPE
  T1                0                  6
  T2                0                 52
  T3                4                 57
  T4                1                 17
D19V6, multiclass
    clus
vv   11P GAIN MUTATED 11P GAIN WILD-TYPE
  N0                0                 44
  N1                3                 54
  N2                2                 22
  N3                0                 15
D19V7, multiclass
    clus
vv   11P GAIN MUTATED 11P GAIN WILD-TYPE
  M0                5                129
  M1                0                 16
  MX                0                  8
D19V8, multiclass
     clus
vv    11P GAIN MUTATED 11P GAIN WILD-TYPE
  I                  0                 24
  II                 0                 37
  III                4                 39
  IV                 1                 25
D19V9, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED      0    5
  11P GAIN WILD-TYPE    5  148
     clus
vv    11P GAIN MUTATED 11P GAIN WILD-TYPE
  NO                 0                  5
  YES                5                148
D19V10, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED      0    5
  11P GAIN WILD-TYPE   10  143
     clus
vv    11P GAIN MUTATED 11P GAIN WILD-TYPE
  NO                 0                 10
  YES                5                143

Clustering(20) Variable = 11q gain mutation analysis
D20V1, survival
                    sevent
clus2                 0  1
  11Q GAIN MUTATED    5  1
  11Q GAIN WILD-TYPE 85 14
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 6                 99 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 1                 14 
$`11Q GAIN MUTATED`
TCGA-BR-6455 TCGA-BR-7704 TCGA-CG-4300 TCGA-CG-4472 TCGA-D7-6528 TCGA-F1-6875 
        1.41         1.25        20.02        12.00         1.68        72.23 

$`11Q GAIN WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-6452 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
        5.62         0.10         0.95         1.35         1.35         0.85 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
        0.82         0.62         0.62         1.71         2.17         0.99 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
        1.22         0.66         1.12         0.76         0.66         0.26 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 
        1.22         1.48         0.46         0.13         1.05         0.82 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 
        0.69         0.16         4.54         0.99         0.95         0.69 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
        0.82         0.69         0.36         0.49         0.30         0.07 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02        52.96         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 
       54.05         4.01        14.01        29.98        47.05        19.07 
TCGA-CG-4455 TCGA-CG-4460 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       12.03        21.99         1.02         8.98        18.94         7.07 
TCGA-CG-4474 TCGA-CG-4477 TCGA-CG-5716 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
        1.02         1.02         1.02         6.94         1.02         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 
        0.99         5.98         0.95        70.06        12.03        15.02 
TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       28.96        31.04        65.10         4.01        55.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99         8.65         3.58         4.54         9.80        15.65 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
        9.63         8.19         6.90         0.69         5.95         6.61 
TCGA-D7-6527 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
        4.14         3.65         4.70         4.04         2.93         4.27 
TCGA-EQ-5647 TCGA-F1-6177 TCGA-F1-6874 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7998 
        0.62         6.54         2.01         0.39         0.20         3.58 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IP-7968 
        6.87         3.55         2.53 

  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
              1.25               0.07 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
             72.23              70.06 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
              6.84               2.93 
[1] "1.2 - 72.2 (6.8)" "0.1 - 70.1 (2.9)"
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
  "11Q GAIN MUTATED" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"11Q GAIN WILD-TYPE"   "11Q GAIN MUTATED" "11Q GAIN WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-CD-5798 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-CD-5799         TCGA-CD-5800         TCGA-CD-5801 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-CD-5802         TCGA-CD-5803         TCGA-CG-4300 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE"   "11Q GAIN MUTATED" 
        TCGA-CG-4301         TCGA-CG-4304         TCGA-CG-4305 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-CG-4306         TCGA-CG-4436         TCGA-CG-4437 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-CG-4438         TCGA-CG-4440         TCGA-CG-4441 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-CG-4443         TCGA-CG-4444         TCGA-CG-4449 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-CG-4455         TCGA-CG-4460         TCGA-CG-4462 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-CG-4465         TCGA-CG-4466         TCGA-CG-4469 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-CG-4472         TCGA-CG-4474         TCGA-CG-4477 
  "11Q GAIN MUTATED" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-CG-5716         TCGA-CG-5717         TCGA-CG-5718 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-CG-5719         TCGA-CG-5720         TCGA-CG-5721 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-CG-5722         TCGA-CG-5723         TCGA-CG-5724 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-CG-5725         TCGA-CG-5726         TCGA-CG-5727 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-CG-5728         TCGA-CG-5730         TCGA-CG-5732 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-CG-5733         TCGA-CG-5734         TCGA-D7-5577 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-D7-5578         TCGA-D7-5579         TCGA-D7-6518 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-D7-6519         TCGA-D7-6520         TCGA-D7-6521 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-D7-6522         TCGA-D7-6524         TCGA-D7-6525 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-D7-6526         TCGA-D7-6527         TCGA-D7-6528 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE"   "11Q GAIN MUTATED" 
        TCGA-D7-6815         TCGA-D7-6817         TCGA-D7-6818 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-D7-6820         TCGA-D7-6822         TCGA-EQ-5647 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-F1-6177         TCGA-F1-6874         TCGA-F1-6875 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE"   "11Q GAIN MUTATED" 
        TCGA-FP-7735         TCGA-FP-7829         TCGA-FP-7998 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-IN-7806         TCGA-IN-7808         TCGA-IP-7968 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
  "11Q GAIN MUTATED" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"11Q GAIN WILD-TYPE"   "11Q GAIN MUTATED" "11Q GAIN WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-CD-5798 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-CD-5799         TCGA-CD-5800         TCGA-CD-5801 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-CD-5802         TCGA-CD-5803         TCGA-CG-4300 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE"   "11Q GAIN MUTATED" 
        TCGA-CG-4301         TCGA-CG-4304         TCGA-CG-4305 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-CG-4306         TCGA-CG-4436         TCGA-CG-4437 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-CG-4438         TCGA-CG-4440         TCGA-CG-4441 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-CG-4443         TCGA-CG-4444         TCGA-CG-4449 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-CG-4455         TCGA-CG-4460         TCGA-CG-4462 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-CG-4465         TCGA-CG-4466         TCGA-CG-4469 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-CG-4472         TCGA-CG-4474         TCGA-CG-4477 
  "11Q GAIN MUTATED" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-CG-5716         TCGA-CG-5717         TCGA-CG-5718 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-CG-5719         TCGA-CG-5720         TCGA-CG-5721 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-CG-5722         TCGA-CG-5723         TCGA-CG-5724 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-CG-5725         TCGA-CG-5726         TCGA-CG-5727 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-CG-5728         TCGA-CG-5730         TCGA-CG-5732 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-CG-5733         TCGA-CG-5734         TCGA-D7-5577 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-D7-5578         TCGA-D7-5579         TCGA-D7-6518 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-D7-6519         TCGA-D7-6520         TCGA-D7-6521 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-D7-6522         TCGA-D7-6524         TCGA-D7-6525 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-D7-6526         TCGA-D7-6527         TCGA-D7-6528 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE"   "11Q GAIN MUTATED" 
        TCGA-D7-6815         TCGA-D7-6817         TCGA-D7-6818 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-D7-6820         TCGA-D7-6822         TCGA-EQ-5647 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-F1-6177         TCGA-F1-6874         TCGA-F1-6875 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE"   "11Q GAIN MUTATED" 
        TCGA-FP-7735         TCGA-FP-7829         TCGA-FP-7998 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-IN-7806         TCGA-IN-7808         TCGA-IP-7968 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
  "11Q GAIN MUTATED" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"11Q GAIN WILD-TYPE"   "11Q GAIN MUTATED" "11Q GAIN WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-CD-5798 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-CD-5799         TCGA-CD-5800         TCGA-CD-5801 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-CD-5802         TCGA-CD-5803         TCGA-CG-4300 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE"   "11Q GAIN MUTATED" 
        TCGA-CG-4301         TCGA-CG-4304         TCGA-CG-4305 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-CG-4306         TCGA-CG-4436         TCGA-CG-4437 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-CG-4438         TCGA-CG-4440         TCGA-CG-4441 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-CG-4443         TCGA-CG-4444         TCGA-CG-4449 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-CG-4455         TCGA-CG-4460         TCGA-CG-4462 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-CG-4465         TCGA-CG-4466         TCGA-CG-4469 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-CG-4472         TCGA-CG-4474         TCGA-CG-4477 
  "11Q GAIN MUTATED" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-CG-5716         TCGA-CG-5717         TCGA-CG-5718 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-CG-5719         TCGA-CG-5720         TCGA-CG-5721 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-CG-5722         TCGA-CG-5723         TCGA-CG-5724 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-CG-5725         TCGA-CG-5726         TCGA-CG-5727 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-CG-5728         TCGA-CG-5730         TCGA-CG-5732 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-CG-5733         TCGA-CG-5734         TCGA-D7-5577 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-D7-5578         TCGA-D7-5579         TCGA-D7-6518 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-D7-6519         TCGA-D7-6520         TCGA-D7-6521 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-D7-6522         TCGA-D7-6524         TCGA-D7-6525 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-D7-6526         TCGA-D7-6527         TCGA-D7-6528 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE"   "11Q GAIN MUTATED" 
        TCGA-D7-6815         TCGA-D7-6817         TCGA-D7-6818 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-D7-6820         TCGA-D7-6822         TCGA-EQ-5647 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-F1-6177         TCGA-F1-6874         TCGA-F1-6875 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE"   "11Q GAIN MUTATED" 
        TCGA-FP-7735         TCGA-FP-7829         TCGA-FP-7998 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-IN-7806         TCGA-IN-7808         TCGA-IP-7968 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
[1] "hr="     "7.7e+07"
D20V2, continuous
D20V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED      3    5
  11Q GAIN WILD-TYPE   57   93
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  FEMALE                3                 57
  MALE                  5                 93
D20V4, multiclass
D20V5, multiclass
    clus
vv   11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  T1                0                  6
  T2                2                 50
  T3                4                 57
  T4                2                 16
D20V6, multiclass
    clus
vv   11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  N0                3                 41
  N1                3                 54
  N2                2                 22
  N3                0                 15
D20V7, multiclass
    clus
vv   11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  M0                8                126
  M1                0                 16
  MX                0                  8
D20V8, multiclass
     clus
vv    11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  I                  2                 22
  II                 1                 36
  III                3                 40
  IV                 2                 24
D20V9, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED      0    8
  11Q GAIN WILD-TYPE    5  145
     clus
vv    11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  NO                 0                  5
  YES                8                145
D20V10, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED      0    8
  11Q GAIN WILD-TYPE   10  140
     clus
vv    11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  NO                 0                 10
  YES                8                140

Clustering(21) Variable = 12p gain mutation analysis
D21V1, survival
                    sevent
clus2                 0  1
  12P GAIN MUTATED   10  2
  12P GAIN WILD-TYPE 80 13
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                12                 93 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                 2                 13 
$`12P GAIN MUTATED`
TCGA-BR-6709 TCGA-BR-6801 TCGA-BR-7723 TCGA-CD-5799 TCGA-CG-4460 TCGA-CG-5724 
        1.22         1.12         4.54         0.69        21.99        12.03 
TCGA-CG-5727 TCGA-D7-6820 TCGA-FP-7735 TCGA-FP-7829 TCGA-IN-7808 TCGA-IP-7968 
       31.04         2.93         0.39         0.20         3.55         2.53 

$`12P GAIN WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-6452 TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6458 
        5.62         0.10         0.95         1.41         1.35         1.35 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
        0.85         0.82         0.62         0.62         1.71         2.17 
TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        0.99         0.66         0.76         0.66         0.26         1.22 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 
        1.48         0.46         1.25         0.13         1.05         0.82 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-CD-5798 
        0.69         0.16         0.99         0.95         0.69         0.82 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CG-4300 TCGA-CG-4301 
        0.36         0.49         0.30         0.07        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02        52.96         8.05        54.05 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 
        4.01        14.01        29.98        47.05        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4474 
        1.02         8.98        18.94         7.07        12.00         1.02 
TCGA-CG-4477 TCGA-CG-5716 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
        1.02         1.02         6.94         1.02         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 
        5.98         0.95        70.06        15.02        28.96        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        55.04        21.07         7.99         8.65         3.58 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
        4.54         9.80        15.65         9.63         8.19         6.90 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
        0.69         5.95         6.61         4.14         1.68         3.65 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6822 TCGA-EQ-5647 TCGA-F1-6177 TCGA-F1-6874 
        4.70         4.04         4.27         0.62         6.54         2.01 
TCGA-F1-6875 TCGA-FP-7998 TCGA-IN-7806 
       72.23         3.58         6.87 

  12P GAIN MUTATED 12P GAIN WILD-TYPE 
              0.20               0.07 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
             31.04              72.23 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
              2.73               3.02 
[1] "0.2 - 31.0 (2.7)" "0.1 - 72.2 (3.0)"
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"12P GAIN WILD-TYPE"   "12P GAIN MUTATED" "12P GAIN WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
  "12P GAIN MUTATED" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"12P GAIN WILD-TYPE"   "12P GAIN MUTATED" "12P GAIN WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-CD-5798 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-CD-5799         TCGA-CD-5800         TCGA-CD-5801 
  "12P GAIN MUTATED" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-CD-5802         TCGA-CD-5803         TCGA-CG-4300 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-CG-4301         TCGA-CG-4304         TCGA-CG-4305 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-CG-4306         TCGA-CG-4436         TCGA-CG-4437 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-CG-4438         TCGA-CG-4440         TCGA-CG-4441 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-CG-4443         TCGA-CG-4444         TCGA-CG-4449 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-CG-4455         TCGA-CG-4460         TCGA-CG-4462 
"12P GAIN WILD-TYPE"   "12P GAIN MUTATED" "12P GAIN WILD-TYPE" 
        TCGA-CG-4465         TCGA-CG-4466         TCGA-CG-4469 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-CG-4472         TCGA-CG-4474         TCGA-CG-4477 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-CG-5716         TCGA-CG-5717         TCGA-CG-5718 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-CG-5719         TCGA-CG-5720         TCGA-CG-5721 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-CG-5722         TCGA-CG-5723         TCGA-CG-5724 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE"   "12P GAIN MUTATED" 
        TCGA-CG-5725         TCGA-CG-5726         TCGA-CG-5727 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE"   "12P GAIN MUTATED" 
        TCGA-CG-5728         TCGA-CG-5730         TCGA-CG-5732 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-CG-5733         TCGA-CG-5734         TCGA-D7-5577 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-D7-5578         TCGA-D7-5579         TCGA-D7-6518 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-D7-6519         TCGA-D7-6520         TCGA-D7-6521 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-D7-6522         TCGA-D7-6524         TCGA-D7-6525 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-D7-6526         TCGA-D7-6527         TCGA-D7-6528 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-D7-6815         TCGA-D7-6817         TCGA-D7-6818 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-D7-6820         TCGA-D7-6822         TCGA-EQ-5647 
  "12P GAIN MUTATED" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-F1-6177         TCGA-F1-6874         TCGA-F1-6875 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-FP-7735         TCGA-FP-7829         TCGA-FP-7998 
  "12P GAIN MUTATED"   "12P GAIN MUTATED" "12P GAIN WILD-TYPE" 
        TCGA-IN-7806         TCGA-IN-7808         TCGA-IP-7968 
"12P GAIN WILD-TYPE"   "12P GAIN MUTATED"   "12P GAIN MUTATED" 
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"12P GAIN WILD-TYPE"   "12P GAIN MUTATED" "12P GAIN WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
  "12P GAIN MUTATED" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"12P GAIN WILD-TYPE"   "12P GAIN MUTATED" "12P GAIN WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-CD-5798 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-CD-5799         TCGA-CD-5800         TCGA-CD-5801 
  "12P GAIN MUTATED" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-CD-5802         TCGA-CD-5803         TCGA-CG-4300 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-CG-4301         TCGA-CG-4304         TCGA-CG-4305 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-CG-4306         TCGA-CG-4436         TCGA-CG-4437 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-CG-4438         TCGA-CG-4440         TCGA-CG-4441 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-CG-4443         TCGA-CG-4444         TCGA-CG-4449 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-CG-4455         TCGA-CG-4460         TCGA-CG-4462 
"12P GAIN WILD-TYPE"   "12P GAIN MUTATED" "12P GAIN WILD-TYPE" 
        TCGA-CG-4465         TCGA-CG-4466         TCGA-CG-4469 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-CG-4472         TCGA-CG-4474         TCGA-CG-4477 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-CG-5716         TCGA-CG-5717         TCGA-CG-5718 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-CG-5719         TCGA-CG-5720         TCGA-CG-5721 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-CG-5722         TCGA-CG-5723         TCGA-CG-5724 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE"   "12P GAIN MUTATED" 
        TCGA-CG-5725         TCGA-CG-5726         TCGA-CG-5727 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE"   "12P GAIN MUTATED" 
        TCGA-CG-5728         TCGA-CG-5730         TCGA-CG-5732 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-CG-5733         TCGA-CG-5734         TCGA-D7-5577 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-D7-5578         TCGA-D7-5579         TCGA-D7-6518 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-D7-6519         TCGA-D7-6520         TCGA-D7-6521 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-D7-6522         TCGA-D7-6524         TCGA-D7-6525 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-D7-6526         TCGA-D7-6527         TCGA-D7-6528 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-D7-6815         TCGA-D7-6817         TCGA-D7-6818 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-D7-6820         TCGA-D7-6822         TCGA-EQ-5647 
  "12P GAIN MUTATED" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-F1-6177         TCGA-F1-6874         TCGA-F1-6875 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-FP-7735         TCGA-FP-7829         TCGA-FP-7998 
  "12P GAIN MUTATED"   "12P GAIN MUTATED" "12P GAIN WILD-TYPE" 
        TCGA-IN-7806         TCGA-IN-7808         TCGA-IP-7968 
"12P GAIN WILD-TYPE"   "12P GAIN MUTATED"   "12P GAIN MUTATED" 
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"12P GAIN WILD-TYPE"   "12P GAIN MUTATED" "12P GAIN WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
  "12P GAIN MUTATED" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"12P GAIN WILD-TYPE"   "12P GAIN MUTATED" "12P GAIN WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-CD-5798 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-CD-5799         TCGA-CD-5800         TCGA-CD-5801 
  "12P GAIN MUTATED" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-CD-5802         TCGA-CD-5803         TCGA-CG-4300 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-CG-4301         TCGA-CG-4304         TCGA-CG-4305 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-CG-4306         TCGA-CG-4436         TCGA-CG-4437 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-CG-4438         TCGA-CG-4440         TCGA-CG-4441 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-CG-4443         TCGA-CG-4444         TCGA-CG-4449 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-CG-4455         TCGA-CG-4460         TCGA-CG-4462 
"12P GAIN WILD-TYPE"   "12P GAIN MUTATED" "12P GAIN WILD-TYPE" 
        TCGA-CG-4465         TCGA-CG-4466         TCGA-CG-4469 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-CG-4472         TCGA-CG-4474         TCGA-CG-4477 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-CG-5716         TCGA-CG-5717         TCGA-CG-5718 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-CG-5719         TCGA-CG-5720         TCGA-CG-5721 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-CG-5722         TCGA-CG-5723         TCGA-CG-5724 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE"   "12P GAIN MUTATED" 
        TCGA-CG-5725         TCGA-CG-5726         TCGA-CG-5727 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE"   "12P GAIN MUTATED" 
        TCGA-CG-5728         TCGA-CG-5730         TCGA-CG-5732 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-CG-5733         TCGA-CG-5734         TCGA-D7-5577 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-D7-5578         TCGA-D7-5579         TCGA-D7-6518 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-D7-6519         TCGA-D7-6520         TCGA-D7-6521 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-D7-6522         TCGA-D7-6524         TCGA-D7-6525 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-D7-6526         TCGA-D7-6527         TCGA-D7-6528 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-D7-6815         TCGA-D7-6817         TCGA-D7-6818 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-D7-6820         TCGA-D7-6822         TCGA-EQ-5647 
  "12P GAIN MUTATED" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-F1-6177         TCGA-F1-6874         TCGA-F1-6875 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-FP-7735         TCGA-FP-7829         TCGA-FP-7998 
  "12P GAIN MUTATED"   "12P GAIN MUTATED" "12P GAIN WILD-TYPE" 
        TCGA-IN-7806         TCGA-IN-7808         TCGA-IP-7968 
"12P GAIN WILD-TYPE"   "12P GAIN MUTATED"   "12P GAIN MUTATED" 
[1] "hr=" "1.3"
D21V2, continuous
D21V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED      4   13
  12P GAIN WILD-TYPE   56   85
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  FEMALE                4                 56
  MALE                 13                 85
D21V4, multiclass
D21V5, multiclass
    clus
vv   12P GAIN MUTATED 12P GAIN WILD-TYPE
  T1                0                  6
  T2                3                 49
  T3                9                 52
  T4                3                 15
D21V6, multiclass
    clus
vv   12P GAIN MUTATED 12P GAIN WILD-TYPE
  N0                4                 40
  N1                6                 51
  N2                4                 20
  N3                2                 13
D21V7, multiclass
    clus
vv   12P GAIN MUTATED 12P GAIN WILD-TYPE
  M0               12                122
  M1                3                 13
  MX                2                  6
D21V8, multiclass
     clus
vv    12P GAIN MUTATED 12P GAIN WILD-TYPE
  I                  1                 23
  II                 6                 31
  III                5                 38
  IV                 3                 23
D21V9, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED      0   17
  12P GAIN WILD-TYPE    5  136
     clus
vv    12P GAIN MUTATED 12P GAIN WILD-TYPE
  NO                 0                  5
  YES               17                136
D21V10, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED      0   17
  12P GAIN WILD-TYPE   10  131
     clus
vv    12P GAIN MUTATED 12P GAIN WILD-TYPE
  NO                 0                 10
  YES               17                131

Clustering(22) Variable = 12q gain mutation analysis
D22V1, survival
                    sevent
clus2                 0  1
  12Q GAIN MUTATED    7  1
  12Q GAIN WILD-TYPE 83 14
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                 8                 97 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                 1                 14 
$`12Q GAIN MUTATED`
TCGA-BR-6709 TCGA-BR-7723 TCGA-CD-5799 TCGA-CG-4460 TCGA-CG-4472 TCGA-CG-5727 
        1.22         4.54         0.69        21.99        12.00        31.04 
TCGA-D7-6527 TCGA-IP-7968 
        4.14         2.53 

$`12Q GAIN WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-6452 TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6458 
        5.62         0.10         0.95         1.41         1.35         1.35 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
        0.85         0.82         0.62         0.62         1.71         2.17 
TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
        0.99         0.66         1.12         0.76         0.66         0.26 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
        1.22         1.48         0.46         1.25         0.13         1.05 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 
        0.82         0.69         0.16         0.99         0.95         0.69 
TCGA-CD-5798 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CG-4300 
        0.82         0.36         0.49         0.30         0.07        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02        52.96         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 
       54.05         4.01        14.01        29.98        47.05        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4474 
       12.03         1.02         8.98        18.94         7.07         1.02 
TCGA-CG-4477 TCGA-CG-5716 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
        1.02         1.02         6.94         1.02         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 
        5.98         0.95        70.06        12.03        15.02        28.96 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        55.04        21.07         7.99         8.65 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
        3.58         4.54         9.80        15.65         9.63         8.19 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6528 TCGA-D7-6815 
        6.90         0.69         5.95         6.61         1.68         3.65 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-EQ-5647 TCGA-F1-6177 
        4.70         4.04         2.93         4.27         0.62         6.54 
TCGA-F1-6874 TCGA-F1-6875 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7998 TCGA-IN-7806 
        2.01        72.23         0.39         0.20         3.58         6.87 
TCGA-IN-7808 
        3.55 

  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
              0.69               0.07 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
             31.04              72.23 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
              4.34               2.17 
[1] "0.7 - 31.0 (4.3)" "0.1 - 72.2 (2.2)"
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-CD-5798 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-CD-5799         TCGA-CD-5800         TCGA-CD-5801 
  "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-CD-5802         TCGA-CD-5803         TCGA-CG-4300 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-CG-4301         TCGA-CG-4304         TCGA-CG-4305 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-CG-4306         TCGA-CG-4436         TCGA-CG-4437 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-CG-4438         TCGA-CG-4440         TCGA-CG-4441 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-CG-4443         TCGA-CG-4444         TCGA-CG-4449 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-CG-4455         TCGA-CG-4460         TCGA-CG-4462 
"12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" 
        TCGA-CG-4465         TCGA-CG-4466         TCGA-CG-4469 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-CG-4472         TCGA-CG-4474         TCGA-CG-4477 
  "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-CG-5716         TCGA-CG-5717         TCGA-CG-5718 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-CG-5719         TCGA-CG-5720         TCGA-CG-5721 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-CG-5722         TCGA-CG-5723         TCGA-CG-5724 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-CG-5725         TCGA-CG-5726         TCGA-CG-5727 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" 
        TCGA-CG-5728         TCGA-CG-5730         TCGA-CG-5732 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-CG-5733         TCGA-CG-5734         TCGA-D7-5577 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-D7-5578         TCGA-D7-5579         TCGA-D7-6518 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-D7-6519         TCGA-D7-6520         TCGA-D7-6521 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-D7-6522         TCGA-D7-6524         TCGA-D7-6525 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-D7-6526         TCGA-D7-6527         TCGA-D7-6528 
"12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" 
        TCGA-D7-6815         TCGA-D7-6817         TCGA-D7-6818 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-D7-6820         TCGA-D7-6822         TCGA-EQ-5647 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-F1-6177         TCGA-F1-6874         TCGA-F1-6875 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-FP-7735         TCGA-FP-7829         TCGA-FP-7998 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-IN-7806         TCGA-IN-7808         TCGA-IP-7968 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" 
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-CD-5798 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-CD-5799         TCGA-CD-5800         TCGA-CD-5801 
  "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-CD-5802         TCGA-CD-5803         TCGA-CG-4300 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-CG-4301         TCGA-CG-4304         TCGA-CG-4305 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-CG-4306         TCGA-CG-4436         TCGA-CG-4437 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-CG-4438         TCGA-CG-4440         TCGA-CG-4441 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-CG-4443         TCGA-CG-4444         TCGA-CG-4449 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-CG-4455         TCGA-CG-4460         TCGA-CG-4462 
"12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" 
        TCGA-CG-4465         TCGA-CG-4466         TCGA-CG-4469 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-CG-4472         TCGA-CG-4474         TCGA-CG-4477 
  "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-CG-5716         TCGA-CG-5717         TCGA-CG-5718 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-CG-5719         TCGA-CG-5720         TCGA-CG-5721 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-CG-5722         TCGA-CG-5723         TCGA-CG-5724 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-CG-5725         TCGA-CG-5726         TCGA-CG-5727 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" 
        TCGA-CG-5728         TCGA-CG-5730         TCGA-CG-5732 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-CG-5733         TCGA-CG-5734         TCGA-D7-5577 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-D7-5578         TCGA-D7-5579         TCGA-D7-6518 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-D7-6519         TCGA-D7-6520         TCGA-D7-6521 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-D7-6522         TCGA-D7-6524         TCGA-D7-6525 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-D7-6526         TCGA-D7-6527         TCGA-D7-6528 
"12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" 
        TCGA-D7-6815         TCGA-D7-6817         TCGA-D7-6818 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-D7-6820         TCGA-D7-6822         TCGA-EQ-5647 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-F1-6177         TCGA-F1-6874         TCGA-F1-6875 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-FP-7735         TCGA-FP-7829         TCGA-FP-7998 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-IN-7806         TCGA-IN-7808         TCGA-IP-7968 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" 
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-CD-5798 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-CD-5799         TCGA-CD-5800         TCGA-CD-5801 
  "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-CD-5802         TCGA-CD-5803         TCGA-CG-4300 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-CG-4301         TCGA-CG-4304         TCGA-CG-4305 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-CG-4306         TCGA-CG-4436         TCGA-CG-4437 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-CG-4438         TCGA-CG-4440         TCGA-CG-4441 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-CG-4443         TCGA-CG-4444         TCGA-CG-4449 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-CG-4455         TCGA-CG-4460         TCGA-CG-4462 
"12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" 
        TCGA-CG-4465         TCGA-CG-4466         TCGA-CG-4469 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-CG-4472         TCGA-CG-4474         TCGA-CG-4477 
  "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-CG-5716         TCGA-CG-5717         TCGA-CG-5718 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-CG-5719         TCGA-CG-5720         TCGA-CG-5721 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-CG-5722         TCGA-CG-5723         TCGA-CG-5724 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-CG-5725         TCGA-CG-5726         TCGA-CG-5727 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" 
        TCGA-CG-5728         TCGA-CG-5730         TCGA-CG-5732 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-CG-5733         TCGA-CG-5734         TCGA-D7-5577 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-D7-5578         TCGA-D7-5579         TCGA-D7-6518 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-D7-6519         TCGA-D7-6520         TCGA-D7-6521 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-D7-6522         TCGA-D7-6524         TCGA-D7-6525 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-D7-6526         TCGA-D7-6527         TCGA-D7-6528 
"12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" 
        TCGA-D7-6815         TCGA-D7-6817         TCGA-D7-6818 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-D7-6820         TCGA-D7-6822         TCGA-EQ-5647 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-F1-6177         TCGA-F1-6874         TCGA-F1-6875 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-FP-7735         TCGA-FP-7829         TCGA-FP-7998 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-IN-7806         TCGA-IN-7808         TCGA-IP-7968 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" 
[1] "hr=" "1.6"
D22V2, continuous
D22V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED      4    7
  12Q GAIN WILD-TYPE   56   91
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  FEMALE                4                 56
  MALE                  7                 91
D22V4, multiclass
D22V5, multiclass
    clus
vv   12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  T1                0                  6
  T2                3                 49
  T3                4                 57
  T4                3                 15
D22V6, multiclass
    clus
vv   12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  N0                2                 42
  N1                4                 53
  N2                4                 20
  N3                0                 15
D22V7, multiclass
    clus
vv   12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  M0                9                125
  M1                1                 15
  MX                1                  7
D22V8, multiclass
     clus
vv    12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  I                  1                 23
  II                 4                 33
  III                2                 41
  IV                 3                 23
D22V9, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED      1   10
  12Q GAIN WILD-TYPE    4  143
     clus
vv    12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  NO                 1                  4
  YES               10                143
D22V10, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED      1   10
  12Q GAIN WILD-TYPE    9  138
     clus
vv    12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  NO                 1                  9
  YES               10                138

Clustering(23) Variable = 13q gain mutation analysis
D23V1, survival
                    sevent
clus2                 0  1
  13Q GAIN MUTATED   21  3
  13Q GAIN WILD-TYPE 69 12
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                24                 81 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                 3                 12 
$`13Q GAIN MUTATED`
TCGA-B7-5818 TCGA-BR-6565 TCGA-BR-6801 TCGA-BR-7197 TCGA-BR-7704 TCGA-BR-7717 
        0.10         0.62         1.12         1.48         1.25         0.69 
TCGA-BR-7723 TCGA-CD-5799 TCGA-CD-5800 TCGA-CG-4300 TCGA-CG-4305 TCGA-CG-4436 
        4.54         0.69         0.36        20.02        15.95        52.96 
TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-5730 TCGA-CG-5732 TCGA-D7-5577 TCGA-D7-6518 
        7.07        12.00         4.01        55.04         8.65         9.80 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6820 TCGA-EQ-5647 TCGA-F1-6875 TCGA-FP-7829 
        6.61         4.14         2.93         0.62        72.23         0.20 

$`13Q GAIN WILD-TYPE`
TCGA-B7-5816 TCGA-BR-6452 TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
        5.62         0.95         1.41         1.35         1.35         0.85 
TCGA-BR-6564 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
        0.82         0.62         1.71         2.17         0.99         1.22 
TCGA-BR-6710 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7703 
        0.66         0.76         0.66         0.26         1.22         0.46 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7722 TCGA-BR-7851 TCGA-BR-7901 
        0.13         1.05         0.82         0.16         0.99         0.95 
TCGA-BR-7957 TCGA-CD-5798 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CG-4301 
        0.69         0.82         0.49         0.30         0.07         3.02 
TCGA-CG-4304 TCGA-CG-4306 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
       27.02         1.02         8.05        54.05         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4460 TCGA-CG-4462 
       29.98        47.05        19.07        12.03        21.99         1.02 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4474 TCGA-CG-4477 TCGA-CG-5716 TCGA-CG-5717 
        8.98        18.94         1.02         1.02         1.02         6.94 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
        1.02         1.02         0.99         5.98         0.95        70.06 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5733 
       12.03        15.02        28.96        31.04        65.10        21.07 
TCGA-CG-5734 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
        7.99         3.58         4.54        15.65         9.63         8.19 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
        6.90         0.69         5.95         1.68         3.65         4.70 
TCGA-D7-6818 TCGA-D7-6822 TCGA-F1-6177 TCGA-F1-6874 TCGA-FP-7735 TCGA-FP-7998 
        4.04         4.27         6.54         2.01         0.39         3.58 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IP-7968 
        6.87         3.55         2.53 

  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
              0.10               0.07 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
             72.23              70.06 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
             4.075              2.170 
[1] "0.1 - 72.2 (4.1)" "0.1 - 70.1 (2.2)"
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
  "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-CD-5798 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-CD-5799         TCGA-CD-5800         TCGA-CD-5801 
  "13Q GAIN MUTATED"   "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" 
        TCGA-CD-5802         TCGA-CD-5803         TCGA-CG-4300 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" 
        TCGA-CG-4301         TCGA-CG-4304         TCGA-CG-4305 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" 
        TCGA-CG-4306         TCGA-CG-4436         TCGA-CG-4437 
"13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" 
        TCGA-CG-4438         TCGA-CG-4440         TCGA-CG-4441 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-CG-4443         TCGA-CG-4444         TCGA-CG-4449 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-CG-4455         TCGA-CG-4460         TCGA-CG-4462 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-CG-4465         TCGA-CG-4466         TCGA-CG-4469 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" 
        TCGA-CG-4472         TCGA-CG-4474         TCGA-CG-4477 
  "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-CG-5716         TCGA-CG-5717         TCGA-CG-5718 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-CG-5719         TCGA-CG-5720         TCGA-CG-5721 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-CG-5722         TCGA-CG-5723         TCGA-CG-5724 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-CG-5725         TCGA-CG-5726         TCGA-CG-5727 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-CG-5728         TCGA-CG-5730         TCGA-CG-5732 
"13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED"   "13Q GAIN MUTATED" 
        TCGA-CG-5733         TCGA-CG-5734         TCGA-D7-5577 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" 
        TCGA-D7-5578         TCGA-D7-5579         TCGA-D7-6518 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" 
        TCGA-D7-6519         TCGA-D7-6520         TCGA-D7-6521 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-D7-6522         TCGA-D7-6524         TCGA-D7-6525 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-D7-6526         TCGA-D7-6527         TCGA-D7-6528 
  "13Q GAIN MUTATED"   "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" 
        TCGA-D7-6815         TCGA-D7-6817         TCGA-D7-6818 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-D7-6820         TCGA-D7-6822         TCGA-EQ-5647 
  "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" 
        TCGA-F1-6177         TCGA-F1-6874         TCGA-F1-6875 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" 
        TCGA-FP-7735         TCGA-FP-7829         TCGA-FP-7998 
"13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" 
        TCGA-IN-7806         TCGA-IN-7808         TCGA-IP-7968 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
  "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-CD-5798 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-CD-5799         TCGA-CD-5800         TCGA-CD-5801 
  "13Q GAIN MUTATED"   "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" 
        TCGA-CD-5802         TCGA-CD-5803         TCGA-CG-4300 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" 
        TCGA-CG-4301         TCGA-CG-4304         TCGA-CG-4305 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" 
        TCGA-CG-4306         TCGA-CG-4436         TCGA-CG-4437 
"13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" 
        TCGA-CG-4438         TCGA-CG-4440         TCGA-CG-4441 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-CG-4443         TCGA-CG-4444         TCGA-CG-4449 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-CG-4455         TCGA-CG-4460         TCGA-CG-4462 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-CG-4465         TCGA-CG-4466         TCGA-CG-4469 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" 
        TCGA-CG-4472         TCGA-CG-4474         TCGA-CG-4477 
  "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-CG-5716         TCGA-CG-5717         TCGA-CG-5718 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-CG-5719         TCGA-CG-5720         TCGA-CG-5721 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-CG-5722         TCGA-CG-5723         TCGA-CG-5724 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-CG-5725         TCGA-CG-5726         TCGA-CG-5727 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-CG-5728         TCGA-CG-5730         TCGA-CG-5732 
"13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED"   "13Q GAIN MUTATED" 
        TCGA-CG-5733         TCGA-CG-5734         TCGA-D7-5577 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" 
        TCGA-D7-5578         TCGA-D7-5579         TCGA-D7-6518 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" 
        TCGA-D7-6519         TCGA-D7-6520         TCGA-D7-6521 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-D7-6522         TCGA-D7-6524         TCGA-D7-6525 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-D7-6526         TCGA-D7-6527         TCGA-D7-6528 
  "13Q GAIN MUTATED"   "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" 
        TCGA-D7-6815         TCGA-D7-6817         TCGA-D7-6818 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-D7-6820         TCGA-D7-6822         TCGA-EQ-5647 
  "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" 
        TCGA-F1-6177         TCGA-F1-6874         TCGA-F1-6875 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" 
        TCGA-FP-7735         TCGA-FP-7829         TCGA-FP-7998 
"13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" 
        TCGA-IN-7806         TCGA-IN-7808         TCGA-IP-7968 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
  "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-CD-5798 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-CD-5799         TCGA-CD-5800         TCGA-CD-5801 
  "13Q GAIN MUTATED"   "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" 
        TCGA-CD-5802         TCGA-CD-5803         TCGA-CG-4300 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" 
        TCGA-CG-4301         TCGA-CG-4304         TCGA-CG-4305 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" 
        TCGA-CG-4306         TCGA-CG-4436         TCGA-CG-4437 
"13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" 
        TCGA-CG-4438         TCGA-CG-4440         TCGA-CG-4441 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-CG-4443         TCGA-CG-4444         TCGA-CG-4449 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-CG-4455         TCGA-CG-4460         TCGA-CG-4462 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-CG-4465         TCGA-CG-4466         TCGA-CG-4469 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" 
        TCGA-CG-4472         TCGA-CG-4474         TCGA-CG-4477 
  "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-CG-5716         TCGA-CG-5717         TCGA-CG-5718 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-CG-5719         TCGA-CG-5720         TCGA-CG-5721 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-CG-5722         TCGA-CG-5723         TCGA-CG-5724 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-CG-5725         TCGA-CG-5726         TCGA-CG-5727 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-CG-5728         TCGA-CG-5730         TCGA-CG-5732 
"13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED"   "13Q GAIN MUTATED" 
        TCGA-CG-5733         TCGA-CG-5734         TCGA-D7-5577 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" 
        TCGA-D7-5578         TCGA-D7-5579         TCGA-D7-6518 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" 
        TCGA-D7-6519         TCGA-D7-6520         TCGA-D7-6521 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-D7-6522         TCGA-D7-6524         TCGA-D7-6525 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-D7-6526         TCGA-D7-6527         TCGA-D7-6528 
  "13Q GAIN MUTATED"   "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" 
        TCGA-D7-6815         TCGA-D7-6817         TCGA-D7-6818 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-D7-6820         TCGA-D7-6822         TCGA-EQ-5647 
  "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" 
        TCGA-F1-6177         TCGA-F1-6874         TCGA-F1-6875 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" 
        TCGA-FP-7735         TCGA-FP-7829         TCGA-FP-7998 
"13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" 
        TCGA-IN-7806         TCGA-IN-7808         TCGA-IP-7968 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
[1] "hr=" "2.1"
D23V2, continuous
D23V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED     12   23
  13Q GAIN WILD-TYPE   48   75
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  FEMALE               12                 48
  MALE                 23                 75
D23V4, multiclass
D23V5, multiclass
    clus
vv   13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  T1                1                  5
  T2               13                 39
  T3               12                 49
  T4                5                 13
D23V6, multiclass
    clus
vv   13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  N0                9                 35
  N1               12                 45
  N2                3                 21
  N3                6                  9
D23V7, multiclass
    clus
vv   13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  M0               32                102
  M1                2                 14
  MX                1                  7
D23V8, multiclass
     clus
vv    13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  I                  4                 20
  II                 9                 28
  III                8                 35
  IV                 7                 19
D23V9, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED      1   34
  13Q GAIN WILD-TYPE    4  119
     clus
vv    13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  NO                 1                  4
  YES               34                119
D23V10, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED      3   32
  13Q GAIN WILD-TYPE    7  116
     clus
vv    13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  NO                 3                  7
  YES               32                116

Clustering(24) Variable = 14q gain mutation analysis
D24V1, survival
                    sevent
clus2                 0  1
  14Q GAIN MUTATED    0  2
  14Q GAIN WILD-TYPE 90 13
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                 2                103 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                 2                 13 
$`14Q GAIN MUTATED`
TCGA-CG-4460 TCGA-EQ-5647 
       21.99         0.62 

$`14Q GAIN WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-6452 TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6458 
        5.62         0.10         0.95         1.41         1.35         1.35 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
        0.85         0.82         0.62         0.62         1.71         2.17 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
        0.99         1.22         0.66         1.12         0.76         0.66 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
        0.26         1.22         1.48         0.46         1.25         0.13 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 
        1.05         0.82         0.69         0.16         4.54         0.99 
TCGA-BR-7901 TCGA-BR-7957 TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
        0.95         0.69         0.82         0.69         0.36         0.49 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
        0.30         0.07        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02        52.96         8.05        54.05         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       29.98        47.05        19.07        12.03         1.02         8.98 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4474 TCGA-CG-4477 TCGA-CG-5716 
       18.94         7.07        12.00         1.02         1.02         1.02 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.94         1.02         1.02         0.99         5.98         0.95 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 
       70.06        12.03        15.02        28.96        31.04        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        55.04        21.07         7.99         8.65         3.58 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
        4.54         9.80        15.65         9.63         8.19         6.90 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
        0.69         5.95         6.61         4.14         1.68         3.65 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-F1-6177 TCGA-F1-6874 
        4.70         4.04         2.93         4.27         6.54         2.01 
TCGA-F1-6875 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7998 TCGA-IN-7806 TCGA-IN-7808 
       72.23         0.39         0.20         3.58         6.87         3.55 
TCGA-IP-7968 
        2.53 

  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
              0.62               0.07 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
             21.99              72.23 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
            11.305              2.930 
[1] "0.6 - 22.0 (11.3)" "0.1 - 72.2 (2.9)" 
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-CD-5798 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CD-5799         TCGA-CD-5800         TCGA-CD-5801 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CD-5802         TCGA-CD-5803         TCGA-CG-4300 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CG-4301         TCGA-CG-4304         TCGA-CG-4305 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CG-4306         TCGA-CG-4436         TCGA-CG-4437 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CG-4438         TCGA-CG-4440         TCGA-CG-4441 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CG-4443         TCGA-CG-4444         TCGA-CG-4449 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CG-4455         TCGA-CG-4460         TCGA-CG-4462 
"14Q GAIN WILD-TYPE"   "14Q GAIN MUTATED" "14Q GAIN WILD-TYPE" 
        TCGA-CG-4465         TCGA-CG-4466         TCGA-CG-4469 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CG-4472         TCGA-CG-4474         TCGA-CG-4477 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CG-5716         TCGA-CG-5717         TCGA-CG-5718 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CG-5719         TCGA-CG-5720         TCGA-CG-5721 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CG-5722         TCGA-CG-5723         TCGA-CG-5724 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CG-5725         TCGA-CG-5726         TCGA-CG-5727 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CG-5728         TCGA-CG-5730         TCGA-CG-5732 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CG-5733         TCGA-CG-5734         TCGA-D7-5577 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-D7-5578         TCGA-D7-5579         TCGA-D7-6518 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-D7-6519         TCGA-D7-6520         TCGA-D7-6521 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-D7-6522         TCGA-D7-6524         TCGA-D7-6525 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-D7-6526         TCGA-D7-6527         TCGA-D7-6528 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-D7-6815         TCGA-D7-6817         TCGA-D7-6818 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-D7-6820         TCGA-D7-6822         TCGA-EQ-5647 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE"   "14Q GAIN MUTATED" 
        TCGA-F1-6177         TCGA-F1-6874         TCGA-F1-6875 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-FP-7735         TCGA-FP-7829         TCGA-FP-7998 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-IN-7806         TCGA-IN-7808         TCGA-IP-7968 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-CD-5798 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CD-5799         TCGA-CD-5800         TCGA-CD-5801 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CD-5802         TCGA-CD-5803         TCGA-CG-4300 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CG-4301         TCGA-CG-4304         TCGA-CG-4305 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CG-4306         TCGA-CG-4436         TCGA-CG-4437 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CG-4438         TCGA-CG-4440         TCGA-CG-4441 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CG-4443         TCGA-CG-4444         TCGA-CG-4449 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CG-4455         TCGA-CG-4460         TCGA-CG-4462 
"14Q GAIN WILD-TYPE"   "14Q GAIN MUTATED" "14Q GAIN WILD-TYPE" 
        TCGA-CG-4465         TCGA-CG-4466         TCGA-CG-4469 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CG-4472         TCGA-CG-4474         TCGA-CG-4477 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CG-5716         TCGA-CG-5717         TCGA-CG-5718 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CG-5719         TCGA-CG-5720         TCGA-CG-5721 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CG-5722         TCGA-CG-5723         TCGA-CG-5724 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CG-5725         TCGA-CG-5726         TCGA-CG-5727 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CG-5728         TCGA-CG-5730         TCGA-CG-5732 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CG-5733         TCGA-CG-5734         TCGA-D7-5577 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-D7-5578         TCGA-D7-5579         TCGA-D7-6518 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-D7-6519         TCGA-D7-6520         TCGA-D7-6521 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-D7-6522         TCGA-D7-6524         TCGA-D7-6525 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-D7-6526         TCGA-D7-6527         TCGA-D7-6528 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-D7-6815         TCGA-D7-6817         TCGA-D7-6818 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-D7-6820         TCGA-D7-6822         TCGA-EQ-5647 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE"   "14Q GAIN MUTATED" 
        TCGA-F1-6177         TCGA-F1-6874         TCGA-F1-6875 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-FP-7735         TCGA-FP-7829         TCGA-FP-7998 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-IN-7806         TCGA-IN-7808         TCGA-IP-7968 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-CD-5798 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CD-5799         TCGA-CD-5800         TCGA-CD-5801 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CD-5802         TCGA-CD-5803         TCGA-CG-4300 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CG-4301         TCGA-CG-4304         TCGA-CG-4305 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CG-4306         TCGA-CG-4436         TCGA-CG-4437 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CG-4438         TCGA-CG-4440         TCGA-CG-4441 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CG-4443         TCGA-CG-4444         TCGA-CG-4449 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CG-4455         TCGA-CG-4460         TCGA-CG-4462 
"14Q GAIN WILD-TYPE"   "14Q GAIN MUTATED" "14Q GAIN WILD-TYPE" 
        TCGA-CG-4465         TCGA-CG-4466         TCGA-CG-4469 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CG-4472         TCGA-CG-4474         TCGA-CG-4477 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CG-5716         TCGA-CG-5717         TCGA-CG-5718 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CG-5719         TCGA-CG-5720         TCGA-CG-5721 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CG-5722         TCGA-CG-5723         TCGA-CG-5724 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CG-5725         TCGA-CG-5726         TCGA-CG-5727 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CG-5728         TCGA-CG-5730         TCGA-CG-5732 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CG-5733         TCGA-CG-5734         TCGA-D7-5577 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-D7-5578         TCGA-D7-5579         TCGA-D7-6518 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-D7-6519         TCGA-D7-6520         TCGA-D7-6521 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-D7-6522         TCGA-D7-6524         TCGA-D7-6525 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-D7-6526         TCGA-D7-6527         TCGA-D7-6528 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-D7-6815         TCGA-D7-6817         TCGA-D7-6818 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-D7-6820         TCGA-D7-6822         TCGA-EQ-5647 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE"   "14Q GAIN MUTATED" 
        TCGA-F1-6177         TCGA-F1-6874         TCGA-F1-6875 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-FP-7735         TCGA-FP-7829         TCGA-FP-7998 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-IN-7806         TCGA-IN-7808         TCGA-IP-7968 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
[1] "Remove cluster labels:" "14Q GAIN MUTATED"      
clus
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                 2                103 
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-CD-5798 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CD-5799         TCGA-CD-5800         TCGA-CD-5801 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CD-5802         TCGA-CD-5803         TCGA-CG-4300 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CG-4301         TCGA-CG-4304         TCGA-CG-4305 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CG-4306         TCGA-CG-4436         TCGA-CG-4437 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CG-4438         TCGA-CG-4440         TCGA-CG-4441 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CG-4443         TCGA-CG-4444         TCGA-CG-4449 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CG-4455         TCGA-CG-4462         TCGA-CG-4465 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CG-4466         TCGA-CG-4469         TCGA-CG-4472 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CG-4474         TCGA-CG-4477         TCGA-CG-5716 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CG-5717         TCGA-CG-5718         TCGA-CG-5719 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CG-5720         TCGA-CG-5721         TCGA-CG-5722 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CG-5723         TCGA-CG-5724         TCGA-CG-5725 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CG-5726         TCGA-CG-5727         TCGA-CG-5728 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CG-5730         TCGA-CG-5732         TCGA-CG-5733 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CG-5734         TCGA-D7-5577         TCGA-D7-5578 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-D7-5579         TCGA-D7-6518         TCGA-D7-6519 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-D7-6520         TCGA-D7-6521         TCGA-D7-6522 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-D7-6524         TCGA-D7-6525         TCGA-D7-6526 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-D7-6527         TCGA-D7-6528         TCGA-D7-6815 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-D7-6817         TCGA-D7-6818         TCGA-D7-6820 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-D7-6822         TCGA-F1-6177         TCGA-F1-6874 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-F1-6875         TCGA-FP-7735         TCGA-FP-7829 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-FP-7998         TCGA-IN-7806         TCGA-IN-7808 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-IP-7968 
"14Q GAIN WILD-TYPE" 
D24V2, continuous
D24V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED      4    0
  14Q GAIN WILD-TYPE   56   98
        clus
vv       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  FEMALE                4                 56
  MALE                  0                 98
D24V4, multiclass
D24V5, multiclass
[1] "Remove cluster labels:" "14Q GAIN MUTATED"      
clus
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                 2                135 
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-4183 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BR-4184         TCGA-BR-4190         TCGA-BR-4201 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BR-4253         TCGA-BR-4255         TCGA-BR-4267 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BR-4277         TCGA-BR-4278         TCGA-BR-4279 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BR-4280         TCGA-BR-4292         TCGA-BR-4294 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BR-4298         TCGA-BR-4357         TCGA-BR-4361 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BR-4363         TCGA-BR-4368         TCGA-BR-4371 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BR-4376         TCGA-BR-6452         TCGA-BR-6453 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BR-6454         TCGA-BR-6455         TCGA-BR-6456 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BR-6457         TCGA-BR-6458         TCGA-BR-6563 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BR-6564         TCGA-BR-6565         TCGA-BR-6566 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BR-6705         TCGA-BR-6706         TCGA-BR-6707 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BR-6709         TCGA-BR-6710         TCGA-BR-6801 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BR-6802         TCGA-BR-6803         TCGA-BR-6852 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BR-7196         TCGA-BR-7197         TCGA-BR-7703 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BR-7704         TCGA-BR-7707         TCGA-BR-7715 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BR-7716         TCGA-BR-7717         TCGA-BR-7722 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BR-7723         TCGA-BR-7851         TCGA-BR-7901 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BR-7957         TCGA-CD-5798         TCGA-CD-5799 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CD-5800         TCGA-CD-5801         TCGA-CD-5802 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CD-5803         TCGA-CD-5804         TCGA-CG-4300 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CG-4301         TCGA-CG-4304         TCGA-CG-4305 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CG-4306         TCGA-CG-4436         TCGA-CG-4437 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CG-4438         TCGA-CG-4440         TCGA-CG-4441 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CG-4442         TCGA-CG-4443         TCGA-CG-4444 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CG-4449         TCGA-CG-4455         TCGA-CG-4462 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CG-4465         TCGA-CG-4466         TCGA-CG-4469 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CG-4472         TCGA-CG-4474         TCGA-CG-4475 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CG-4476         TCGA-CG-4477         TCGA-CG-5716 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CG-5717         TCGA-CG-5718         TCGA-CG-5719 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CG-5720         TCGA-CG-5721         TCGA-CG-5722 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CG-5723         TCGA-CG-5724         TCGA-CG-5725 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CG-5726         TCGA-CG-5727         TCGA-CG-5728 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CG-5730         TCGA-CG-5732         TCGA-CG-5733 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CG-5734         TCGA-D7-5577         TCGA-D7-5578 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-D7-5579         TCGA-D7-6518         TCGA-D7-6519 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-D7-6520         TCGA-D7-6521         TCGA-D7-6522 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-D7-6524         TCGA-D7-6525         TCGA-D7-6526 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-D7-6527         TCGA-D7-6528         TCGA-D7-6815 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-D7-6817         TCGA-D7-6818         TCGA-D7-6820 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-D7-6822         TCGA-F1-6177         TCGA-F1-6874 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-F1-6875         TCGA-FP-7735         TCGA-FP-7829 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-FP-7998         TCGA-HF-7131         TCGA-HF-7132 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-HF-7133         TCGA-HF-7134         TCGA-HF-7136 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-IN-7806         TCGA-IN-7808         TCGA-IP-7968 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
D24V6, multiclass
[1] "Remove cluster labels:" "14Q GAIN MUTATED"      
clus
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                 2                138 
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-4183 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BR-4184         TCGA-BR-4188         TCGA-BR-4190 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BR-4191         TCGA-BR-4195         TCGA-BR-4199 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BR-4200         TCGA-BR-4253         TCGA-BR-4255 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BR-4256         TCGA-BR-4261         TCGA-BR-4267 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BR-4278         TCGA-BR-4279         TCGA-BR-4280 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BR-4281         TCGA-BR-4298         TCGA-BR-4361 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BR-4362         TCGA-BR-4367         TCGA-BR-4368 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BR-4376         TCGA-BR-6452         TCGA-BR-6453 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BR-6454         TCGA-BR-6455         TCGA-BR-6456 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BR-6457         TCGA-BR-6458         TCGA-BR-6563 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BR-6564         TCGA-BR-6565         TCGA-BR-6566 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BR-6705         TCGA-BR-6706         TCGA-BR-6707 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BR-6709         TCGA-BR-6710         TCGA-BR-6801 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BR-6802         TCGA-BR-6803         TCGA-BR-6852 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BR-7196         TCGA-BR-7197         TCGA-BR-7703 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BR-7704         TCGA-BR-7707         TCGA-BR-7715 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BR-7716         TCGA-BR-7717         TCGA-BR-7722 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BR-7723         TCGA-BR-7851         TCGA-BR-7901 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BR-7957         TCGA-CD-5798         TCGA-CD-5799 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CD-5800         TCGA-CD-5801         TCGA-CD-5802 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CD-5803         TCGA-CD-5804         TCGA-CG-4300 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CG-4301         TCGA-CG-4304         TCGA-CG-4305 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CG-4306         TCGA-CG-4436         TCGA-CG-4437 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CG-4438         TCGA-CG-4440         TCGA-CG-4441 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CG-4442         TCGA-CG-4443         TCGA-CG-4444 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CG-4449         TCGA-CG-4455         TCGA-CG-4462 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CG-4465         TCGA-CG-4466         TCGA-CG-4469 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CG-4472         TCGA-CG-4474         TCGA-CG-4475 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CG-4476         TCGA-CG-4477         TCGA-CG-5716 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CG-5717         TCGA-CG-5718         TCGA-CG-5719 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CG-5720         TCGA-CG-5721         TCGA-CG-5722 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CG-5723         TCGA-CG-5724         TCGA-CG-5725 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CG-5726         TCGA-CG-5727         TCGA-CG-5728 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CG-5730         TCGA-CG-5732         TCGA-CG-5733 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CG-5734         TCGA-D7-5577         TCGA-D7-5578 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-D7-5579         TCGA-D7-6518         TCGA-D7-6519 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-D7-6520         TCGA-D7-6521         TCGA-D7-6522 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-D7-6524         TCGA-D7-6525         TCGA-D7-6526 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-D7-6527         TCGA-D7-6528         TCGA-D7-6815 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-D7-6817         TCGA-D7-6818         TCGA-D7-6820 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-D7-6822         TCGA-F1-6177         TCGA-F1-6874 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-F1-6875         TCGA-FP-7735         TCGA-FP-7829 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-FP-7998         TCGA-HF-7131         TCGA-HF-7132 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-HF-7133         TCGA-HF-7134         TCGA-HF-7136 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-IN-7806         TCGA-IN-7808         TCGA-IP-7968 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
D24V7, multiclass
    clus
vv   14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  M0                2                132
  M1                2                 14
  MX                0                  8
D24V8, multiclass
[1] "Remove cluster labels:" "14Q GAIN MUTATED"      
clus
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                 2                128 
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-4183 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BR-4184         TCGA-BR-4190         TCGA-BR-4253 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BR-4255         TCGA-BR-4267         TCGA-BR-4278 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BR-4279         TCGA-BR-4280         TCGA-BR-4298 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BR-4361         TCGA-BR-4368         TCGA-BR-4376 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BR-6452         TCGA-BR-6453         TCGA-BR-6454 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6456         TCGA-BR-6457 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BR-6458         TCGA-BR-6563         TCGA-BR-6564 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BR-6565         TCGA-BR-6566         TCGA-BR-6705 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BR-6706         TCGA-BR-6707         TCGA-BR-6709 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BR-6710         TCGA-BR-6801         TCGA-BR-6802 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BR-6803         TCGA-BR-6852         TCGA-BR-7196 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BR-7197         TCGA-BR-7703         TCGA-BR-7704 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BR-7707         TCGA-BR-7715         TCGA-BR-7716 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BR-7717         TCGA-BR-7722         TCGA-BR-7723 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BR-7851         TCGA-BR-7901         TCGA-BR-7957 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CD-5798         TCGA-CD-5799         TCGA-CD-5800 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CD-5801         TCGA-CD-5802         TCGA-CD-5803 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CD-5804         TCGA-CG-4300         TCGA-CG-4301 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CG-4304         TCGA-CG-4305         TCGA-CG-4306 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CG-4436         TCGA-CG-4437         TCGA-CG-4438 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CG-4440         TCGA-CG-4441         TCGA-CG-4442 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CG-4443         TCGA-CG-4444         TCGA-CG-4449 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CG-4455         TCGA-CG-4462         TCGA-CG-4465 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CG-4466         TCGA-CG-4469         TCGA-CG-4472 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CG-4474         TCGA-CG-4475         TCGA-CG-4476 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CG-4477         TCGA-CG-5716         TCGA-CG-5717 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CG-5718         TCGA-CG-5719         TCGA-CG-5720 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CG-5721         TCGA-CG-5722         TCGA-CG-5723 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CG-5724         TCGA-CG-5725         TCGA-CG-5726 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CG-5727         TCGA-CG-5728         TCGA-CG-5730 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CG-5732         TCGA-CG-5733         TCGA-CG-5734 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-D7-5577         TCGA-D7-5578         TCGA-D7-5579 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-D7-6518         TCGA-D7-6519         TCGA-D7-6520 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-D7-6521         TCGA-D7-6522         TCGA-D7-6524 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-D7-6525         TCGA-D7-6526         TCGA-D7-6527 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-D7-6528         TCGA-D7-6815         TCGA-D7-6817 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-D7-6818         TCGA-D7-6820         TCGA-D7-6822 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-F1-6177         TCGA-F1-6874         TCGA-F1-6875 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-FP-7735         TCGA-FP-7829         TCGA-FP-7998 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-HF-7131         TCGA-HF-7132         TCGA-HF-7133 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-HF-7134         TCGA-HF-7136         TCGA-IN-7806 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-IN-7808         TCGA-IP-7968 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
D24V9, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED      0    4
  14Q GAIN WILD-TYPE    5  149
     clus
vv    14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  NO                 0                  5
  YES                4                149
D24V10, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED      0    4
  14Q GAIN WILD-TYPE   10  144
     clus
vv    14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  NO                 0                 10
  YES                4                144

Clustering(25) Variable = 15q gain mutation analysis
D25V1, survival
                    sevent
clus2                 0  1
  15Q GAIN MUTATED    5  1
  15Q GAIN WILD-TYPE 85 14
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                 6                 99 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                 1                 14 
$`15Q GAIN MUTATED`
TCGA-BR-7197 TCGA-CG-5727 TCGA-D7-6520 TCGA-D7-6528 TCGA-F1-6875 TCGA-IN-7808 
        1.48        31.04         9.63         1.68        72.23         3.55 

$`15Q GAIN WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-6452 TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6458 
        5.62         0.10         0.95         1.41         1.35         1.35 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
        0.85         0.82         0.62         0.62         1.71         2.17 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
        0.99         1.22         0.66         1.12         0.76         0.66 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
        0.26         1.22         0.46         1.25         0.13         1.05 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 
        0.82         0.69         0.16         4.54         0.99         0.95 
TCGA-BR-7957 TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        0.69         0.82         0.69         0.36         0.49         0.30 
TCGA-CD-5803 TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
        0.07        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
       52.96         8.05        54.05         4.01        14.01        29.98 
TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4460 TCGA-CG-4462 TCGA-CG-4465 
       47.05        19.07        12.03        21.99         1.02         8.98 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4474 TCGA-CG-4477 TCGA-CG-5716 
       18.94         7.07        12.00         1.02         1.02         1.02 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.94         1.02         1.02         0.99         5.98         0.95 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 
       70.06        12.03        15.02        28.96        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       55.04        21.07         7.99         8.65         3.58         4.54 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
        9.80        15.65         8.19         6.90         0.69         5.95 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
        6.61         4.14         3.65         4.70         4.04         2.93 
TCGA-D7-6822 TCGA-EQ-5647 TCGA-F1-6177 TCGA-F1-6874 TCGA-FP-7735 TCGA-FP-7829 
        4.27         0.62         6.54         2.01         0.39         0.20 
TCGA-FP-7998 TCGA-IN-7806 TCGA-IP-7968 
        3.58         6.87         2.53 

  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
              1.48               0.07 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
             72.23              70.06 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
              6.59               2.53 
[1] "1.5 - 72.2 (6.6)" "0.1 - 70.1 (2.5)"
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-CD-5798 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-CD-5799         TCGA-CD-5800         TCGA-CD-5801 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-CD-5802         TCGA-CD-5803         TCGA-CG-4300 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-CG-4301         TCGA-CG-4304         TCGA-CG-4305 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-CG-4306         TCGA-CG-4436         TCGA-CG-4437 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-CG-4438         TCGA-CG-4440         TCGA-CG-4441 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-CG-4443         TCGA-CG-4444         TCGA-CG-4449 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-CG-4455         TCGA-CG-4460         TCGA-CG-4462 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-CG-4465         TCGA-CG-4466         TCGA-CG-4469 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-CG-4472         TCGA-CG-4474         TCGA-CG-4477 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-CG-5716         TCGA-CG-5717         TCGA-CG-5718 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-CG-5719         TCGA-CG-5720         TCGA-CG-5721 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-CG-5722         TCGA-CG-5723         TCGA-CG-5724 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-CG-5725         TCGA-CG-5726         TCGA-CG-5727 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" 
        TCGA-CG-5728         TCGA-CG-5730         TCGA-CG-5732 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-CG-5733         TCGA-CG-5734         TCGA-D7-5577 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-D7-5578         TCGA-D7-5579         TCGA-D7-6518 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-D7-6519         TCGA-D7-6520         TCGA-D7-6521 
"15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" "15Q GAIN WILD-TYPE" 
        TCGA-D7-6522         TCGA-D7-6524         TCGA-D7-6525 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-D7-6526         TCGA-D7-6527         TCGA-D7-6528 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" 
        TCGA-D7-6815         TCGA-D7-6817         TCGA-D7-6818 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-D7-6820         TCGA-D7-6822         TCGA-EQ-5647 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-F1-6177         TCGA-F1-6874         TCGA-F1-6875 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" 
        TCGA-FP-7735         TCGA-FP-7829         TCGA-FP-7998 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-IN-7806         TCGA-IN-7808         TCGA-IP-7968 
"15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" "15Q GAIN WILD-TYPE" 
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-CD-5798 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-CD-5799         TCGA-CD-5800         TCGA-CD-5801 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-CD-5802         TCGA-CD-5803         TCGA-CG-4300 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-CG-4301         TCGA-CG-4304         TCGA-CG-4305 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-CG-4306         TCGA-CG-4436         TCGA-CG-4437 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-CG-4438         TCGA-CG-4440         TCGA-CG-4441 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-CG-4443         TCGA-CG-4444         TCGA-CG-4449 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-CG-4455         TCGA-CG-4460         TCGA-CG-4462 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-CG-4465         TCGA-CG-4466         TCGA-CG-4469 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-CG-4472         TCGA-CG-4474         TCGA-CG-4477 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-CG-5716         TCGA-CG-5717         TCGA-CG-5718 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-CG-5719         TCGA-CG-5720         TCGA-CG-5721 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-CG-5722         TCGA-CG-5723         TCGA-CG-5724 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-CG-5725         TCGA-CG-5726         TCGA-CG-5727 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" 
        TCGA-CG-5728         TCGA-CG-5730         TCGA-CG-5732 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-CG-5733         TCGA-CG-5734         TCGA-D7-5577 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-D7-5578         TCGA-D7-5579         TCGA-D7-6518 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-D7-6519         TCGA-D7-6520         TCGA-D7-6521 
"15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" "15Q GAIN WILD-TYPE" 
        TCGA-D7-6522         TCGA-D7-6524         TCGA-D7-6525 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-D7-6526         TCGA-D7-6527         TCGA-D7-6528 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" 
        TCGA-D7-6815         TCGA-D7-6817         TCGA-D7-6818 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-D7-6820         TCGA-D7-6822         TCGA-EQ-5647 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-F1-6177         TCGA-F1-6874         TCGA-F1-6875 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" 
        TCGA-FP-7735         TCGA-FP-7829         TCGA-FP-7998 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-IN-7806         TCGA-IN-7808         TCGA-IP-7968 
"15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" "15Q GAIN WILD-TYPE" 
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-CD-5798 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-CD-5799         TCGA-CD-5800         TCGA-CD-5801 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-CD-5802         TCGA-CD-5803         TCGA-CG-4300 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-CG-4301         TCGA-CG-4304         TCGA-CG-4305 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-CG-4306         TCGA-CG-4436         TCGA-CG-4437 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-CG-4438         TCGA-CG-4440         TCGA-CG-4441 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-CG-4443         TCGA-CG-4444         TCGA-CG-4449 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-CG-4455         TCGA-CG-4460         TCGA-CG-4462 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-CG-4465         TCGA-CG-4466         TCGA-CG-4469 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-CG-4472         TCGA-CG-4474         TCGA-CG-4477 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-CG-5716         TCGA-CG-5717         TCGA-CG-5718 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-CG-5719         TCGA-CG-5720         TCGA-CG-5721 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-CG-5722         TCGA-CG-5723         TCGA-CG-5724 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-CG-5725         TCGA-CG-5726         TCGA-CG-5727 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" 
        TCGA-CG-5728         TCGA-CG-5730         TCGA-CG-5732 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-CG-5733         TCGA-CG-5734         TCGA-D7-5577 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-D7-5578         TCGA-D7-5579         TCGA-D7-6518 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-D7-6519         TCGA-D7-6520         TCGA-D7-6521 
"15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" "15Q GAIN WILD-TYPE" 
        TCGA-D7-6522         TCGA-D7-6524         TCGA-D7-6525 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-D7-6526         TCGA-D7-6527         TCGA-D7-6528 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" 
        TCGA-D7-6815         TCGA-D7-6817         TCGA-D7-6818 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-D7-6820         TCGA-D7-6822         TCGA-EQ-5647 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-F1-6177         TCGA-F1-6874         TCGA-F1-6875 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" 
        TCGA-FP-7735         TCGA-FP-7829         TCGA-FP-7998 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-IN-7806         TCGA-IN-7808         TCGA-IP-7968 
"15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" "15Q GAIN WILD-TYPE" 
[1] "hr="     "8.1e+07"
D25V2, continuous
D25V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED      1    6
  15Q GAIN WILD-TYPE   59   92
        clus
vv       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  FEMALE                1                 59
  MALE                  6                 92
D25V4, multiclass
D25V5, multiclass
    clus
vv   15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  T1                0                  6
  T2                3                 49
  T3                4                 57
  T4                0                 18
D25V6, multiclass
    clus
vv   15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  N0                5                 39
  N1                0                 57
  N2                1                 23
  N3                1                 14
D25V7, multiclass
    clus
vv   15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  M0                6                128
  M1                1                 15
  MX                0                  8
D25V8, multiclass
     clus
vv    15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  I                  2                 22
  II                 3                 34
  III                2                 41
  IV                 0                 26
D25V9, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED      0    7
  15Q GAIN WILD-TYPE    5  146
     clus
vv    15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  NO                 0                  5
  YES                7                146
D25V10, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED      0    7
  15Q GAIN WILD-TYPE   10  141
     clus
vv    15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  NO                 0                 10
  YES                7                141

Clustering(26) Variable = 16p gain mutation analysis
D26V1, survival
                    sevent
clus2                 0  1
  16P GAIN MUTATED    9  1
  16P GAIN WILD-TYPE 81 14
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                10                 95 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                 1                 14 
$`16P GAIN MUTATED`
TCGA-CG-4438 TCGA-CG-4460 TCGA-CG-4472 TCGA-CG-5719 TCGA-D7-6521 TCGA-D7-6526 
       54.05        21.99        12.00         1.02         8.19         6.61 
TCGA-D7-6817 TCGA-D7-6818 TCGA-FP-7735 TCGA-IP-7968 
        4.70         4.04         0.39         2.53 

$`16P GAIN WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-6452 TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6458 
        5.62         0.10         0.95         1.41         1.35         1.35 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
        0.85         0.82         0.62         0.62         1.71         2.17 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
        0.99         1.22         0.66         1.12         0.76         0.66 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
        0.26         1.22         1.48         0.46         1.25         0.13 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 
        1.05         0.82         0.69         0.16         4.54         0.99 
TCGA-BR-7901 TCGA-BR-7957 TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
        0.95         0.69         0.82         0.69         0.36         0.49 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
        0.30         0.07        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        1.02        52.96         8.05         4.01        14.01        29.98 
TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       47.05        19.07        12.03         1.02         8.98        18.94 
TCGA-CG-4469 TCGA-CG-4474 TCGA-CG-4477 TCGA-CG-5716 TCGA-CG-5717 TCGA-CG-5718 
        7.07         1.02         1.02         1.02         6.94         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 
        0.99         5.98         0.95        70.06        12.03        15.02 
TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       28.96        31.04        65.10         4.01        55.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99         8.65         3.58         4.54         9.80        15.65 
TCGA-D7-6520 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6527 TCGA-D7-6528 
        9.63         6.90         0.69         5.95         4.14         1.68 
TCGA-D7-6815 TCGA-D7-6820 TCGA-D7-6822 TCGA-EQ-5647 TCGA-F1-6177 TCGA-F1-6874 
        3.65         2.93         4.27         0.62         6.54         2.01 
TCGA-F1-6875 TCGA-FP-7829 TCGA-FP-7998 TCGA-IN-7806 TCGA-IN-7808 
       72.23         0.20         3.58         6.87         3.55 

  16P GAIN MUTATED 16P GAIN WILD-TYPE 
              0.39               0.07 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
             54.05              72.23 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
             5.655              2.010 
[1] "0.4 - 54.0 (5.7)" "0.1 - 72.2 (2.0)"
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-CD-5798 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-CD-5799         TCGA-CD-5800         TCGA-CD-5801 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-CD-5802         TCGA-CD-5803         TCGA-CG-4300 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-CG-4301         TCGA-CG-4304         TCGA-CG-4305 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-CG-4306         TCGA-CG-4436         TCGA-CG-4437 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-CG-4438         TCGA-CG-4440         TCGA-CG-4441 
  "16P GAIN MUTATED" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-CG-4443         TCGA-CG-4444         TCGA-CG-4449 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-CG-4455         TCGA-CG-4460         TCGA-CG-4462 
"16P GAIN WILD-TYPE"   "16P GAIN MUTATED" "16P GAIN WILD-TYPE" 
        TCGA-CG-4465         TCGA-CG-4466         TCGA-CG-4469 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-CG-4472         TCGA-CG-4474         TCGA-CG-4477 
  "16P GAIN MUTATED" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-CG-5716         TCGA-CG-5717         TCGA-CG-5718 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-CG-5719         TCGA-CG-5720         TCGA-CG-5721 
  "16P GAIN MUTATED" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-CG-5722         TCGA-CG-5723         TCGA-CG-5724 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-CG-5725         TCGA-CG-5726         TCGA-CG-5727 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-CG-5728         TCGA-CG-5730         TCGA-CG-5732 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-CG-5733         TCGA-CG-5734         TCGA-D7-5577 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-D7-5578         TCGA-D7-5579         TCGA-D7-6518 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-D7-6519         TCGA-D7-6520         TCGA-D7-6521 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE"   "16P GAIN MUTATED" 
        TCGA-D7-6522         TCGA-D7-6524         TCGA-D7-6525 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-D7-6526         TCGA-D7-6527         TCGA-D7-6528 
  "16P GAIN MUTATED" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-D7-6815         TCGA-D7-6817         TCGA-D7-6818 
"16P GAIN WILD-TYPE"   "16P GAIN MUTATED"   "16P GAIN MUTATED" 
        TCGA-D7-6820         TCGA-D7-6822         TCGA-EQ-5647 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-F1-6177         TCGA-F1-6874         TCGA-F1-6875 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-FP-7735         TCGA-FP-7829         TCGA-FP-7998 
  "16P GAIN MUTATED" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-IN-7806         TCGA-IN-7808         TCGA-IP-7968 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE"   "16P GAIN MUTATED" 
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-CD-5798 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-CD-5799         TCGA-CD-5800         TCGA-CD-5801 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-CD-5802         TCGA-CD-5803         TCGA-CG-4300 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-CG-4301         TCGA-CG-4304         TCGA-CG-4305 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-CG-4306         TCGA-CG-4436         TCGA-CG-4437 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-CG-4438         TCGA-CG-4440         TCGA-CG-4441 
  "16P GAIN MUTATED" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-CG-4443         TCGA-CG-4444         TCGA-CG-4449 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-CG-4455         TCGA-CG-4460         TCGA-CG-4462 
"16P GAIN WILD-TYPE"   "16P GAIN MUTATED" "16P GAIN WILD-TYPE" 
        TCGA-CG-4465         TCGA-CG-4466         TCGA-CG-4469 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-CG-4472         TCGA-CG-4474         TCGA-CG-4477 
  "16P GAIN MUTATED" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-CG-5716         TCGA-CG-5717         TCGA-CG-5718 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-CG-5719         TCGA-CG-5720         TCGA-CG-5721 
  "16P GAIN MUTATED" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-CG-5722         TCGA-CG-5723         TCGA-CG-5724 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-CG-5725         TCGA-CG-5726         TCGA-CG-5727 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-CG-5728         TCGA-CG-5730         TCGA-CG-5732 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-CG-5733         TCGA-CG-5734         TCGA-D7-5577 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-D7-5578         TCGA-D7-5579         TCGA-D7-6518 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-D7-6519         TCGA-D7-6520         TCGA-D7-6521 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE"   "16P GAIN MUTATED" 
        TCGA-D7-6522         TCGA-D7-6524         TCGA-D7-6525 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-D7-6526         TCGA-D7-6527         TCGA-D7-6528 
  "16P GAIN MUTATED" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-D7-6815         TCGA-D7-6817         TCGA-D7-6818 
"16P GAIN WILD-TYPE"   "16P GAIN MUTATED"   "16P GAIN MUTATED" 
        TCGA-D7-6820         TCGA-D7-6822         TCGA-EQ-5647 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-F1-6177         TCGA-F1-6874         TCGA-F1-6875 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-FP-7735         TCGA-FP-7829         TCGA-FP-7998 
  "16P GAIN MUTATED" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-IN-7806         TCGA-IN-7808         TCGA-IP-7968 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE"   "16P GAIN MUTATED" 
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-CD-5798 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-CD-5799         TCGA-CD-5800         TCGA-CD-5801 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-CD-5802         TCGA-CD-5803         TCGA-CG-4300 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-CG-4301         TCGA-CG-4304         TCGA-CG-4305 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-CG-4306         TCGA-CG-4436         TCGA-CG-4437 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-CG-4438         TCGA-CG-4440         TCGA-CG-4441 
  "16P GAIN MUTATED" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-CG-4443         TCGA-CG-4444         TCGA-CG-4449 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-CG-4455         TCGA-CG-4460         TCGA-CG-4462 
"16P GAIN WILD-TYPE"   "16P GAIN MUTATED" "16P GAIN WILD-TYPE" 
        TCGA-CG-4465         TCGA-CG-4466         TCGA-CG-4469 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-CG-4472         TCGA-CG-4474         TCGA-CG-4477 
  "16P GAIN MUTATED" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-CG-5716         TCGA-CG-5717         TCGA-CG-5718 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-CG-5719         TCGA-CG-5720         TCGA-CG-5721 
  "16P GAIN MUTATED" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-CG-5722         TCGA-CG-5723         TCGA-CG-5724 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-CG-5725         TCGA-CG-5726         TCGA-CG-5727 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-CG-5728         TCGA-CG-5730         TCGA-CG-5732 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-CG-5733         TCGA-CG-5734         TCGA-D7-5577 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-D7-5578         TCGA-D7-5579         TCGA-D7-6518 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-D7-6519         TCGA-D7-6520         TCGA-D7-6521 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE"   "16P GAIN MUTATED" 
        TCGA-D7-6522         TCGA-D7-6524         TCGA-D7-6525 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-D7-6526         TCGA-D7-6527         TCGA-D7-6528 
  "16P GAIN MUTATED" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-D7-6815         TCGA-D7-6817         TCGA-D7-6818 
"16P GAIN WILD-TYPE"   "16P GAIN MUTATED"   "16P GAIN MUTATED" 
        TCGA-D7-6820         TCGA-D7-6822         TCGA-EQ-5647 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-F1-6177         TCGA-F1-6874         TCGA-F1-6875 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-FP-7735         TCGA-FP-7829         TCGA-FP-7998 
  "16P GAIN MUTATED" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-IN-7806         TCGA-IN-7808         TCGA-IP-7968 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE"   "16P GAIN MUTATED" 
[1] "hr=" "1.8"
D26V2, continuous
D26V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED      4    8
  16P GAIN WILD-TYPE   56   90
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  FEMALE                4                 56
  MALE                  8                 90
D26V4, multiclass
D26V5, multiclass
    clus
vv   16P GAIN MUTATED 16P GAIN WILD-TYPE
  T1                0                  6
  T2                4                 48
  T3                3                 58
  T4                5                 13
D26V6, multiclass
    clus
vv   16P GAIN MUTATED 16P GAIN WILD-TYPE
  N0                2                 42
  N1                3                 54
  N2                5                 19
  N3                2                 13
D26V7, multiclass
    clus
vv   16P GAIN MUTATED 16P GAIN WILD-TYPE
  M0                8                126
  M1                2                 14
  MX                2                  6
D26V8, multiclass
     clus
vv    16P GAIN MUTATED 16P GAIN WILD-TYPE
  I                  1                 23
  II                 0                 37
  III                5                 38
  IV                 6                 20
D26V9, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED      1   11
  16P GAIN WILD-TYPE    4  142
     clus
vv    16P GAIN MUTATED 16P GAIN WILD-TYPE
  NO                 1                  4
  YES               11                142
D26V10, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED      3    9
  16P GAIN WILD-TYPE    7  139
     clus
vv    16P GAIN MUTATED 16P GAIN WILD-TYPE
  NO                 3                  7
  YES                9                139

Clustering(27) Variable = 16q gain mutation analysis
D27V1, survival
                    sevent
clus2                 0  1
  16Q GAIN MUTATED    5  1
  16Q GAIN WILD-TYPE 85 14
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                 6                 99 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                 1                 14 
$`16Q GAIN MUTATED`
TCGA-CG-4438 TCGA-CG-4460 TCGA-CG-4472 TCGA-CG-5719 TCGA-D7-6521 TCGA-FP-7735 
       54.05        21.99        12.00         1.02         8.19         0.39 

$`16Q GAIN WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-6452 TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6458 
        5.62         0.10         0.95         1.41         1.35         1.35 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
        0.85         0.82         0.62         0.62         1.71         2.17 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
        0.99         1.22         0.66         1.12         0.76         0.66 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
        0.26         1.22         1.48         0.46         1.25         0.13 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 
        1.05         0.82         0.69         0.16         4.54         0.99 
TCGA-BR-7901 TCGA-BR-7957 TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
        0.95         0.69         0.82         0.69         0.36         0.49 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
        0.30         0.07        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        1.02        52.96         8.05         4.01        14.01        29.98 
TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       47.05        19.07        12.03         1.02         8.98        18.94 
TCGA-CG-4469 TCGA-CG-4474 TCGA-CG-4477 TCGA-CG-5716 TCGA-CG-5717 TCGA-CG-5718 
        7.07         1.02         1.02         1.02         6.94         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 
        0.99         5.98         0.95        70.06        12.03        15.02 
TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       28.96        31.04        65.10         4.01        55.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99         8.65         3.58         4.54         9.80        15.65 
TCGA-D7-6520 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
        9.63         6.90         0.69         5.95         6.61         4.14 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
        1.68         3.65         4.70         4.04         2.93         4.27 
TCGA-EQ-5647 TCGA-F1-6177 TCGA-F1-6874 TCGA-F1-6875 TCGA-FP-7829 TCGA-FP-7998 
        0.62         6.54         2.01        72.23         0.20         3.58 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IP-7968 
        6.87         3.55         2.53 

  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
              0.39               0.07 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
             54.05              72.23 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
            10.095              2.530 
[1] "0.4 - 54.0 (10.1)" "0.1 - 72.2 (2.5)" 
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-CD-5798 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-CD-5799         TCGA-CD-5800         TCGA-CD-5801 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-CD-5802         TCGA-CD-5803         TCGA-CG-4300 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-CG-4301         TCGA-CG-4304         TCGA-CG-4305 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-CG-4306         TCGA-CG-4436         TCGA-CG-4437 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-CG-4438         TCGA-CG-4440         TCGA-CG-4441 
  "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-CG-4443         TCGA-CG-4444         TCGA-CG-4449 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-CG-4455         TCGA-CG-4460         TCGA-CG-4462 
"16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" 
        TCGA-CG-4465         TCGA-CG-4466         TCGA-CG-4469 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-CG-4472         TCGA-CG-4474         TCGA-CG-4477 
  "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-CG-5716         TCGA-CG-5717         TCGA-CG-5718 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-CG-5719         TCGA-CG-5720         TCGA-CG-5721 
  "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-CG-5722         TCGA-CG-5723         TCGA-CG-5724 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-CG-5725         TCGA-CG-5726         TCGA-CG-5727 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-CG-5728         TCGA-CG-5730         TCGA-CG-5732 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-CG-5733         TCGA-CG-5734         TCGA-D7-5577 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-D7-5578         TCGA-D7-5579         TCGA-D7-6518 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-D7-6519         TCGA-D7-6520         TCGA-D7-6521 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" 
        TCGA-D7-6522         TCGA-D7-6524         TCGA-D7-6525 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-D7-6526         TCGA-D7-6527         TCGA-D7-6528 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-D7-6815         TCGA-D7-6817         TCGA-D7-6818 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-D7-6820         TCGA-D7-6822         TCGA-EQ-5647 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-F1-6177         TCGA-F1-6874         TCGA-F1-6875 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-FP-7735         TCGA-FP-7829         TCGA-FP-7998 
  "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-IN-7806         TCGA-IN-7808         TCGA-IP-7968 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-CD-5798 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-CD-5799         TCGA-CD-5800         TCGA-CD-5801 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-CD-5802         TCGA-CD-5803         TCGA-CG-4300 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-CG-4301         TCGA-CG-4304         TCGA-CG-4305 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-CG-4306         TCGA-CG-4436         TCGA-CG-4437 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-CG-4438         TCGA-CG-4440         TCGA-CG-4441 
  "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-CG-4443         TCGA-CG-4444         TCGA-CG-4449 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-CG-4455         TCGA-CG-4460         TCGA-CG-4462 
"16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" 
        TCGA-CG-4465         TCGA-CG-4466         TCGA-CG-4469 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-CG-4472         TCGA-CG-4474         TCGA-CG-4477 
  "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-CG-5716         TCGA-CG-5717         TCGA-CG-5718 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-CG-5719         TCGA-CG-5720         TCGA-CG-5721 
  "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-CG-5722         TCGA-CG-5723         TCGA-CG-5724 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-CG-5725         TCGA-CG-5726         TCGA-CG-5727 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-CG-5728         TCGA-CG-5730         TCGA-CG-5732 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-CG-5733         TCGA-CG-5734         TCGA-D7-5577 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-D7-5578         TCGA-D7-5579         TCGA-D7-6518 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-D7-6519         TCGA-D7-6520         TCGA-D7-6521 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" 
        TCGA-D7-6522         TCGA-D7-6524         TCGA-D7-6525 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-D7-6526         TCGA-D7-6527         TCGA-D7-6528 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-D7-6815         TCGA-D7-6817         TCGA-D7-6818 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-D7-6820         TCGA-D7-6822         TCGA-EQ-5647 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-F1-6177         TCGA-F1-6874         TCGA-F1-6875 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-FP-7735         TCGA-FP-7829         TCGA-FP-7998 
  "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-IN-7806         TCGA-IN-7808         TCGA-IP-7968 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-CD-5798 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-CD-5799         TCGA-CD-5800         TCGA-CD-5801 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-CD-5802         TCGA-CD-5803         TCGA-CG-4300 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-CG-4301         TCGA-CG-4304         TCGA-CG-4305 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-CG-4306         TCGA-CG-4436         TCGA-CG-4437 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-CG-4438         TCGA-CG-4440         TCGA-CG-4441 
  "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-CG-4443         TCGA-CG-4444         TCGA-CG-4449 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-CG-4455         TCGA-CG-4460         TCGA-CG-4462 
"16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" 
        TCGA-CG-4465         TCGA-CG-4466         TCGA-CG-4469 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-CG-4472         TCGA-CG-4474         TCGA-CG-4477 
  "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-CG-5716         TCGA-CG-5717         TCGA-CG-5718 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-CG-5719         TCGA-CG-5720         TCGA-CG-5721 
  "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-CG-5722         TCGA-CG-5723         TCGA-CG-5724 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-CG-5725         TCGA-CG-5726         TCGA-CG-5727 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-CG-5728         TCGA-CG-5730         TCGA-CG-5732 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-CG-5733         TCGA-CG-5734         TCGA-D7-5577 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-D7-5578         TCGA-D7-5579         TCGA-D7-6518 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-D7-6519         TCGA-D7-6520         TCGA-D7-6521 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" 
        TCGA-D7-6522         TCGA-D7-6524         TCGA-D7-6525 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-D7-6526         TCGA-D7-6527         TCGA-D7-6528 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-D7-6815         TCGA-D7-6817         TCGA-D7-6818 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-D7-6820         TCGA-D7-6822         TCGA-EQ-5647 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-F1-6177         TCGA-F1-6874         TCGA-F1-6875 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-FP-7735         TCGA-FP-7829         TCGA-FP-7998 
  "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-IN-7806         TCGA-IN-7808         TCGA-IP-7968 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
[1] "hr=" "1.6"
D27V2, continuous
D27V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED      3    4
  16Q GAIN WILD-TYPE   57   94
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  FEMALE                3                 57
  MALE                  4                 94
D27V4, multiclass
D27V5, multiclass
    clus
vv   16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  T1                0                  6
  T2                2                 50
  T3                0                 61
  T4                5                 13
D27V6, multiclass
    clus
vv   16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  N0                2                 42
  N1                2                 55
  N2                3                 21
  N3                0                 15
D27V7, multiclass
    clus
vv   16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  M0                4                130
  M1                2                 14
  MX                1                  7
D27V8, multiclass
     clus
vv    16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  I                  1                 23
  II                 0                 37
  III                1                 42
  IV                 5                 21
D27V9, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED      0    7
  16Q GAIN WILD-TYPE    5  146
     clus
vv    16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  NO                 0                  5
  YES                7                146
D27V10, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED      1    6
  16Q GAIN WILD-TYPE    9  142
     clus
vv    16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  NO                 1                  9
  YES                6                142

Clustering(28) Variable = 17p gain mutation analysis
D28V1, survival
                    sevent
clus2                 0  1
  17P GAIN MUTATED    2  3
  17P GAIN WILD-TYPE 88 12
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                 5                100 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                 3                 12 
$`17P GAIN MUTATED`
TCGA-CG-4460 TCGA-CG-5724 TCGA-D7-6817 TCGA-EQ-5647 TCGA-FP-7829 
       21.99        12.03         4.70         0.62         0.20 

$`17P GAIN WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-6452 TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6458 
        5.62         0.10         0.95         1.41         1.35         1.35 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
        0.85         0.82         0.62         0.62         1.71         2.17 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
        0.99         1.22         0.66         1.12         0.76         0.66 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
        0.26         1.22         1.48         0.46         1.25         0.13 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 
        1.05         0.82         0.69         0.16         4.54         0.99 
TCGA-BR-7901 TCGA-BR-7957 TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
        0.95         0.69         0.82         0.69         0.36         0.49 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
        0.30         0.07        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02        52.96         8.05        54.05         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       29.98        47.05        19.07        12.03         1.02         8.98 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4474 TCGA-CG-4477 TCGA-CG-5716 
       18.94         7.07        12.00         1.02         1.02         1.02 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.94         1.02         1.02         0.99         5.98         0.95 
TCGA-CG-5723 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 
       70.06        15.02        28.96        31.04        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       55.04        21.07         7.99         8.65         3.58         4.54 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
        9.80        15.65         9.63         8.19         6.90         0.69 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6818 
        5.95         6.61         4.14         1.68         3.65         4.04 
TCGA-D7-6820 TCGA-D7-6822 TCGA-F1-6177 TCGA-F1-6874 TCGA-F1-6875 TCGA-FP-7735 
        2.93         4.27         6.54         2.01        72.23         0.39 
TCGA-FP-7998 TCGA-IN-7806 TCGA-IN-7808 TCGA-IP-7968 
        3.58         6.87         3.55         2.53 

  17P GAIN MUTATED 17P GAIN WILD-TYPE 
              0.20               0.07 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
             21.99              72.23 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
              4.70               2.73 
[1] "0.2 - 22.0 (4.7)" "0.1 - 72.2 (2.7)"
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-CD-5798 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-CD-5799         TCGA-CD-5800         TCGA-CD-5801 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-CD-5802         TCGA-CD-5803         TCGA-CG-4300 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-CG-4301         TCGA-CG-4304         TCGA-CG-4305 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-CG-4306         TCGA-CG-4436         TCGA-CG-4437 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-CG-4438         TCGA-CG-4440         TCGA-CG-4441 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-CG-4443         TCGA-CG-4444         TCGA-CG-4449 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-CG-4455         TCGA-CG-4460         TCGA-CG-4462 
"17P GAIN WILD-TYPE"   "17P GAIN MUTATED" "17P GAIN WILD-TYPE" 
        TCGA-CG-4465         TCGA-CG-4466         TCGA-CG-4469 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-CG-4472         TCGA-CG-4474         TCGA-CG-4477 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-CG-5716         TCGA-CG-5717         TCGA-CG-5718 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-CG-5719         TCGA-CG-5720         TCGA-CG-5721 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-CG-5722         TCGA-CG-5723         TCGA-CG-5724 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE"   "17P GAIN MUTATED" 
        TCGA-CG-5725         TCGA-CG-5726         TCGA-CG-5727 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-CG-5728         TCGA-CG-5730         TCGA-CG-5732 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-CG-5733         TCGA-CG-5734         TCGA-D7-5577 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-D7-5578         TCGA-D7-5579         TCGA-D7-6518 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-D7-6519         TCGA-D7-6520         TCGA-D7-6521 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-D7-6522         TCGA-D7-6524         TCGA-D7-6525 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-D7-6526         TCGA-D7-6527         TCGA-D7-6528 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-D7-6815         TCGA-D7-6817         TCGA-D7-6818 
"17P GAIN WILD-TYPE"   "17P GAIN MUTATED" "17P GAIN WILD-TYPE" 
        TCGA-D7-6820         TCGA-D7-6822         TCGA-EQ-5647 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE"   "17P GAIN MUTATED" 
        TCGA-F1-6177         TCGA-F1-6874         TCGA-F1-6875 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-FP-7735         TCGA-FP-7829         TCGA-FP-7998 
"17P GAIN WILD-TYPE"   "17P GAIN MUTATED" "17P GAIN WILD-TYPE" 
        TCGA-IN-7806         TCGA-IN-7808         TCGA-IP-7968 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-CD-5798 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-CD-5799         TCGA-CD-5800         TCGA-CD-5801 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-CD-5802         TCGA-CD-5803         TCGA-CG-4300 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-CG-4301         TCGA-CG-4304         TCGA-CG-4305 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-CG-4306         TCGA-CG-4436         TCGA-CG-4437 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-CG-4438         TCGA-CG-4440         TCGA-CG-4441 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-CG-4443         TCGA-CG-4444         TCGA-CG-4449 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-CG-4455         TCGA-CG-4460         TCGA-CG-4462 
"17P GAIN WILD-TYPE"   "17P GAIN MUTATED" "17P GAIN WILD-TYPE" 
        TCGA-CG-4465         TCGA-CG-4466         TCGA-CG-4469 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-CG-4472         TCGA-CG-4474         TCGA-CG-4477 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-CG-5716         TCGA-CG-5717         TCGA-CG-5718 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-CG-5719         TCGA-CG-5720         TCGA-CG-5721 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-CG-5722         TCGA-CG-5723         TCGA-CG-5724 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE"   "17P GAIN MUTATED" 
        TCGA-CG-5725         TCGA-CG-5726         TCGA-CG-5727 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-CG-5728         TCGA-CG-5730         TCGA-CG-5732 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-CG-5733         TCGA-CG-5734         TCGA-D7-5577 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-D7-5578         TCGA-D7-5579         TCGA-D7-6518 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-D7-6519         TCGA-D7-6520         TCGA-D7-6521 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-D7-6522         TCGA-D7-6524         TCGA-D7-6525 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-D7-6526         TCGA-D7-6527         TCGA-D7-6528 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-D7-6815         TCGA-D7-6817         TCGA-D7-6818 
"17P GAIN WILD-TYPE"   "17P GAIN MUTATED" "17P GAIN WILD-TYPE" 
        TCGA-D7-6820         TCGA-D7-6822         TCGA-EQ-5647 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE"   "17P GAIN MUTATED" 
        TCGA-F1-6177         TCGA-F1-6874         TCGA-F1-6875 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-FP-7735         TCGA-FP-7829         TCGA-FP-7998 
"17P GAIN WILD-TYPE"   "17P GAIN MUTATED" "17P GAIN WILD-TYPE" 
        TCGA-IN-7806         TCGA-IN-7808         TCGA-IP-7968 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-CD-5798 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-CD-5799         TCGA-CD-5800         TCGA-CD-5801 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-CD-5802         TCGA-CD-5803         TCGA-CG-4300 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-CG-4301         TCGA-CG-4304         TCGA-CG-4305 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-CG-4306         TCGA-CG-4436         TCGA-CG-4437 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-CG-4438         TCGA-CG-4440         TCGA-CG-4441 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-CG-4443         TCGA-CG-4444         TCGA-CG-4449 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-CG-4455         TCGA-CG-4460         TCGA-CG-4462 
"17P GAIN WILD-TYPE"   "17P GAIN MUTATED" "17P GAIN WILD-TYPE" 
        TCGA-CG-4465         TCGA-CG-4466         TCGA-CG-4469 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-CG-4472         TCGA-CG-4474         TCGA-CG-4477 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-CG-5716         TCGA-CG-5717         TCGA-CG-5718 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-CG-5719         TCGA-CG-5720         TCGA-CG-5721 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-CG-5722         TCGA-CG-5723         TCGA-CG-5724 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE"   "17P GAIN MUTATED" 
        TCGA-CG-5725         TCGA-CG-5726         TCGA-CG-5727 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-CG-5728         TCGA-CG-5730         TCGA-CG-5732 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-CG-5733         TCGA-CG-5734         TCGA-D7-5577 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-D7-5578         TCGA-D7-5579         TCGA-D7-6518 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-D7-6519         TCGA-D7-6520         TCGA-D7-6521 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-D7-6522         TCGA-D7-6524         TCGA-D7-6525 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-D7-6526         TCGA-D7-6527         TCGA-D7-6528 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-D7-6815         TCGA-D7-6817         TCGA-D7-6818 
"17P GAIN WILD-TYPE"   "17P GAIN MUTATED" "17P GAIN WILD-TYPE" 
        TCGA-D7-6820         TCGA-D7-6822         TCGA-EQ-5647 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE"   "17P GAIN MUTATED" 
        TCGA-F1-6177         TCGA-F1-6874         TCGA-F1-6875 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-FP-7735         TCGA-FP-7829         TCGA-FP-7998 
"17P GAIN WILD-TYPE"   "17P GAIN MUTATED" "17P GAIN WILD-TYPE" 
        TCGA-IN-7806         TCGA-IN-7808         TCGA-IP-7968 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
[1] "hr=" "4.6"
D28V2, continuous
D28V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED      2    3
  17P GAIN WILD-TYPE   58   95
        clus
vv       17P GAIN MUTATED 17P GAIN WILD-TYPE
  FEMALE                2                 58
  MALE                  3                 95
D28V4, multiclass
D28V5, multiclass
    clus
vv   17P GAIN MUTATED 17P GAIN WILD-TYPE
  T1                0                  6
  T2                1                 51
  T3                2                 59
  T4                2                 16
D28V6, multiclass
    clus
vv   17P GAIN MUTATED 17P GAIN WILD-TYPE
  N0                0                 44
  N1                2                 55
  N2                0                 24
  N3                3                 12
D28V7, multiclass
    clus
vv   17P GAIN MUTATED 17P GAIN WILD-TYPE
  M0                2                132
  M1                3                 13
  MX                0                  8
D28V8, multiclass
     clus
vv    17P GAIN MUTATED 17P GAIN WILD-TYPE
  I                  0                 24
  II                 0                 37
  III                2                 41
  IV                 3                 23
D28V9, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED      0    5
  17P GAIN WILD-TYPE    5  148
     clus
vv    17P GAIN MUTATED 17P GAIN WILD-TYPE
  NO                 0                  5
  YES                5                148
D28V10, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED      0    5
  17P GAIN WILD-TYPE   10  143
     clus
vv    17P GAIN MUTATED 17P GAIN WILD-TYPE
  NO                 0                 10
  YES                5                143

Clustering(29) Variable = 17q gain mutation analysis
D29V1, survival
                    sevent
clus2                 0  1
  17Q GAIN MUTATED    4  4
  17Q GAIN WILD-TYPE 86 11
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                 8                 97 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                 4                 11 
$`17Q GAIN MUTATED`
TCGA-B7-5818 TCGA-CG-4460 TCGA-CG-5719 TCGA-CG-5724 TCGA-D7-6817 TCGA-EQ-5647 
        0.10        21.99         1.02        12.03         4.70         0.62 
TCGA-F1-6875 TCGA-FP-7829 
       72.23         0.20 

$`17Q GAIN WILD-TYPE`
TCGA-B7-5816 TCGA-BR-6452 TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
        5.62         0.95         1.41         1.35         1.35         0.85 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
        0.82         0.62         0.62         1.71         2.17         0.99 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
        1.22         0.66         1.12         0.76         0.66         0.26 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
        1.22         1.48         0.46         1.25         0.13         1.05 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 
        0.82         0.69         0.16         4.54         0.99         0.95 
TCGA-BR-7957 TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        0.69         0.82         0.69         0.36         0.49         0.30 
TCGA-CD-5803 TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
        0.07        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
       52.96         8.05        54.05         4.01        14.01        29.98 
TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       47.05        19.07        12.03         1.02         8.98        18.94 
TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4474 TCGA-CG-4477 TCGA-CG-5716 TCGA-CG-5717 
        7.07        12.00         1.02         1.02         1.02         6.94 
TCGA-CG-5718 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5725 
        1.02         0.99         5.98         0.95        70.06        15.02 
TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       28.96        31.04        65.10         4.01        55.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99         8.65         3.58         4.54         9.80        15.65 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
        9.63         8.19         6.90         0.69         5.95         6.61 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
        4.14         1.68         3.65         4.04         2.93         4.27 
TCGA-F1-6177 TCGA-F1-6874 TCGA-FP-7735 TCGA-FP-7998 TCGA-IN-7806 TCGA-IN-7808 
        6.54         2.01         0.39         3.58         6.87         3.55 
TCGA-IP-7968 
        2.53 

  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
              0.10               0.07 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
             72.23              70.06 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
              2.86               2.93 
[1] "0.1 - 72.2 (2.9)" "0.1 - 70.1 (2.9)"
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-CD-5798 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-CD-5799         TCGA-CD-5800         TCGA-CD-5801 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-CD-5802         TCGA-CD-5803         TCGA-CG-4300 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-CG-4301         TCGA-CG-4304         TCGA-CG-4305 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-CG-4306         TCGA-CG-4436         TCGA-CG-4437 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-CG-4438         TCGA-CG-4440         TCGA-CG-4441 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-CG-4443         TCGA-CG-4444         TCGA-CG-4449 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-CG-4455         TCGA-CG-4460         TCGA-CG-4462 
"17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" 
        TCGA-CG-4465         TCGA-CG-4466         TCGA-CG-4469 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-CG-4472         TCGA-CG-4474         TCGA-CG-4477 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-CG-5716         TCGA-CG-5717         TCGA-CG-5718 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-CG-5719         TCGA-CG-5720         TCGA-CG-5721 
  "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-CG-5722         TCGA-CG-5723         TCGA-CG-5724 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
        TCGA-CG-5725         TCGA-CG-5726         TCGA-CG-5727 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-CG-5728         TCGA-CG-5730         TCGA-CG-5732 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-CG-5733         TCGA-CG-5734         TCGA-D7-5577 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-D7-5578         TCGA-D7-5579         TCGA-D7-6518 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-D7-6519         TCGA-D7-6520         TCGA-D7-6521 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-D7-6522         TCGA-D7-6524         TCGA-D7-6525 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-D7-6526         TCGA-D7-6527         TCGA-D7-6528 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-D7-6815         TCGA-D7-6817         TCGA-D7-6818 
"17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" 
        TCGA-D7-6820         TCGA-D7-6822         TCGA-EQ-5647 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
        TCGA-F1-6177         TCGA-F1-6874         TCGA-F1-6875 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
        TCGA-FP-7735         TCGA-FP-7829         TCGA-FP-7998 
"17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" 
        TCGA-IN-7806         TCGA-IN-7808         TCGA-IP-7968 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-CD-5798 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-CD-5799         TCGA-CD-5800         TCGA-CD-5801 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-CD-5802         TCGA-CD-5803         TCGA-CG-4300 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-CG-4301         TCGA-CG-4304         TCGA-CG-4305 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-CG-4306         TCGA-CG-4436         TCGA-CG-4437 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-CG-4438         TCGA-CG-4440         TCGA-CG-4441 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-CG-4443         TCGA-CG-4444         TCGA-CG-4449 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-CG-4455         TCGA-CG-4460         TCGA-CG-4462 
"17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" 
        TCGA-CG-4465         TCGA-CG-4466         TCGA-CG-4469 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-CG-4472         TCGA-CG-4474         TCGA-CG-4477 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-CG-5716         TCGA-CG-5717         TCGA-CG-5718 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-CG-5719         TCGA-CG-5720         TCGA-CG-5721 
  "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-CG-5722         TCGA-CG-5723         TCGA-CG-5724 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
        TCGA-CG-5725         TCGA-CG-5726         TCGA-CG-5727 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-CG-5728         TCGA-CG-5730         TCGA-CG-5732 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-CG-5733         TCGA-CG-5734         TCGA-D7-5577 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-D7-5578         TCGA-D7-5579         TCGA-D7-6518 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-D7-6519         TCGA-D7-6520         TCGA-D7-6521 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-D7-6522         TCGA-D7-6524         TCGA-D7-6525 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-D7-6526         TCGA-D7-6527         TCGA-D7-6528 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-D7-6815         TCGA-D7-6817         TCGA-D7-6818 
"17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" 
        TCGA-D7-6820         TCGA-D7-6822         TCGA-EQ-5647 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
        TCGA-F1-6177         TCGA-F1-6874         TCGA-F1-6875 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
        TCGA-FP-7735         TCGA-FP-7829         TCGA-FP-7998 
"17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" 
        TCGA-IN-7806         TCGA-IN-7808         TCGA-IP-7968 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-CD-5798 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-CD-5799         TCGA-CD-5800         TCGA-CD-5801 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-CD-5802         TCGA-CD-5803         TCGA-CG-4300 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-CG-4301         TCGA-CG-4304         TCGA-CG-4305 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-CG-4306         TCGA-CG-4436         TCGA-CG-4437 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-CG-4438         TCGA-CG-4440         TCGA-CG-4441 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-CG-4443         TCGA-CG-4444         TCGA-CG-4449 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-CG-4455         TCGA-CG-4460         TCGA-CG-4462 
"17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" 
        TCGA-CG-4465         TCGA-CG-4466         TCGA-CG-4469 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-CG-4472         TCGA-CG-4474         TCGA-CG-4477 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-CG-5716         TCGA-CG-5717         TCGA-CG-5718 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-CG-5719         TCGA-CG-5720         TCGA-CG-5721 
  "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-CG-5722         TCGA-CG-5723         TCGA-CG-5724 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
        TCGA-CG-5725         TCGA-CG-5726         TCGA-CG-5727 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-CG-5728         TCGA-CG-5730         TCGA-CG-5732 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-CG-5733         TCGA-CG-5734         TCGA-D7-5577 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-D7-5578         TCGA-D7-5579         TCGA-D7-6518 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-D7-6519         TCGA-D7-6520         TCGA-D7-6521 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-D7-6522         TCGA-D7-6524         TCGA-D7-6525 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-D7-6526         TCGA-D7-6527         TCGA-D7-6528 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-D7-6815         TCGA-D7-6817         TCGA-D7-6818 
"17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" 
        TCGA-D7-6820         TCGA-D7-6822         TCGA-EQ-5647 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
        TCGA-F1-6177         TCGA-F1-6874         TCGA-F1-6875 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
        TCGA-FP-7735         TCGA-FP-7829         TCGA-FP-7998 
"17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" 
        TCGA-IN-7806         TCGA-IN-7808         TCGA-IP-7968 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
[1] "hr=" "2.4"
D29V2, continuous
D29V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED      4    6
  17Q GAIN WILD-TYPE   56   92
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  FEMALE                4                 56
  MALE                  6                 92
D29V4, multiclass
D29V5, multiclass
    clus
vv   17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  T1                0                  6
  T2                3                 49
  T3                3                 58
  T4                3                 15
D29V6, multiclass
    clus
vv   17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  N0                4                 40
  N1                2                 55
  N2                0                 24
  N3                3                 12
D29V7, multiclass
    clus
vv   17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  M0                6                128
  M1                4                 12
  MX                0                  8
D29V8, multiclass
     clus
vv    17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  I                  2                 22
  II                 1                 36
  III                2                 41
  IV                 4                 22
D29V9, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED      0   10
  17Q GAIN WILD-TYPE    5  143
     clus
vv    17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  NO                 0                  5
  YES               10                143
D29V10, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED      0   10
  17Q GAIN WILD-TYPE   10  138
     clus
vv    17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  NO                 0                 10
  YES               10                138

Clustering(30) Variable = 18p gain mutation analysis
D30V1, survival
                    sevent
clus2                 0  1
  18P GAIN MUTATED    6  1
  18P GAIN WILD-TYPE 84 14
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                 7                 98 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                 1                 14 
$`18P GAIN MUTATED`
TCGA-BR-7722 TCGA-BR-7901 TCGA-CD-5799 TCGA-CG-4460 TCGA-CG-4474 TCGA-D7-6528 
        0.16         0.95         0.69        21.99         1.02         1.68 
TCGA-D7-6817 
        4.70 

$`18P GAIN WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-6452 TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6458 
        5.62         0.10         0.95         1.41         1.35         1.35 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
        0.85         0.82         0.62         0.62         1.71         2.17 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
        0.99         1.22         0.66         1.12         0.76         0.66 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
        0.26         1.22         1.48         0.46         1.25         0.13 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7957 
        1.05         0.82         0.69         4.54         0.99         0.69 
TCGA-CD-5798 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CG-4300 
        0.82         0.36         0.49         0.30         0.07        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02        52.96         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 
       54.05         4.01        14.01        29.98        47.05        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 
       12.03         1.02         8.98        18.94         7.07        12.00 
TCGA-CG-4477 TCGA-CG-5716 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
        1.02         1.02         6.94         1.02         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 
        5.98         0.95        70.06        12.03        15.02        28.96 
TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       31.04        65.10         4.01        55.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
        8.65         3.58         4.54         9.80        15.65         9.63 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
        8.19         6.90         0.69         5.95         6.61         4.14 
TCGA-D7-6815 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-EQ-5647 TCGA-F1-6177 
        3.65         4.04         2.93         4.27         0.62         6.54 
TCGA-F1-6874 TCGA-F1-6875 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7998 TCGA-IN-7806 
        2.01        72.23         0.39         0.20         3.58         6.87 
TCGA-IN-7808 TCGA-IP-7968 
        3.55         2.53 

  18P GAIN MUTATED 18P GAIN WILD-TYPE 
              0.16               0.07 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
             21.99              72.23 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
             1.020              3.285 
[1] "0.2 - 22.0 (1.0)" "0.1 - 72.2 (3.3)"
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
  "18P GAIN MUTATED" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-CD-5798 
  "18P GAIN MUTATED" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-CD-5799         TCGA-CD-5800         TCGA-CD-5801 
  "18P GAIN MUTATED" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-CD-5802         TCGA-CD-5803         TCGA-CG-4300 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-CG-4301         TCGA-CG-4304         TCGA-CG-4305 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-CG-4306         TCGA-CG-4436         TCGA-CG-4437 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-CG-4438         TCGA-CG-4440         TCGA-CG-4441 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-CG-4443         TCGA-CG-4444         TCGA-CG-4449 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-CG-4455         TCGA-CG-4460         TCGA-CG-4462 
"18P GAIN WILD-TYPE"   "18P GAIN MUTATED" "18P GAIN WILD-TYPE" 
        TCGA-CG-4465         TCGA-CG-4466         TCGA-CG-4469 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-CG-4472         TCGA-CG-4474         TCGA-CG-4477 
"18P GAIN WILD-TYPE"   "18P GAIN MUTATED" "18P GAIN WILD-TYPE" 
        TCGA-CG-5716         TCGA-CG-5717         TCGA-CG-5718 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-CG-5719         TCGA-CG-5720         TCGA-CG-5721 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-CG-5722         TCGA-CG-5723         TCGA-CG-5724 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-CG-5725         TCGA-CG-5726         TCGA-CG-5727 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-CG-5728         TCGA-CG-5730         TCGA-CG-5732 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-CG-5733         TCGA-CG-5734         TCGA-D7-5577 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-D7-5578         TCGA-D7-5579         TCGA-D7-6518 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-D7-6519         TCGA-D7-6520         TCGA-D7-6521 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-D7-6522         TCGA-D7-6524         TCGA-D7-6525 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-D7-6526         TCGA-D7-6527         TCGA-D7-6528 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE"   "18P GAIN MUTATED" 
        TCGA-D7-6815         TCGA-D7-6817         TCGA-D7-6818 
"18P GAIN WILD-TYPE"   "18P GAIN MUTATED" "18P GAIN WILD-TYPE" 
        TCGA-D7-6820         TCGA-D7-6822         TCGA-EQ-5647 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-F1-6177         TCGA-F1-6874         TCGA-F1-6875 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-FP-7735         TCGA-FP-7829         TCGA-FP-7998 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-IN-7806         TCGA-IN-7808         TCGA-IP-7968 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
  "18P GAIN MUTATED" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-CD-5798 
  "18P GAIN MUTATED" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-CD-5799         TCGA-CD-5800         TCGA-CD-5801 
  "18P GAIN MUTATED" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-CD-5802         TCGA-CD-5803         TCGA-CG-4300 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-CG-4301         TCGA-CG-4304         TCGA-CG-4305 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-CG-4306         TCGA-CG-4436         TCGA-CG-4437 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-CG-4438         TCGA-CG-4440         TCGA-CG-4441 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-CG-4443         TCGA-CG-4444         TCGA-CG-4449 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-CG-4455         TCGA-CG-4460         TCGA-CG-4462 
"18P GAIN WILD-TYPE"   "18P GAIN MUTATED" "18P GAIN WILD-TYPE" 
        TCGA-CG-4465         TCGA-CG-4466         TCGA-CG-4469 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-CG-4472         TCGA-CG-4474         TCGA-CG-4477 
"18P GAIN WILD-TYPE"   "18P GAIN MUTATED" "18P GAIN WILD-TYPE" 
        TCGA-CG-5716         TCGA-CG-5717         TCGA-CG-5718 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-CG-5719         TCGA-CG-5720         TCGA-CG-5721 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-CG-5722         TCGA-CG-5723         TCGA-CG-5724 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-CG-5725         TCGA-CG-5726         TCGA-CG-5727 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-CG-5728         TCGA-CG-5730         TCGA-CG-5732 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-CG-5733         TCGA-CG-5734         TCGA-D7-5577 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-D7-5578         TCGA-D7-5579         TCGA-D7-6518 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-D7-6519         TCGA-D7-6520         TCGA-D7-6521 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-D7-6522         TCGA-D7-6524         TCGA-D7-6525 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-D7-6526         TCGA-D7-6527         TCGA-D7-6528 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE"   "18P GAIN MUTATED" 
        TCGA-D7-6815         TCGA-D7-6817         TCGA-D7-6818 
"18P GAIN WILD-TYPE"   "18P GAIN MUTATED" "18P GAIN WILD-TYPE" 
        TCGA-D7-6820         TCGA-D7-6822         TCGA-EQ-5647 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-F1-6177         TCGA-F1-6874         TCGA-F1-6875 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-FP-7735         TCGA-FP-7829         TCGA-FP-7998 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-IN-7806         TCGA-IN-7808         TCGA-IP-7968 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
  "18P GAIN MUTATED" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-CD-5798 
  "18P GAIN MUTATED" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-CD-5799         TCGA-CD-5800         TCGA-CD-5801 
  "18P GAIN MUTATED" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-CD-5802         TCGA-CD-5803         TCGA-CG-4300 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-CG-4301         TCGA-CG-4304         TCGA-CG-4305 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-CG-4306         TCGA-CG-4436         TCGA-CG-4437 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-CG-4438         TCGA-CG-4440         TCGA-CG-4441 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-CG-4443         TCGA-CG-4444         TCGA-CG-4449 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-CG-4455         TCGA-CG-4460         TCGA-CG-4462 
"18P GAIN WILD-TYPE"   "18P GAIN MUTATED" "18P GAIN WILD-TYPE" 
        TCGA-CG-4465         TCGA-CG-4466         TCGA-CG-4469 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-CG-4472         TCGA-CG-4474         TCGA-CG-4477 
"18P GAIN WILD-TYPE"   "18P GAIN MUTATED" "18P GAIN WILD-TYPE" 
        TCGA-CG-5716         TCGA-CG-5717         TCGA-CG-5718 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-CG-5719         TCGA-CG-5720         TCGA-CG-5721 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-CG-5722         TCGA-CG-5723         TCGA-CG-5724 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-CG-5725         TCGA-CG-5726         TCGA-CG-5727 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-CG-5728         TCGA-CG-5730         TCGA-CG-5732 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-CG-5733         TCGA-CG-5734         TCGA-D7-5577 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-D7-5578         TCGA-D7-5579         TCGA-D7-6518 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-D7-6519         TCGA-D7-6520         TCGA-D7-6521 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-D7-6522         TCGA-D7-6524         TCGA-D7-6525 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-D7-6526         TCGA-D7-6527         TCGA-D7-6528 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE"   "18P GAIN MUTATED" 
        TCGA-D7-6815         TCGA-D7-6817         TCGA-D7-6818 
"18P GAIN WILD-TYPE"   "18P GAIN MUTATED" "18P GAIN WILD-TYPE" 
        TCGA-D7-6820         TCGA-D7-6822         TCGA-EQ-5647 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-F1-6177         TCGA-F1-6874         TCGA-F1-6875 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-FP-7735         TCGA-FP-7829         TCGA-FP-7998 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-IN-7806         TCGA-IN-7808         TCGA-IP-7968 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
[1] "hr=" "1.6"
D30V2, continuous
D30V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED      8   10
  18P GAIN WILD-TYPE   52   88
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  FEMALE                8                 52
  MALE                 10                 88
D30V4, multiclass
D30V5, multiclass
    clus
vv   18P GAIN MUTATED 18P GAIN WILD-TYPE
  T1                0                  6
  T2                4                 48
  T3                7                 54
  T4                2                 16
D30V6, multiclass
    clus
vv   18P GAIN MUTATED 18P GAIN WILD-TYPE
  N0                1                 43
  N1               11                 46
  N2                1                 23
  N3                2                 13
D30V7, multiclass
    clus
vv   18P GAIN MUTATED 18P GAIN WILD-TYPE
  M0               15                119
  M1                2                 14
  MX                1                  7
D30V8, multiclass
     clus
vv    18P GAIN MUTATED 18P GAIN WILD-TYPE
  I                  1                 23
  II                 2                 35
  III                7                 36
  IV                 3                 23
D30V9, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED      1   17
  18P GAIN WILD-TYPE    4  136
     clus
vv    18P GAIN MUTATED 18P GAIN WILD-TYPE
  NO                 1                  4
  YES               17                136
D30V10, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED      1   17
  18P GAIN WILD-TYPE    9  131
     clus
vv    18P GAIN MUTATED 18P GAIN WILD-TYPE
  NO                 1                  9
  YES               17                131

Clustering(31) Variable = 18q gain mutation analysis
D31V1, survival
                    sevent
clus2                 0  1
  18Q GAIN MUTATED    4  1
  18Q GAIN WILD-TYPE 86 14
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 5                100 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 1                 14 
$`18Q GAIN MUTATED`
TCGA-CD-5799 TCGA-CG-4460 TCGA-CG-4474 TCGA-D7-6528 TCGA-D7-6817 
        0.69        21.99         1.02         1.68         4.70 

$`18Q GAIN WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-6452 TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6458 
        5.62         0.10         0.95         1.41         1.35         1.35 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
        0.85         0.82         0.62         0.62         1.71         2.17 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
        0.99         1.22         0.66         1.12         0.76         0.66 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
        0.26         1.22         1.48         0.46         1.25         0.13 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 
        1.05         0.82         0.69         0.16         4.54         0.99 
TCGA-BR-7901 TCGA-BR-7957 TCGA-CD-5798 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        0.95         0.69         0.82         0.36         0.49         0.30 
TCGA-CD-5803 TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
        0.07        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
       52.96         8.05        54.05         4.01        14.01        29.98 
TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       47.05        19.07        12.03         1.02         8.98        18.94 
TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4477 TCGA-CG-5716 TCGA-CG-5717 TCGA-CG-5718 
        7.07        12.00         1.02         1.02         6.94         1.02 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
        1.02         0.99         5.98         0.95        70.06        12.03 
TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       15.02        28.96        31.04        65.10         4.01        55.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99         8.65         3.58         4.54         9.80 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       15.65         9.63         8.19         6.90         0.69         5.95 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6815 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
        6.61         4.14         3.65         4.04         2.93         4.27 
TCGA-EQ-5647 TCGA-F1-6177 TCGA-F1-6874 TCGA-F1-6875 TCGA-FP-7735 TCGA-FP-7829 
        0.62         6.54         2.01        72.23         0.39         0.20 
TCGA-FP-7998 TCGA-IN-7806 TCGA-IN-7808 TCGA-IP-7968 
        3.58         6.87         3.55         2.53 

  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
              0.69               0.07 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
             21.99              72.23 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
             1.680              2.975 
[1] "0.7 - 22.0 (1.7)" "0.1 - 72.2 (3.0)"
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-CD-5798 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-CD-5799         TCGA-CD-5800         TCGA-CD-5801 
  "18Q GAIN MUTATED" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-CD-5802         TCGA-CD-5803         TCGA-CG-4300 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-CG-4301         TCGA-CG-4304         TCGA-CG-4305 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-CG-4306         TCGA-CG-4436         TCGA-CG-4437 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-CG-4438         TCGA-CG-4440         TCGA-CG-4441 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-CG-4443         TCGA-CG-4444         TCGA-CG-4449 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-CG-4455         TCGA-CG-4460         TCGA-CG-4462 
"18Q GAIN WILD-TYPE"   "18Q GAIN MUTATED" "18Q GAIN WILD-TYPE" 
        TCGA-CG-4465         TCGA-CG-4466         TCGA-CG-4469 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-CG-4472         TCGA-CG-4474         TCGA-CG-4477 
"18Q GAIN WILD-TYPE"   "18Q GAIN MUTATED" "18Q GAIN WILD-TYPE" 
        TCGA-CG-5716         TCGA-CG-5717         TCGA-CG-5718 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-CG-5719         TCGA-CG-5720         TCGA-CG-5721 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-CG-5722         TCGA-CG-5723         TCGA-CG-5724 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-CG-5725         TCGA-CG-5726         TCGA-CG-5727 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-CG-5728         TCGA-CG-5730         TCGA-CG-5732 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-CG-5733         TCGA-CG-5734         TCGA-D7-5577 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-D7-5578         TCGA-D7-5579         TCGA-D7-6518 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-D7-6519         TCGA-D7-6520         TCGA-D7-6521 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-D7-6522         TCGA-D7-6524         TCGA-D7-6525 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-D7-6526         TCGA-D7-6527         TCGA-D7-6528 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE"   "18Q GAIN MUTATED" 
        TCGA-D7-6815         TCGA-D7-6817         TCGA-D7-6818 
"18Q GAIN WILD-TYPE"   "18Q GAIN MUTATED" "18Q GAIN WILD-TYPE" 
        TCGA-D7-6820         TCGA-D7-6822         TCGA-EQ-5647 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-F1-6177         TCGA-F1-6874         TCGA-F1-6875 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-FP-7735         TCGA-FP-7829         TCGA-FP-7998 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-IN-7806         TCGA-IN-7808         TCGA-IP-7968 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-CD-5798 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-CD-5799         TCGA-CD-5800         TCGA-CD-5801 
  "18Q GAIN MUTATED" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-CD-5802         TCGA-CD-5803         TCGA-CG-4300 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-CG-4301         TCGA-CG-4304         TCGA-CG-4305 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-CG-4306         TCGA-CG-4436         TCGA-CG-4437 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-CG-4438         TCGA-CG-4440         TCGA-CG-4441 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-CG-4443         TCGA-CG-4444         TCGA-CG-4449 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-CG-4455         TCGA-CG-4460         TCGA-CG-4462 
"18Q GAIN WILD-TYPE"   "18Q GAIN MUTATED" "18Q GAIN WILD-TYPE" 
        TCGA-CG-4465         TCGA-CG-4466         TCGA-CG-4469 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-CG-4472         TCGA-CG-4474         TCGA-CG-4477 
"18Q GAIN WILD-TYPE"   "18Q GAIN MUTATED" "18Q GAIN WILD-TYPE" 
        TCGA-CG-5716         TCGA-CG-5717         TCGA-CG-5718 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-CG-5719         TCGA-CG-5720         TCGA-CG-5721 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-CG-5722         TCGA-CG-5723         TCGA-CG-5724 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-CG-5725         TCGA-CG-5726         TCGA-CG-5727 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-CG-5728         TCGA-CG-5730         TCGA-CG-5732 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-CG-5733         TCGA-CG-5734         TCGA-D7-5577 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-D7-5578         TCGA-D7-5579         TCGA-D7-6518 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-D7-6519         TCGA-D7-6520         TCGA-D7-6521 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-D7-6522         TCGA-D7-6524         TCGA-D7-6525 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-D7-6526         TCGA-D7-6527         TCGA-D7-6528 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE"   "18Q GAIN MUTATED" 
        TCGA-D7-6815         TCGA-D7-6817         TCGA-D7-6818 
"18Q GAIN WILD-TYPE"   "18Q GAIN MUTATED" "18Q GAIN WILD-TYPE" 
        TCGA-D7-6820         TCGA-D7-6822         TCGA-EQ-5647 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-F1-6177         TCGA-F1-6874         TCGA-F1-6875 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-FP-7735         TCGA-FP-7829         TCGA-FP-7998 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-IN-7806         TCGA-IN-7808         TCGA-IP-7968 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-CD-5798 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-CD-5799         TCGA-CD-5800         TCGA-CD-5801 
  "18Q GAIN MUTATED" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-CD-5802         TCGA-CD-5803         TCGA-CG-4300 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-CG-4301         TCGA-CG-4304         TCGA-CG-4305 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-CG-4306         TCGA-CG-4436         TCGA-CG-4437 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-CG-4438         TCGA-CG-4440         TCGA-CG-4441 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-CG-4443         TCGA-CG-4444         TCGA-CG-4449 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-CG-4455         TCGA-CG-4460         TCGA-CG-4462 
"18Q GAIN WILD-TYPE"   "18Q GAIN MUTATED" "18Q GAIN WILD-TYPE" 
        TCGA-CG-4465         TCGA-CG-4466         TCGA-CG-4469 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-CG-4472         TCGA-CG-4474         TCGA-CG-4477 
"18Q GAIN WILD-TYPE"   "18Q GAIN MUTATED" "18Q GAIN WILD-TYPE" 
        TCGA-CG-5716         TCGA-CG-5717         TCGA-CG-5718 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-CG-5719         TCGA-CG-5720         TCGA-CG-5721 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-CG-5722         TCGA-CG-5723         TCGA-CG-5724 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-CG-5725         TCGA-CG-5726         TCGA-CG-5727 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-CG-5728         TCGA-CG-5730         TCGA-CG-5732 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-CG-5733         TCGA-CG-5734         TCGA-D7-5577 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-D7-5578         TCGA-D7-5579         TCGA-D7-6518 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-D7-6519         TCGA-D7-6520         TCGA-D7-6521 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-D7-6522         TCGA-D7-6524         TCGA-D7-6525 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-D7-6526         TCGA-D7-6527         TCGA-D7-6528 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE"   "18Q GAIN MUTATED" 
        TCGA-D7-6815         TCGA-D7-6817         TCGA-D7-6818 
"18Q GAIN WILD-TYPE"   "18Q GAIN MUTATED" "18Q GAIN WILD-TYPE" 
        TCGA-D7-6820         TCGA-D7-6822         TCGA-EQ-5647 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-F1-6177         TCGA-F1-6874         TCGA-F1-6875 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-FP-7735         TCGA-FP-7829         TCGA-FP-7998 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-IN-7806         TCGA-IN-7808         TCGA-IP-7968 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
[1] "hr=" "1.6"
D31V2, continuous
D31V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      5    3
  18Q GAIN WILD-TYPE   55   95
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  FEMALE                5                 55
  MALE                  3                 95
D31V4, multiclass
D31V5, multiclass
    clus
vv   18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  T1                0                  6
  T2                3                 49
  T3                1                 60
  T4                2                 16
D31V6, multiclass
    clus
vv   18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  N0                1                 43
  N1                3                 54
  N2                1                 23
  N3                1                 14
D31V7, multiclass
    clus
vv   18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  M0                5                129
  M1                2                 14
  MX                1                  7
D31V8, multiclass
     clus
vv    18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  I                  1                 23
  II                 1                 36
  III                2                 41
  IV                 2                 24
D31V9, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      0    8
  18Q GAIN WILD-TYPE    5  145
     clus
vv    18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  NO                 0                  5
  YES                8                145
D31V10, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      0    8
  18Q GAIN WILD-TYPE   10  140
     clus
vv    18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  NO                 0                 10
  YES                8                140

Clustering(32) Variable = 19p gain mutation analysis
D32V1, survival
                    sevent
clus2                 0  1
  19P GAIN MUTATED    6  1
  19P GAIN WILD-TYPE 84 14
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                 7                 98 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                 1                 14 
$`19P GAIN MUTATED`
TCGA-CG-4460 TCGA-CG-4474 TCGA-CG-5722 TCGA-CG-5730 TCGA-D7-5577 TCGA-D7-6518 
       21.99         1.02         0.95         4.01         8.65         9.80 
TCGA-D7-6521 
        8.19 

$`19P GAIN WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-6452 TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6458 
        5.62         0.10         0.95         1.41         1.35         1.35 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
        0.85         0.82         0.62         0.62         1.71         2.17 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
        0.99         1.22         0.66         1.12         0.76         0.66 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
        0.26         1.22         1.48         0.46         1.25         0.13 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 
        1.05         0.82         0.69         0.16         4.54         0.99 
TCGA-BR-7901 TCGA-BR-7957 TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
        0.95         0.69         0.82         0.69         0.36         0.49 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
        0.30         0.07        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02        52.96         8.05        54.05         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       29.98        47.05        19.07        12.03         1.02         8.98 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4477 TCGA-CG-5716 TCGA-CG-5717 
       18.94         7.07        12.00         1.02         1.02         6.94 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5723 TCGA-CG-5724 
        1.02         1.02         0.99         5.98        70.06        12.03 
TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5732 TCGA-CG-5733 
       15.02        28.96        31.04        65.10        55.04        21.07 
TCGA-CG-5734 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6522 
        7.99         3.58         4.54        15.65         9.63         6.90 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
        0.69         5.95         6.61         4.14         1.68         3.65 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-EQ-5647 TCGA-F1-6177 
        4.70         4.04         2.93         4.27         0.62         6.54 
TCGA-F1-6874 TCGA-F1-6875 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7998 TCGA-IN-7806 
        2.01        72.23         0.39         0.20         3.58         6.87 
TCGA-IN-7808 TCGA-IP-7968 
        3.55         2.53 

  19P GAIN MUTATED 19P GAIN WILD-TYPE 
              0.95               0.07 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
             21.99              72.23 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
              8.19               2.35 
[1] "0.9 - 22.0 (8.2)" "0.1 - 72.2 (2.3)"
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-CD-5798 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-CD-5799         TCGA-CD-5800         TCGA-CD-5801 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-CD-5802         TCGA-CD-5803         TCGA-CG-4300 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-CG-4301         TCGA-CG-4304         TCGA-CG-4305 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-CG-4306         TCGA-CG-4436         TCGA-CG-4437 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-CG-4438         TCGA-CG-4440         TCGA-CG-4441 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-CG-4443         TCGA-CG-4444         TCGA-CG-4449 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-CG-4455         TCGA-CG-4460         TCGA-CG-4462 
"19P GAIN WILD-TYPE"   "19P GAIN MUTATED" "19P GAIN WILD-TYPE" 
        TCGA-CG-4465         TCGA-CG-4466         TCGA-CG-4469 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-CG-4472         TCGA-CG-4474         TCGA-CG-4477 
"19P GAIN WILD-TYPE"   "19P GAIN MUTATED" "19P GAIN WILD-TYPE" 
        TCGA-CG-5716         TCGA-CG-5717         TCGA-CG-5718 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-CG-5719         TCGA-CG-5720         TCGA-CG-5721 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-CG-5722         TCGA-CG-5723         TCGA-CG-5724 
  "19P GAIN MUTATED" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-CG-5725         TCGA-CG-5726         TCGA-CG-5727 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-CG-5728         TCGA-CG-5730         TCGA-CG-5732 
"19P GAIN WILD-TYPE"   "19P GAIN MUTATED" "19P GAIN WILD-TYPE" 
        TCGA-CG-5733         TCGA-CG-5734         TCGA-D7-5577 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE"   "19P GAIN MUTATED" 
        TCGA-D7-5578         TCGA-D7-5579         TCGA-D7-6518 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE"   "19P GAIN MUTATED" 
        TCGA-D7-6519         TCGA-D7-6520         TCGA-D7-6521 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE"   "19P GAIN MUTATED" 
        TCGA-D7-6522         TCGA-D7-6524         TCGA-D7-6525 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-D7-6526         TCGA-D7-6527         TCGA-D7-6528 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-D7-6815         TCGA-D7-6817         TCGA-D7-6818 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-D7-6820         TCGA-D7-6822         TCGA-EQ-5647 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-F1-6177         TCGA-F1-6874         TCGA-F1-6875 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-FP-7735         TCGA-FP-7829         TCGA-FP-7998 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-IN-7806         TCGA-IN-7808         TCGA-IP-7968 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-CD-5798 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-CD-5799         TCGA-CD-5800         TCGA-CD-5801 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-CD-5802         TCGA-CD-5803         TCGA-CG-4300 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-CG-4301         TCGA-CG-4304         TCGA-CG-4305 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-CG-4306         TCGA-CG-4436         TCGA-CG-4437 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-CG-4438         TCGA-CG-4440         TCGA-CG-4441 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-CG-4443         TCGA-CG-4444         TCGA-CG-4449 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-CG-4455         TCGA-CG-4460         TCGA-CG-4462 
"19P GAIN WILD-TYPE"   "19P GAIN MUTATED" "19P GAIN WILD-TYPE" 
        TCGA-CG-4465         TCGA-CG-4466         TCGA-CG-4469 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-CG-4472         TCGA-CG-4474         TCGA-CG-4477 
"19P GAIN WILD-TYPE"   "19P GAIN MUTATED" "19P GAIN WILD-TYPE" 
        TCGA-CG-5716         TCGA-CG-5717         TCGA-CG-5718 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-CG-5719         TCGA-CG-5720         TCGA-CG-5721 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-CG-5722         TCGA-CG-5723         TCGA-CG-5724 
  "19P GAIN MUTATED" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-CG-5725         TCGA-CG-5726         TCGA-CG-5727 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-CG-5728         TCGA-CG-5730         TCGA-CG-5732 
"19P GAIN WILD-TYPE"   "19P GAIN MUTATED" "19P GAIN WILD-TYPE" 
        TCGA-CG-5733         TCGA-CG-5734         TCGA-D7-5577 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE"   "19P GAIN MUTATED" 
        TCGA-D7-5578         TCGA-D7-5579         TCGA-D7-6518 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE"   "19P GAIN MUTATED" 
        TCGA-D7-6519         TCGA-D7-6520         TCGA-D7-6521 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE"   "19P GAIN MUTATED" 
        TCGA-D7-6522         TCGA-D7-6524         TCGA-D7-6525 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-D7-6526         TCGA-D7-6527         TCGA-D7-6528 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-D7-6815         TCGA-D7-6817         TCGA-D7-6818 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-D7-6820         TCGA-D7-6822         TCGA-EQ-5647 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-F1-6177         TCGA-F1-6874         TCGA-F1-6875 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-FP-7735         TCGA-FP-7829         TCGA-FP-7998 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-IN-7806         TCGA-IN-7808         TCGA-IP-7968 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-CD-5798 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-CD-5799         TCGA-CD-5800         TCGA-CD-5801 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-CD-5802         TCGA-CD-5803         TCGA-CG-4300 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-CG-4301         TCGA-CG-4304         TCGA-CG-4305 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-CG-4306         TCGA-CG-4436         TCGA-CG-4437 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-CG-4438         TCGA-CG-4440         TCGA-CG-4441 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-CG-4443         TCGA-CG-4444         TCGA-CG-4449 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-CG-4455         TCGA-CG-4460         TCGA-CG-4462 
"19P GAIN WILD-TYPE"   "19P GAIN MUTATED" "19P GAIN WILD-TYPE" 
        TCGA-CG-4465         TCGA-CG-4466         TCGA-CG-4469 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-CG-4472         TCGA-CG-4474         TCGA-CG-4477 
"19P GAIN WILD-TYPE"   "19P GAIN MUTATED" "19P GAIN WILD-TYPE" 
        TCGA-CG-5716         TCGA-CG-5717         TCGA-CG-5718 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-CG-5719         TCGA-CG-5720         TCGA-CG-5721 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-CG-5722         TCGA-CG-5723         TCGA-CG-5724 
  "19P GAIN MUTATED" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-CG-5725         TCGA-CG-5726         TCGA-CG-5727 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-CG-5728         TCGA-CG-5730         TCGA-CG-5732 
"19P GAIN WILD-TYPE"   "19P GAIN MUTATED" "19P GAIN WILD-TYPE" 
        TCGA-CG-5733         TCGA-CG-5734         TCGA-D7-5577 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE"   "19P GAIN MUTATED" 
        TCGA-D7-5578         TCGA-D7-5579         TCGA-D7-6518 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE"   "19P GAIN MUTATED" 
        TCGA-D7-6519         TCGA-D7-6520         TCGA-D7-6521 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE"   "19P GAIN MUTATED" 
        TCGA-D7-6522         TCGA-D7-6524         TCGA-D7-6525 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-D7-6526         TCGA-D7-6527         TCGA-D7-6528 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-D7-6815         TCGA-D7-6817         TCGA-D7-6818 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-D7-6820         TCGA-D7-6822         TCGA-EQ-5647 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-F1-6177         TCGA-F1-6874         TCGA-F1-6875 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-FP-7735         TCGA-FP-7829         TCGA-FP-7998 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-IN-7806         TCGA-IN-7808         TCGA-IP-7968 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
[1] "hr=" "1.1"
D32V2, continuous
D32V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED      8    2
  19P GAIN WILD-TYPE   52   96
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  FEMALE                8                 52
  MALE                  2                 96
D32V4, multiclass
D32V5, multiclass
    clus
vv   19P GAIN MUTATED 19P GAIN WILD-TYPE
  T1                0                  6
  T2                5                 47
  T3                3                 58
  T4                2                 16
D32V6, multiclass
    clus
vv   19P GAIN MUTATED 19P GAIN WILD-TYPE
  N0                0                 44
  N1                4                 53
  N2                3                 21
  N3                2                 13
D32V7, multiclass
    clus
vv   19P GAIN MUTATED 19P GAIN WILD-TYPE
  M0                6                128
  M1                4                 12
  MX                0                  8
D32V8, multiclass
     clus
vv    19P GAIN MUTATED 19P GAIN WILD-TYPE
  I                  0                 24
  II                 1                 36
  III                3                 40
  IV                 5                 21
D32V9, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED      0   10
  19P GAIN WILD-TYPE    5  143
     clus
vv    19P GAIN MUTATED 19P GAIN WILD-TYPE
  NO                 0                  5
  YES               10                143
D32V10, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED      2    8
  19P GAIN WILD-TYPE    8  140
     clus
vv    19P GAIN MUTATED 19P GAIN WILD-TYPE
  NO                 2                  8
  YES                8                140

Clustering(33) Variable = 19q gain mutation analysis
D33V1, survival
                    sevent
clus2                 0  1
  19Q GAIN MUTATED    9  2
  19Q GAIN WILD-TYPE 81 13
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                11                 94 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                 2                 13 
$`19Q GAIN MUTATED`
TCGA-BR-7716 TCGA-CG-4438 TCGA-CG-4460 TCGA-CG-4474 TCGA-CG-5722 TCGA-CG-5730 
        0.82        54.05        21.99         1.02         0.95         4.01 
TCGA-D7-5577 TCGA-D7-6518 TCGA-D7-6521 TCGA-D7-6822 TCGA-F1-6875 
        8.65         9.80         8.19         4.27        72.23 

$`19Q GAIN WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-6452 TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6458 
        5.62         0.10         0.95         1.41         1.35         1.35 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
        0.85         0.82         0.62         0.62         1.71         2.17 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
        0.99         1.22         0.66         1.12         0.76         0.66 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
        0.26         1.22         1.48         0.46         1.25         0.13 
TCGA-BR-7715 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 
        1.05         0.69         0.16         4.54         0.99         0.95 
TCGA-BR-7957 TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        0.69         0.82         0.69         0.36         0.49         0.30 
TCGA-CD-5803 TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
        0.07        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 
       52.96         8.05         4.01        14.01        29.98        47.05 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         1.02         8.98        18.94         7.07 
TCGA-CG-4472 TCGA-CG-4477 TCGA-CG-5716 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
       12.00         1.02         1.02         6.94         1.02         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 
        0.99         5.98        70.06        12.03        15.02        28.96 
TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5578 
       31.04        65.10        55.04        21.07         7.99         3.58 
TCGA-D7-5579 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
        4.54        15.65         9.63         6.90         0.69         5.95 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
        6.61         4.14         1.68         3.65         4.70         4.04 
TCGA-D7-6820 TCGA-EQ-5647 TCGA-F1-6177 TCGA-F1-6874 TCGA-FP-7735 TCGA-FP-7829 
        2.93         0.62         6.54         2.01         0.39         0.20 
TCGA-FP-7998 TCGA-IN-7806 TCGA-IN-7808 TCGA-IP-7968 
        3.58         6.87         3.55         2.53 

  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
              0.82               0.07 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
             72.23              70.06 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
              8.19               2.09 
[1] "0.8 - 72.2 (8.2)" "0.1 - 70.1 (2.1)"
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
"19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-CD-5798 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-CD-5799         TCGA-CD-5800         TCGA-CD-5801 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-CD-5802         TCGA-CD-5803         TCGA-CG-4300 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-CG-4301         TCGA-CG-4304         TCGA-CG-4305 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-CG-4306         TCGA-CG-4436         TCGA-CG-4437 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-CG-4438         TCGA-CG-4440         TCGA-CG-4441 
  "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-CG-4443         TCGA-CG-4444         TCGA-CG-4449 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-CG-4455         TCGA-CG-4460         TCGA-CG-4462 
"19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" 
        TCGA-CG-4465         TCGA-CG-4466         TCGA-CG-4469 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-CG-4472         TCGA-CG-4474         TCGA-CG-4477 
"19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" 
        TCGA-CG-5716         TCGA-CG-5717         TCGA-CG-5718 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-CG-5719         TCGA-CG-5720         TCGA-CG-5721 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-CG-5722         TCGA-CG-5723         TCGA-CG-5724 
  "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-CG-5725         TCGA-CG-5726         TCGA-CG-5727 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-CG-5728         TCGA-CG-5730         TCGA-CG-5732 
"19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" 
        TCGA-CG-5733         TCGA-CG-5734         TCGA-D7-5577 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" 
        TCGA-D7-5578         TCGA-D7-5579         TCGA-D7-6518 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" 
        TCGA-D7-6519         TCGA-D7-6520         TCGA-D7-6521 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" 
        TCGA-D7-6522         TCGA-D7-6524         TCGA-D7-6525 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-D7-6526         TCGA-D7-6527         TCGA-D7-6528 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-D7-6815         TCGA-D7-6817         TCGA-D7-6818 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-D7-6820         TCGA-D7-6822         TCGA-EQ-5647 
"19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" 
        TCGA-F1-6177         TCGA-F1-6874         TCGA-F1-6875 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" 
        TCGA-FP-7735         TCGA-FP-7829         TCGA-FP-7998 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-IN-7806         TCGA-IN-7808         TCGA-IP-7968 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
"19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-CD-5798 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-CD-5799         TCGA-CD-5800         TCGA-CD-5801 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-CD-5802         TCGA-CD-5803         TCGA-CG-4300 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-CG-4301         TCGA-CG-4304         TCGA-CG-4305 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-CG-4306         TCGA-CG-4436         TCGA-CG-4437 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-CG-4438         TCGA-CG-4440         TCGA-CG-4441 
  "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-CG-4443         TCGA-CG-4444         TCGA-CG-4449 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-CG-4455         TCGA-CG-4460         TCGA-CG-4462 
"19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" 
        TCGA-CG-4465         TCGA-CG-4466         TCGA-CG-4469 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-CG-4472         TCGA-CG-4474         TCGA-CG-4477 
"19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" 
        TCGA-CG-5716         TCGA-CG-5717         TCGA-CG-5718 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-CG-5719         TCGA-CG-5720         TCGA-CG-5721 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-CG-5722         TCGA-CG-5723         TCGA-CG-5724 
  "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-CG-5725         TCGA-CG-5726         TCGA-CG-5727 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-CG-5728         TCGA-CG-5730         TCGA-CG-5732 
"19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" 
        TCGA-CG-5733         TCGA-CG-5734         TCGA-D7-5577 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" 
        TCGA-D7-5578         TCGA-D7-5579         TCGA-D7-6518 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" 
        TCGA-D7-6519         TCGA-D7-6520         TCGA-D7-6521 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" 
        TCGA-D7-6522         TCGA-D7-6524         TCGA-D7-6525 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-D7-6526         TCGA-D7-6527         TCGA-D7-6528 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-D7-6815         TCGA-D7-6817         TCGA-D7-6818 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-D7-6820         TCGA-D7-6822         TCGA-EQ-5647 
"19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" 
        TCGA-F1-6177         TCGA-F1-6874         TCGA-F1-6875 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" 
        TCGA-FP-7735         TCGA-FP-7829         TCGA-FP-7998 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-IN-7806         TCGA-IN-7808         TCGA-IP-7968 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
"19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-CD-5798 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-CD-5799         TCGA-CD-5800         TCGA-CD-5801 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-CD-5802         TCGA-CD-5803         TCGA-CG-4300 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-CG-4301         TCGA-CG-4304         TCGA-CG-4305 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-CG-4306         TCGA-CG-4436         TCGA-CG-4437 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-CG-4438         TCGA-CG-4440         TCGA-CG-4441 
  "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-CG-4443         TCGA-CG-4444         TCGA-CG-4449 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-CG-4455         TCGA-CG-4460         TCGA-CG-4462 
"19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" 
        TCGA-CG-4465         TCGA-CG-4466         TCGA-CG-4469 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-CG-4472         TCGA-CG-4474         TCGA-CG-4477 
"19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" 
        TCGA-CG-5716         TCGA-CG-5717         TCGA-CG-5718 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-CG-5719         TCGA-CG-5720         TCGA-CG-5721 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-CG-5722         TCGA-CG-5723         TCGA-CG-5724 
  "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-CG-5725         TCGA-CG-5726         TCGA-CG-5727 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-CG-5728         TCGA-CG-5730         TCGA-CG-5732 
"19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" 
        TCGA-CG-5733         TCGA-CG-5734         TCGA-D7-5577 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" 
        TCGA-D7-5578         TCGA-D7-5579         TCGA-D7-6518 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" 
        TCGA-D7-6519         TCGA-D7-6520         TCGA-D7-6521 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" 
        TCGA-D7-6522         TCGA-D7-6524         TCGA-D7-6525 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-D7-6526         TCGA-D7-6527         TCGA-D7-6528 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-D7-6815         TCGA-D7-6817         TCGA-D7-6818 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-D7-6820         TCGA-D7-6822         TCGA-EQ-5647 
"19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" 
        TCGA-F1-6177         TCGA-F1-6874         TCGA-F1-6875 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" 
        TCGA-FP-7735         TCGA-FP-7829         TCGA-FP-7998 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-IN-7806         TCGA-IN-7808         TCGA-IP-7968 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
[1] "hr=" "2.7"
D33V2, continuous
D33V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED     11    6
  19Q GAIN WILD-TYPE   49   92
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  FEMALE               11                 49
  MALE                  6                 92
D33V4, multiclass
D33V5, multiclass
    clus
vv   19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  T1                0                  6
  T2                8                 44
  T3                4                 57
  T4                4                 14
D33V6, multiclass
    clus
vv   19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  N0                2                 42
  N1                6                 51
  N2                4                 20
  N3                3                 12
D33V7, multiclass
    clus
vv   19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  M0               13                121
  M1                4                 12
  MX                0                  8
D33V8, multiclass
     clus
vv    19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  I                  2                 22
  II                 2                 35
  III                3                 40
  IV                 8                 18
D33V9, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED      1   16
  19Q GAIN WILD-TYPE    4  137
     clus
vv    19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  NO                 1                  4
  YES               16                137
D33V10, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED      3   14
  19Q GAIN WILD-TYPE    7  134
     clus
vv    19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  NO                 3                  7
  YES               14                134

Clustering(34) Variable = 20p gain mutation analysis
D34V1, survival
                    sevent
clus2                 0  1
  20P GAIN MUTATED   40  5
  20P GAIN WILD-TYPE 50 10
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                45                 60 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                 5                 10 
$`20P GAIN MUTATED`
TCGA-BR-6455 TCGA-BR-6458 TCGA-BR-6565 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6801 
        1.41         1.35         0.62         2.17         0.99         1.12 
TCGA-BR-7197 TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
        1.48         1.25         1.05         0.69         0.16         4.54 
TCGA-BR-7901 TCGA-CD-5799 TCGA-CD-5801 TCGA-CG-4300 TCGA-CG-4304 TCGA-CG-4305 
        0.95         0.69         0.49        20.02        27.02        15.95 
TCGA-CG-4436 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4444 TCGA-CG-4455 
       52.96        54.05         4.01        14.01        47.05        12.03 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-5718 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5730 
       18.94         7.07         1.02        28.96        31.04         4.01 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6521 TCGA-D7-6525 
        8.65         3.58         4.54         9.80         8.19         5.95 
TCGA-D7-6528 TCGA-D7-6818 TCGA-D7-6822 TCGA-F1-6874 TCGA-F1-6875 TCGA-FP-7829 
        1.68         4.04         4.27         2.01        72.23         0.20 
TCGA-FP-7998 TCGA-IN-7806 TCGA-IN-7808 
        3.58         6.87         3.55 

$`20P GAIN WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-6452 TCGA-BR-6457 TCGA-BR-6563 TCGA-BR-6564 
        5.62         0.10         0.95         1.35         0.85         0.82 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6802 TCGA-BR-6803 
        0.62         1.71         1.22         0.66         0.76         0.66 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7716 TCGA-BR-7851 
        0.26         1.22         0.46         0.13         0.82         0.99 
TCGA-BR-7957 TCGA-CD-5798 TCGA-CD-5800 TCGA-CD-5802 TCGA-CD-5803 TCGA-CG-4301 
        0.69         0.82         0.36         0.30         0.07         3.02 
TCGA-CG-4306 TCGA-CG-4437 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4460 TCGA-CG-4462 
        1.02         8.05        29.98        19.07        21.99         1.02 
TCGA-CG-4465 TCGA-CG-4472 TCGA-CG-4474 TCGA-CG-4477 TCGA-CG-5716 TCGA-CG-5717 
        8.98        12.00         1.02         1.02         1.02         6.94 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
        1.02         0.99         5.98         0.95        70.06        12.03 
TCGA-CG-5725 TCGA-CG-5728 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-6519 
       15.02        65.10        55.04        21.07         7.99        15.65 
TCGA-D7-6520 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6815 
        9.63         6.90         0.69         6.61         4.14         3.65 
TCGA-D7-6817 TCGA-D7-6820 TCGA-EQ-5647 TCGA-F1-6177 TCGA-FP-7735 TCGA-IP-7968 
        4.70         2.93         0.62         6.54         0.39         2.53 

  20P GAIN MUTATED 20P GAIN WILD-TYPE 
              0.16               0.07 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
             72.23              70.06 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
              4.01               1.22 
[1] "0.2 - 72.2 (4.0)" "0.1 - 70.1 (1.2)"
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
  "20P GAIN MUTATED"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-CD-5798 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-CD-5799         TCGA-CD-5800         TCGA-CD-5801 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-CD-5802         TCGA-CD-5803         TCGA-CG-4300 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-CG-4301         TCGA-CG-4304         TCGA-CG-4305 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED"   "20P GAIN MUTATED" 
        TCGA-CG-4306         TCGA-CG-4436         TCGA-CG-4437 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-CG-4438         TCGA-CG-4440         TCGA-CG-4441 
  "20P GAIN MUTATED"   "20P GAIN MUTATED"   "20P GAIN MUTATED" 
        TCGA-CG-4443         TCGA-CG-4444         TCGA-CG-4449 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-CG-4455         TCGA-CG-4460         TCGA-CG-4462 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-CG-4465         TCGA-CG-4466         TCGA-CG-4469 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED"   "20P GAIN MUTATED" 
        TCGA-CG-4472         TCGA-CG-4474         TCGA-CG-4477 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-CG-5716         TCGA-CG-5717         TCGA-CG-5718 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-CG-5719         TCGA-CG-5720         TCGA-CG-5721 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-CG-5722         TCGA-CG-5723         TCGA-CG-5724 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-CG-5725         TCGA-CG-5726         TCGA-CG-5727 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED"   "20P GAIN MUTATED" 
        TCGA-CG-5728         TCGA-CG-5730         TCGA-CG-5732 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-CG-5733         TCGA-CG-5734         TCGA-D7-5577 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-D7-5578         TCGA-D7-5579         TCGA-D7-6518 
  "20P GAIN MUTATED"   "20P GAIN MUTATED"   "20P GAIN MUTATED" 
        TCGA-D7-6519         TCGA-D7-6520         TCGA-D7-6521 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-D7-6522         TCGA-D7-6524         TCGA-D7-6525 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-D7-6526         TCGA-D7-6527         TCGA-D7-6528 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-D7-6815         TCGA-D7-6817         TCGA-D7-6818 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-D7-6820         TCGA-D7-6822         TCGA-EQ-5647 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-F1-6177         TCGA-F1-6874         TCGA-F1-6875 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED"   "20P GAIN MUTATED" 
        TCGA-FP-7735         TCGA-FP-7829         TCGA-FP-7998 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED"   "20P GAIN MUTATED" 
        TCGA-IN-7806         TCGA-IN-7808         TCGA-IP-7968 
  "20P GAIN MUTATED"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
  "20P GAIN MUTATED"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-CD-5798 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-CD-5799         TCGA-CD-5800         TCGA-CD-5801 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-CD-5802         TCGA-CD-5803         TCGA-CG-4300 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-CG-4301         TCGA-CG-4304         TCGA-CG-4305 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED"   "20P GAIN MUTATED" 
        TCGA-CG-4306         TCGA-CG-4436         TCGA-CG-4437 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-CG-4438         TCGA-CG-4440         TCGA-CG-4441 
  "20P GAIN MUTATED"   "20P GAIN MUTATED"   "20P GAIN MUTATED" 
        TCGA-CG-4443         TCGA-CG-4444         TCGA-CG-4449 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-CG-4455         TCGA-CG-4460         TCGA-CG-4462 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-CG-4465         TCGA-CG-4466         TCGA-CG-4469 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED"   "20P GAIN MUTATED" 
        TCGA-CG-4472         TCGA-CG-4474         TCGA-CG-4477 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-CG-5716         TCGA-CG-5717         TCGA-CG-5718 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-CG-5719         TCGA-CG-5720         TCGA-CG-5721 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-CG-5722         TCGA-CG-5723         TCGA-CG-5724 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-CG-5725         TCGA-CG-5726         TCGA-CG-5727 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED"   "20P GAIN MUTATED" 
        TCGA-CG-5728         TCGA-CG-5730         TCGA-CG-5732 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-CG-5733         TCGA-CG-5734         TCGA-D7-5577 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-D7-5578         TCGA-D7-5579         TCGA-D7-6518 
  "20P GAIN MUTATED"   "20P GAIN MUTATED"   "20P GAIN MUTATED" 
        TCGA-D7-6519         TCGA-D7-6520         TCGA-D7-6521 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-D7-6522         TCGA-D7-6524         TCGA-D7-6525 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-D7-6526         TCGA-D7-6527         TCGA-D7-6528 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-D7-6815         TCGA-D7-6817         TCGA-D7-6818 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-D7-6820         TCGA-D7-6822         TCGA-EQ-5647 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-F1-6177         TCGA-F1-6874         TCGA-F1-6875 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED"   "20P GAIN MUTATED" 
        TCGA-FP-7735         TCGA-FP-7829         TCGA-FP-7998 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED"   "20P GAIN MUTATED" 
        TCGA-IN-7806         TCGA-IN-7808         TCGA-IP-7968 
  "20P GAIN MUTATED"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
  "20P GAIN MUTATED"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-CD-5798 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-CD-5799         TCGA-CD-5800         TCGA-CD-5801 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-CD-5802         TCGA-CD-5803         TCGA-CG-4300 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-CG-4301         TCGA-CG-4304         TCGA-CG-4305 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED"   "20P GAIN MUTATED" 
        TCGA-CG-4306         TCGA-CG-4436         TCGA-CG-4437 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-CG-4438         TCGA-CG-4440         TCGA-CG-4441 
  "20P GAIN MUTATED"   "20P GAIN MUTATED"   "20P GAIN MUTATED" 
        TCGA-CG-4443         TCGA-CG-4444         TCGA-CG-4449 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-CG-4455         TCGA-CG-4460         TCGA-CG-4462 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-CG-4465         TCGA-CG-4466         TCGA-CG-4469 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED"   "20P GAIN MUTATED" 
        TCGA-CG-4472         TCGA-CG-4474         TCGA-CG-4477 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-CG-5716         TCGA-CG-5717         TCGA-CG-5718 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-CG-5719         TCGA-CG-5720         TCGA-CG-5721 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-CG-5722         TCGA-CG-5723         TCGA-CG-5724 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-CG-5725         TCGA-CG-5726         TCGA-CG-5727 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED"   "20P GAIN MUTATED" 
        TCGA-CG-5728         TCGA-CG-5730         TCGA-CG-5732 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-CG-5733         TCGA-CG-5734         TCGA-D7-5577 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-D7-5578         TCGA-D7-5579         TCGA-D7-6518 
  "20P GAIN MUTATED"   "20P GAIN MUTATED"   "20P GAIN MUTATED" 
        TCGA-D7-6519         TCGA-D7-6520         TCGA-D7-6521 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-D7-6522         TCGA-D7-6524         TCGA-D7-6525 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-D7-6526         TCGA-D7-6527         TCGA-D7-6528 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-D7-6815         TCGA-D7-6817         TCGA-D7-6818 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-D7-6820         TCGA-D7-6822         TCGA-EQ-5647 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-F1-6177         TCGA-F1-6874         TCGA-F1-6875 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED"   "20P GAIN MUTATED" 
        TCGA-FP-7735         TCGA-FP-7829         TCGA-FP-7998 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED"   "20P GAIN MUTATED" 
        TCGA-IN-7806         TCGA-IN-7808         TCGA-IP-7968 
  "20P GAIN MUTATED"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
[1] "hr=" "2.7"
D34V2, continuous
D34V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED     16   49
  20P GAIN WILD-TYPE   44   49
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  FEMALE               16                 44
  MALE                 49                 49
D34V4, multiclass
D34V5, multiclass
    clus
vv   20P GAIN MUTATED 20P GAIN WILD-TYPE
  T1                1                  5
  T2               23                 29
  T3               28                 33
  T4                5                 13
D34V6, multiclass
    clus
vv   20P GAIN MUTATED 20P GAIN WILD-TYPE
  N0               15                 29
  N1               23                 34
  N2                9                 15
  N3                8                  7
D34V7, multiclass
    clus
vv   20P GAIN MUTATED 20P GAIN WILD-TYPE
  M0               59                 75
  M1                3                 13
  MX                3                  5
D34V8, multiclass
     clus
vv    20P GAIN MUTATED 20P GAIN WILD-TYPE
  I                  8                 16
  II                14                 23
  III               23                 20
  IV                 7                 19
D34V9, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED      1   64
  20P GAIN WILD-TYPE    4   89
     clus
vv    20P GAIN MUTATED 20P GAIN WILD-TYPE
  NO                 1                  4
  YES               64                 89
D34V10, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED      5   60
  20P GAIN WILD-TYPE    5   88
     clus
vv    20P GAIN MUTATED 20P GAIN WILD-TYPE
  NO                 5                  5
  YES               60                 88

Clustering(35) Variable = 20q gain mutation analysis
D35V1, survival
                    sevent
clus2                 0  1
  20Q GAIN MUTATED   47  6
  20Q GAIN WILD-TYPE 43  9
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                53                 52 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                 6                  9 
$`20Q GAIN MUTATED`
TCGA-BR-6455 TCGA-BR-6458 TCGA-BR-6565 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6801 
        1.41         1.35         0.62         2.17         0.99         1.12 
TCGA-BR-7197 TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
        1.48         1.25         1.05         0.69         0.16         4.54 
TCGA-BR-7901 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CG-4300 TCGA-CG-4304 
        0.95         0.69         0.36         0.49        20.02        27.02 
TCGA-CG-4305 TCGA-CG-4436 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4444 
       15.95        52.96        54.05         4.01        14.01        47.05 
TCGA-CG-4455 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-5718 TCGA-CG-5724 TCGA-CG-5726 
       12.03        18.94         7.07         1.02        12.03        28.96 
TCGA-CG-5727 TCGA-CG-5730 TCGA-CG-5732 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       31.04         4.01        55.04         8.65         3.58         4.54 
TCGA-D7-6518 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6528 
        9.80         9.63         8.19         5.95         6.61         1.68 
TCGA-D7-6815 TCGA-D7-6818 TCGA-D7-6822 TCGA-F1-6874 TCGA-F1-6875 TCGA-FP-7735 
        3.65         4.04         4.27         2.01        72.23         0.39 
TCGA-FP-7829 TCGA-FP-7998 TCGA-IN-7806 TCGA-IN-7808 TCGA-IP-7968 
        0.20         3.58         6.87         3.55         2.53 

$`20Q GAIN WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-6452 TCGA-BR-6457 TCGA-BR-6563 TCGA-BR-6564 
        5.62         0.10         0.95         1.35         0.85         0.82 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6802 TCGA-BR-6803 
        0.62         1.71         1.22         0.66         0.76         0.66 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7716 TCGA-BR-7851 
        0.26         1.22         0.46         0.13         0.82         0.99 
TCGA-BR-7957 TCGA-CD-5798 TCGA-CD-5802 TCGA-CD-5803 TCGA-CG-4301 TCGA-CG-4306 
        0.69         0.82         0.30         0.07         3.02         1.02 
TCGA-CG-4437 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4460 TCGA-CG-4462 TCGA-CG-4465 
        8.05        29.98        19.07        21.99         1.02         8.98 
TCGA-CG-4472 TCGA-CG-4474 TCGA-CG-4477 TCGA-CG-5716 TCGA-CG-5717 TCGA-CG-5719 
       12.00         1.02         1.02         1.02         6.94         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5725 TCGA-CG-5728 
        0.99         5.98         0.95        70.06        15.02        65.10 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-6519 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6527 
       21.07         7.99        15.65         6.90         0.69         4.14 
TCGA-D7-6817 TCGA-D7-6820 TCGA-EQ-5647 TCGA-F1-6177 
        4.70         2.93         0.62         6.54 

  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
              0.16               0.07 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
             72.23              70.06 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
              4.01               1.02 
[1] "0.2 - 72.2 (4.0)" "0.1 - 70.1 (1.0)"
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-CD-5798 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-CD-5799         TCGA-CD-5800         TCGA-CD-5801 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-CD-5802         TCGA-CD-5803         TCGA-CG-4300 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-CG-4301         TCGA-CG-4304         TCGA-CG-4305 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-CG-4306         TCGA-CG-4436         TCGA-CG-4437 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-CG-4438         TCGA-CG-4440         TCGA-CG-4441 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-CG-4443         TCGA-CG-4444         TCGA-CG-4449 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-CG-4455         TCGA-CG-4460         TCGA-CG-4462 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-CG-4465         TCGA-CG-4466         TCGA-CG-4469 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-CG-4472         TCGA-CG-4474         TCGA-CG-4477 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-CG-5716         TCGA-CG-5717         TCGA-CG-5718 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-CG-5719         TCGA-CG-5720         TCGA-CG-5721 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-CG-5722         TCGA-CG-5723         TCGA-CG-5724 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-CG-5725         TCGA-CG-5726         TCGA-CG-5727 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-CG-5728         TCGA-CG-5730         TCGA-CG-5732 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-CG-5733         TCGA-CG-5734         TCGA-D7-5577 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-D7-5578         TCGA-D7-5579         TCGA-D7-6518 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-D7-6519         TCGA-D7-6520         TCGA-D7-6521 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-D7-6522         TCGA-D7-6524         TCGA-D7-6525 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-D7-6526         TCGA-D7-6527         TCGA-D7-6528 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-D7-6815         TCGA-D7-6817         TCGA-D7-6818 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-D7-6820         TCGA-D7-6822         TCGA-EQ-5647 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-F1-6177         TCGA-F1-6874         TCGA-F1-6875 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-FP-7735         TCGA-FP-7829         TCGA-FP-7998 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-IN-7806         TCGA-IN-7808         TCGA-IP-7968 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-CD-5798 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-CD-5799         TCGA-CD-5800         TCGA-CD-5801 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-CD-5802         TCGA-CD-5803         TCGA-CG-4300 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-CG-4301         TCGA-CG-4304         TCGA-CG-4305 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-CG-4306         TCGA-CG-4436         TCGA-CG-4437 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-CG-4438         TCGA-CG-4440         TCGA-CG-4441 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-CG-4443         TCGA-CG-4444         TCGA-CG-4449 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-CG-4455         TCGA-CG-4460         TCGA-CG-4462 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-CG-4465         TCGA-CG-4466         TCGA-CG-4469 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-CG-4472         TCGA-CG-4474         TCGA-CG-4477 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-CG-5716         TCGA-CG-5717         TCGA-CG-5718 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-CG-5719         TCGA-CG-5720         TCGA-CG-5721 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-CG-5722         TCGA-CG-5723         TCGA-CG-5724 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-CG-5725         TCGA-CG-5726         TCGA-CG-5727 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-CG-5728         TCGA-CG-5730         TCGA-CG-5732 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-CG-5733         TCGA-CG-5734         TCGA-D7-5577 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-D7-5578         TCGA-D7-5579         TCGA-D7-6518 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-D7-6519         TCGA-D7-6520         TCGA-D7-6521 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-D7-6522         TCGA-D7-6524         TCGA-D7-6525 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-D7-6526         TCGA-D7-6527         TCGA-D7-6528 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-D7-6815         TCGA-D7-6817         TCGA-D7-6818 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-D7-6820         TCGA-D7-6822         TCGA-EQ-5647 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-F1-6177         TCGA-F1-6874         TCGA-F1-6875 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-FP-7735         TCGA-FP-7829         TCGA-FP-7998 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-IN-7806         TCGA-IN-7808         TCGA-IP-7968 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-CD-5798 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-CD-5799         TCGA-CD-5800         TCGA-CD-5801 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-CD-5802         TCGA-CD-5803         TCGA-CG-4300 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-CG-4301         TCGA-CG-4304         TCGA-CG-4305 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-CG-4306         TCGA-CG-4436         TCGA-CG-4437 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-CG-4438         TCGA-CG-4440         TCGA-CG-4441 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-CG-4443         TCGA-CG-4444         TCGA-CG-4449 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-CG-4455         TCGA-CG-4460         TCGA-CG-4462 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-CG-4465         TCGA-CG-4466         TCGA-CG-4469 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-CG-4472         TCGA-CG-4474         TCGA-CG-4477 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-CG-5716         TCGA-CG-5717         TCGA-CG-5718 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-CG-5719         TCGA-CG-5720         TCGA-CG-5721 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-CG-5722         TCGA-CG-5723         TCGA-CG-5724 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-CG-5725         TCGA-CG-5726         TCGA-CG-5727 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-CG-5728         TCGA-CG-5730         TCGA-CG-5732 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-CG-5733         TCGA-CG-5734         TCGA-D7-5577 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-D7-5578         TCGA-D7-5579         TCGA-D7-6518 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-D7-6519         TCGA-D7-6520         TCGA-D7-6521 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-D7-6522         TCGA-D7-6524         TCGA-D7-6525 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-D7-6526         TCGA-D7-6527         TCGA-D7-6528 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-D7-6815         TCGA-D7-6817         TCGA-D7-6818 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-D7-6820         TCGA-D7-6822         TCGA-EQ-5647 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-F1-6177         TCGA-F1-6874         TCGA-F1-6875 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-FP-7735         TCGA-FP-7829         TCGA-FP-7998 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-IN-7806         TCGA-IN-7808         TCGA-IP-7968 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
[1] "hr=" "2.8"
D35V2, continuous
D35V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED     23   59
  20Q GAIN WILD-TYPE   37   39
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  FEMALE               23                 37
  MALE                 59                 39
D35V4, multiclass
D35V5, multiclass
    clus
vv   20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  T1                2                  4
  T2               29                 23
  T3               36                 25
  T4                5                 13
D35V6, multiclass
    clus
vv   20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  N0               20                 24
  N1               27                 30
  N2               13                 11
  N3               11                  4
D35V7, multiclass
    clus
vv   20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  M0               72                 62
  M1                4                 12
  MX                6                  2
D35V8, multiclass
     clus
vv    20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  I                 11                 13
  II                18                 19
  III               28                 15
  IV                10                 16
D35V9, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED      3   79
  20Q GAIN WILD-TYPE    2   74
     clus
vv    20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  NO                 3                  2
  YES               79                 74
D35V10, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED      8   74
  20Q GAIN WILD-TYPE    2   74
     clus
vv    20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  NO                 8                  2
  YES               74                 74

Clustering(36) Variable = 22q gain mutation analysis
D36V1, survival
                    sevent
clus2                 0  1
  22Q GAIN MUTATED    3  0
  22Q GAIN WILD-TYPE 87 15
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                 3                102 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                 0                 15 
$`22Q GAIN MUTATED`
TCGA-B7-5818 TCGA-BR-7704 TCGA-BR-7723 
        0.10         1.25         4.54 

$`22Q GAIN WILD-TYPE`
TCGA-B7-5816 TCGA-BR-6452 TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
        5.62         0.95         1.41         1.35         1.35         0.85 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
        0.82         0.62         0.62         1.71         2.17         0.99 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
        1.22         0.66         1.12         0.76         0.66         0.26 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 
        1.22         1.48         0.46         0.13         1.05         0.82 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-CD-5798 
        0.69         0.16         0.99         0.95         0.69         0.82 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CG-4300 
        0.69         0.36         0.49         0.30         0.07        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02        52.96         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 
       54.05         4.01        14.01        29.98        47.05        19.07 
TCGA-CG-4455 TCGA-CG-4460 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       12.03        21.99         1.02         8.98        18.94         7.07 
TCGA-CG-4472 TCGA-CG-4474 TCGA-CG-4477 TCGA-CG-5716 TCGA-CG-5717 TCGA-CG-5718 
       12.00         1.02         1.02         1.02         6.94         1.02 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
        1.02         0.99         5.98         0.95        70.06        12.03 
TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       15.02        28.96        31.04        65.10         4.01        55.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99         8.65         3.58         4.54         9.80 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       15.65         9.63         8.19         6.90         0.69         5.95 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
        6.61         4.14         1.68         3.65         4.70         4.04 
TCGA-D7-6820 TCGA-D7-6822 TCGA-EQ-5647 TCGA-F1-6177 TCGA-F1-6874 TCGA-F1-6875 
        2.93         4.27         0.62         6.54         2.01        72.23 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7998 TCGA-IN-7806 TCGA-IN-7808 TCGA-IP-7968 
        0.39         0.20         3.58         6.87         3.55         2.53 

  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
              0.10               0.07 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
              4.54              72.23 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
             1.250              2.975 
[1] "0.1 - 4.5 (1.2)"  "0.1 - 72.2 (3.0)"
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-CD-5798 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-CD-5799         TCGA-CD-5800         TCGA-CD-5801 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-CD-5802         TCGA-CD-5803         TCGA-CG-4300 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-CG-4301         TCGA-CG-4304         TCGA-CG-4305 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-CG-4306         TCGA-CG-4436         TCGA-CG-4437 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-CG-4438         TCGA-CG-4440         TCGA-CG-4441 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-CG-4443         TCGA-CG-4444         TCGA-CG-4449 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-CG-4455         TCGA-CG-4460         TCGA-CG-4462 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-CG-4465         TCGA-CG-4466         TCGA-CG-4469 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-CG-4472         TCGA-CG-4474         TCGA-CG-4477 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-CG-5716         TCGA-CG-5717         TCGA-CG-5718 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-CG-5719         TCGA-CG-5720         TCGA-CG-5721 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-CG-5722         TCGA-CG-5723         TCGA-CG-5724 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-CG-5725         TCGA-CG-5726         TCGA-CG-5727 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-CG-5728         TCGA-CG-5730         TCGA-CG-5732 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-CG-5733         TCGA-CG-5734         TCGA-D7-5577 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-D7-5578         TCGA-D7-5579         TCGA-D7-6518 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-D7-6519         TCGA-D7-6520         TCGA-D7-6521 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-D7-6522         TCGA-D7-6524         TCGA-D7-6525 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-D7-6526         TCGA-D7-6527         TCGA-D7-6528 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-D7-6815         TCGA-D7-6817         TCGA-D7-6818 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-D7-6820         TCGA-D7-6822         TCGA-EQ-5647 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-F1-6177         TCGA-F1-6874         TCGA-F1-6875 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-FP-7735         TCGA-FP-7829         TCGA-FP-7998 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-IN-7806         TCGA-IN-7808         TCGA-IP-7968 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-CD-5798 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-CD-5799         TCGA-CD-5800         TCGA-CD-5801 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-CD-5802         TCGA-CD-5803         TCGA-CG-4300 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-CG-4301         TCGA-CG-4304         TCGA-CG-4305 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-CG-4306         TCGA-CG-4436         TCGA-CG-4437 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-CG-4438         TCGA-CG-4440         TCGA-CG-4441 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-CG-4443         TCGA-CG-4444         TCGA-CG-4449 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-CG-4455         TCGA-CG-4460         TCGA-CG-4462 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-CG-4465         TCGA-CG-4466         TCGA-CG-4469 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-CG-4472         TCGA-CG-4474         TCGA-CG-4477 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-CG-5716         TCGA-CG-5717         TCGA-CG-5718 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-CG-5719         TCGA-CG-5720         TCGA-CG-5721 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-CG-5722         TCGA-CG-5723         TCGA-CG-5724 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-CG-5725         TCGA-CG-5726         TCGA-CG-5727 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-CG-5728         TCGA-CG-5730         TCGA-CG-5732 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-CG-5733         TCGA-CG-5734         TCGA-D7-5577 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-D7-5578         TCGA-D7-5579         TCGA-D7-6518 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-D7-6519         TCGA-D7-6520         TCGA-D7-6521 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-D7-6522         TCGA-D7-6524         TCGA-D7-6525 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-D7-6526         TCGA-D7-6527         TCGA-D7-6528 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-D7-6815         TCGA-D7-6817         TCGA-D7-6818 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-D7-6820         TCGA-D7-6822         TCGA-EQ-5647 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-F1-6177         TCGA-F1-6874         TCGA-F1-6875 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-FP-7735         TCGA-FP-7829         TCGA-FP-7998 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-IN-7806         TCGA-IN-7808         TCGA-IP-7968 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-CD-5798 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-CD-5799         TCGA-CD-5800         TCGA-CD-5801 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-CD-5802         TCGA-CD-5803         TCGA-CG-4300 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-CG-4301         TCGA-CG-4304         TCGA-CG-4305 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-CG-4306         TCGA-CG-4436         TCGA-CG-4437 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-CG-4438         TCGA-CG-4440         TCGA-CG-4441 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-CG-4443         TCGA-CG-4444         TCGA-CG-4449 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-CG-4455         TCGA-CG-4460         TCGA-CG-4462 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-CG-4465         TCGA-CG-4466         TCGA-CG-4469 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-CG-4472         TCGA-CG-4474         TCGA-CG-4477 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-CG-5716         TCGA-CG-5717         TCGA-CG-5718 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-CG-5719         TCGA-CG-5720         TCGA-CG-5721 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-CG-5722         TCGA-CG-5723         TCGA-CG-5724 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-CG-5725         TCGA-CG-5726         TCGA-CG-5727 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-CG-5728         TCGA-CG-5730         TCGA-CG-5732 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-CG-5733         TCGA-CG-5734         TCGA-D7-5577 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-D7-5578         TCGA-D7-5579         TCGA-D7-6518 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-D7-6519         TCGA-D7-6520         TCGA-D7-6521 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-D7-6522         TCGA-D7-6524         TCGA-D7-6525 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-D7-6526         TCGA-D7-6527         TCGA-D7-6528 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-D7-6815         TCGA-D7-6817         TCGA-D7-6818 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-D7-6820         TCGA-D7-6822         TCGA-EQ-5647 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-F1-6177         TCGA-F1-6874         TCGA-F1-6875 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-FP-7735         TCGA-FP-7829         TCGA-FP-7998 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-IN-7806         TCGA-IN-7808         TCGA-IP-7968 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
[1] "hr="     "9200000"
D36V2, continuous
D36V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED      2    2
  22Q GAIN WILD-TYPE   58   96
        clus
vv       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  FEMALE                2                 58
  MALE                  2                 96
D36V4, multiclass
D36V5, multiclass
    clus
vv   22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  T1                0                  6
  T2                1                 51
  T3                2                 59
  T4                0                 18
D36V6, multiclass
    clus
vv   22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  N0                2                 42
  N1                0                 57
  N2                1                 23
  N3                0                 15
D36V7, multiclass
    clus
vv   22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  M0                4                130
  M1                0                 16
  MX                0                  8
D36V8, multiclass
     clus
vv    22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  I                  1                 23
  II                 2                 35
  III                0                 43
  IV                 0                 26
D36V9, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED      0    4
  22Q GAIN WILD-TYPE    5  149
     clus
vv    22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  NO                 0                  5
  YES                4                149
D36V10, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED      0    4
  22Q GAIN WILD-TYPE   10  144
     clus
vv    22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  NO                 0                 10
  YES                4                144

Clustering(37) Variable = 1p loss mutation analysis
D37V1, survival
                   sevent
clus2                0  1
  1P LOSS MUTATED    4  2
  1P LOSS WILD-TYPE 86 13
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
                6                99 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
                2                13 
$`1P LOSS MUTATED`
TCGA-CG-4301 TCGA-CG-5719 TCGA-CG-5724 TCGA-CG-5730 TCGA-D7-6519 TCGA-EQ-5647 
        3.02         1.02        12.03         4.01        15.65         0.62 

$`1P LOSS WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-6452 TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6458 
        5.62         0.10         0.95         1.41         1.35         1.35 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
        0.85         0.82         0.62         0.62         1.71         2.17 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
        0.99         1.22         0.66         1.12         0.76         0.66 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
        0.26         1.22         1.48         0.46         1.25         0.13 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 
        1.05         0.82         0.69         0.16         4.54         0.99 
TCGA-BR-7901 TCGA-BR-7957 TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
        0.95         0.69         0.82         0.69         0.36         0.49 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CG-4300 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
        0.30         0.07        20.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
       52.96         8.05        54.05         4.01        14.01        29.98 
TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4460 TCGA-CG-4462 TCGA-CG-4465 
       47.05        19.07        12.03        21.99         1.02         8.98 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4474 TCGA-CG-4477 TCGA-CG-5716 
       18.94         7.07        12.00         1.02         1.02         1.02 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
        6.94         1.02         0.99         5.98         0.95        70.06 
TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5732 TCGA-CG-5733 
       15.02        28.96        31.04        65.10        55.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6520 
        7.99         8.65         3.58         4.54         9.80         9.63 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
        8.19         6.90         0.69         5.95         6.61         4.14 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
        1.68         3.65         4.70         4.04         2.93         4.27 
TCGA-F1-6177 TCGA-F1-6874 TCGA-F1-6875 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7998 
        6.54         2.01        72.23         0.39         0.20         3.58 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IP-7968 
        6.87         3.55         2.53 

  1P LOSS MUTATED 1P LOSS WILD-TYPE 
             0.62              0.07 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
            15.65             72.23 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
            3.515             2.530 
[1] "0.6 - 15.7 (3.5)" "0.1 - 72.2 (2.5)"
       TCGA-B7-5816        TCGA-B7-5818        TCGA-BR-6452        TCGA-BR-6455 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BR-6457        TCGA-BR-6458        TCGA-BR-6563        TCGA-BR-6564 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BR-6565        TCGA-BR-6566        TCGA-BR-6705        TCGA-BR-6706 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BR-6707        TCGA-BR-6709        TCGA-BR-6710        TCGA-BR-6801 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BR-6802        TCGA-BR-6803        TCGA-BR-6852        TCGA-BR-7196 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BR-7197        TCGA-BR-7703        TCGA-BR-7704        TCGA-BR-7707 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BR-7715        TCGA-BR-7716        TCGA-BR-7717        TCGA-BR-7722 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BR-7723        TCGA-BR-7851        TCGA-BR-7901        TCGA-BR-7957 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-CD-5798        TCGA-CD-5799        TCGA-CD-5800        TCGA-CD-5801 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-CD-5802        TCGA-CD-5803        TCGA-CG-4300        TCGA-CG-4301 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" 
       TCGA-CG-4304        TCGA-CG-4305        TCGA-CG-4306        TCGA-CG-4436 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-CG-4437        TCGA-CG-4438        TCGA-CG-4440        TCGA-CG-4441 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-CG-4443        TCGA-CG-4444        TCGA-CG-4449        TCGA-CG-4455 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-CG-4460        TCGA-CG-4462        TCGA-CG-4465        TCGA-CG-4466 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-CG-4469        TCGA-CG-4472        TCGA-CG-4474        TCGA-CG-4477 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-CG-5716        TCGA-CG-5717        TCGA-CG-5718        TCGA-CG-5719 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" 
       TCGA-CG-5720        TCGA-CG-5721        TCGA-CG-5722        TCGA-CG-5723 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-CG-5724        TCGA-CG-5725        TCGA-CG-5726        TCGA-CG-5727 
  "1P LOSS MUTATED" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-CG-5728        TCGA-CG-5730        TCGA-CG-5732        TCGA-CG-5733 
"1P LOSS WILD-TYPE"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-CG-5734        TCGA-D7-5577        TCGA-D7-5578        TCGA-D7-5579 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-D7-6518        TCGA-D7-6519        TCGA-D7-6520        TCGA-D7-6521 
"1P LOSS WILD-TYPE"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-D7-6522        TCGA-D7-6524        TCGA-D7-6525        TCGA-D7-6526 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-D7-6527        TCGA-D7-6528        TCGA-D7-6815        TCGA-D7-6817 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-D7-6818        TCGA-D7-6820        TCGA-D7-6822        TCGA-EQ-5647 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" 
       TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875        TCGA-FP-7735 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-FP-7829        TCGA-FP-7998        TCGA-IN-7806        TCGA-IN-7808 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-IP-7968 
"1P LOSS WILD-TYPE" 
       TCGA-B7-5816        TCGA-B7-5818        TCGA-BR-6452        TCGA-BR-6455 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BR-6457        TCGA-BR-6458        TCGA-BR-6563        TCGA-BR-6564 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BR-6565        TCGA-BR-6566        TCGA-BR-6705        TCGA-BR-6706 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BR-6707        TCGA-BR-6709        TCGA-BR-6710        TCGA-BR-6801 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BR-6802        TCGA-BR-6803        TCGA-BR-6852        TCGA-BR-7196 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BR-7197        TCGA-BR-7703        TCGA-BR-7704        TCGA-BR-7707 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BR-7715        TCGA-BR-7716        TCGA-BR-7717        TCGA-BR-7722 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BR-7723        TCGA-BR-7851        TCGA-BR-7901        TCGA-BR-7957 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-CD-5798        TCGA-CD-5799        TCGA-CD-5800        TCGA-CD-5801 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-CD-5802        TCGA-CD-5803        TCGA-CG-4300        TCGA-CG-4301 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" 
       TCGA-CG-4304        TCGA-CG-4305        TCGA-CG-4306        TCGA-CG-4436 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-CG-4437        TCGA-CG-4438        TCGA-CG-4440        TCGA-CG-4441 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-CG-4443        TCGA-CG-4444        TCGA-CG-4449        TCGA-CG-4455 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-CG-4460        TCGA-CG-4462        TCGA-CG-4465        TCGA-CG-4466 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-CG-4469        TCGA-CG-4472        TCGA-CG-4474        TCGA-CG-4477 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-CG-5716        TCGA-CG-5717        TCGA-CG-5718        TCGA-CG-5719 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" 
       TCGA-CG-5720        TCGA-CG-5721        TCGA-CG-5722        TCGA-CG-5723 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-CG-5724        TCGA-CG-5725        TCGA-CG-5726        TCGA-CG-5727 
  "1P LOSS MUTATED" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-CG-5728        TCGA-CG-5730        TCGA-CG-5732        TCGA-CG-5733 
"1P LOSS WILD-TYPE"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-CG-5734        TCGA-D7-5577        TCGA-D7-5578        TCGA-D7-5579 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-D7-6518        TCGA-D7-6519        TCGA-D7-6520        TCGA-D7-6521 
"1P LOSS WILD-TYPE"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-D7-6522        TCGA-D7-6524        TCGA-D7-6525        TCGA-D7-6526 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-D7-6527        TCGA-D7-6528        TCGA-D7-6815        TCGA-D7-6817 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-D7-6818        TCGA-D7-6820        TCGA-D7-6822        TCGA-EQ-5647 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" 
       TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875        TCGA-FP-7735 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-FP-7829        TCGA-FP-7998        TCGA-IN-7806        TCGA-IN-7808 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-IP-7968 
"1P LOSS WILD-TYPE" 
       TCGA-B7-5816        TCGA-B7-5818        TCGA-BR-6452        TCGA-BR-6455 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BR-6457        TCGA-BR-6458        TCGA-BR-6563        TCGA-BR-6564 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BR-6565        TCGA-BR-6566        TCGA-BR-6705        TCGA-BR-6706 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BR-6707        TCGA-BR-6709        TCGA-BR-6710        TCGA-BR-6801 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BR-6802        TCGA-BR-6803        TCGA-BR-6852        TCGA-BR-7196 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BR-7197        TCGA-BR-7703        TCGA-BR-7704        TCGA-BR-7707 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BR-7715        TCGA-BR-7716        TCGA-BR-7717        TCGA-BR-7722 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BR-7723        TCGA-BR-7851        TCGA-BR-7901        TCGA-BR-7957 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-CD-5798        TCGA-CD-5799        TCGA-CD-5800        TCGA-CD-5801 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-CD-5802        TCGA-CD-5803        TCGA-CG-4300        TCGA-CG-4301 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" 
       TCGA-CG-4304        TCGA-CG-4305        TCGA-CG-4306        TCGA-CG-4436 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-CG-4437        TCGA-CG-4438        TCGA-CG-4440        TCGA-CG-4441 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-CG-4443        TCGA-CG-4444        TCGA-CG-4449        TCGA-CG-4455 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-CG-4460        TCGA-CG-4462        TCGA-CG-4465        TCGA-CG-4466 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-CG-4469        TCGA-CG-4472        TCGA-CG-4474        TCGA-CG-4477 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-CG-5716        TCGA-CG-5717        TCGA-CG-5718        TCGA-CG-5719 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" 
       TCGA-CG-5720        TCGA-CG-5721        TCGA-CG-5722        TCGA-CG-5723 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-CG-5724        TCGA-CG-5725        TCGA-CG-5726        TCGA-CG-5727 
  "1P LOSS MUTATED" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-CG-5728        TCGA-CG-5730        TCGA-CG-5732        TCGA-CG-5733 
"1P LOSS WILD-TYPE"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-CG-5734        TCGA-D7-5577        TCGA-D7-5578        TCGA-D7-5579 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-D7-6518        TCGA-D7-6519        TCGA-D7-6520        TCGA-D7-6521 
"1P LOSS WILD-TYPE"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-D7-6522        TCGA-D7-6524        TCGA-D7-6525        TCGA-D7-6526 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-D7-6527        TCGA-D7-6528        TCGA-D7-6815        TCGA-D7-6817 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-D7-6818        TCGA-D7-6820        TCGA-D7-6822        TCGA-EQ-5647 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" 
       TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875        TCGA-FP-7735 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-FP-7829        TCGA-FP-7998        TCGA-IN-7806        TCGA-IN-7808 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-IP-7968 
"1P LOSS WILD-TYPE" 
[1] "hr=" "3.2"
D37V2, continuous
D37V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED      5    3
  1P LOSS WILD-TYPE   55   95
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  FEMALE               5                55
  MALE                 3                95
D37V4, multiclass
D37V5, multiclass
    clus
vv   1P LOSS MUTATED 1P LOSS WILD-TYPE
  T1               0                 6
  T2               3                49
  T3               1                60
  T4               3                15
D37V6, multiclass
    clus
vv   1P LOSS MUTATED 1P LOSS WILD-TYPE
  N0               1                43
  N1               3                54
  N2               0                24
  N3               2                13
D37V7, multiclass
    clus
vv   1P LOSS MUTATED 1P LOSS WILD-TYPE
  M0               3               131
  M1               5                11
  MX               0                 8
D37V8, multiclass
     clus
vv    1P LOSS MUTATED 1P LOSS WILD-TYPE
  I                 0                24
  II                0                37
  III               1                42
  IV                5                21
D37V9, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED      0    8
  1P LOSS WILD-TYPE    5  145
     clus
vv    1P LOSS MUTATED 1P LOSS WILD-TYPE
  NO                0                 5
  YES               8               145
D37V10, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED      0    8
  1P LOSS WILD-TYPE   10  140
     clus
vv    1P LOSS MUTATED 1P LOSS WILD-TYPE
  NO                0                10
  YES               8               140

Clustering(38) Variable = 1q loss mutation analysis
D38V1, survival
                   sevent
clus2                0  1
  1Q LOSS MUTATED    2  1
  1Q LOSS WILD-TYPE 88 14
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
                3               102 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
                1                14 
$`1Q LOSS MUTATED`
TCGA-CG-5719 TCGA-CG-5724 TCGA-D7-6519 
        1.02        12.03        15.65 

$`1Q LOSS WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-6452 TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6458 
        5.62         0.10         0.95         1.41         1.35         1.35 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
        0.85         0.82         0.62         0.62         1.71         2.17 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
        0.99         1.22         0.66         1.12         0.76         0.66 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
        0.26         1.22         1.48         0.46         1.25         0.13 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 
        1.05         0.82         0.69         0.16         4.54         0.99 
TCGA-BR-7901 TCGA-BR-7957 TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
        0.95         0.69         0.82         0.69         0.36         0.49 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
        0.30         0.07        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02        52.96         8.05        54.05         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4460 TCGA-CG-4462 
       29.98        47.05        19.07        12.03        21.99         1.02 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4474 TCGA-CG-4477 
        8.98        18.94         7.07        12.00         1.02         1.02 
TCGA-CG-5716 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        1.02         6.94         1.02         0.99         5.98         0.95 
TCGA-CG-5723 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 
       70.06        15.02        28.96        31.04        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       55.04        21.07         7.99         8.65         3.58         4.54 
TCGA-D7-6518 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
        9.80         9.63         8.19         6.90         0.69         5.95 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
        6.61         4.14         1.68         3.65         4.70         4.04 
TCGA-D7-6820 TCGA-D7-6822 TCGA-EQ-5647 TCGA-F1-6177 TCGA-F1-6874 TCGA-F1-6875 
        2.93         4.27         0.62         6.54         2.01        72.23 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7998 TCGA-IN-7806 TCGA-IN-7808 TCGA-IP-7968 
        0.39         0.20         3.58         6.87         3.55         2.53 

  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
             1.02              0.07 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
            15.65             72.23 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
            12.03              2.73 
[1] "1.0 - 15.7 (12.0)" "0.1 - 72.2 (2.7)" 
       TCGA-B7-5816        TCGA-B7-5818        TCGA-BR-6452        TCGA-BR-6455 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BR-6457        TCGA-BR-6458        TCGA-BR-6563        TCGA-BR-6564 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BR-6565        TCGA-BR-6566        TCGA-BR-6705        TCGA-BR-6706 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BR-6707        TCGA-BR-6709        TCGA-BR-6710        TCGA-BR-6801 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BR-6802        TCGA-BR-6803        TCGA-BR-6852        TCGA-BR-7196 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BR-7197        TCGA-BR-7703        TCGA-BR-7704        TCGA-BR-7707 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BR-7715        TCGA-BR-7716        TCGA-BR-7717        TCGA-BR-7722 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BR-7723        TCGA-BR-7851        TCGA-BR-7901        TCGA-BR-7957 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-CD-5798        TCGA-CD-5799        TCGA-CD-5800        TCGA-CD-5801 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-CD-5802        TCGA-CD-5803        TCGA-CG-4300        TCGA-CG-4301 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-CG-4304        TCGA-CG-4305        TCGA-CG-4306        TCGA-CG-4436 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-CG-4437        TCGA-CG-4438        TCGA-CG-4440        TCGA-CG-4441 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-CG-4443        TCGA-CG-4444        TCGA-CG-4449        TCGA-CG-4455 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-CG-4460        TCGA-CG-4462        TCGA-CG-4465        TCGA-CG-4466 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-CG-4469        TCGA-CG-4472        TCGA-CG-4474        TCGA-CG-4477 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-CG-5716        TCGA-CG-5717        TCGA-CG-5718        TCGA-CG-5719 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE"   "1Q LOSS MUTATED" 
       TCGA-CG-5720        TCGA-CG-5721        TCGA-CG-5722        TCGA-CG-5723 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-CG-5724        TCGA-CG-5725        TCGA-CG-5726        TCGA-CG-5727 
  "1Q LOSS MUTATED" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-CG-5728        TCGA-CG-5730        TCGA-CG-5732        TCGA-CG-5733 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-CG-5734        TCGA-D7-5577        TCGA-D7-5578        TCGA-D7-5579 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-D7-6518        TCGA-D7-6519        TCGA-D7-6520        TCGA-D7-6521 
"1Q LOSS WILD-TYPE"   "1Q LOSS MUTATED" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-D7-6522        TCGA-D7-6524        TCGA-D7-6525        TCGA-D7-6526 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-D7-6527        TCGA-D7-6528        TCGA-D7-6815        TCGA-D7-6817 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-D7-6818        TCGA-D7-6820        TCGA-D7-6822        TCGA-EQ-5647 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875        TCGA-FP-7735 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-FP-7829        TCGA-FP-7998        TCGA-IN-7806        TCGA-IN-7808 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-IP-7968 
"1Q LOSS WILD-TYPE" 
       TCGA-B7-5816        TCGA-B7-5818        TCGA-BR-6452        TCGA-BR-6455 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BR-6457        TCGA-BR-6458        TCGA-BR-6563        TCGA-BR-6564 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BR-6565        TCGA-BR-6566        TCGA-BR-6705        TCGA-BR-6706 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BR-6707        TCGA-BR-6709        TCGA-BR-6710        TCGA-BR-6801 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BR-6802        TCGA-BR-6803        TCGA-BR-6852        TCGA-BR-7196 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BR-7197        TCGA-BR-7703        TCGA-BR-7704        TCGA-BR-7707 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BR-7715        TCGA-BR-7716        TCGA-BR-7717        TCGA-BR-7722 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BR-7723        TCGA-BR-7851        TCGA-BR-7901        TCGA-BR-7957 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-CD-5798        TCGA-CD-5799        TCGA-CD-5800        TCGA-CD-5801 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-CD-5802        TCGA-CD-5803        TCGA-CG-4300        TCGA-CG-4301 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-CG-4304        TCGA-CG-4305        TCGA-CG-4306        TCGA-CG-4436 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-CG-4437        TCGA-CG-4438        TCGA-CG-4440        TCGA-CG-4441 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-CG-4443        TCGA-CG-4444        TCGA-CG-4449        TCGA-CG-4455 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-CG-4460        TCGA-CG-4462        TCGA-CG-4465        TCGA-CG-4466 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-CG-4469        TCGA-CG-4472        TCGA-CG-4474        TCGA-CG-4477 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-CG-5716        TCGA-CG-5717        TCGA-CG-5718        TCGA-CG-5719 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE"   "1Q LOSS MUTATED" 
       TCGA-CG-5720        TCGA-CG-5721        TCGA-CG-5722        TCGA-CG-5723 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-CG-5724        TCGA-CG-5725        TCGA-CG-5726        TCGA-CG-5727 
  "1Q LOSS MUTATED" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-CG-5728        TCGA-CG-5730        TCGA-CG-5732        TCGA-CG-5733 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-CG-5734        TCGA-D7-5577        TCGA-D7-5578        TCGA-D7-5579 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-D7-6518        TCGA-D7-6519        TCGA-D7-6520        TCGA-D7-6521 
"1Q LOSS WILD-TYPE"   "1Q LOSS MUTATED" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-D7-6522        TCGA-D7-6524        TCGA-D7-6525        TCGA-D7-6526 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-D7-6527        TCGA-D7-6528        TCGA-D7-6815        TCGA-D7-6817 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-D7-6818        TCGA-D7-6820        TCGA-D7-6822        TCGA-EQ-5647 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875        TCGA-FP-7735 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-FP-7829        TCGA-FP-7998        TCGA-IN-7806        TCGA-IN-7808 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-IP-7968 
"1Q LOSS WILD-TYPE" 
       TCGA-B7-5816        TCGA-B7-5818        TCGA-BR-6452        TCGA-BR-6455 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BR-6457        TCGA-BR-6458        TCGA-BR-6563        TCGA-BR-6564 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BR-6565        TCGA-BR-6566        TCGA-BR-6705        TCGA-BR-6706 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BR-6707        TCGA-BR-6709        TCGA-BR-6710        TCGA-BR-6801 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BR-6802        TCGA-BR-6803        TCGA-BR-6852        TCGA-BR-7196 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BR-7197        TCGA-BR-7703        TCGA-BR-7704        TCGA-BR-7707 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BR-7715        TCGA-BR-7716        TCGA-BR-7717        TCGA-BR-7722 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BR-7723        TCGA-BR-7851        TCGA-BR-7901        TCGA-BR-7957 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-CD-5798        TCGA-CD-5799        TCGA-CD-5800        TCGA-CD-5801 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-CD-5802        TCGA-CD-5803        TCGA-CG-4300        TCGA-CG-4301 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-CG-4304        TCGA-CG-4305        TCGA-CG-4306        TCGA-CG-4436 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-CG-4437        TCGA-CG-4438        TCGA-CG-4440        TCGA-CG-4441 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-CG-4443        TCGA-CG-4444        TCGA-CG-4449        TCGA-CG-4455 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-CG-4460        TCGA-CG-4462        TCGA-CG-4465        TCGA-CG-4466 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-CG-4469        TCGA-CG-4472        TCGA-CG-4474        TCGA-CG-4477 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-CG-5716        TCGA-CG-5717        TCGA-CG-5718        TCGA-CG-5719 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE"   "1Q LOSS MUTATED" 
       TCGA-CG-5720        TCGA-CG-5721        TCGA-CG-5722        TCGA-CG-5723 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-CG-5724        TCGA-CG-5725        TCGA-CG-5726        TCGA-CG-5727 
  "1Q LOSS MUTATED" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-CG-5728        TCGA-CG-5730        TCGA-CG-5732        TCGA-CG-5733 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-CG-5734        TCGA-D7-5577        TCGA-D7-5578        TCGA-D7-5579 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-D7-6518        TCGA-D7-6519        TCGA-D7-6520        TCGA-D7-6521 
"1Q LOSS WILD-TYPE"   "1Q LOSS MUTATED" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-D7-6522        TCGA-D7-6524        TCGA-D7-6525        TCGA-D7-6526 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-D7-6527        TCGA-D7-6528        TCGA-D7-6815        TCGA-D7-6817 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-D7-6818        TCGA-D7-6820        TCGA-D7-6822        TCGA-EQ-5647 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875        TCGA-FP-7735 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-FP-7829        TCGA-FP-7998        TCGA-IN-7806        TCGA-IN-7808 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-IP-7968 
"1Q LOSS WILD-TYPE" 
[1] "hr=" "1.7"
D38V2, continuous
D38V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED      2    2
  1Q LOSS WILD-TYPE   58   96
        clus
vv       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  FEMALE               2                58
  MALE                 2                96
D38V4, multiclass
D38V5, multiclass
    clus
vv   1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  T1               0                 6
  T2               1                51
  T3               1                60
  T4               1                17
D38V6, multiclass
    clus
vv   1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  N0               1                43
  N1               1                56
  N2               0                24
  N3               1                14
D38V7, multiclass
    clus
vv   1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  M0               2               132
  M1               2                14
  MX               0                 8
D38V8, multiclass
     clus
vv    1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  I                 0                24
  II                0                37
  III               1                42
  IV                2                24
D38V9, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED      0    4
  1Q LOSS WILD-TYPE    5  149
     clus
vv    1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  NO                0                 5
  YES               4               149
D38V10, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED      0    4
  1Q LOSS WILD-TYPE   10  144
     clus
vv    1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  NO                0                10
  YES               4               144

Clustering(39) Variable = 3p loss mutation analysis
D39V1, survival
                   sevent
clus2                0  1
  3P LOSS MUTATED    9  1
  3P LOSS WILD-TYPE 81 14
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               10                95 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
                1                14 
$`3P LOSS MUTATED`
TCGA-BR-6458 TCGA-BR-7715 TCGA-CG-4438 TCGA-CG-4466 TCGA-CG-5725 TCGA-CG-5730 
        1.35         1.05        54.05        18.94        15.02         4.01 
TCGA-D7-6525 TCGA-D7-6528 TCGA-FP-7829 TCGA-IN-7806 
        5.95         1.68         0.20         6.87 

$`3P LOSS WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-6452 TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6563 
        5.62         0.10         0.95         1.41         1.35         0.85 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
        0.82         0.62         0.62         1.71         2.17         0.99 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
        1.22         0.66         1.12         0.76         0.66         0.26 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7716 
        1.22         1.48         0.46         1.25         0.13         0.82 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 
        0.69         0.16         4.54         0.99         0.95         0.69 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
        0.82         0.69         0.36         0.49         0.30         0.07 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02        52.96 
TCGA-CG-4437 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 
        8.05         4.01        14.01        29.98        47.05        19.07 
TCGA-CG-4455 TCGA-CG-4460 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4469 TCGA-CG-4472 
       12.03        21.99         1.02         8.98         7.07        12.00 
TCGA-CG-4474 TCGA-CG-4477 TCGA-CG-5716 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
        1.02         1.02         1.02         6.94         1.02         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 
        0.99         5.98         0.95        70.06        12.03        28.96 
TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       31.04        65.10        55.04        21.07         7.99         8.65 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
        3.58         4.54         9.80        15.65         9.63         8.19 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6815 TCGA-D7-6817 
        6.90         0.69         6.61         4.14         3.65         4.70 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-EQ-5647 TCGA-F1-6177 TCGA-F1-6874 
        4.04         2.93         4.27         0.62         6.54         2.01 
TCGA-F1-6875 TCGA-FP-7735 TCGA-FP-7998 TCGA-IN-7808 TCGA-IP-7968 
       72.23         0.39         3.58         3.55         2.53 

  3P LOSS MUTATED 3P LOSS WILD-TYPE 
             0.20              0.07 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
            54.05             72.23 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
             4.98              2.53 
[1] "0.2 - 54.0 (5.0)" "0.1 - 72.2 (2.5)"
       TCGA-B7-5816        TCGA-B7-5818        TCGA-BR-6452        TCGA-BR-6455 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-BR-6457        TCGA-BR-6458        TCGA-BR-6563        TCGA-BR-6564 
"3P LOSS WILD-TYPE"   "3P LOSS MUTATED" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-BR-6565        TCGA-BR-6566        TCGA-BR-6705        TCGA-BR-6706 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-BR-6707        TCGA-BR-6709        TCGA-BR-6710        TCGA-BR-6801 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-BR-6802        TCGA-BR-6803        TCGA-BR-6852        TCGA-BR-7196 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-BR-7197        TCGA-BR-7703        TCGA-BR-7704        TCGA-BR-7707 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-BR-7715        TCGA-BR-7716        TCGA-BR-7717        TCGA-BR-7722 
  "3P LOSS MUTATED" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-BR-7723        TCGA-BR-7851        TCGA-BR-7901        TCGA-BR-7957 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-CD-5798        TCGA-CD-5799        TCGA-CD-5800        TCGA-CD-5801 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-CD-5802        TCGA-CD-5803        TCGA-CG-4300        TCGA-CG-4301 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-CG-4304        TCGA-CG-4305        TCGA-CG-4306        TCGA-CG-4436 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-CG-4437        TCGA-CG-4438        TCGA-CG-4440        TCGA-CG-4441 
"3P LOSS WILD-TYPE"   "3P LOSS MUTATED" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-CG-4443        TCGA-CG-4444        TCGA-CG-4449        TCGA-CG-4455 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-CG-4460        TCGA-CG-4462        TCGA-CG-4465        TCGA-CG-4466 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE"   "3P LOSS MUTATED" 
       TCGA-CG-4469        TCGA-CG-4472        TCGA-CG-4474        TCGA-CG-4477 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-CG-5716        TCGA-CG-5717        TCGA-CG-5718        TCGA-CG-5719 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-CG-5720        TCGA-CG-5721        TCGA-CG-5722        TCGA-CG-5723 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-CG-5724        TCGA-CG-5725        TCGA-CG-5726        TCGA-CG-5727 
"3P LOSS WILD-TYPE"   "3P LOSS MUTATED" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-CG-5728        TCGA-CG-5730        TCGA-CG-5732        TCGA-CG-5733 
"3P LOSS WILD-TYPE"   "3P LOSS MUTATED" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-CG-5734        TCGA-D7-5577        TCGA-D7-5578        TCGA-D7-5579 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-D7-6518        TCGA-D7-6519        TCGA-D7-6520        TCGA-D7-6521 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-D7-6522        TCGA-D7-6524        TCGA-D7-6525        TCGA-D7-6526 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE"   "3P LOSS MUTATED" "3P LOSS WILD-TYPE" 
       TCGA-D7-6527        TCGA-D7-6528        TCGA-D7-6815        TCGA-D7-6817 
"3P LOSS WILD-TYPE"   "3P LOSS MUTATED" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-D7-6818        TCGA-D7-6820        TCGA-D7-6822        TCGA-EQ-5647 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875        TCGA-FP-7735 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-FP-7829        TCGA-FP-7998        TCGA-IN-7806        TCGA-IN-7808 
  "3P LOSS MUTATED" "3P LOSS WILD-TYPE"   "3P LOSS MUTATED" "3P LOSS WILD-TYPE" 
       TCGA-IP-7968 
"3P LOSS WILD-TYPE" 
       TCGA-B7-5816        TCGA-B7-5818        TCGA-BR-6452        TCGA-BR-6455 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-BR-6457        TCGA-BR-6458        TCGA-BR-6563        TCGA-BR-6564 
"3P LOSS WILD-TYPE"   "3P LOSS MUTATED" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-BR-6565        TCGA-BR-6566        TCGA-BR-6705        TCGA-BR-6706 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-BR-6707        TCGA-BR-6709        TCGA-BR-6710        TCGA-BR-6801 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-BR-6802        TCGA-BR-6803        TCGA-BR-6852        TCGA-BR-7196 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-BR-7197        TCGA-BR-7703        TCGA-BR-7704        TCGA-BR-7707 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-BR-7715        TCGA-BR-7716        TCGA-BR-7717        TCGA-BR-7722 
  "3P LOSS MUTATED" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-BR-7723        TCGA-BR-7851        TCGA-BR-7901        TCGA-BR-7957 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-CD-5798        TCGA-CD-5799        TCGA-CD-5800        TCGA-CD-5801 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-CD-5802        TCGA-CD-5803        TCGA-CG-4300        TCGA-CG-4301 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-CG-4304        TCGA-CG-4305        TCGA-CG-4306        TCGA-CG-4436 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-CG-4437        TCGA-CG-4438        TCGA-CG-4440        TCGA-CG-4441 
"3P LOSS WILD-TYPE"   "3P LOSS MUTATED" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-CG-4443        TCGA-CG-4444        TCGA-CG-4449        TCGA-CG-4455 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-CG-4460        TCGA-CG-4462        TCGA-CG-4465        TCGA-CG-4466 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE"   "3P LOSS MUTATED" 
       TCGA-CG-4469        TCGA-CG-4472        TCGA-CG-4474        TCGA-CG-4477 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-CG-5716        TCGA-CG-5717        TCGA-CG-5718        TCGA-CG-5719 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-CG-5720        TCGA-CG-5721        TCGA-CG-5722        TCGA-CG-5723 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-CG-5724        TCGA-CG-5725        TCGA-CG-5726        TCGA-CG-5727 
"3P LOSS WILD-TYPE"   "3P LOSS MUTATED" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-CG-5728        TCGA-CG-5730        TCGA-CG-5732        TCGA-CG-5733 
"3P LOSS WILD-TYPE"   "3P LOSS MUTATED" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-CG-5734        TCGA-D7-5577        TCGA-D7-5578        TCGA-D7-5579 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-D7-6518        TCGA-D7-6519        TCGA-D7-6520        TCGA-D7-6521 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-D7-6522        TCGA-D7-6524        TCGA-D7-6525        TCGA-D7-6526 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE"   "3P LOSS MUTATED" "3P LOSS WILD-TYPE" 
       TCGA-D7-6527        TCGA-D7-6528        TCGA-D7-6815        TCGA-D7-6817 
"3P LOSS WILD-TYPE"   "3P LOSS MUTATED" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-D7-6818        TCGA-D7-6820        TCGA-D7-6822        TCGA-EQ-5647 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875        TCGA-FP-7735 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-FP-7829        TCGA-FP-7998        TCGA-IN-7806        TCGA-IN-7808 
  "3P LOSS MUTATED" "3P LOSS WILD-TYPE"   "3P LOSS MUTATED" "3P LOSS WILD-TYPE" 
       TCGA-IP-7968 
"3P LOSS WILD-TYPE" 
       TCGA-B7-5816        TCGA-B7-5818        TCGA-BR-6452        TCGA-BR-6455 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-BR-6457        TCGA-BR-6458        TCGA-BR-6563        TCGA-BR-6564 
"3P LOSS WILD-TYPE"   "3P LOSS MUTATED" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-BR-6565        TCGA-BR-6566        TCGA-BR-6705        TCGA-BR-6706 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-BR-6707        TCGA-BR-6709        TCGA-BR-6710        TCGA-BR-6801 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-BR-6802        TCGA-BR-6803        TCGA-BR-6852        TCGA-BR-7196 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-BR-7197        TCGA-BR-7703        TCGA-BR-7704        TCGA-BR-7707 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-BR-7715        TCGA-BR-7716        TCGA-BR-7717        TCGA-BR-7722 
  "3P LOSS MUTATED" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-BR-7723        TCGA-BR-7851        TCGA-BR-7901        TCGA-BR-7957 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-CD-5798        TCGA-CD-5799        TCGA-CD-5800        TCGA-CD-5801 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-CD-5802        TCGA-CD-5803        TCGA-CG-4300        TCGA-CG-4301 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-CG-4304        TCGA-CG-4305        TCGA-CG-4306        TCGA-CG-4436 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-CG-4437        TCGA-CG-4438        TCGA-CG-4440        TCGA-CG-4441 
"3P LOSS WILD-TYPE"   "3P LOSS MUTATED" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-CG-4443        TCGA-CG-4444        TCGA-CG-4449        TCGA-CG-4455 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-CG-4460        TCGA-CG-4462        TCGA-CG-4465        TCGA-CG-4466 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE"   "3P LOSS MUTATED" 
       TCGA-CG-4469        TCGA-CG-4472        TCGA-CG-4474        TCGA-CG-4477 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-CG-5716        TCGA-CG-5717        TCGA-CG-5718        TCGA-CG-5719 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-CG-5720        TCGA-CG-5721        TCGA-CG-5722        TCGA-CG-5723 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-CG-5724        TCGA-CG-5725        TCGA-CG-5726        TCGA-CG-5727 
"3P LOSS WILD-TYPE"   "3P LOSS MUTATED" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-CG-5728        TCGA-CG-5730        TCGA-CG-5732        TCGA-CG-5733 
"3P LOSS WILD-TYPE"   "3P LOSS MUTATED" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-CG-5734        TCGA-D7-5577        TCGA-D7-5578        TCGA-D7-5579 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-D7-6518        TCGA-D7-6519        TCGA-D7-6520        TCGA-D7-6521 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-D7-6522        TCGA-D7-6524        TCGA-D7-6525        TCGA-D7-6526 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE"   "3P LOSS MUTATED" "3P LOSS WILD-TYPE" 
       TCGA-D7-6527        TCGA-D7-6528        TCGA-D7-6815        TCGA-D7-6817 
"3P LOSS WILD-TYPE"   "3P LOSS MUTATED" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-D7-6818        TCGA-D7-6820        TCGA-D7-6822        TCGA-EQ-5647 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875        TCGA-FP-7735 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-FP-7829        TCGA-FP-7998        TCGA-IN-7806        TCGA-IN-7808 
  "3P LOSS MUTATED" "3P LOSS WILD-TYPE"   "3P LOSS MUTATED" "3P LOSS WILD-TYPE" 
       TCGA-IP-7968 
"3P LOSS WILD-TYPE" 
[1] "hr=" "1.6"
D39V2, continuous
D39V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED      5    6
  3P LOSS WILD-TYPE   55   92
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  FEMALE               5                55
  MALE                 6                92
D39V4, multiclass
D39V5, multiclass
    clus
vv   3P LOSS MUTATED 3P LOSS WILD-TYPE
  T1               0                 6
  T2               5                47
  T3               4                57
  T4               1                17
D39V6, multiclass
    clus
vv   3P LOSS MUTATED 3P LOSS WILD-TYPE
  N0               4                40
  N1               4                53
  N2               2                22
  N3               0                15
D39V7, multiclass
    clus
vv   3P LOSS MUTATED 3P LOSS WILD-TYPE
  M0              10               124
  M1               1                15
  MX               0                 8
D39V8, multiclass
     clus
vv    3P LOSS MUTATED 3P LOSS WILD-TYPE
  I                 3                21
  II                2                35
  III               3                40
  IV                2                24
D39V9, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED      0   11
  3P LOSS WILD-TYPE    5  142
     clus
vv    3P LOSS MUTATED 3P LOSS WILD-TYPE
  NO                0                 5
  YES              11               142
D39V10, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED      1   10
  3P LOSS WILD-TYPE    9  138
     clus
vv    3P LOSS MUTATED 3P LOSS WILD-TYPE
  NO                1                 9
  YES              10               138

Clustering(40) Variable = 3q loss mutation analysis
D40V1, survival
                   sevent
clus2                0  1
  3Q LOSS MUTATED    5  1
  3Q LOSS WILD-TYPE 85 14
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
                6                99 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
                1                14 
$`3Q LOSS MUTATED`
TCGA-BR-7715 TCGA-CG-4438 TCGA-CG-4466 TCGA-CG-5725 TCGA-FP-7829 TCGA-IN-7806 
        1.05        54.05        18.94        15.02         0.20         6.87 

$`3Q LOSS WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-6452 TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6458 
        5.62         0.10         0.95         1.41         1.35         1.35 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
        0.85         0.82         0.62         0.62         1.71         2.17 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
        0.99         1.22         0.66         1.12         0.76         0.66 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
        0.26         1.22         1.48         0.46         1.25         0.13 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 
        0.82         0.69         0.16         4.54         0.99         0.95 
TCGA-BR-7957 TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        0.69         0.82         0.69         0.36         0.49         0.30 
TCGA-CD-5803 TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
        0.07        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 
       52.96         8.05         4.01        14.01        29.98        47.05 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4460 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4469 
       19.07        12.03        21.99         1.02         8.98         7.07 
TCGA-CG-4472 TCGA-CG-4474 TCGA-CG-4477 TCGA-CG-5716 TCGA-CG-5717 TCGA-CG-5718 
       12.00         1.02         1.02         1.02         6.94         1.02 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
        1.02         0.99         5.98         0.95        70.06        12.03 
TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       28.96        31.04        65.10         4.01        55.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99         8.65         3.58         4.54         9.80        15.65 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
        9.63         8.19         6.90         0.69         5.95         6.61 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
        4.14         1.68         3.65         4.70         4.04         2.93 
TCGA-D7-6822 TCGA-EQ-5647 TCGA-F1-6177 TCGA-F1-6874 TCGA-F1-6875 TCGA-FP-7735 
        4.27         0.62         6.54         2.01        72.23         0.39 
TCGA-FP-7998 TCGA-IN-7808 TCGA-IP-7968 
        3.58         3.55         2.53 

  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
             0.20              0.07 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
            54.05             72.23 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
           10.945             2.530 
[1] "0.2 - 54.0 (10.9)" "0.1 - 72.2 (2.5)" 
       TCGA-B7-5816        TCGA-B7-5818        TCGA-BR-6452        TCGA-BR-6455 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-BR-6457        TCGA-BR-6458        TCGA-BR-6563        TCGA-BR-6564 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-BR-6565        TCGA-BR-6566        TCGA-BR-6705        TCGA-BR-6706 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-BR-6707        TCGA-BR-6709        TCGA-BR-6710        TCGA-BR-6801 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-BR-6802        TCGA-BR-6803        TCGA-BR-6852        TCGA-BR-7196 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-BR-7197        TCGA-BR-7703        TCGA-BR-7704        TCGA-BR-7707 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-BR-7715        TCGA-BR-7716        TCGA-BR-7717        TCGA-BR-7722 
  "3Q LOSS MUTATED" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-BR-7723        TCGA-BR-7851        TCGA-BR-7901        TCGA-BR-7957 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-CD-5798        TCGA-CD-5799        TCGA-CD-5800        TCGA-CD-5801 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-CD-5802        TCGA-CD-5803        TCGA-CG-4300        TCGA-CG-4301 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-CG-4304        TCGA-CG-4305        TCGA-CG-4306        TCGA-CG-4436 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-CG-4437        TCGA-CG-4438        TCGA-CG-4440        TCGA-CG-4441 
"3Q LOSS WILD-TYPE"   "3Q LOSS MUTATED" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-CG-4443        TCGA-CG-4444        TCGA-CG-4449        TCGA-CG-4455 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-CG-4460        TCGA-CG-4462        TCGA-CG-4465        TCGA-CG-4466 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE"   "3Q LOSS MUTATED" 
       TCGA-CG-4469        TCGA-CG-4472        TCGA-CG-4474        TCGA-CG-4477 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-CG-5716        TCGA-CG-5717        TCGA-CG-5718        TCGA-CG-5719 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-CG-5720        TCGA-CG-5721        TCGA-CG-5722        TCGA-CG-5723 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-CG-5724        TCGA-CG-5725        TCGA-CG-5726        TCGA-CG-5727 
"3Q LOSS WILD-TYPE"   "3Q LOSS MUTATED" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-CG-5728        TCGA-CG-5730        TCGA-CG-5732        TCGA-CG-5733 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-CG-5734        TCGA-D7-5577        TCGA-D7-5578        TCGA-D7-5579 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-D7-6518        TCGA-D7-6519        TCGA-D7-6520        TCGA-D7-6521 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-D7-6522        TCGA-D7-6524        TCGA-D7-6525        TCGA-D7-6526 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-D7-6527        TCGA-D7-6528        TCGA-D7-6815        TCGA-D7-6817 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-D7-6818        TCGA-D7-6820        TCGA-D7-6822        TCGA-EQ-5647 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875        TCGA-FP-7735 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-FP-7829        TCGA-FP-7998        TCGA-IN-7806        TCGA-IN-7808 
  "3Q LOSS MUTATED" "3Q LOSS WILD-TYPE"   "3Q LOSS MUTATED" "3Q LOSS WILD-TYPE" 
       TCGA-IP-7968 
"3Q LOSS WILD-TYPE" 
       TCGA-B7-5816        TCGA-B7-5818        TCGA-BR-6452        TCGA-BR-6455 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-BR-6457        TCGA-BR-6458        TCGA-BR-6563        TCGA-BR-6564 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-BR-6565        TCGA-BR-6566        TCGA-BR-6705        TCGA-BR-6706 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-BR-6707        TCGA-BR-6709        TCGA-BR-6710        TCGA-BR-6801 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-BR-6802        TCGA-BR-6803        TCGA-BR-6852        TCGA-BR-7196 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-BR-7197        TCGA-BR-7703        TCGA-BR-7704        TCGA-BR-7707 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-BR-7715        TCGA-BR-7716        TCGA-BR-7717        TCGA-BR-7722 
  "3Q LOSS MUTATED" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-BR-7723        TCGA-BR-7851        TCGA-BR-7901        TCGA-BR-7957 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-CD-5798        TCGA-CD-5799        TCGA-CD-5800        TCGA-CD-5801 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-CD-5802        TCGA-CD-5803        TCGA-CG-4300        TCGA-CG-4301 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-CG-4304        TCGA-CG-4305        TCGA-CG-4306        TCGA-CG-4436 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-CG-4437        TCGA-CG-4438        TCGA-CG-4440        TCGA-CG-4441 
"3Q LOSS WILD-TYPE"   "3Q LOSS MUTATED" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-CG-4443        TCGA-CG-4444        TCGA-CG-4449        TCGA-CG-4455 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-CG-4460        TCGA-CG-4462        TCGA-CG-4465        TCGA-CG-4466 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE"   "3Q LOSS MUTATED" 
       TCGA-CG-4469        TCGA-CG-4472        TCGA-CG-4474        TCGA-CG-4477 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-CG-5716        TCGA-CG-5717        TCGA-CG-5718        TCGA-CG-5719 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-CG-5720        TCGA-CG-5721        TCGA-CG-5722        TCGA-CG-5723 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-CG-5724        TCGA-CG-5725        TCGA-CG-5726        TCGA-CG-5727 
"3Q LOSS WILD-TYPE"   "3Q LOSS MUTATED" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-CG-5728        TCGA-CG-5730        TCGA-CG-5732        TCGA-CG-5733 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-CG-5734        TCGA-D7-5577        TCGA-D7-5578        TCGA-D7-5579 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-D7-6518        TCGA-D7-6519        TCGA-D7-6520        TCGA-D7-6521 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-D7-6522        TCGA-D7-6524        TCGA-D7-6525        TCGA-D7-6526 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-D7-6527        TCGA-D7-6528        TCGA-D7-6815        TCGA-D7-6817 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-D7-6818        TCGA-D7-6820        TCGA-D7-6822        TCGA-EQ-5647 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875        TCGA-FP-7735 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-FP-7829        TCGA-FP-7998        TCGA-IN-7806        TCGA-IN-7808 
  "3Q LOSS MUTATED" "3Q LOSS WILD-TYPE"   "3Q LOSS MUTATED" "3Q LOSS WILD-TYPE" 
       TCGA-IP-7968 
"3Q LOSS WILD-TYPE" 
       TCGA-B7-5816        TCGA-B7-5818        TCGA-BR-6452        TCGA-BR-6455 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-BR-6457        TCGA-BR-6458        TCGA-BR-6563        TCGA-BR-6564 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-BR-6565        TCGA-BR-6566        TCGA-BR-6705        TCGA-BR-6706 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-BR-6707        TCGA-BR-6709        TCGA-BR-6710        TCGA-BR-6801 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-BR-6802        TCGA-BR-6803        TCGA-BR-6852        TCGA-BR-7196 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-BR-7197        TCGA-BR-7703        TCGA-BR-7704        TCGA-BR-7707 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-BR-7715        TCGA-BR-7716        TCGA-BR-7717        TCGA-BR-7722 
  "3Q LOSS MUTATED" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-BR-7723        TCGA-BR-7851        TCGA-BR-7901        TCGA-BR-7957 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-CD-5798        TCGA-CD-5799        TCGA-CD-5800        TCGA-CD-5801 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-CD-5802        TCGA-CD-5803        TCGA-CG-4300        TCGA-CG-4301 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-CG-4304        TCGA-CG-4305        TCGA-CG-4306        TCGA-CG-4436 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-CG-4437        TCGA-CG-4438        TCGA-CG-4440        TCGA-CG-4441 
"3Q LOSS WILD-TYPE"   "3Q LOSS MUTATED" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-CG-4443        TCGA-CG-4444        TCGA-CG-4449        TCGA-CG-4455 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-CG-4460        TCGA-CG-4462        TCGA-CG-4465        TCGA-CG-4466 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE"   "3Q LOSS MUTATED" 
       TCGA-CG-4469        TCGA-CG-4472        TCGA-CG-4474        TCGA-CG-4477 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-CG-5716        TCGA-CG-5717        TCGA-CG-5718        TCGA-CG-5719 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-CG-5720        TCGA-CG-5721        TCGA-CG-5722        TCGA-CG-5723 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-CG-5724        TCGA-CG-5725        TCGA-CG-5726        TCGA-CG-5727 
"3Q LOSS WILD-TYPE"   "3Q LOSS MUTATED" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-CG-5728        TCGA-CG-5730        TCGA-CG-5732        TCGA-CG-5733 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-CG-5734        TCGA-D7-5577        TCGA-D7-5578        TCGA-D7-5579 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-D7-6518        TCGA-D7-6519        TCGA-D7-6520        TCGA-D7-6521 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-D7-6522        TCGA-D7-6524        TCGA-D7-6525        TCGA-D7-6526 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-D7-6527        TCGA-D7-6528        TCGA-D7-6815        TCGA-D7-6817 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-D7-6818        TCGA-D7-6820        TCGA-D7-6822        TCGA-EQ-5647 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875        TCGA-FP-7735 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-FP-7829        TCGA-FP-7998        TCGA-IN-7806        TCGA-IN-7808 
  "3Q LOSS MUTATED" "3Q LOSS WILD-TYPE"   "3Q LOSS MUTATED" "3Q LOSS WILD-TYPE" 
       TCGA-IP-7968 
"3Q LOSS WILD-TYPE" 
[1] "hr=" "1.4"
D40V2, continuous
D40V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED      2    5
  3Q LOSS WILD-TYPE   58   93
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  FEMALE               2                58
  MALE                 5                93
D40V4, multiclass
D40V5, multiclass
    clus
vv   3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  T1               0                 6
  T2               2                50
  T3               3                58
  T4               1                17
D40V6, multiclass
    clus
vv   3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  N0               3                41
  N1               2                55
  N2               1                23
  N3               0                15
D40V7, multiclass
    clus
vv   3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  M0               7               127
  M1               0                16
  MX               0                 8
D40V8, multiclass
     clus
vv    3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  I                 2                22
  II                1                36
  III               2                41
  IV                1                25
D40V9, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED      0    7
  3Q LOSS WILD-TYPE    5  146
     clus
vv    3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  NO                0                 5
  YES               7               146
D40V10, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED      0    7
  3Q LOSS WILD-TYPE   10  141
     clus
vv    3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  NO                0                10
  YES               7               141

Clustering(41) Variable = 4p loss mutation analysis
D41V1, survival
                   sevent
clus2                0  1
  4P LOSS MUTATED   13  3
  4P LOSS WILD-TYPE 77 12
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               16                89 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
                3                12 
$`4P LOSS MUTATED`
TCGA-BR-7197 TCGA-BR-7723 TCGA-CD-5799 TCGA-CD-5802 TCGA-CG-4300 TCGA-CG-4438 
        1.48         4.54         0.69         0.30        20.02        54.05 
TCGA-CG-4440 TCGA-CG-4449 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5725 
        4.01        19.07        18.94         7.07         1.02        15.02 
TCGA-D7-6519 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6820 
       15.65         4.14         1.68         2.93 

$`4P LOSS WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-6452 TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6458 
        5.62         0.10         0.95         1.41         1.35         1.35 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
        0.85         0.82         0.62         0.62         1.71         2.17 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
        0.99         1.22         0.66         1.12         0.76         0.66 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
        0.26         1.22         0.46         1.25         0.13         1.05 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 
        0.82         0.69         0.16         0.99         0.95         0.69 
TCGA-CD-5798 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5803 TCGA-CG-4301 TCGA-CG-4304 
        0.82         0.36         0.49         0.07         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4441 TCGA-CG-4443 
       15.95         1.02        52.96         8.05        14.01        29.98 
TCGA-CG-4444 TCGA-CG-4455 TCGA-CG-4460 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4472 
       47.05        12.03        21.99         1.02         8.98        12.00 
TCGA-CG-4474 TCGA-CG-5716 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
        1.02         1.02         6.94         1.02         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 
        5.98         0.95        70.06        12.03        28.96        31.04 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        55.04        21.07         7.99         8.65 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
        3.58         4.54         9.80         9.63         8.19         6.90 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
        0.69         5.95         6.61         3.65         4.70         4.04 
TCGA-D7-6822 TCGA-EQ-5647 TCGA-F1-6177 TCGA-F1-6874 TCGA-F1-6875 TCGA-FP-7735 
        4.27         0.62         6.54         2.01        72.23         0.39 
TCGA-FP-7829 TCGA-FP-7998 TCGA-IN-7806 TCGA-IN-7808 TCGA-IP-7968 
        0.20         3.58         6.87         3.55         2.53 

  4P LOSS MUTATED 4P LOSS WILD-TYPE 
             0.30              0.07 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
            54.05             72.23 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
             4.34              2.01 
[1] "0.3 - 54.0 (4.3)" "0.1 - 72.2 (2.0)"
       TCGA-B7-5816        TCGA-B7-5818        TCGA-BR-6452        TCGA-BR-6455 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-BR-6457        TCGA-BR-6458        TCGA-BR-6563        TCGA-BR-6564 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-BR-6565        TCGA-BR-6566        TCGA-BR-6705        TCGA-BR-6706 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-BR-6707        TCGA-BR-6709        TCGA-BR-6710        TCGA-BR-6801 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-BR-6802        TCGA-BR-6803        TCGA-BR-6852        TCGA-BR-7196 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-BR-7197        TCGA-BR-7703        TCGA-BR-7704        TCGA-BR-7707 
  "4P LOSS MUTATED" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-BR-7715        TCGA-BR-7716        TCGA-BR-7717        TCGA-BR-7722 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-BR-7723        TCGA-BR-7851        TCGA-BR-7901        TCGA-BR-7957 
  "4P LOSS MUTATED" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-CD-5798        TCGA-CD-5799        TCGA-CD-5800        TCGA-CD-5801 
"4P LOSS WILD-TYPE"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-CD-5802        TCGA-CD-5803        TCGA-CG-4300        TCGA-CG-4301 
  "4P LOSS MUTATED" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" 
       TCGA-CG-4304        TCGA-CG-4305        TCGA-CG-4306        TCGA-CG-4436 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-CG-4437        TCGA-CG-4438        TCGA-CG-4440        TCGA-CG-4441 
"4P LOSS WILD-TYPE"   "4P LOSS MUTATED"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" 
       TCGA-CG-4443        TCGA-CG-4444        TCGA-CG-4449        TCGA-CG-4455 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" 
       TCGA-CG-4460        TCGA-CG-4462        TCGA-CG-4465        TCGA-CG-4466 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" 
       TCGA-CG-4469        TCGA-CG-4472        TCGA-CG-4474        TCGA-CG-4477 
  "4P LOSS MUTATED" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" 
       TCGA-CG-5716        TCGA-CG-5717        TCGA-CG-5718        TCGA-CG-5719 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-CG-5720        TCGA-CG-5721        TCGA-CG-5722        TCGA-CG-5723 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-CG-5724        TCGA-CG-5725        TCGA-CG-5726        TCGA-CG-5727 
"4P LOSS WILD-TYPE"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-CG-5728        TCGA-CG-5730        TCGA-CG-5732        TCGA-CG-5733 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-CG-5734        TCGA-D7-5577        TCGA-D7-5578        TCGA-D7-5579 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-D7-6518        TCGA-D7-6519        TCGA-D7-6520        TCGA-D7-6521 
"4P LOSS WILD-TYPE"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-D7-6522        TCGA-D7-6524        TCGA-D7-6525        TCGA-D7-6526 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-D7-6527        TCGA-D7-6528        TCGA-D7-6815        TCGA-D7-6817 
  "4P LOSS MUTATED"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-D7-6818        TCGA-D7-6820        TCGA-D7-6822        TCGA-EQ-5647 
"4P LOSS WILD-TYPE"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875        TCGA-FP-7735 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-FP-7829        TCGA-FP-7998        TCGA-IN-7806        TCGA-IN-7808 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-IP-7968 
"4P LOSS WILD-TYPE" 
       TCGA-B7-5816        TCGA-B7-5818        TCGA-BR-6452        TCGA-BR-6455 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-BR-6457        TCGA-BR-6458        TCGA-BR-6563        TCGA-BR-6564 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-BR-6565        TCGA-BR-6566        TCGA-BR-6705        TCGA-BR-6706 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-BR-6707        TCGA-BR-6709        TCGA-BR-6710        TCGA-BR-6801 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-BR-6802        TCGA-BR-6803        TCGA-BR-6852        TCGA-BR-7196 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-BR-7197        TCGA-BR-7703        TCGA-BR-7704        TCGA-BR-7707 
  "4P LOSS MUTATED" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-BR-7715        TCGA-BR-7716        TCGA-BR-7717        TCGA-BR-7722 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-BR-7723        TCGA-BR-7851        TCGA-BR-7901        TCGA-BR-7957 
  "4P LOSS MUTATED" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-CD-5798        TCGA-CD-5799        TCGA-CD-5800        TCGA-CD-5801 
"4P LOSS WILD-TYPE"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-CD-5802        TCGA-CD-5803        TCGA-CG-4300        TCGA-CG-4301 
  "4P LOSS MUTATED" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" 
       TCGA-CG-4304        TCGA-CG-4305        TCGA-CG-4306        TCGA-CG-4436 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-CG-4437        TCGA-CG-4438        TCGA-CG-4440        TCGA-CG-4441 
"4P LOSS WILD-TYPE"   "4P LOSS MUTATED"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" 
       TCGA-CG-4443        TCGA-CG-4444        TCGA-CG-4449        TCGA-CG-4455 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" 
       TCGA-CG-4460        TCGA-CG-4462        TCGA-CG-4465        TCGA-CG-4466 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" 
       TCGA-CG-4469        TCGA-CG-4472        TCGA-CG-4474        TCGA-CG-4477 
  "4P LOSS MUTATED" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" 
       TCGA-CG-5716        TCGA-CG-5717        TCGA-CG-5718        TCGA-CG-5719 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-CG-5720        TCGA-CG-5721        TCGA-CG-5722        TCGA-CG-5723 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-CG-5724        TCGA-CG-5725        TCGA-CG-5726        TCGA-CG-5727 
"4P LOSS WILD-TYPE"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-CG-5728        TCGA-CG-5730        TCGA-CG-5732        TCGA-CG-5733 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-CG-5734        TCGA-D7-5577        TCGA-D7-5578        TCGA-D7-5579 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-D7-6518        TCGA-D7-6519        TCGA-D7-6520        TCGA-D7-6521 
"4P LOSS WILD-TYPE"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-D7-6522        TCGA-D7-6524        TCGA-D7-6525        TCGA-D7-6526 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-D7-6527        TCGA-D7-6528        TCGA-D7-6815        TCGA-D7-6817 
  "4P LOSS MUTATED"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-D7-6818        TCGA-D7-6820        TCGA-D7-6822        TCGA-EQ-5647 
"4P LOSS WILD-TYPE"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875        TCGA-FP-7735 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-FP-7829        TCGA-FP-7998        TCGA-IN-7806        TCGA-IN-7808 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-IP-7968 
"4P LOSS WILD-TYPE" 
       TCGA-B7-5816        TCGA-B7-5818        TCGA-BR-6452        TCGA-BR-6455 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-BR-6457        TCGA-BR-6458        TCGA-BR-6563        TCGA-BR-6564 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-BR-6565        TCGA-BR-6566        TCGA-BR-6705        TCGA-BR-6706 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-BR-6707        TCGA-BR-6709        TCGA-BR-6710        TCGA-BR-6801 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-BR-6802        TCGA-BR-6803        TCGA-BR-6852        TCGA-BR-7196 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-BR-7197        TCGA-BR-7703        TCGA-BR-7704        TCGA-BR-7707 
  "4P LOSS MUTATED" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-BR-7715        TCGA-BR-7716        TCGA-BR-7717        TCGA-BR-7722 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-BR-7723        TCGA-BR-7851        TCGA-BR-7901        TCGA-BR-7957 
  "4P LOSS MUTATED" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-CD-5798        TCGA-CD-5799        TCGA-CD-5800        TCGA-CD-5801 
"4P LOSS WILD-TYPE"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-CD-5802        TCGA-CD-5803        TCGA-CG-4300        TCGA-CG-4301 
  "4P LOSS MUTATED" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" 
       TCGA-CG-4304        TCGA-CG-4305        TCGA-CG-4306        TCGA-CG-4436 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-CG-4437        TCGA-CG-4438        TCGA-CG-4440        TCGA-CG-4441 
"4P LOSS WILD-TYPE"   "4P LOSS MUTATED"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" 
       TCGA-CG-4443        TCGA-CG-4444        TCGA-CG-4449        TCGA-CG-4455 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" 
       TCGA-CG-4460        TCGA-CG-4462        TCGA-CG-4465        TCGA-CG-4466 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" 
       TCGA-CG-4469        TCGA-CG-4472        TCGA-CG-4474        TCGA-CG-4477 
  "4P LOSS MUTATED" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" 
       TCGA-CG-5716        TCGA-CG-5717        TCGA-CG-5718        TCGA-CG-5719 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-CG-5720        TCGA-CG-5721        TCGA-CG-5722        TCGA-CG-5723 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-CG-5724        TCGA-CG-5725        TCGA-CG-5726        TCGA-CG-5727 
"4P LOSS WILD-TYPE"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-CG-5728        TCGA-CG-5730        TCGA-CG-5732        TCGA-CG-5733 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-CG-5734        TCGA-D7-5577        TCGA-D7-5578        TCGA-D7-5579 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-D7-6518        TCGA-D7-6519        TCGA-D7-6520        TCGA-D7-6521 
"4P LOSS WILD-TYPE"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-D7-6522        TCGA-D7-6524        TCGA-D7-6525        TCGA-D7-6526 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-D7-6527        TCGA-D7-6528        TCGA-D7-6815        TCGA-D7-6817 
  "4P LOSS MUTATED"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-D7-6818        TCGA-D7-6820        TCGA-D7-6822        TCGA-EQ-5647 
"4P LOSS WILD-TYPE"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875        TCGA-FP-7735 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-FP-7829        TCGA-FP-7998        TCGA-IN-7806        TCGA-IN-7808 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-IP-7968 
"4P LOSS WILD-TYPE" 
[1] "hr=" "1.1"
D41V2, continuous
D41V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED      6   17
  4P LOSS WILD-TYPE   54   81
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  FEMALE               6                54
  MALE                17                81
D41V4, multiclass
D41V5, multiclass
    clus
vv   4P LOSS MUTATED 4P LOSS WILD-TYPE
  T1               0                 6
  T2              12                40
  T3               9                52
  T4               1                17
D41V6, multiclass
    clus
vv   4P LOSS MUTATED 4P LOSS WILD-TYPE
  N0               7                37
  N1               7                50
  N2               3                21
  N3               3                12
D41V7, multiclass
    clus
vv   4P LOSS MUTATED 4P LOSS WILD-TYPE
  M0              22               112
  M1               1                15
  MX               0                 8
D41V8, multiclass
     clus
vv    4P LOSS MUTATED 4P LOSS WILD-TYPE
  I                 4                20
  II                9                28
  III               3                40
  IV                4                22
D41V9, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED      2   21
  4P LOSS WILD-TYPE    3  132
     clus
vv    4P LOSS MUTATED 4P LOSS WILD-TYPE
  NO                2                 3
  YES              21               132
D41V10, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED      2   21
  4P LOSS WILD-TYPE    8  127
     clus
vv    4P LOSS MUTATED 4P LOSS WILD-TYPE
  NO                2                 8
  YES              21               127

Clustering(42) Variable = 4q loss mutation analysis
D42V1, survival
                   sevent
clus2                0  1
  4Q LOSS MUTATED   14  2
  4Q LOSS WILD-TYPE 76 13
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               16                89 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
                2                13 
$`4Q LOSS MUTATED`
TCGA-BR-6458 TCGA-BR-7723 TCGA-CD-5799 TCGA-CD-5802 TCGA-CG-4438 TCGA-CG-4440 
        1.35         4.54         0.69         0.30        54.05         4.01 
TCGA-CG-4449 TCGA-CG-4466 TCGA-CG-4477 TCGA-CG-5725 TCGA-CG-5730 TCGA-D7-6519 
       19.07        18.94         1.02        15.02         4.01        15.65 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6820 
        4.14         1.68         3.65         2.93 

$`4Q LOSS WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-6452 TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6563 
        5.62         0.10         0.95         1.41         1.35         0.85 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
        0.82         0.62         0.62         1.71         2.17         0.99 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
        1.22         0.66         1.12         0.76         0.66         0.26 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
        1.22         1.48         0.46         1.25         0.13         1.05 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 
        0.82         0.69         0.16         0.99         0.95         0.69 
TCGA-CD-5798 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5803 TCGA-CG-4300 TCGA-CG-4301 
        0.82         0.36         0.49         0.07        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4441 
       27.02        15.95         1.02        52.96         8.05        14.01 
TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4455 TCGA-CG-4460 TCGA-CG-4462 TCGA-CG-4465 
       29.98        47.05        12.03        21.99         1.02         8.98 
TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4474 TCGA-CG-5716 TCGA-CG-5717 TCGA-CG-5718 
        7.07        12.00         1.02         1.02         6.94         1.02 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
        1.02         0.99         5.98         0.95        70.06        12.03 
TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       28.96        31.04        65.10        55.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6520 TCGA-D7-6521 
        8.65         3.58         4.54         9.80         9.63         8.19 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6817 TCGA-D7-6818 
        6.90         0.69         5.95         6.61         4.70         4.04 
TCGA-D7-6822 TCGA-EQ-5647 TCGA-F1-6177 TCGA-F1-6874 TCGA-F1-6875 TCGA-FP-7735 
        4.27         0.62         6.54         2.01        72.23         0.39 
TCGA-FP-7829 TCGA-FP-7998 TCGA-IN-7806 TCGA-IN-7808 TCGA-IP-7968 
        0.20         3.58         6.87         3.55         2.53 

  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
             0.30              0.07 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
            54.05             72.23 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
             4.01              2.01 
[1] "0.3 - 54.0 (4.0)" "0.1 - 72.2 (2.0)"
       TCGA-B7-5816        TCGA-B7-5818        TCGA-BR-6452        TCGA-BR-6455 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-BR-6457        TCGA-BR-6458        TCGA-BR-6563        TCGA-BR-6564 
"4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-BR-6565        TCGA-BR-6566        TCGA-BR-6705        TCGA-BR-6706 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-BR-6707        TCGA-BR-6709        TCGA-BR-6710        TCGA-BR-6801 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-BR-6802        TCGA-BR-6803        TCGA-BR-6852        TCGA-BR-7196 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-BR-7197        TCGA-BR-7703        TCGA-BR-7704        TCGA-BR-7707 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-BR-7715        TCGA-BR-7716        TCGA-BR-7717        TCGA-BR-7722 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-BR-7723        TCGA-BR-7851        TCGA-BR-7901        TCGA-BR-7957 
  "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-CD-5798        TCGA-CD-5799        TCGA-CD-5800        TCGA-CD-5801 
"4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-CD-5802        TCGA-CD-5803        TCGA-CG-4300        TCGA-CG-4301 
  "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-CG-4304        TCGA-CG-4305        TCGA-CG-4306        TCGA-CG-4436 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-CG-4437        TCGA-CG-4438        TCGA-CG-4440        TCGA-CG-4441 
"4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" 
       TCGA-CG-4443        TCGA-CG-4444        TCGA-CG-4449        TCGA-CG-4455 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" 
       TCGA-CG-4460        TCGA-CG-4462        TCGA-CG-4465        TCGA-CG-4466 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" 
       TCGA-CG-4469        TCGA-CG-4472        TCGA-CG-4474        TCGA-CG-4477 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" 
       TCGA-CG-5716        TCGA-CG-5717        TCGA-CG-5718        TCGA-CG-5719 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-CG-5720        TCGA-CG-5721        TCGA-CG-5722        TCGA-CG-5723 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-CG-5724        TCGA-CG-5725        TCGA-CG-5726        TCGA-CG-5727 
"4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-CG-5728        TCGA-CG-5730        TCGA-CG-5732        TCGA-CG-5733 
"4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-CG-5734        TCGA-D7-5577        TCGA-D7-5578        TCGA-D7-5579 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-D7-6518        TCGA-D7-6519        TCGA-D7-6520        TCGA-D7-6521 
"4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-D7-6522        TCGA-D7-6524        TCGA-D7-6525        TCGA-D7-6526 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-D7-6527        TCGA-D7-6528        TCGA-D7-6815        TCGA-D7-6817 
  "4Q LOSS MUTATED"   "4Q LOSS MUTATED"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" 
       TCGA-D7-6818        TCGA-D7-6820        TCGA-D7-6822        TCGA-EQ-5647 
"4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875        TCGA-FP-7735 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-FP-7829        TCGA-FP-7998        TCGA-IN-7806        TCGA-IN-7808 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-IP-7968 
"4Q LOSS WILD-TYPE" 
       TCGA-B7-5816        TCGA-B7-5818        TCGA-BR-6452        TCGA-BR-6455 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-BR-6457        TCGA-BR-6458        TCGA-BR-6563        TCGA-BR-6564 
"4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-BR-6565        TCGA-BR-6566        TCGA-BR-6705        TCGA-BR-6706 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-BR-6707        TCGA-BR-6709        TCGA-BR-6710        TCGA-BR-6801 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-BR-6802        TCGA-BR-6803        TCGA-BR-6852        TCGA-BR-7196 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-BR-7197        TCGA-BR-7703        TCGA-BR-7704        TCGA-BR-7707 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-BR-7715        TCGA-BR-7716        TCGA-BR-7717        TCGA-BR-7722 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-BR-7723        TCGA-BR-7851        TCGA-BR-7901        TCGA-BR-7957 
  "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-CD-5798        TCGA-CD-5799        TCGA-CD-5800        TCGA-CD-5801 
"4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-CD-5802        TCGA-CD-5803        TCGA-CG-4300        TCGA-CG-4301 
  "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-CG-4304        TCGA-CG-4305        TCGA-CG-4306        TCGA-CG-4436 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-CG-4437        TCGA-CG-4438        TCGA-CG-4440        TCGA-CG-4441 
"4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" 
       TCGA-CG-4443        TCGA-CG-4444        TCGA-CG-4449        TCGA-CG-4455 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" 
       TCGA-CG-4460        TCGA-CG-4462        TCGA-CG-4465        TCGA-CG-4466 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" 
       TCGA-CG-4469        TCGA-CG-4472        TCGA-CG-4474        TCGA-CG-4477 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" 
       TCGA-CG-5716        TCGA-CG-5717        TCGA-CG-5718        TCGA-CG-5719 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-CG-5720        TCGA-CG-5721        TCGA-CG-5722        TCGA-CG-5723 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-CG-5724        TCGA-CG-5725        TCGA-CG-5726        TCGA-CG-5727 
"4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-CG-5728        TCGA-CG-5730        TCGA-CG-5732        TCGA-CG-5733 
"4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-CG-5734        TCGA-D7-5577        TCGA-D7-5578        TCGA-D7-5579 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-D7-6518        TCGA-D7-6519        TCGA-D7-6520        TCGA-D7-6521 
"4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-D7-6522        TCGA-D7-6524        TCGA-D7-6525        TCGA-D7-6526 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-D7-6527        TCGA-D7-6528        TCGA-D7-6815        TCGA-D7-6817 
  "4Q LOSS MUTATED"   "4Q LOSS MUTATED"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" 
       TCGA-D7-6818        TCGA-D7-6820        TCGA-D7-6822        TCGA-EQ-5647 
"4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875        TCGA-FP-7735 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-FP-7829        TCGA-FP-7998        TCGA-IN-7806        TCGA-IN-7808 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-IP-7968 
"4Q LOSS WILD-TYPE" 
       TCGA-B7-5816        TCGA-B7-5818        TCGA-BR-6452        TCGA-BR-6455 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-BR-6457        TCGA-BR-6458        TCGA-BR-6563        TCGA-BR-6564 
"4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-BR-6565        TCGA-BR-6566        TCGA-BR-6705        TCGA-BR-6706 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-BR-6707        TCGA-BR-6709        TCGA-BR-6710        TCGA-BR-6801 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-BR-6802        TCGA-BR-6803        TCGA-BR-6852        TCGA-BR-7196 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-BR-7197        TCGA-BR-7703        TCGA-BR-7704        TCGA-BR-7707 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-BR-7715        TCGA-BR-7716        TCGA-BR-7717        TCGA-BR-7722 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-BR-7723        TCGA-BR-7851        TCGA-BR-7901        TCGA-BR-7957 
  "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-CD-5798        TCGA-CD-5799        TCGA-CD-5800        TCGA-CD-5801 
"4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-CD-5802        TCGA-CD-5803        TCGA-CG-4300        TCGA-CG-4301 
  "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-CG-4304        TCGA-CG-4305        TCGA-CG-4306        TCGA-CG-4436 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-CG-4437        TCGA-CG-4438        TCGA-CG-4440        TCGA-CG-4441 
"4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" 
       TCGA-CG-4443        TCGA-CG-4444        TCGA-CG-4449        TCGA-CG-4455 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" 
       TCGA-CG-4460        TCGA-CG-4462        TCGA-CG-4465        TCGA-CG-4466 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" 
       TCGA-CG-4469        TCGA-CG-4472        TCGA-CG-4474        TCGA-CG-4477 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" 
       TCGA-CG-5716        TCGA-CG-5717        TCGA-CG-5718        TCGA-CG-5719 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-CG-5720        TCGA-CG-5721        TCGA-CG-5722        TCGA-CG-5723 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-CG-5724        TCGA-CG-5725        TCGA-CG-5726        TCGA-CG-5727 
"4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-CG-5728        TCGA-CG-5730        TCGA-CG-5732        TCGA-CG-5733 
"4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-CG-5734        TCGA-D7-5577        TCGA-D7-5578        TCGA-D7-5579 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-D7-6518        TCGA-D7-6519        TCGA-D7-6520        TCGA-D7-6521 
"4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-D7-6522        TCGA-D7-6524        TCGA-D7-6525        TCGA-D7-6526 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-D7-6527        TCGA-D7-6528        TCGA-D7-6815        TCGA-D7-6817 
  "4Q LOSS MUTATED"   "4Q LOSS MUTATED"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" 
       TCGA-D7-6818        TCGA-D7-6820        TCGA-D7-6822        TCGA-EQ-5647 
"4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875        TCGA-FP-7735 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-FP-7829        TCGA-FP-7998        TCGA-IN-7806        TCGA-IN-7808 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-IP-7968 
"4Q LOSS WILD-TYPE" 
[1] "hr=" "1.2"
D42V2, continuous
D42V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED      9   13
  4Q LOSS WILD-TYPE   51   85
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  FEMALE               9                51
  MALE                13                85
D42V4, multiclass
D42V5, multiclass
    clus
vv   4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  T1               0                 6
  T2              13                39
  T3               7                54
  T4               1                17
D42V6, multiclass
    clus
vv   4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  N0               5                39
  N1               9                48
  N2               3                21
  N3               2                13
D42V7, multiclass
    clus
vv   4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  M0              20               114
  M1               2                14
  MX               0                 8
D42V8, multiclass
     clus
vv    4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  I                 4                20
  II                8                29
  III               3                40
  IV                4                22
D42V9, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED      2   20
  4Q LOSS WILD-TYPE    3  133
     clus
vv    4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  NO                2                 3
  YES              20               133
D42V10, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED      2   20
  4Q LOSS WILD-TYPE    8  128
     clus
vv    4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  NO                2                 8
  YES              20               128

Clustering(43) Variable = 5p loss mutation analysis
D43V1, survival
                   sevent
clus2                0  1
  5P LOSS MUTATED    6  0
  5P LOSS WILD-TYPE 84 15
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
                6                99 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
                0                15 
$`5P LOSS MUTATED`
TCGA-BR-6458 TCGA-CD-5800 TCGA-CG-4449 TCGA-D7-6520 TCGA-D7-6815 TCGA-IN-7806 
        1.35         0.36        19.07         9.63         3.65         6.87 

$`5P LOSS WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-6452 TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6563 
        5.62         0.10         0.95         1.41         1.35         0.85 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
        0.82         0.62         0.62         1.71         2.17         0.99 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
        1.22         0.66         1.12         0.76         0.66         0.26 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
        1.22         1.48         0.46         1.25         0.13         1.05 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 
        0.82         0.69         0.16         4.54         0.99         0.95 
TCGA-BR-7957 TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
        0.69         0.82         0.69         0.49         0.30         0.07 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02        52.96 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 
        8.05        54.05         4.01        14.01        29.98        47.05 
TCGA-CG-4455 TCGA-CG-4460 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       12.03        21.99         1.02         8.98        18.94         7.07 
TCGA-CG-4472 TCGA-CG-4474 TCGA-CG-4477 TCGA-CG-5716 TCGA-CG-5717 TCGA-CG-5718 
       12.00         1.02         1.02         1.02         6.94         1.02 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
        1.02         0.99         5.98         0.95        70.06        12.03 
TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       15.02        28.96        31.04        65.10         4.01        55.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99         8.65         3.58         4.54         9.80 
TCGA-D7-6519 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       15.65         8.19         6.90         0.69         5.95         6.61 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
        4.14         1.68         4.70         4.04         2.93         4.27 
TCGA-EQ-5647 TCGA-F1-6177 TCGA-F1-6874 TCGA-F1-6875 TCGA-FP-7735 TCGA-FP-7829 
        0.62         6.54         2.01        72.23         0.39         0.20 
TCGA-FP-7998 TCGA-IN-7808 TCGA-IP-7968 
        3.58         3.55         2.53 

  5P LOSS MUTATED 5P LOSS WILD-TYPE 
             0.36              0.07 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
            19.07             72.23 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
             5.26              2.53 
[1] "0.4 - 19.1 (5.3)" "0.1 - 72.2 (2.5)"
       TCGA-B7-5816        TCGA-B7-5818        TCGA-BR-6452        TCGA-BR-6455 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-BR-6457        TCGA-BR-6458        TCGA-BR-6563        TCGA-BR-6564 
"5P LOSS WILD-TYPE"   "5P LOSS MUTATED" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-BR-6565        TCGA-BR-6566        TCGA-BR-6705        TCGA-BR-6706 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-BR-6707        TCGA-BR-6709        TCGA-BR-6710        TCGA-BR-6801 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-BR-6802        TCGA-BR-6803        TCGA-BR-6852        TCGA-BR-7196 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-BR-7197        TCGA-BR-7703        TCGA-BR-7704        TCGA-BR-7707 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-BR-7715        TCGA-BR-7716        TCGA-BR-7717        TCGA-BR-7722 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-BR-7723        TCGA-BR-7851        TCGA-BR-7901        TCGA-BR-7957 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-CD-5798        TCGA-CD-5799        TCGA-CD-5800        TCGA-CD-5801 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE"   "5P LOSS MUTATED" "5P LOSS WILD-TYPE" 
       TCGA-CD-5802        TCGA-CD-5803        TCGA-CG-4300        TCGA-CG-4301 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-CG-4304        TCGA-CG-4305        TCGA-CG-4306        TCGA-CG-4436 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-CG-4437        TCGA-CG-4438        TCGA-CG-4440        TCGA-CG-4441 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-CG-4443        TCGA-CG-4444        TCGA-CG-4449        TCGA-CG-4455 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE"   "5P LOSS MUTATED" "5P LOSS WILD-TYPE" 
       TCGA-CG-4460        TCGA-CG-4462        TCGA-CG-4465        TCGA-CG-4466 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-CG-4469        TCGA-CG-4472        TCGA-CG-4474        TCGA-CG-4477 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-CG-5716        TCGA-CG-5717        TCGA-CG-5718        TCGA-CG-5719 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-CG-5720        TCGA-CG-5721        TCGA-CG-5722        TCGA-CG-5723 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-CG-5724        TCGA-CG-5725        TCGA-CG-5726        TCGA-CG-5727 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-CG-5728        TCGA-CG-5730        TCGA-CG-5732        TCGA-CG-5733 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-CG-5734        TCGA-D7-5577        TCGA-D7-5578        TCGA-D7-5579 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-D7-6518        TCGA-D7-6519        TCGA-D7-6520        TCGA-D7-6521 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE"   "5P LOSS MUTATED" "5P LOSS WILD-TYPE" 
       TCGA-D7-6522        TCGA-D7-6524        TCGA-D7-6525        TCGA-D7-6526 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-D7-6527        TCGA-D7-6528        TCGA-D7-6815        TCGA-D7-6817 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE"   "5P LOSS MUTATED" "5P LOSS WILD-TYPE" 
       TCGA-D7-6818        TCGA-D7-6820        TCGA-D7-6822        TCGA-EQ-5647 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875        TCGA-FP-7735 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-FP-7829        TCGA-FP-7998        TCGA-IN-7806        TCGA-IN-7808 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE"   "5P LOSS MUTATED" "5P LOSS WILD-TYPE" 
       TCGA-IP-7968 
"5P LOSS WILD-TYPE" 
       TCGA-B7-5816        TCGA-B7-5818        TCGA-BR-6452        TCGA-BR-6455 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-BR-6457        TCGA-BR-6458        TCGA-BR-6563        TCGA-BR-6564 
"5P LOSS WILD-TYPE"   "5P LOSS MUTATED" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-BR-6565        TCGA-BR-6566        TCGA-BR-6705        TCGA-BR-6706 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-BR-6707        TCGA-BR-6709        TCGA-BR-6710        TCGA-BR-6801 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-BR-6802        TCGA-BR-6803        TCGA-BR-6852        TCGA-BR-7196 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-BR-7197        TCGA-BR-7703        TCGA-BR-7704        TCGA-BR-7707 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-BR-7715        TCGA-BR-7716        TCGA-BR-7717        TCGA-BR-7722 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-BR-7723        TCGA-BR-7851        TCGA-BR-7901        TCGA-BR-7957 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-CD-5798        TCGA-CD-5799        TCGA-CD-5800        TCGA-CD-5801 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE"   "5P LOSS MUTATED" "5P LOSS WILD-TYPE" 
       TCGA-CD-5802        TCGA-CD-5803        TCGA-CG-4300        TCGA-CG-4301 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-CG-4304        TCGA-CG-4305        TCGA-CG-4306        TCGA-CG-4436 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-CG-4437        TCGA-CG-4438        TCGA-CG-4440        TCGA-CG-4441 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-CG-4443        TCGA-CG-4444        TCGA-CG-4449        TCGA-CG-4455 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE"   "5P LOSS MUTATED" "5P LOSS WILD-TYPE" 
       TCGA-CG-4460        TCGA-CG-4462        TCGA-CG-4465        TCGA-CG-4466 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-CG-4469        TCGA-CG-4472        TCGA-CG-4474        TCGA-CG-4477 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-CG-5716        TCGA-CG-5717        TCGA-CG-5718        TCGA-CG-5719 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-CG-5720        TCGA-CG-5721        TCGA-CG-5722        TCGA-CG-5723 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-CG-5724        TCGA-CG-5725        TCGA-CG-5726        TCGA-CG-5727 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-CG-5728        TCGA-CG-5730        TCGA-CG-5732        TCGA-CG-5733 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-CG-5734        TCGA-D7-5577        TCGA-D7-5578        TCGA-D7-5579 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-D7-6518        TCGA-D7-6519        TCGA-D7-6520        TCGA-D7-6521 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE"   "5P LOSS MUTATED" "5P LOSS WILD-TYPE" 
       TCGA-D7-6522        TCGA-D7-6524        TCGA-D7-6525        TCGA-D7-6526 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-D7-6527        TCGA-D7-6528        TCGA-D7-6815        TCGA-D7-6817 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE"   "5P LOSS MUTATED" "5P LOSS WILD-TYPE" 
       TCGA-D7-6818        TCGA-D7-6820        TCGA-D7-6822        TCGA-EQ-5647 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875        TCGA-FP-7735 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-FP-7829        TCGA-FP-7998        TCGA-IN-7806        TCGA-IN-7808 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE"   "5P LOSS MUTATED" "5P LOSS WILD-TYPE" 
       TCGA-IP-7968 
"5P LOSS WILD-TYPE" 
       TCGA-B7-5816        TCGA-B7-5818        TCGA-BR-6452        TCGA-BR-6455 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-BR-6457        TCGA-BR-6458        TCGA-BR-6563        TCGA-BR-6564 
"5P LOSS WILD-TYPE"   "5P LOSS MUTATED" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-BR-6565        TCGA-BR-6566        TCGA-BR-6705        TCGA-BR-6706 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-BR-6707        TCGA-BR-6709        TCGA-BR-6710        TCGA-BR-6801 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-BR-6802        TCGA-BR-6803        TCGA-BR-6852        TCGA-BR-7196 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-BR-7197        TCGA-BR-7703        TCGA-BR-7704        TCGA-BR-7707 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-BR-7715        TCGA-BR-7716        TCGA-BR-7717        TCGA-BR-7722 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-BR-7723        TCGA-BR-7851        TCGA-BR-7901        TCGA-BR-7957 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-CD-5798        TCGA-CD-5799        TCGA-CD-5800        TCGA-CD-5801 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE"   "5P LOSS MUTATED" "5P LOSS WILD-TYPE" 
       TCGA-CD-5802        TCGA-CD-5803        TCGA-CG-4300        TCGA-CG-4301 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-CG-4304        TCGA-CG-4305        TCGA-CG-4306        TCGA-CG-4436 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-CG-4437        TCGA-CG-4438        TCGA-CG-4440        TCGA-CG-4441 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-CG-4443        TCGA-CG-4444        TCGA-CG-4449        TCGA-CG-4455 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE"   "5P LOSS MUTATED" "5P LOSS WILD-TYPE" 
       TCGA-CG-4460        TCGA-CG-4462        TCGA-CG-4465        TCGA-CG-4466 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-CG-4469        TCGA-CG-4472        TCGA-CG-4474        TCGA-CG-4477 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-CG-5716        TCGA-CG-5717        TCGA-CG-5718        TCGA-CG-5719 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-CG-5720        TCGA-CG-5721        TCGA-CG-5722        TCGA-CG-5723 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-CG-5724        TCGA-CG-5725        TCGA-CG-5726        TCGA-CG-5727 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-CG-5728        TCGA-CG-5730        TCGA-CG-5732        TCGA-CG-5733 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-CG-5734        TCGA-D7-5577        TCGA-D7-5578        TCGA-D7-5579 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-D7-6518        TCGA-D7-6519        TCGA-D7-6520        TCGA-D7-6521 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE"   "5P LOSS MUTATED" "5P LOSS WILD-TYPE" 
       TCGA-D7-6522        TCGA-D7-6524        TCGA-D7-6525        TCGA-D7-6526 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-D7-6527        TCGA-D7-6528        TCGA-D7-6815        TCGA-D7-6817 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE"   "5P LOSS MUTATED" "5P LOSS WILD-TYPE" 
       TCGA-D7-6818        TCGA-D7-6820        TCGA-D7-6822        TCGA-EQ-5647 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875        TCGA-FP-7735 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-FP-7829        TCGA-FP-7998        TCGA-IN-7806        TCGA-IN-7808 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE"   "5P LOSS MUTATED" "5P LOSS WILD-TYPE" 
       TCGA-IP-7968 
"5P LOSS WILD-TYPE" 
[1] "hr="     "2.7e+07"
D43V2, continuous
D43V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED      3    5
  5P LOSS WILD-TYPE   57   93
        clus
vv       5P LOSS MUTATED 5P LOSS WILD-TYPE
  FEMALE               3                57
  MALE                 5                93
D43V4, multiclass
D43V5, multiclass
    clus
vv   5P LOSS MUTATED 5P LOSS WILD-TYPE
  T1               0                 6
  T2               3                49
  T3               3                58
  T4               0                18
D43V6, multiclass
    clus
vv   5P LOSS MUTATED 5P LOSS WILD-TYPE
  N0               1                43
  N1               4                53
  N2               2                22
  N3               0                15
D43V7, multiclass
    clus
vv   5P LOSS MUTATED 5P LOSS WILD-TYPE
  M0               8               126
  M1               0                16
  MX               0                 8
D43V8, multiclass
     clus
vv    5P LOSS MUTATED 5P LOSS WILD-TYPE
  I                 0                24
  II                3                34
  III               3                40
  IV                0                26
D43V9, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED      0    8
  5P LOSS WILD-TYPE    5  145
     clus
vv    5P LOSS MUTATED 5P LOSS WILD-TYPE
  NO                0                 5
  YES               8               145
D43V10, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED      0    8
  5P LOSS WILD-TYPE   10  140
     clus
vv    5P LOSS MUTATED 5P LOSS WILD-TYPE
  NO                0                10
  YES               8               140

Clustering(44) Variable = 5q loss mutation analysis
D44V1, survival
                   sevent
clus2                0  1
  5Q LOSS MUTATED   13  1
  5Q LOSS WILD-TYPE 77 14
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               14                91 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
                1                14 
$`5Q LOSS MUTATED`
TCGA-BR-6458 TCGA-BR-7197 TCGA-BR-7901 TCGA-CD-5800 TCGA-CG-4304 TCGA-CG-4449 
        1.35         1.48         0.95         0.36        27.02        19.07 
TCGA-CG-5718 TCGA-D7-6520 TCGA-D7-6527 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6822 
        1.02         9.63         4.14         3.65         4.70         4.27 
TCGA-F1-6875 TCGA-IN-7806 
       72.23         6.87 

$`5Q LOSS WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-6452 TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6563 
        5.62         0.10         0.95         1.41         1.35         0.85 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
        0.82         0.62         0.62         1.71         2.17         0.99 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
        1.22         0.66         1.12         0.76         0.66         0.26 
TCGA-BR-7196 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 
        1.22         0.46         1.25         0.13         1.05         0.82 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7957 TCGA-CD-5798 
        0.69         0.16         4.54         0.99         0.69         0.82 
TCGA-CD-5799 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CG-4300 TCGA-CG-4301 
        0.69         0.49         0.30         0.07        20.02         3.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02        52.96         8.05        54.05         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4455 TCGA-CG-4460 TCGA-CG-4462 
       14.01        29.98        47.05        12.03        21.99         1.02 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4474 TCGA-CG-4477 
        8.98        18.94         7.07        12.00         1.02         1.02 
TCGA-CG-5716 TCGA-CG-5717 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        1.02         6.94         1.02         0.99         5.98         0.95 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 
       70.06        12.03        15.02        28.96        31.04        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        55.04        21.07         7.99         8.65         3.58 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
        4.54         9.80        15.65         8.19         6.90         0.69 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6528 TCGA-D7-6818 TCGA-D7-6820 TCGA-EQ-5647 
        5.95         6.61         1.68         4.04         2.93         0.62 
TCGA-F1-6177 TCGA-F1-6874 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7998 TCGA-IN-7808 
        6.54         2.01         0.39         0.20         3.58         3.55 
TCGA-IP-7968 
        2.53 

  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
             0.36              0.07 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
            72.23             70.06 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
            4.205             2.170 
[1] "0.4 - 72.2 (4.2)" "0.1 - 70.1 (2.2)"
       TCGA-B7-5816        TCGA-B7-5818        TCGA-BR-6452        TCGA-BR-6455 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-BR-6457        TCGA-BR-6458        TCGA-BR-6563        TCGA-BR-6564 
"5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-BR-6565        TCGA-BR-6566        TCGA-BR-6705        TCGA-BR-6706 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-BR-6707        TCGA-BR-6709        TCGA-BR-6710        TCGA-BR-6801 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-BR-6802        TCGA-BR-6803        TCGA-BR-6852        TCGA-BR-7196 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-BR-7197        TCGA-BR-7703        TCGA-BR-7704        TCGA-BR-7707 
  "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-BR-7715        TCGA-BR-7716        TCGA-BR-7717        TCGA-BR-7722 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-BR-7723        TCGA-BR-7851        TCGA-BR-7901        TCGA-BR-7957 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" 
       TCGA-CD-5798        TCGA-CD-5799        TCGA-CD-5800        TCGA-CD-5801 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" 
       TCGA-CD-5802        TCGA-CD-5803        TCGA-CG-4300        TCGA-CG-4301 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-CG-4304        TCGA-CG-4305        TCGA-CG-4306        TCGA-CG-4436 
  "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-CG-4437        TCGA-CG-4438        TCGA-CG-4440        TCGA-CG-4441 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-CG-4443        TCGA-CG-4444        TCGA-CG-4449        TCGA-CG-4455 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" 
       TCGA-CG-4460        TCGA-CG-4462        TCGA-CG-4465        TCGA-CG-4466 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-CG-4469        TCGA-CG-4472        TCGA-CG-4474        TCGA-CG-4477 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-CG-5716        TCGA-CG-5717        TCGA-CG-5718        TCGA-CG-5719 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" 
       TCGA-CG-5720        TCGA-CG-5721        TCGA-CG-5722        TCGA-CG-5723 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-CG-5724        TCGA-CG-5725        TCGA-CG-5726        TCGA-CG-5727 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-CG-5728        TCGA-CG-5730        TCGA-CG-5732        TCGA-CG-5733 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-CG-5734        TCGA-D7-5577        TCGA-D7-5578        TCGA-D7-5579 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-D7-6518        TCGA-D7-6519        TCGA-D7-6520        TCGA-D7-6521 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" 
       TCGA-D7-6522        TCGA-D7-6524        TCGA-D7-6525        TCGA-D7-6526 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-D7-6527        TCGA-D7-6528        TCGA-D7-6815        TCGA-D7-6817 
  "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED"   "5Q LOSS MUTATED" 
       TCGA-D7-6818        TCGA-D7-6820        TCGA-D7-6822        TCGA-EQ-5647 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" 
       TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875        TCGA-FP-7735 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" 
       TCGA-FP-7829        TCGA-FP-7998        TCGA-IN-7806        TCGA-IN-7808 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" 
       TCGA-IP-7968 
"5Q LOSS WILD-TYPE" 
       TCGA-B7-5816        TCGA-B7-5818        TCGA-BR-6452        TCGA-BR-6455 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-BR-6457        TCGA-BR-6458        TCGA-BR-6563        TCGA-BR-6564 
"5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-BR-6565        TCGA-BR-6566        TCGA-BR-6705        TCGA-BR-6706 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-BR-6707        TCGA-BR-6709        TCGA-BR-6710        TCGA-BR-6801 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-BR-6802        TCGA-BR-6803        TCGA-BR-6852        TCGA-BR-7196 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-BR-7197        TCGA-BR-7703        TCGA-BR-7704        TCGA-BR-7707 
  "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-BR-7715        TCGA-BR-7716        TCGA-BR-7717        TCGA-BR-7722 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-BR-7723        TCGA-BR-7851        TCGA-BR-7901        TCGA-BR-7957 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" 
       TCGA-CD-5798        TCGA-CD-5799        TCGA-CD-5800        TCGA-CD-5801 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" 
       TCGA-CD-5802        TCGA-CD-5803        TCGA-CG-4300        TCGA-CG-4301 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-CG-4304        TCGA-CG-4305        TCGA-CG-4306        TCGA-CG-4436 
  "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-CG-4437        TCGA-CG-4438        TCGA-CG-4440        TCGA-CG-4441 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-CG-4443        TCGA-CG-4444        TCGA-CG-4449        TCGA-CG-4455 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" 
       TCGA-CG-4460        TCGA-CG-4462        TCGA-CG-4465        TCGA-CG-4466 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-CG-4469        TCGA-CG-4472        TCGA-CG-4474        TCGA-CG-4477 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-CG-5716        TCGA-CG-5717        TCGA-CG-5718        TCGA-CG-5719 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" 
       TCGA-CG-5720        TCGA-CG-5721        TCGA-CG-5722        TCGA-CG-5723 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-CG-5724        TCGA-CG-5725        TCGA-CG-5726        TCGA-CG-5727 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-CG-5728        TCGA-CG-5730        TCGA-CG-5732        TCGA-CG-5733 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-CG-5734        TCGA-D7-5577        TCGA-D7-5578        TCGA-D7-5579 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-D7-6518        TCGA-D7-6519        TCGA-D7-6520        TCGA-D7-6521 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" 
       TCGA-D7-6522        TCGA-D7-6524        TCGA-D7-6525        TCGA-D7-6526 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-D7-6527        TCGA-D7-6528        TCGA-D7-6815        TCGA-D7-6817 
  "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED"   "5Q LOSS MUTATED" 
       TCGA-D7-6818        TCGA-D7-6820        TCGA-D7-6822        TCGA-EQ-5647 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" 
       TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875        TCGA-FP-7735 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" 
       TCGA-FP-7829        TCGA-FP-7998        TCGA-IN-7806        TCGA-IN-7808 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" 
       TCGA-IP-7968 
"5Q LOSS WILD-TYPE" 
       TCGA-B7-5816        TCGA-B7-5818        TCGA-BR-6452        TCGA-BR-6455 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-BR-6457        TCGA-BR-6458        TCGA-BR-6563        TCGA-BR-6564 
"5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-BR-6565        TCGA-BR-6566        TCGA-BR-6705        TCGA-BR-6706 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-BR-6707        TCGA-BR-6709        TCGA-BR-6710        TCGA-BR-6801 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-BR-6802        TCGA-BR-6803        TCGA-BR-6852        TCGA-BR-7196 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-BR-7197        TCGA-BR-7703        TCGA-BR-7704        TCGA-BR-7707 
  "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-BR-7715        TCGA-BR-7716        TCGA-BR-7717        TCGA-BR-7722 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-BR-7723        TCGA-BR-7851        TCGA-BR-7901        TCGA-BR-7957 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" 
       TCGA-CD-5798        TCGA-CD-5799        TCGA-CD-5800        TCGA-CD-5801 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" 
       TCGA-CD-5802        TCGA-CD-5803        TCGA-CG-4300        TCGA-CG-4301 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-CG-4304        TCGA-CG-4305        TCGA-CG-4306        TCGA-CG-4436 
  "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-CG-4437        TCGA-CG-4438        TCGA-CG-4440        TCGA-CG-4441 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-CG-4443        TCGA-CG-4444        TCGA-CG-4449        TCGA-CG-4455 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" 
       TCGA-CG-4460        TCGA-CG-4462        TCGA-CG-4465        TCGA-CG-4466 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-CG-4469        TCGA-CG-4472        TCGA-CG-4474        TCGA-CG-4477 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-CG-5716        TCGA-CG-5717        TCGA-CG-5718        TCGA-CG-5719 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" 
       TCGA-CG-5720        TCGA-CG-5721        TCGA-CG-5722        TCGA-CG-5723 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-CG-5724        TCGA-CG-5725        TCGA-CG-5726        TCGA-CG-5727 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-CG-5728        TCGA-CG-5730        TCGA-CG-5732        TCGA-CG-5733 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-CG-5734        TCGA-D7-5577        TCGA-D7-5578        TCGA-D7-5579 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-D7-6518        TCGA-D7-6519        TCGA-D7-6520        TCGA-D7-6521 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" 
       TCGA-D7-6522        TCGA-D7-6524        TCGA-D7-6525        TCGA-D7-6526 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-D7-6527        TCGA-D7-6528        TCGA-D7-6815        TCGA-D7-6817 
  "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED"   "5Q LOSS MUTATED" 
       TCGA-D7-6818        TCGA-D7-6820        TCGA-D7-6822        TCGA-EQ-5647 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" 
       TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875        TCGA-FP-7735 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" 
       TCGA-FP-7829        TCGA-FP-7998        TCGA-IN-7806        TCGA-IN-7808 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" 
       TCGA-IP-7968 
"5Q LOSS WILD-TYPE" 
[1] "hr="     "2.3e+08"
D44V2, continuous
D44V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED      5   13
  5Q LOSS WILD-TYPE   55   85
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  FEMALE               5                55
  MALE                13                85
D44V4, multiclass
D44V5, multiclass
    clus
vv   5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  T1               0                 6
  T2               9                43
  T3               5                56
  T4               0                18
D44V6, multiclass
    clus
vv   5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  N0               5                39
  N1               8                49
  N2               2                22
  N3               1                14
D44V7, multiclass
    clus
vv   5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  M0              18               116
  M1               0                16
  MX               0                 8
D44V8, multiclass
     clus
vv    5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  I                 3                21
  II                6                31
  III               5                38
  IV                0                26
D44V9, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED      1   17
  5Q LOSS WILD-TYPE    4  136
     clus
vv    5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  NO                1                 4
  YES              17               136
D44V10, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED      1   17
  5Q LOSS WILD-TYPE    9  131
     clus
vv    5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  NO                1                 9
  YES              17               131

Clustering(45) Variable = 6p loss mutation analysis
D45V1, survival
                   sevent
clus2                0  1
  6P LOSS MUTATED    4  1
  6P LOSS WILD-TYPE 86 14
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
                5               100 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
                1                14 
$`6P LOSS MUTATED`
TCGA-CG-5719 TCGA-CG-5725 TCGA-D7-6520 TCGA-D7-6525 TCGA-D7-6815 
        1.02        15.02         9.63         5.95         3.65 

$`6P LOSS WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-6452 TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6458 
        5.62         0.10         0.95         1.41         1.35         1.35 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
        0.85         0.82         0.62         0.62         1.71         2.17 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
        0.99         1.22         0.66         1.12         0.76         0.66 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
        0.26         1.22         1.48         0.46         1.25         0.13 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 
        1.05         0.82         0.69         0.16         4.54         0.99 
TCGA-BR-7901 TCGA-BR-7957 TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
        0.95         0.69         0.82         0.69         0.36         0.49 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
        0.30         0.07        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02        52.96         8.05        54.05         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4460 TCGA-CG-4462 
       29.98        47.05        19.07        12.03        21.99         1.02 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4474 TCGA-CG-4477 
        8.98        18.94         7.07        12.00         1.02         1.02 
TCGA-CG-5716 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        1.02         6.94         1.02         0.99         5.98         0.95 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 
       70.06        12.03        28.96        31.04        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       55.04        21.07         7.99         8.65         3.58         4.54 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6526 
        9.80        15.65         8.19         6.90         0.69         6.61 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
        4.14         1.68         4.70         4.04         2.93         4.27 
TCGA-EQ-5647 TCGA-F1-6177 TCGA-F1-6874 TCGA-F1-6875 TCGA-FP-7735 TCGA-FP-7829 
        0.62         6.54         2.01        72.23         0.39         0.20 
TCGA-FP-7998 TCGA-IN-7806 TCGA-IN-7808 TCGA-IP-7968 
        3.58         6.87         3.55         2.53 

  6P LOSS MUTATED 6P LOSS WILD-TYPE 
             1.02              0.07 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
            15.02             72.23 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
             5.95              2.35 
[1] "1.0 - 15.0 (6.0)" "0.1 - 72.2 (2.3)"
       TCGA-B7-5816        TCGA-B7-5818        TCGA-BR-6452        TCGA-BR-6455 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-BR-6457        TCGA-BR-6458        TCGA-BR-6563        TCGA-BR-6564 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-BR-6565        TCGA-BR-6566        TCGA-BR-6705        TCGA-BR-6706 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-BR-6707        TCGA-BR-6709        TCGA-BR-6710        TCGA-BR-6801 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-BR-6802        TCGA-BR-6803        TCGA-BR-6852        TCGA-BR-7196 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-BR-7197        TCGA-BR-7703        TCGA-BR-7704        TCGA-BR-7707 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-BR-7715        TCGA-BR-7716        TCGA-BR-7717        TCGA-BR-7722 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-BR-7723        TCGA-BR-7851        TCGA-BR-7901        TCGA-BR-7957 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-CD-5798        TCGA-CD-5799        TCGA-CD-5800        TCGA-CD-5801 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-CD-5802        TCGA-CD-5803        TCGA-CG-4300        TCGA-CG-4301 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-CG-4304        TCGA-CG-4305        TCGA-CG-4306        TCGA-CG-4436 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-CG-4437        TCGA-CG-4438        TCGA-CG-4440        TCGA-CG-4441 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-CG-4443        TCGA-CG-4444        TCGA-CG-4449        TCGA-CG-4455 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-CG-4460        TCGA-CG-4462        TCGA-CG-4465        TCGA-CG-4466 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-CG-4469        TCGA-CG-4472        TCGA-CG-4474        TCGA-CG-4477 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-CG-5716        TCGA-CG-5717        TCGA-CG-5718        TCGA-CG-5719 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE"   "6P LOSS MUTATED" 
       TCGA-CG-5720        TCGA-CG-5721        TCGA-CG-5722        TCGA-CG-5723 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-CG-5724        TCGA-CG-5725        TCGA-CG-5726        TCGA-CG-5727 
"6P LOSS WILD-TYPE"   "6P LOSS MUTATED" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-CG-5728        TCGA-CG-5730        TCGA-CG-5732        TCGA-CG-5733 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-CG-5734        TCGA-D7-5577        TCGA-D7-5578        TCGA-D7-5579 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-D7-6518        TCGA-D7-6519        TCGA-D7-6520        TCGA-D7-6521 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE"   "6P LOSS MUTATED" "6P LOSS WILD-TYPE" 
       TCGA-D7-6522        TCGA-D7-6524        TCGA-D7-6525        TCGA-D7-6526 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE"   "6P LOSS MUTATED" "6P LOSS WILD-TYPE" 
       TCGA-D7-6527        TCGA-D7-6528        TCGA-D7-6815        TCGA-D7-6817 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE"   "6P LOSS MUTATED" "6P LOSS WILD-TYPE" 
       TCGA-D7-6818        TCGA-D7-6820        TCGA-D7-6822        TCGA-EQ-5647 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875        TCGA-FP-7735 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-FP-7829        TCGA-FP-7998        TCGA-IN-7806        TCGA-IN-7808 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-IP-7968 
"6P LOSS WILD-TYPE" 
       TCGA-B7-5816        TCGA-B7-5818        TCGA-BR-6452        TCGA-BR-6455 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-BR-6457        TCGA-BR-6458        TCGA-BR-6563        TCGA-BR-6564 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-BR-6565        TCGA-BR-6566        TCGA-BR-6705        TCGA-BR-6706 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-BR-6707        TCGA-BR-6709        TCGA-BR-6710        TCGA-BR-6801 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-BR-6802        TCGA-BR-6803        TCGA-BR-6852        TCGA-BR-7196 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-BR-7197        TCGA-BR-7703        TCGA-BR-7704        TCGA-BR-7707 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-BR-7715        TCGA-BR-7716        TCGA-BR-7717        TCGA-BR-7722 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-BR-7723        TCGA-BR-7851        TCGA-BR-7901        TCGA-BR-7957 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-CD-5798        TCGA-CD-5799        TCGA-CD-5800        TCGA-CD-5801 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-CD-5802        TCGA-CD-5803        TCGA-CG-4300        TCGA-CG-4301 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-CG-4304        TCGA-CG-4305        TCGA-CG-4306        TCGA-CG-4436 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-CG-4437        TCGA-CG-4438        TCGA-CG-4440        TCGA-CG-4441 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-CG-4443        TCGA-CG-4444        TCGA-CG-4449        TCGA-CG-4455 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-CG-4460        TCGA-CG-4462        TCGA-CG-4465        TCGA-CG-4466 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-CG-4469        TCGA-CG-4472        TCGA-CG-4474        TCGA-CG-4477 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-CG-5716        TCGA-CG-5717        TCGA-CG-5718        TCGA-CG-5719 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE"   "6P LOSS MUTATED" 
       TCGA-CG-5720        TCGA-CG-5721        TCGA-CG-5722        TCGA-CG-5723 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-CG-5724        TCGA-CG-5725        TCGA-CG-5726        TCGA-CG-5727 
"6P LOSS WILD-TYPE"   "6P LOSS MUTATED" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-CG-5728        TCGA-CG-5730        TCGA-CG-5732        TCGA-CG-5733 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-CG-5734        TCGA-D7-5577        TCGA-D7-5578        TCGA-D7-5579 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-D7-6518        TCGA-D7-6519        TCGA-D7-6520        TCGA-D7-6521 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE"   "6P LOSS MUTATED" "6P LOSS WILD-TYPE" 
       TCGA-D7-6522        TCGA-D7-6524        TCGA-D7-6525        TCGA-D7-6526 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE"   "6P LOSS MUTATED" "6P LOSS WILD-TYPE" 
       TCGA-D7-6527        TCGA-D7-6528        TCGA-D7-6815        TCGA-D7-6817 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE"   "6P LOSS MUTATED" "6P LOSS WILD-TYPE" 
       TCGA-D7-6818        TCGA-D7-6820        TCGA-D7-6822        TCGA-EQ-5647 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875        TCGA-FP-7735 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-FP-7829        TCGA-FP-7998        TCGA-IN-7806        TCGA-IN-7808 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-IP-7968 
"6P LOSS WILD-TYPE" 
       TCGA-B7-5816        TCGA-B7-5818        TCGA-BR-6452        TCGA-BR-6455 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-BR-6457        TCGA-BR-6458        TCGA-BR-6563        TCGA-BR-6564 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-BR-6565        TCGA-BR-6566        TCGA-BR-6705        TCGA-BR-6706 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-BR-6707        TCGA-BR-6709        TCGA-BR-6710        TCGA-BR-6801 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-BR-6802        TCGA-BR-6803        TCGA-BR-6852        TCGA-BR-7196 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-BR-7197        TCGA-BR-7703        TCGA-BR-7704        TCGA-BR-7707 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-BR-7715        TCGA-BR-7716        TCGA-BR-7717        TCGA-BR-7722 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-BR-7723        TCGA-BR-7851        TCGA-BR-7901        TCGA-BR-7957 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-CD-5798        TCGA-CD-5799        TCGA-CD-5800        TCGA-CD-5801 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-CD-5802        TCGA-CD-5803        TCGA-CG-4300        TCGA-CG-4301 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-CG-4304        TCGA-CG-4305        TCGA-CG-4306        TCGA-CG-4436 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-CG-4437        TCGA-CG-4438        TCGA-CG-4440        TCGA-CG-4441 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-CG-4443        TCGA-CG-4444        TCGA-CG-4449        TCGA-CG-4455 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-CG-4460        TCGA-CG-4462        TCGA-CG-4465        TCGA-CG-4466 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-CG-4469        TCGA-CG-4472        TCGA-CG-4474        TCGA-CG-4477 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-CG-5716        TCGA-CG-5717        TCGA-CG-5718        TCGA-CG-5719 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE"   "6P LOSS MUTATED" 
       TCGA-CG-5720        TCGA-CG-5721        TCGA-CG-5722        TCGA-CG-5723 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-CG-5724        TCGA-CG-5725        TCGA-CG-5726        TCGA-CG-5727 
"6P LOSS WILD-TYPE"   "6P LOSS MUTATED" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-CG-5728        TCGA-CG-5730        TCGA-CG-5732        TCGA-CG-5733 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-CG-5734        TCGA-D7-5577        TCGA-D7-5578        TCGA-D7-5579 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-D7-6518        TCGA-D7-6519        TCGA-D7-6520        TCGA-D7-6521 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE"   "6P LOSS MUTATED" "6P LOSS WILD-TYPE" 
       TCGA-D7-6522        TCGA-D7-6524        TCGA-D7-6525        TCGA-D7-6526 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE"   "6P LOSS MUTATED" "6P LOSS WILD-TYPE" 
       TCGA-D7-6527        TCGA-D7-6528        TCGA-D7-6815        TCGA-D7-6817 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE"   "6P LOSS MUTATED" "6P LOSS WILD-TYPE" 
       TCGA-D7-6818        TCGA-D7-6820        TCGA-D7-6822        TCGA-EQ-5647 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875        TCGA-FP-7735 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-FP-7829        TCGA-FP-7998        TCGA-IN-7806        TCGA-IN-7808 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-IP-7968 
"6P LOSS WILD-TYPE" 
[1] "hr=" "1.5"
D45V2, continuous
D45V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED      4    4
  6P LOSS WILD-TYPE   56   94
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  FEMALE               4                56
  MALE                 4                94
D45V4, multiclass
D45V5, multiclass
    clus
vv   6P LOSS MUTATED 6P LOSS WILD-TYPE
  T1               0                 6
  T2               5                47
  T3               1                60
  T4               1                17
D45V6, multiclass
    clus
vv   6P LOSS MUTATED 6P LOSS WILD-TYPE
  N0               2                42
  N1               0                57
  N2               3                21
  N3               0                15
D45V7, multiclass
    clus
vv   6P LOSS MUTATED 6P LOSS WILD-TYPE
  M0               6               128
  M1               1                15
  MX               1                 7
D45V8, multiclass
     clus
vv    6P LOSS MUTATED 6P LOSS WILD-TYPE
  I                 1                23
  II                0                37
  III               3                40
  IV                1                25
D45V9, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED      0    8
  6P LOSS WILD-TYPE    5  145
     clus
vv    6P LOSS MUTATED 6P LOSS WILD-TYPE
  NO                0                 5
  YES               8               145
D45V10, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED      1    7
  6P LOSS WILD-TYPE    9  141
     clus
vv    6P LOSS MUTATED 6P LOSS WILD-TYPE
  NO                1                 9
  YES               7               141

Clustering(46) Variable = 6q loss mutation analysis
D46V1, survival
                   sevent
clus2                0  1
  6Q LOSS MUTATED    6  1
  6Q LOSS WILD-TYPE 84 14
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
                7                98 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
                1                14 
$`6Q LOSS MUTATED`
TCGA-BR-7722 TCGA-CG-4443 TCGA-CG-5719 TCGA-CG-5725 TCGA-D7-6520 TCGA-D7-6525 
        0.16        29.98         1.02        15.02         9.63         5.95 
TCGA-D7-6815 
        3.65 

$`6Q LOSS WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-6452 TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6458 
        5.62         0.10         0.95         1.41         1.35         1.35 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
        0.85         0.82         0.62         0.62         1.71         2.17 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
        0.99         1.22         0.66         1.12         0.76         0.66 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
        0.26         1.22         1.48         0.46         1.25         0.13 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 
        1.05         0.82         0.69         4.54         0.99         0.95 
TCGA-BR-7957 TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        0.69         0.82         0.69         0.36         0.49         0.30 
TCGA-CD-5803 TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
        0.07        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4444 
       52.96         8.05        54.05         4.01        14.01        47.05 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4460 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       19.07        12.03        21.99         1.02         8.98        18.94 
TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4474 TCGA-CG-4477 TCGA-CG-5716 TCGA-CG-5717 
        7.07        12.00         1.02         1.02         1.02         6.94 
TCGA-CG-5718 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
        1.02         0.99         5.98         0.95        70.06        12.03 
TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       28.96        31.04        65.10         4.01        55.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99         8.65         3.58         4.54         9.80        15.65 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
        8.19         6.90         0.69         6.61         4.14         1.68 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-EQ-5647 TCGA-F1-6177 
        4.70         4.04         2.93         4.27         0.62         6.54 
TCGA-F1-6874 TCGA-F1-6875 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7998 TCGA-IN-7806 
        2.01        72.23         0.39         0.20         3.58         6.87 
TCGA-IN-7808 TCGA-IP-7968 
        3.55         2.53 

  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
             0.16              0.07 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
            29.98             72.23 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
             5.95              2.35 
[1] "0.2 - 30.0 (6.0)" "0.1 - 72.2 (2.3)"
       TCGA-B7-5816        TCGA-B7-5818        TCGA-BR-6452        TCGA-BR-6455 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-BR-6457        TCGA-BR-6458        TCGA-BR-6563        TCGA-BR-6564 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-BR-6565        TCGA-BR-6566        TCGA-BR-6705        TCGA-BR-6706 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-BR-6707        TCGA-BR-6709        TCGA-BR-6710        TCGA-BR-6801 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-BR-6802        TCGA-BR-6803        TCGA-BR-6852        TCGA-BR-7196 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-BR-7197        TCGA-BR-7703        TCGA-BR-7704        TCGA-BR-7707 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-BR-7715        TCGA-BR-7716        TCGA-BR-7717        TCGA-BR-7722 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" 
       TCGA-BR-7723        TCGA-BR-7851        TCGA-BR-7901        TCGA-BR-7957 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-CD-5798        TCGA-CD-5799        TCGA-CD-5800        TCGA-CD-5801 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-CD-5802        TCGA-CD-5803        TCGA-CG-4300        TCGA-CG-4301 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-CG-4304        TCGA-CG-4305        TCGA-CG-4306        TCGA-CG-4436 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-CG-4437        TCGA-CG-4438        TCGA-CG-4440        TCGA-CG-4441 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-CG-4443        TCGA-CG-4444        TCGA-CG-4449        TCGA-CG-4455 
  "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-CG-4460        TCGA-CG-4462        TCGA-CG-4465        TCGA-CG-4466 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-CG-4469        TCGA-CG-4472        TCGA-CG-4474        TCGA-CG-4477 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-CG-5716        TCGA-CG-5717        TCGA-CG-5718        TCGA-CG-5719 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" 
       TCGA-CG-5720        TCGA-CG-5721        TCGA-CG-5722        TCGA-CG-5723 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-CG-5724        TCGA-CG-5725        TCGA-CG-5726        TCGA-CG-5727 
"6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-CG-5728        TCGA-CG-5730        TCGA-CG-5732        TCGA-CG-5733 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-CG-5734        TCGA-D7-5577        TCGA-D7-5578        TCGA-D7-5579 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-D7-6518        TCGA-D7-6519        TCGA-D7-6520        TCGA-D7-6521 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" 
       TCGA-D7-6522        TCGA-D7-6524        TCGA-D7-6525        TCGA-D7-6526 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" 
       TCGA-D7-6527        TCGA-D7-6528        TCGA-D7-6815        TCGA-D7-6817 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" 
       TCGA-D7-6818        TCGA-D7-6820        TCGA-D7-6822        TCGA-EQ-5647 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875        TCGA-FP-7735 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-FP-7829        TCGA-FP-7998        TCGA-IN-7806        TCGA-IN-7808 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-IP-7968 
"6Q LOSS WILD-TYPE" 
       TCGA-B7-5816        TCGA-B7-5818        TCGA-BR-6452        TCGA-BR-6455 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-BR-6457        TCGA-BR-6458        TCGA-BR-6563        TCGA-BR-6564 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-BR-6565        TCGA-BR-6566        TCGA-BR-6705        TCGA-BR-6706 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-BR-6707        TCGA-BR-6709        TCGA-BR-6710        TCGA-BR-6801 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-BR-6802        TCGA-BR-6803        TCGA-BR-6852        TCGA-BR-7196 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-BR-7197        TCGA-BR-7703        TCGA-BR-7704        TCGA-BR-7707 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-BR-7715        TCGA-BR-7716        TCGA-BR-7717        TCGA-BR-7722 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" 
       TCGA-BR-7723        TCGA-BR-7851        TCGA-BR-7901        TCGA-BR-7957 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-CD-5798        TCGA-CD-5799        TCGA-CD-5800        TCGA-CD-5801 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-CD-5802        TCGA-CD-5803        TCGA-CG-4300        TCGA-CG-4301 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-CG-4304        TCGA-CG-4305        TCGA-CG-4306        TCGA-CG-4436 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-CG-4437        TCGA-CG-4438        TCGA-CG-4440        TCGA-CG-4441 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-CG-4443        TCGA-CG-4444        TCGA-CG-4449        TCGA-CG-4455 
  "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-CG-4460        TCGA-CG-4462        TCGA-CG-4465        TCGA-CG-4466 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-CG-4469        TCGA-CG-4472        TCGA-CG-4474        TCGA-CG-4477 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-CG-5716        TCGA-CG-5717        TCGA-CG-5718        TCGA-CG-5719 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" 
       TCGA-CG-5720        TCGA-CG-5721        TCGA-CG-5722        TCGA-CG-5723 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-CG-5724        TCGA-CG-5725        TCGA-CG-5726        TCGA-CG-5727 
"6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-CG-5728        TCGA-CG-5730        TCGA-CG-5732        TCGA-CG-5733 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-CG-5734        TCGA-D7-5577        TCGA-D7-5578        TCGA-D7-5579 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-D7-6518        TCGA-D7-6519        TCGA-D7-6520        TCGA-D7-6521 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" 
       TCGA-D7-6522        TCGA-D7-6524        TCGA-D7-6525        TCGA-D7-6526 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" 
       TCGA-D7-6527        TCGA-D7-6528        TCGA-D7-6815        TCGA-D7-6817 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" 
       TCGA-D7-6818        TCGA-D7-6820        TCGA-D7-6822        TCGA-EQ-5647 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875        TCGA-FP-7735 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-FP-7829        TCGA-FP-7998        TCGA-IN-7806        TCGA-IN-7808 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-IP-7968 
"6Q LOSS WILD-TYPE" 
       TCGA-B7-5816        TCGA-B7-5818        TCGA-BR-6452        TCGA-BR-6455 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-BR-6457        TCGA-BR-6458        TCGA-BR-6563        TCGA-BR-6564 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-BR-6565        TCGA-BR-6566        TCGA-BR-6705        TCGA-BR-6706 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-BR-6707        TCGA-BR-6709        TCGA-BR-6710        TCGA-BR-6801 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-BR-6802        TCGA-BR-6803        TCGA-BR-6852        TCGA-BR-7196 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-BR-7197        TCGA-BR-7703        TCGA-BR-7704        TCGA-BR-7707 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-BR-7715        TCGA-BR-7716        TCGA-BR-7717        TCGA-BR-7722 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" 
       TCGA-BR-7723        TCGA-BR-7851        TCGA-BR-7901        TCGA-BR-7957 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-CD-5798        TCGA-CD-5799        TCGA-CD-5800        TCGA-CD-5801 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-CD-5802        TCGA-CD-5803        TCGA-CG-4300        TCGA-CG-4301 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-CG-4304        TCGA-CG-4305        TCGA-CG-4306        TCGA-CG-4436 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-CG-4437        TCGA-CG-4438        TCGA-CG-4440        TCGA-CG-4441 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-CG-4443        TCGA-CG-4444        TCGA-CG-4449        TCGA-CG-4455 
  "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-CG-4460        TCGA-CG-4462        TCGA-CG-4465        TCGA-CG-4466 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-CG-4469        TCGA-CG-4472        TCGA-CG-4474        TCGA-CG-4477 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-CG-5716        TCGA-CG-5717        TCGA-CG-5718        TCGA-CG-5719 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" 
       TCGA-CG-5720        TCGA-CG-5721        TCGA-CG-5722        TCGA-CG-5723 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-CG-5724        TCGA-CG-5725        TCGA-CG-5726        TCGA-CG-5727 
"6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-CG-5728        TCGA-CG-5730        TCGA-CG-5732        TCGA-CG-5733 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-CG-5734        TCGA-D7-5577        TCGA-D7-5578        TCGA-D7-5579 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-D7-6518        TCGA-D7-6519        TCGA-D7-6520        TCGA-D7-6521 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" 
       TCGA-D7-6522        TCGA-D7-6524        TCGA-D7-6525        TCGA-D7-6526 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" 
       TCGA-D7-6527        TCGA-D7-6528        TCGA-D7-6815        TCGA-D7-6817 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" 
       TCGA-D7-6818        TCGA-D7-6820        TCGA-D7-6822        TCGA-EQ-5647 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875        TCGA-FP-7735 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-FP-7829        TCGA-FP-7998        TCGA-IN-7806        TCGA-IN-7808 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-IP-7968 
"6Q LOSS WILD-TYPE" 
[1] "hr=" "1.3"
D46V2, continuous
D46V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED      4    8
  6Q LOSS WILD-TYPE   56   90
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  FEMALE               4                56
  MALE                 8                90
D46V4, multiclass
D46V5, multiclass
    clus
vv   6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  T1               1                 5
  T2               6                46
  T3               3                58
  T4               1                17
D46V6, multiclass
    clus
vv   6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  N0               4                40
  N1               2                55
  N2               3                21
  N3               0                15
D46V7, multiclass
    clus
vv   6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  M0              10               124
  M1               1                15
  MX               1                 7
D46V8, multiclass
     clus
vv    6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  I                 3                21
  II                0                37
  III               5                38
  IV                1                25
D46V9, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED      0   12
  6Q LOSS WILD-TYPE    5  141
     clus
vv    6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  NO                0                 5
  YES              12               141
D46V10, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED      1   11
  6Q LOSS WILD-TYPE    9  137
     clus
vv    6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  NO                1                 9
  YES              11               137

Clustering(47) Variable = 7p loss mutation analysis
D47V1, survival
                   sevent
clus2                0  1
  7P LOSS MUTATED    3  0
  7P LOSS WILD-TYPE 87 15
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
                3               102 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
                0                15 
$`7P LOSS MUTATED`
TCGA-BR-7723 TCGA-CG-4438 TCGA-CG-4443 
        4.54        54.05        29.98 

$`7P LOSS WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-6452 TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6458 
        5.62         0.10         0.95         1.41         1.35         1.35 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
        0.85         0.82         0.62         0.62         1.71         2.17 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
        0.99         1.22         0.66         1.12         0.76         0.66 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
        0.26         1.22         1.48         0.46         1.25         0.13 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7851 TCGA-BR-7901 
        1.05         0.82         0.69         0.16         0.99         0.95 
TCGA-BR-7957 TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        0.69         0.82         0.69         0.36         0.49         0.30 
TCGA-CD-5803 TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
        0.07        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4444 TCGA-CG-4449 
       52.96         8.05         4.01        14.01        47.05        19.07 
TCGA-CG-4455 TCGA-CG-4460 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       12.03        21.99         1.02         8.98        18.94         7.07 
TCGA-CG-4472 TCGA-CG-4474 TCGA-CG-4477 TCGA-CG-5716 TCGA-CG-5717 TCGA-CG-5718 
       12.00         1.02         1.02         1.02         6.94         1.02 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
        1.02         0.99         5.98         0.95        70.06        12.03 
TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       15.02        28.96        31.04        65.10         4.01        55.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99         8.65         3.58         4.54         9.80 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       15.65         9.63         8.19         6.90         0.69         5.95 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
        6.61         4.14         1.68         3.65         4.70         4.04 
TCGA-D7-6820 TCGA-D7-6822 TCGA-EQ-5647 TCGA-F1-6177 TCGA-F1-6874 TCGA-F1-6875 
        2.93         4.27         0.62         6.54         2.01        72.23 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7998 TCGA-IN-7806 TCGA-IN-7808 TCGA-IP-7968 
        0.39         0.20         3.58         6.87         3.55         2.53 

  7P LOSS MUTATED 7P LOSS WILD-TYPE 
             4.54              0.07 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
            54.05             72.23 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
            29.98              2.35 
[1] "4.5 - 54.0 (30.0)" "0.1 - 72.2 (2.3)" 
       TCGA-B7-5816        TCGA-B7-5818        TCGA-BR-6452        TCGA-BR-6455 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-BR-6457        TCGA-BR-6458        TCGA-BR-6563        TCGA-BR-6564 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-BR-6565        TCGA-BR-6566        TCGA-BR-6705        TCGA-BR-6706 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-BR-6707        TCGA-BR-6709        TCGA-BR-6710        TCGA-BR-6801 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-BR-6802        TCGA-BR-6803        TCGA-BR-6852        TCGA-BR-7196 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-BR-7197        TCGA-BR-7703        TCGA-BR-7704        TCGA-BR-7707 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-BR-7715        TCGA-BR-7716        TCGA-BR-7717        TCGA-BR-7722 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-BR-7723        TCGA-BR-7851        TCGA-BR-7901        TCGA-BR-7957 
  "7P LOSS MUTATED" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-CD-5798        TCGA-CD-5799        TCGA-CD-5800        TCGA-CD-5801 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-CD-5802        TCGA-CD-5803        TCGA-CG-4300        TCGA-CG-4301 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-CG-4304        TCGA-CG-4305        TCGA-CG-4306        TCGA-CG-4436 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-CG-4437        TCGA-CG-4438        TCGA-CG-4440        TCGA-CG-4441 
"7P LOSS WILD-TYPE"   "7P LOSS MUTATED" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-CG-4443        TCGA-CG-4444        TCGA-CG-4449        TCGA-CG-4455 
  "7P LOSS MUTATED" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-CG-4460        TCGA-CG-4462        TCGA-CG-4465        TCGA-CG-4466 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-CG-4469        TCGA-CG-4472        TCGA-CG-4474        TCGA-CG-4477 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-CG-5716        TCGA-CG-5717        TCGA-CG-5718        TCGA-CG-5719 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-CG-5720        TCGA-CG-5721        TCGA-CG-5722        TCGA-CG-5723 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-CG-5724        TCGA-CG-5725        TCGA-CG-5726        TCGA-CG-5727 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-CG-5728        TCGA-CG-5730        TCGA-CG-5732        TCGA-CG-5733 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-CG-5734        TCGA-D7-5577        TCGA-D7-5578        TCGA-D7-5579 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-D7-6518        TCGA-D7-6519        TCGA-D7-6520        TCGA-D7-6521 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-D7-6522        TCGA-D7-6524        TCGA-D7-6525        TCGA-D7-6526 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-D7-6527        TCGA-D7-6528        TCGA-D7-6815        TCGA-D7-6817 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-D7-6818        TCGA-D7-6820        TCGA-D7-6822        TCGA-EQ-5647 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875        TCGA-FP-7735 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-FP-7829        TCGA-FP-7998        TCGA-IN-7806        TCGA-IN-7808 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-IP-7968 
"7P LOSS WILD-TYPE" 
       TCGA-B7-5816        TCGA-B7-5818        TCGA-BR-6452        TCGA-BR-6455 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-BR-6457        TCGA-BR-6458        TCGA-BR-6563        TCGA-BR-6564 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-BR-6565        TCGA-BR-6566        TCGA-BR-6705        TCGA-BR-6706 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-BR-6707        TCGA-BR-6709        TCGA-BR-6710        TCGA-BR-6801 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-BR-6802        TCGA-BR-6803        TCGA-BR-6852        TCGA-BR-7196 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-BR-7197        TCGA-BR-7703        TCGA-BR-7704        TCGA-BR-7707 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-BR-7715        TCGA-BR-7716        TCGA-BR-7717        TCGA-BR-7722 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-BR-7723        TCGA-BR-7851        TCGA-BR-7901        TCGA-BR-7957 
  "7P LOSS MUTATED" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-CD-5798        TCGA-CD-5799        TCGA-CD-5800        TCGA-CD-5801 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-CD-5802        TCGA-CD-5803        TCGA-CG-4300        TCGA-CG-4301 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-CG-4304        TCGA-CG-4305        TCGA-CG-4306        TCGA-CG-4436 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-CG-4437        TCGA-CG-4438        TCGA-CG-4440        TCGA-CG-4441 
"7P LOSS WILD-TYPE"   "7P LOSS MUTATED" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-CG-4443        TCGA-CG-4444        TCGA-CG-4449        TCGA-CG-4455 
  "7P LOSS MUTATED" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-CG-4460        TCGA-CG-4462        TCGA-CG-4465        TCGA-CG-4466 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-CG-4469        TCGA-CG-4472        TCGA-CG-4474        TCGA-CG-4477 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-CG-5716        TCGA-CG-5717        TCGA-CG-5718        TCGA-CG-5719 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-CG-5720        TCGA-CG-5721        TCGA-CG-5722        TCGA-CG-5723 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-CG-5724        TCGA-CG-5725        TCGA-CG-5726        TCGA-CG-5727 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-CG-5728        TCGA-CG-5730        TCGA-CG-5732        TCGA-CG-5733 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-CG-5734        TCGA-D7-5577        TCGA-D7-5578        TCGA-D7-5579 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-D7-6518        TCGA-D7-6519        TCGA-D7-6520        TCGA-D7-6521 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-D7-6522        TCGA-D7-6524        TCGA-D7-6525        TCGA-D7-6526 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-D7-6527        TCGA-D7-6528        TCGA-D7-6815        TCGA-D7-6817 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-D7-6818        TCGA-D7-6820        TCGA-D7-6822        TCGA-EQ-5647 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875        TCGA-FP-7735 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-FP-7829        TCGA-FP-7998        TCGA-IN-7806        TCGA-IN-7808 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-IP-7968 
"7P LOSS WILD-TYPE" 
       TCGA-B7-5816        TCGA-B7-5818        TCGA-BR-6452        TCGA-BR-6455 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-BR-6457        TCGA-BR-6458        TCGA-BR-6563        TCGA-BR-6564 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-BR-6565        TCGA-BR-6566        TCGA-BR-6705        TCGA-BR-6706 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-BR-6707        TCGA-BR-6709        TCGA-BR-6710        TCGA-BR-6801 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-BR-6802        TCGA-BR-6803        TCGA-BR-6852        TCGA-BR-7196 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-BR-7197        TCGA-BR-7703        TCGA-BR-7704        TCGA-BR-7707 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-BR-7715        TCGA-BR-7716        TCGA-BR-7717        TCGA-BR-7722 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-BR-7723        TCGA-BR-7851        TCGA-BR-7901        TCGA-BR-7957 
  "7P LOSS MUTATED" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-CD-5798        TCGA-CD-5799        TCGA-CD-5800        TCGA-CD-5801 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-CD-5802        TCGA-CD-5803        TCGA-CG-4300        TCGA-CG-4301 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-CG-4304        TCGA-CG-4305        TCGA-CG-4306        TCGA-CG-4436 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-CG-4437        TCGA-CG-4438        TCGA-CG-4440        TCGA-CG-4441 
"7P LOSS WILD-TYPE"   "7P LOSS MUTATED" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-CG-4443        TCGA-CG-4444        TCGA-CG-4449        TCGA-CG-4455 
  "7P LOSS MUTATED" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-CG-4460        TCGA-CG-4462        TCGA-CG-4465        TCGA-CG-4466 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-CG-4469        TCGA-CG-4472        TCGA-CG-4474        TCGA-CG-4477 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-CG-5716        TCGA-CG-5717        TCGA-CG-5718        TCGA-CG-5719 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-CG-5720        TCGA-CG-5721        TCGA-CG-5722        TCGA-CG-5723 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-CG-5724        TCGA-CG-5725        TCGA-CG-5726        TCGA-CG-5727 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-CG-5728        TCGA-CG-5730        TCGA-CG-5732        TCGA-CG-5733 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-CG-5734        TCGA-D7-5577        TCGA-D7-5578        TCGA-D7-5579 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-D7-6518        TCGA-D7-6519        TCGA-D7-6520        TCGA-D7-6521 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-D7-6522        TCGA-D7-6524        TCGA-D7-6525        TCGA-D7-6526 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-D7-6527        TCGA-D7-6528        TCGA-D7-6815        TCGA-D7-6817 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-D7-6818        TCGA-D7-6820        TCGA-D7-6822        TCGA-EQ-5647 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875        TCGA-FP-7735 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-FP-7829        TCGA-FP-7998        TCGA-IN-7806        TCGA-IN-7808 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-IP-7968 
"7P LOSS WILD-TYPE" 
[1] "hr="   "8e+07"
D47V2, continuous
D47V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED      0    3
  7P LOSS WILD-TYPE   60   95
        clus
vv       7P LOSS MUTATED 7P LOSS WILD-TYPE
  FEMALE               0                60
  MALE                 3                95
D47V4, multiclass
D47V5, multiclass
    clus
vv   7P LOSS MUTATED 7P LOSS WILD-TYPE
  T1               1                 5
  T2               0                52
  T3               1                60
  T4               1                17
D47V6, multiclass
    clus
vv   7P LOSS MUTATED 7P LOSS WILD-TYPE
  N0               1                43
  N1               0                57
  N2               2                22
  N3               0                15
D47V7, multiclass
    clus
vv   7P LOSS MUTATED 7P LOSS WILD-TYPE
  M0               3               131
  M1               0                16
  MX               0                 8
D47V8, multiclass
     clus
vv    7P LOSS MUTATED 7P LOSS WILD-TYPE
  I                 1                23
  II                1                36
  III               0                43
  IV                1                25
D47V9, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED      0    3
  7P LOSS WILD-TYPE    5  150
     clus
vv    7P LOSS MUTATED 7P LOSS WILD-TYPE
  NO                0                 5
  YES               3               150
D47V10, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED      0    3
  7P LOSS WILD-TYPE   10  145
     clus
vv    7P LOSS MUTATED 7P LOSS WILD-TYPE
  NO                0                10
  YES               3               145

Clustering(48) Variable = 7q loss mutation analysis
D48V1, survival
                   sevent
clus2                0  1
  7Q LOSS MUTATED    5  0
  7Q LOSS WILD-TYPE 85 15
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
                5               100 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
                0                15 
$`7Q LOSS MUTATED`
TCGA-BR-7723 TCGA-CG-4438 TCGA-CG-4443 TCGA-D7-6820 TCGA-FP-7829 
        4.54        54.05        29.98         2.93         0.20 

$`7Q LOSS WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-6452 TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6458 
        5.62         0.10         0.95         1.41         1.35         1.35 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
        0.85         0.82         0.62         0.62         1.71         2.17 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
        0.99         1.22         0.66         1.12         0.76         0.66 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
        0.26         1.22         1.48         0.46         1.25         0.13 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7851 TCGA-BR-7901 
        1.05         0.82         0.69         0.16         0.99         0.95 
TCGA-BR-7957 TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        0.69         0.82         0.69         0.36         0.49         0.30 
TCGA-CD-5803 TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
        0.07        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4444 TCGA-CG-4449 
       52.96         8.05         4.01        14.01        47.05        19.07 
TCGA-CG-4455 TCGA-CG-4460 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       12.03        21.99         1.02         8.98        18.94         7.07 
TCGA-CG-4472 TCGA-CG-4474 TCGA-CG-4477 TCGA-CG-5716 TCGA-CG-5717 TCGA-CG-5718 
       12.00         1.02         1.02         1.02         6.94         1.02 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
        1.02         0.99         5.98         0.95        70.06        12.03 
TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       15.02        28.96        31.04        65.10         4.01        55.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99         8.65         3.58         4.54         9.80 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       15.65         9.63         8.19         6.90         0.69         5.95 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
        6.61         4.14         1.68         3.65         4.70         4.04 
TCGA-D7-6822 TCGA-EQ-5647 TCGA-F1-6177 TCGA-F1-6874 TCGA-F1-6875 TCGA-FP-7735 
        4.27         0.62         6.54         2.01        72.23         0.39 
TCGA-FP-7998 TCGA-IN-7806 TCGA-IN-7808 TCGA-IP-7968 
        3.58         6.87         3.55         2.53 

  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
             0.20              0.07 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
            54.05             72.23 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
             4.54              2.35 
[1] "0.2 - 54.0 (4.5)" "0.1 - 72.2 (2.3)"
       TCGA-B7-5816        TCGA-B7-5818        TCGA-BR-6452        TCGA-BR-6455 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-BR-6457        TCGA-BR-6458        TCGA-BR-6563        TCGA-BR-6564 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-BR-6565        TCGA-BR-6566        TCGA-BR-6705        TCGA-BR-6706 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-BR-6707        TCGA-BR-6709        TCGA-BR-6710        TCGA-BR-6801 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-BR-6802        TCGA-BR-6803        TCGA-BR-6852        TCGA-BR-7196 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-BR-7197        TCGA-BR-7703        TCGA-BR-7704        TCGA-BR-7707 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-BR-7715        TCGA-BR-7716        TCGA-BR-7717        TCGA-BR-7722 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-BR-7723        TCGA-BR-7851        TCGA-BR-7901        TCGA-BR-7957 
  "7Q LOSS MUTATED" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-CD-5798        TCGA-CD-5799        TCGA-CD-5800        TCGA-CD-5801 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-CD-5802        TCGA-CD-5803        TCGA-CG-4300        TCGA-CG-4301 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-CG-4304        TCGA-CG-4305        TCGA-CG-4306        TCGA-CG-4436 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-CG-4437        TCGA-CG-4438        TCGA-CG-4440        TCGA-CG-4441 
"7Q LOSS WILD-TYPE"   "7Q LOSS MUTATED" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-CG-4443        TCGA-CG-4444        TCGA-CG-4449        TCGA-CG-4455 
  "7Q LOSS MUTATED" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-CG-4460        TCGA-CG-4462        TCGA-CG-4465        TCGA-CG-4466 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-CG-4469        TCGA-CG-4472        TCGA-CG-4474        TCGA-CG-4477 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-CG-5716        TCGA-CG-5717        TCGA-CG-5718        TCGA-CG-5719 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-CG-5720        TCGA-CG-5721        TCGA-CG-5722        TCGA-CG-5723 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-CG-5724        TCGA-CG-5725        TCGA-CG-5726        TCGA-CG-5727 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-CG-5728        TCGA-CG-5730        TCGA-CG-5732        TCGA-CG-5733 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-CG-5734        TCGA-D7-5577        TCGA-D7-5578        TCGA-D7-5579 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-D7-6518        TCGA-D7-6519        TCGA-D7-6520        TCGA-D7-6521 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-D7-6522        TCGA-D7-6524        TCGA-D7-6525        TCGA-D7-6526 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-D7-6527        TCGA-D7-6528        TCGA-D7-6815        TCGA-D7-6817 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-D7-6818        TCGA-D7-6820        TCGA-D7-6822        TCGA-EQ-5647 
"7Q LOSS WILD-TYPE"   "7Q LOSS MUTATED" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875        TCGA-FP-7735 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-FP-7829        TCGA-FP-7998        TCGA-IN-7806        TCGA-IN-7808 
  "7Q LOSS MUTATED" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-IP-7968 
"7Q LOSS WILD-TYPE" 
       TCGA-B7-5816        TCGA-B7-5818        TCGA-BR-6452        TCGA-BR-6455 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-BR-6457        TCGA-BR-6458        TCGA-BR-6563        TCGA-BR-6564 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-BR-6565        TCGA-BR-6566        TCGA-BR-6705        TCGA-BR-6706 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-BR-6707        TCGA-BR-6709        TCGA-BR-6710        TCGA-BR-6801 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-BR-6802        TCGA-BR-6803        TCGA-BR-6852        TCGA-BR-7196 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-BR-7197        TCGA-BR-7703        TCGA-BR-7704        TCGA-BR-7707 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-BR-7715        TCGA-BR-7716        TCGA-BR-7717        TCGA-BR-7722 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-BR-7723        TCGA-BR-7851        TCGA-BR-7901        TCGA-BR-7957 
  "7Q LOSS MUTATED" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-CD-5798        TCGA-CD-5799        TCGA-CD-5800        TCGA-CD-5801 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-CD-5802        TCGA-CD-5803        TCGA-CG-4300        TCGA-CG-4301 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-CG-4304        TCGA-CG-4305        TCGA-CG-4306        TCGA-CG-4436 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-CG-4437        TCGA-CG-4438        TCGA-CG-4440        TCGA-CG-4441 
"7Q LOSS WILD-TYPE"   "7Q LOSS MUTATED" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-CG-4443        TCGA-CG-4444        TCGA-CG-4449        TCGA-CG-4455 
  "7Q LOSS MUTATED" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-CG-4460        TCGA-CG-4462        TCGA-CG-4465        TCGA-CG-4466 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-CG-4469        TCGA-CG-4472        TCGA-CG-4474        TCGA-CG-4477 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-CG-5716        TCGA-CG-5717        TCGA-CG-5718        TCGA-CG-5719 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-CG-5720        TCGA-CG-5721        TCGA-CG-5722        TCGA-CG-5723 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-CG-5724        TCGA-CG-5725        TCGA-CG-5726        TCGA-CG-5727 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-CG-5728        TCGA-CG-5730        TCGA-CG-5732        TCGA-CG-5733 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-CG-5734        TCGA-D7-5577        TCGA-D7-5578        TCGA-D7-5579 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-D7-6518        TCGA-D7-6519        TCGA-D7-6520        TCGA-D7-6521 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-D7-6522        TCGA-D7-6524        TCGA-D7-6525        TCGA-D7-6526 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-D7-6527        TCGA-D7-6528        TCGA-D7-6815        TCGA-D7-6817 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-D7-6818        TCGA-D7-6820        TCGA-D7-6822        TCGA-EQ-5647 
"7Q LOSS WILD-TYPE"   "7Q LOSS MUTATED" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875        TCGA-FP-7735 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-FP-7829        TCGA-FP-7998        TCGA-IN-7806        TCGA-IN-7808 
  "7Q LOSS MUTATED" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-IP-7968 
"7Q LOSS WILD-TYPE" 
       TCGA-B7-5816        TCGA-B7-5818        TCGA-BR-6452        TCGA-BR-6455 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-BR-6457        TCGA-BR-6458        TCGA-BR-6563        TCGA-BR-6564 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-BR-6565        TCGA-BR-6566        TCGA-BR-6705        TCGA-BR-6706 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-BR-6707        TCGA-BR-6709        TCGA-BR-6710        TCGA-BR-6801 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-BR-6802        TCGA-BR-6803        TCGA-BR-6852        TCGA-BR-7196 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-BR-7197        TCGA-BR-7703        TCGA-BR-7704        TCGA-BR-7707 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-BR-7715        TCGA-BR-7716        TCGA-BR-7717        TCGA-BR-7722 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-BR-7723        TCGA-BR-7851        TCGA-BR-7901        TCGA-BR-7957 
  "7Q LOSS MUTATED" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-CD-5798        TCGA-CD-5799        TCGA-CD-5800        TCGA-CD-5801 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-CD-5802        TCGA-CD-5803        TCGA-CG-4300        TCGA-CG-4301 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-CG-4304        TCGA-CG-4305        TCGA-CG-4306        TCGA-CG-4436 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-CG-4437        TCGA-CG-4438        TCGA-CG-4440        TCGA-CG-4441 
"7Q LOSS WILD-TYPE"   "7Q LOSS MUTATED" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-CG-4443        TCGA-CG-4444        TCGA-CG-4449        TCGA-CG-4455 
  "7Q LOSS MUTATED" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-CG-4460        TCGA-CG-4462        TCGA-CG-4465        TCGA-CG-4466 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-CG-4469        TCGA-CG-4472        TCGA-CG-4474        TCGA-CG-4477 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-CG-5716        TCGA-CG-5717        TCGA-CG-5718        TCGA-CG-5719 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-CG-5720        TCGA-CG-5721        TCGA-CG-5722        TCGA-CG-5723 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-CG-5724        TCGA-CG-5725        TCGA-CG-5726        TCGA-CG-5727 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-CG-5728        TCGA-CG-5730        TCGA-CG-5732        TCGA-CG-5733 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-CG-5734        TCGA-D7-5577        TCGA-D7-5578        TCGA-D7-5579 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-D7-6518        TCGA-D7-6519        TCGA-D7-6520        TCGA-D7-6521 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-D7-6522        TCGA-D7-6524        TCGA-D7-6525        TCGA-D7-6526 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-D7-6527        TCGA-D7-6528        TCGA-D7-6815        TCGA-D7-6817 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-D7-6818        TCGA-D7-6820        TCGA-D7-6822        TCGA-EQ-5647 
"7Q LOSS WILD-TYPE"   "7Q LOSS MUTATED" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875        TCGA-FP-7735 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-FP-7829        TCGA-FP-7998        TCGA-IN-7806        TCGA-IN-7808 
  "7Q LOSS MUTATED" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-IP-7968 
"7Q LOSS WILD-TYPE" 
[1] "hr="   "8e+07"
D48V2, continuous
D48V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED      0    5
  7Q LOSS WILD-TYPE   60   93
        clus
vv       7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  FEMALE               0                60
  MALE                 5                93
D48V4, multiclass
D48V5, multiclass
    clus
vv   7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  T1               1                 5
  T2               1                51
  T3               2                59
  T4               1                17
D48V6, multiclass
    clus
vv   7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  N0               1                43
  N1               2                55
  N2               2                22
  N3               0                15
D48V7, multiclass
    clus
vv   7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  M0               5               129
  M1               0                16
  MX               0                 8
D48V8, multiclass
     clus
vv    7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  I                 1                23
  II                2                35
  III               1                42
  IV                1                25
D48V9, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED      0    5
  7Q LOSS WILD-TYPE    5  148
     clus
vv    7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  NO                0                 5
  YES               5               148
D48V10, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED      0    5
  7Q LOSS WILD-TYPE   10  143
     clus
vv    7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  NO                0                10
  YES               5               143

Clustering(49) Variable = 8p loss mutation analysis
D49V1, survival
                   sevent
clus2                0  1
  8P LOSS MUTATED    8  0
  8P LOSS WILD-TYPE 82 15
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
                8                97 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
                0                15 
$`8P LOSS MUTATED`
TCGA-BR-7716 TCGA-CG-4301 TCGA-CG-4436 TCGA-CG-4444 TCGA-CG-4449 TCGA-D7-6528 
        0.82         3.02        52.96        47.05        19.07         1.68 
TCGA-F1-6177 TCGA-IP-7968 
        6.54         2.53 

$`8P LOSS WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-6452 TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6458 
        5.62         0.10         0.95         1.41         1.35         1.35 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
        0.85         0.82         0.62         0.62         1.71         2.17 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
        0.99         1.22         0.66         1.12         0.76         0.66 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
        0.26         1.22         1.48         0.46         1.25         0.13 
TCGA-BR-7715 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 
        1.05         0.69         0.16         4.54         0.99         0.95 
TCGA-BR-7957 TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        0.69         0.82         0.69         0.36         0.49         0.30 
TCGA-CD-5803 TCGA-CG-4300 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4437 
        0.07        20.02        27.02        15.95         1.02         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4455 TCGA-CG-4460 
       54.05         4.01        14.01        29.98        12.03        21.99 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4474 
        1.02         8.98        18.94         7.07        12.00         1.02 
TCGA-CG-4477 TCGA-CG-5716 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
        1.02         1.02         6.94         1.02         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 
        5.98         0.95        70.06        12.03        15.02        28.96 
TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       31.04        65.10         4.01        55.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
        8.65         3.58         4.54         9.80        15.65         9.63 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
        8.19         6.90         0.69         5.95         6.61         4.14 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-EQ-5647 
        3.65         4.70         4.04         2.93         4.27         0.62 
TCGA-F1-6874 TCGA-F1-6875 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7998 TCGA-IN-7806 
        2.01        72.23         0.39         0.20         3.58         6.87 
TCGA-IN-7808 
        3.55 

  8P LOSS MUTATED 8P LOSS WILD-TYPE 
             0.82              0.07 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
            52.96             72.23 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
             4.78              2.17 
[1] "0.8 - 53.0 (4.8)" "0.1 - 72.2 (2.2)"
       TCGA-B7-5816        TCGA-B7-5818        TCGA-BR-6452        TCGA-BR-6455 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-BR-6457        TCGA-BR-6458        TCGA-BR-6563        TCGA-BR-6564 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-BR-6565        TCGA-BR-6566        TCGA-BR-6705        TCGA-BR-6706 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-BR-6707        TCGA-BR-6709        TCGA-BR-6710        TCGA-BR-6801 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-BR-6802        TCGA-BR-6803        TCGA-BR-6852        TCGA-BR-7196 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-BR-7197        TCGA-BR-7703        TCGA-BR-7704        TCGA-BR-7707 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-BR-7715        TCGA-BR-7716        TCGA-BR-7717        TCGA-BR-7722 
"8P LOSS WILD-TYPE"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-BR-7723        TCGA-BR-7851        TCGA-BR-7901        TCGA-BR-7957 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-CD-5798        TCGA-CD-5799        TCGA-CD-5800        TCGA-CD-5801 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-CD-5802        TCGA-CD-5803        TCGA-CG-4300        TCGA-CG-4301 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" 
       TCGA-CG-4304        TCGA-CG-4305        TCGA-CG-4306        TCGA-CG-4436 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" 
       TCGA-CG-4437        TCGA-CG-4438        TCGA-CG-4440        TCGA-CG-4441 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-CG-4443        TCGA-CG-4444        TCGA-CG-4449        TCGA-CG-4455 
"8P LOSS WILD-TYPE"   "8P LOSS MUTATED"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" 
       TCGA-CG-4460        TCGA-CG-4462        TCGA-CG-4465        TCGA-CG-4466 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-CG-4469        TCGA-CG-4472        TCGA-CG-4474        TCGA-CG-4477 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-CG-5716        TCGA-CG-5717        TCGA-CG-5718        TCGA-CG-5719 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-CG-5720        TCGA-CG-5721        TCGA-CG-5722        TCGA-CG-5723 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-CG-5724        TCGA-CG-5725        TCGA-CG-5726        TCGA-CG-5727 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-CG-5728        TCGA-CG-5730        TCGA-CG-5732        TCGA-CG-5733 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-CG-5734        TCGA-D7-5577        TCGA-D7-5578        TCGA-D7-5579 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-D7-6518        TCGA-D7-6519        TCGA-D7-6520        TCGA-D7-6521 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-D7-6522        TCGA-D7-6524        TCGA-D7-6525        TCGA-D7-6526 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-D7-6527        TCGA-D7-6528        TCGA-D7-6815        TCGA-D7-6817 
"8P LOSS WILD-TYPE"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-D7-6818        TCGA-D7-6820        TCGA-D7-6822        TCGA-EQ-5647 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875        TCGA-FP-7735 
  "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-FP-7829        TCGA-FP-7998        TCGA-IN-7806        TCGA-IN-7808 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-IP-7968 
  "8P LOSS MUTATED" 
       TCGA-B7-5816        TCGA-B7-5818        TCGA-BR-6452        TCGA-BR-6455 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-BR-6457        TCGA-BR-6458        TCGA-BR-6563        TCGA-BR-6564 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-BR-6565        TCGA-BR-6566        TCGA-BR-6705        TCGA-BR-6706 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-BR-6707        TCGA-BR-6709        TCGA-BR-6710        TCGA-BR-6801 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-BR-6802        TCGA-BR-6803        TCGA-BR-6852        TCGA-BR-7196 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-BR-7197        TCGA-BR-7703        TCGA-BR-7704        TCGA-BR-7707 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-BR-7715        TCGA-BR-7716        TCGA-BR-7717        TCGA-BR-7722 
"8P LOSS WILD-TYPE"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-BR-7723        TCGA-BR-7851        TCGA-BR-7901        TCGA-BR-7957 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-CD-5798        TCGA-CD-5799        TCGA-CD-5800        TCGA-CD-5801 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-CD-5802        TCGA-CD-5803        TCGA-CG-4300        TCGA-CG-4301 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" 
       TCGA-CG-4304        TCGA-CG-4305        TCGA-CG-4306        TCGA-CG-4436 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" 
       TCGA-CG-4437        TCGA-CG-4438        TCGA-CG-4440        TCGA-CG-4441 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-CG-4443        TCGA-CG-4444        TCGA-CG-4449        TCGA-CG-4455 
"8P LOSS WILD-TYPE"   "8P LOSS MUTATED"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" 
       TCGA-CG-4460        TCGA-CG-4462        TCGA-CG-4465        TCGA-CG-4466 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-CG-4469        TCGA-CG-4472        TCGA-CG-4474        TCGA-CG-4477 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-CG-5716        TCGA-CG-5717        TCGA-CG-5718        TCGA-CG-5719 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-CG-5720        TCGA-CG-5721        TCGA-CG-5722        TCGA-CG-5723 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-CG-5724        TCGA-CG-5725        TCGA-CG-5726        TCGA-CG-5727 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-CG-5728        TCGA-CG-5730        TCGA-CG-5732        TCGA-CG-5733 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-CG-5734        TCGA-D7-5577        TCGA-D7-5578        TCGA-D7-5579 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-D7-6518        TCGA-D7-6519        TCGA-D7-6520        TCGA-D7-6521 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-D7-6522        TCGA-D7-6524        TCGA-D7-6525        TCGA-D7-6526 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-D7-6527        TCGA-D7-6528        TCGA-D7-6815        TCGA-D7-6817 
"8P LOSS WILD-TYPE"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-D7-6818        TCGA-D7-6820        TCGA-D7-6822        TCGA-EQ-5647 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875        TCGA-FP-7735 
  "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-FP-7829        TCGA-FP-7998        TCGA-IN-7806        TCGA-IN-7808 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-IP-7968 
  "8P LOSS MUTATED" 
       TCGA-B7-5816        TCGA-B7-5818        TCGA-BR-6452        TCGA-BR-6455 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-BR-6457        TCGA-BR-6458        TCGA-BR-6563        TCGA-BR-6564 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-BR-6565        TCGA-BR-6566        TCGA-BR-6705        TCGA-BR-6706 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-BR-6707        TCGA-BR-6709        TCGA-BR-6710        TCGA-BR-6801 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-BR-6802        TCGA-BR-6803        TCGA-BR-6852        TCGA-BR-7196 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-BR-7197        TCGA-BR-7703        TCGA-BR-7704        TCGA-BR-7707 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-BR-7715        TCGA-BR-7716        TCGA-BR-7717        TCGA-BR-7722 
"8P LOSS WILD-TYPE"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-BR-7723        TCGA-BR-7851        TCGA-BR-7901        TCGA-BR-7957 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-CD-5798        TCGA-CD-5799        TCGA-CD-5800        TCGA-CD-5801 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-CD-5802        TCGA-CD-5803        TCGA-CG-4300        TCGA-CG-4301 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" 
       TCGA-CG-4304        TCGA-CG-4305        TCGA-CG-4306        TCGA-CG-4436 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" 
       TCGA-CG-4437        TCGA-CG-4438        TCGA-CG-4440        TCGA-CG-4441 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-CG-4443        TCGA-CG-4444        TCGA-CG-4449        TCGA-CG-4455 
"8P LOSS WILD-TYPE"   "8P LOSS MUTATED"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" 
       TCGA-CG-4460        TCGA-CG-4462        TCGA-CG-4465        TCGA-CG-4466 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-CG-4469        TCGA-CG-4472        TCGA-CG-4474        TCGA-CG-4477 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-CG-5716        TCGA-CG-5717        TCGA-CG-5718        TCGA-CG-5719 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-CG-5720        TCGA-CG-5721        TCGA-CG-5722        TCGA-CG-5723 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-CG-5724        TCGA-CG-5725        TCGA-CG-5726        TCGA-CG-5727 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-CG-5728        TCGA-CG-5730        TCGA-CG-5732        TCGA-CG-5733 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-CG-5734        TCGA-D7-5577        TCGA-D7-5578        TCGA-D7-5579 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-D7-6518        TCGA-D7-6519        TCGA-D7-6520        TCGA-D7-6521 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-D7-6522        TCGA-D7-6524        TCGA-D7-6525        TCGA-D7-6526 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-D7-6527        TCGA-D7-6528        TCGA-D7-6815        TCGA-D7-6817 
"8P LOSS WILD-TYPE"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-D7-6818        TCGA-D7-6820        TCGA-D7-6822        TCGA-EQ-5647 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875        TCGA-FP-7735 
  "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-FP-7829        TCGA-FP-7998        TCGA-IN-7806        TCGA-IN-7808 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-IP-7968 
  "8P LOSS MUTATED" 
[1] "hr="     "8.3e+07"
D49V2, continuous
D49V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED      4    9
  8P LOSS WILD-TYPE   56   89
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  FEMALE               4                56
  MALE                 9                89
D49V4, multiclass
D49V5, multiclass
    clus
vv   8P LOSS MUTATED 8P LOSS WILD-TYPE
  T1               1                 5
  T2               5                47
  T3               2                59
  T4               2                16
D49V6, multiclass
    clus
vv   8P LOSS MUTATED 8P LOSS WILD-TYPE
  N0               2                42
  N1               7                50
  N2               2                22
  N3               0                15
D49V7, multiclass
    clus
vv   8P LOSS MUTATED 8P LOSS WILD-TYPE
  M0              10               124
  M1               1                15
  MX               2                 6
D49V8, multiclass
     clus
vv    8P LOSS MUTATED 8P LOSS WILD-TYPE
  I                 3                21
  II                2                35
  III               2                41
  IV                2                24
D49V9, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED      0   13
  8P LOSS WILD-TYPE    5  140
     clus
vv    8P LOSS MUTATED 8P LOSS WILD-TYPE
  NO                0                 5
  YES              13               140
D49V10, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED      0   13
  8P LOSS WILD-TYPE   10  135
     clus
vv    8P LOSS MUTATED 8P LOSS WILD-TYPE
  NO                0                10
  YES              13               135

Clustering(50) Variable = 8q loss mutation analysis
D50V1, survival
                   sevent
clus2                0  1
  8Q LOSS MUTATED    1  0
  8Q LOSS WILD-TYPE 89 15
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                1               104 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                0                15 
$`8Q LOSS MUTATED`
TCGA-D7-6528 
        1.68 

$`8Q LOSS WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-6452 TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6458 
        5.62         0.10         0.95         1.41         1.35         1.35 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
        0.85         0.82         0.62         0.62         1.71         2.17 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
        0.99         1.22         0.66         1.12         0.76         0.66 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
        0.26         1.22         1.48         0.46         1.25         0.13 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 
        1.05         0.82         0.69         0.16         4.54         0.99 
TCGA-BR-7901 TCGA-BR-7957 TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
        0.95         0.69         0.82         0.69         0.36         0.49 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
        0.30         0.07        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02        52.96         8.05        54.05         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4460 TCGA-CG-4462 
       29.98        47.05        19.07        12.03        21.99         1.02 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4474 TCGA-CG-4477 
        8.98        18.94         7.07        12.00         1.02         1.02 
TCGA-CG-5716 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
        1.02         6.94         1.02         1.02         0.99         5.98 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5727 
        0.95        70.06        12.03        15.02        28.96        31.04 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        55.04        21.07         7.99         8.65 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
        3.58         4.54         9.80        15.65         9.63         8.19 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6815 
        6.90         0.69         5.95         6.61         4.14         3.65 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-EQ-5647 TCGA-F1-6177 
        4.70         4.04         2.93         4.27         0.62         6.54 
TCGA-F1-6874 TCGA-F1-6875 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7998 TCGA-IN-7806 
        2.01        72.23         0.39         0.20         3.58         6.87 
TCGA-IN-7808 TCGA-IP-7968 
        3.55         2.53 

  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
             1.68              0.07 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
             1.68             72.23 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
            1.680             2.975 
[1] "1.7 - 1.7 (1.7)"  "0.1 - 72.2 (3.0)"
       TCGA-B7-5816        TCGA-B7-5818        TCGA-BR-6452        TCGA-BR-6455 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BR-6457        TCGA-BR-6458        TCGA-BR-6563        TCGA-BR-6564 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BR-6565        TCGA-BR-6566        TCGA-BR-6705        TCGA-BR-6706 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BR-6707        TCGA-BR-6709        TCGA-BR-6710        TCGA-BR-6801 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BR-6802        TCGA-BR-6803        TCGA-BR-6852        TCGA-BR-7196 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BR-7197        TCGA-BR-7703        TCGA-BR-7704        TCGA-BR-7707 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BR-7715        TCGA-BR-7716        TCGA-BR-7717        TCGA-BR-7722 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BR-7723        TCGA-BR-7851        TCGA-BR-7901        TCGA-BR-7957 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-CD-5798        TCGA-CD-5799        TCGA-CD-5800        TCGA-CD-5801 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-CD-5802        TCGA-CD-5803        TCGA-CG-4300        TCGA-CG-4301 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-CG-4304        TCGA-CG-4305        TCGA-CG-4306        TCGA-CG-4436 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-CG-4437        TCGA-CG-4438        TCGA-CG-4440        TCGA-CG-4441 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-CG-4443        TCGA-CG-4444        TCGA-CG-4449        TCGA-CG-4455 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-CG-4460        TCGA-CG-4462        TCGA-CG-4465        TCGA-CG-4466 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-CG-4469        TCGA-CG-4472        TCGA-CG-4474        TCGA-CG-4477 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-CG-5716        TCGA-CG-5717        TCGA-CG-5718        TCGA-CG-5719 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-CG-5720        TCGA-CG-5721        TCGA-CG-5722        TCGA-CG-5723 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-CG-5724        TCGA-CG-5725        TCGA-CG-5726        TCGA-CG-5727 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-CG-5728        TCGA-CG-5730        TCGA-CG-5732        TCGA-CG-5733 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-CG-5734        TCGA-D7-5577        TCGA-D7-5578        TCGA-D7-5579 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-D7-6518        TCGA-D7-6519        TCGA-D7-6520        TCGA-D7-6521 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-D7-6522        TCGA-D7-6524        TCGA-D7-6525        TCGA-D7-6526 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-D7-6527        TCGA-D7-6528        TCGA-D7-6815        TCGA-D7-6817 
"8Q LOSS WILD-TYPE"   "8Q LOSS MUTATED" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-D7-6818        TCGA-D7-6820        TCGA-D7-6822        TCGA-EQ-5647 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875        TCGA-FP-7735 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-FP-7829        TCGA-FP-7998        TCGA-IN-7806        TCGA-IN-7808 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-IP-7968 
"8Q LOSS WILD-TYPE" 
       TCGA-B7-5816        TCGA-B7-5818        TCGA-BR-6452        TCGA-BR-6455 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BR-6457        TCGA-BR-6458        TCGA-BR-6563        TCGA-BR-6564 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BR-6565        TCGA-BR-6566        TCGA-BR-6705        TCGA-BR-6706 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BR-6707        TCGA-BR-6709        TCGA-BR-6710        TCGA-BR-6801 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BR-6802        TCGA-BR-6803        TCGA-BR-6852        TCGA-BR-7196 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BR-7197        TCGA-BR-7703        TCGA-BR-7704        TCGA-BR-7707 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BR-7715        TCGA-BR-7716        TCGA-BR-7717        TCGA-BR-7722 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BR-7723        TCGA-BR-7851        TCGA-BR-7901        TCGA-BR-7957 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-CD-5798        TCGA-CD-5799        TCGA-CD-5800        TCGA-CD-5801 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-CD-5802        TCGA-CD-5803        TCGA-CG-4300        TCGA-CG-4301 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-CG-4304        TCGA-CG-4305        TCGA-CG-4306        TCGA-CG-4436 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-CG-4437        TCGA-CG-4438        TCGA-CG-4440        TCGA-CG-4441 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-CG-4443        TCGA-CG-4444        TCGA-CG-4449        TCGA-CG-4455 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-CG-4460        TCGA-CG-4462        TCGA-CG-4465        TCGA-CG-4466 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-CG-4469        TCGA-CG-4472        TCGA-CG-4474        TCGA-CG-4477 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-CG-5716        TCGA-CG-5717        TCGA-CG-5718        TCGA-CG-5719 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-CG-5720        TCGA-CG-5721        TCGA-CG-5722        TCGA-CG-5723 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-CG-5724        TCGA-CG-5725        TCGA-CG-5726        TCGA-CG-5727 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-CG-5728        TCGA-CG-5730        TCGA-CG-5732        TCGA-CG-5733 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-CG-5734        TCGA-D7-5577        TCGA-D7-5578        TCGA-D7-5579 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-D7-6518        TCGA-D7-6519        TCGA-D7-6520        TCGA-D7-6521 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-D7-6522        TCGA-D7-6524        TCGA-D7-6525        TCGA-D7-6526 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-D7-6527        TCGA-D7-6528        TCGA-D7-6815        TCGA-D7-6817 
"8Q LOSS WILD-TYPE"   "8Q LOSS MUTATED" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-D7-6818        TCGA-D7-6820        TCGA-D7-6822        TCGA-EQ-5647 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875        TCGA-FP-7735 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-FP-7829        TCGA-FP-7998        TCGA-IN-7806        TCGA-IN-7808 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-IP-7968 
"8Q LOSS WILD-TYPE" 
       TCGA-B7-5816        TCGA-B7-5818        TCGA-BR-6452        TCGA-BR-6455 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BR-6457        TCGA-BR-6458        TCGA-BR-6563        TCGA-BR-6564 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BR-6565        TCGA-BR-6566        TCGA-BR-6705        TCGA-BR-6706 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BR-6707        TCGA-BR-6709        TCGA-BR-6710        TCGA-BR-6801 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BR-6802        TCGA-BR-6803        TCGA-BR-6852        TCGA-BR-7196 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BR-7197        TCGA-BR-7703        TCGA-BR-7704        TCGA-BR-7707 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BR-7715        TCGA-BR-7716        TCGA-BR-7717        TCGA-BR-7722 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BR-7723        TCGA-BR-7851        TCGA-BR-7901        TCGA-BR-7957 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-CD-5798        TCGA-CD-5799        TCGA-CD-5800        TCGA-CD-5801 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-CD-5802        TCGA-CD-5803        TCGA-CG-4300        TCGA-CG-4301 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-CG-4304        TCGA-CG-4305        TCGA-CG-4306        TCGA-CG-4436 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-CG-4437        TCGA-CG-4438        TCGA-CG-4440        TCGA-CG-4441 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-CG-4443        TCGA-CG-4444        TCGA-CG-4449        TCGA-CG-4455 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-CG-4460        TCGA-CG-4462        TCGA-CG-4465        TCGA-CG-4466 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-CG-4469        TCGA-CG-4472        TCGA-CG-4474        TCGA-CG-4477 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-CG-5716        TCGA-CG-5717        TCGA-CG-5718        TCGA-CG-5719 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-CG-5720        TCGA-CG-5721        TCGA-CG-5722        TCGA-CG-5723 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-CG-5724        TCGA-CG-5725        TCGA-CG-5726        TCGA-CG-5727 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-CG-5728        TCGA-CG-5730        TCGA-CG-5732        TCGA-CG-5733 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-CG-5734        TCGA-D7-5577        TCGA-D7-5578        TCGA-D7-5579 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-D7-6518        TCGA-D7-6519        TCGA-D7-6520        TCGA-D7-6521 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-D7-6522        TCGA-D7-6524        TCGA-D7-6525        TCGA-D7-6526 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-D7-6527        TCGA-D7-6528        TCGA-D7-6815        TCGA-D7-6817 
"8Q LOSS WILD-TYPE"   "8Q LOSS MUTATED" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-D7-6818        TCGA-D7-6820        TCGA-D7-6822        TCGA-EQ-5647 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875        TCGA-FP-7735 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-FP-7829        TCGA-FP-7998        TCGA-IN-7806        TCGA-IN-7808 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-IP-7968 
"8Q LOSS WILD-TYPE" 
[1] "Remove cluster labels:" "8Q LOSS MUTATED"       
clus
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                1               104 
       TCGA-B7-5816        TCGA-B7-5818        TCGA-BR-6452        TCGA-BR-6455 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BR-6457        TCGA-BR-6458        TCGA-BR-6563        TCGA-BR-6564 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BR-6565        TCGA-BR-6566        TCGA-BR-6705        TCGA-BR-6706 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BR-6707        TCGA-BR-6709        TCGA-BR-6710        TCGA-BR-6801 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BR-6802        TCGA-BR-6803        TCGA-BR-6852        TCGA-BR-7196 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BR-7197        TCGA-BR-7703        TCGA-BR-7704        TCGA-BR-7707 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BR-7715        TCGA-BR-7716        TCGA-BR-7717        TCGA-BR-7722 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BR-7723        TCGA-BR-7851        TCGA-BR-7901        TCGA-BR-7957 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-CD-5798        TCGA-CD-5799        TCGA-CD-5800        TCGA-CD-5801 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-CD-5802        TCGA-CD-5803        TCGA-CG-4300        TCGA-CG-4301 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-CG-4304        TCGA-CG-4305        TCGA-CG-4306        TCGA-CG-4436 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-CG-4437        TCGA-CG-4438        TCGA-CG-4440        TCGA-CG-4441 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-CG-4443        TCGA-CG-4444        TCGA-CG-4449        TCGA-CG-4455 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-CG-4460        TCGA-CG-4462        TCGA-CG-4465        TCGA-CG-4466 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-CG-4469        TCGA-CG-4472        TCGA-CG-4474        TCGA-CG-4477 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-CG-5716        TCGA-CG-5717        TCGA-CG-5718        TCGA-CG-5719 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-CG-5720        TCGA-CG-5721        TCGA-CG-5722        TCGA-CG-5723 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-CG-5724        TCGA-CG-5725        TCGA-CG-5726        TCGA-CG-5727 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-CG-5728        TCGA-CG-5730        TCGA-CG-5732        TCGA-CG-5733 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-CG-5734        TCGA-D7-5577        TCGA-D7-5578        TCGA-D7-5579 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-D7-6518        TCGA-D7-6519        TCGA-D7-6520        TCGA-D7-6521 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-D7-6522        TCGA-D7-6524        TCGA-D7-6525        TCGA-D7-6526 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-D7-6527        TCGA-D7-6815        TCGA-D7-6817        TCGA-D7-6818 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-D7-6820        TCGA-D7-6822        TCGA-EQ-5647        TCGA-F1-6177 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-F1-6874        TCGA-F1-6875        TCGA-FP-7735        TCGA-FP-7829 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-FP-7998        TCGA-IN-7806        TCGA-IN-7808        TCGA-IP-7968 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
D50V2, continuous
D50V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED      2    2
  8Q LOSS WILD-TYPE   58   96
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  FEMALE               2                58
  MALE                 2                96
D50V4, multiclass
D50V5, multiclass
[1] "Remove cluster labels:" "8Q LOSS MUTATED"       
clus
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                2               135 
       TCGA-B7-5816        TCGA-B7-5818        TCGA-BR-4183        TCGA-BR-4184 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BR-4190        TCGA-BR-4201        TCGA-BR-4253        TCGA-BR-4255 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BR-4267        TCGA-BR-4277        TCGA-BR-4278        TCGA-BR-4279 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BR-4280        TCGA-BR-4292        TCGA-BR-4298        TCGA-BR-4357 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BR-4361        TCGA-BR-4363        TCGA-BR-4368        TCGA-BR-4371 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BR-4376        TCGA-BR-6452        TCGA-BR-6453        TCGA-BR-6454 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BR-6455        TCGA-BR-6456        TCGA-BR-6457        TCGA-BR-6458 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BR-6563        TCGA-BR-6564        TCGA-BR-6565        TCGA-BR-6566 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BR-6705        TCGA-BR-6706        TCGA-BR-6707        TCGA-BR-6709 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BR-6710        TCGA-BR-6801        TCGA-BR-6802        TCGA-BR-6803 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BR-6852        TCGA-BR-7196        TCGA-BR-7197        TCGA-BR-7703 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BR-7704        TCGA-BR-7707        TCGA-BR-7715        TCGA-BR-7716 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BR-7717        TCGA-BR-7722        TCGA-BR-7723        TCGA-BR-7851 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BR-7901        TCGA-BR-7957        TCGA-CD-5798        TCGA-CD-5799 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-CD-5800        TCGA-CD-5801        TCGA-CD-5802        TCGA-CD-5803 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-CD-5804        TCGA-CG-4300        TCGA-CG-4301        TCGA-CG-4304 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-CG-4305        TCGA-CG-4306        TCGA-CG-4436        TCGA-CG-4437 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-CG-4438        TCGA-CG-4440        TCGA-CG-4441        TCGA-CG-4442 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-CG-4443        TCGA-CG-4444        TCGA-CG-4449        TCGA-CG-4455 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-CG-4460        TCGA-CG-4462        TCGA-CG-4465        TCGA-CG-4466 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-CG-4469        TCGA-CG-4472        TCGA-CG-4474        TCGA-CG-4475 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-CG-4476        TCGA-CG-4477        TCGA-CG-5716        TCGA-CG-5717 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-CG-5718        TCGA-CG-5719        TCGA-CG-5720        TCGA-CG-5721 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-CG-5722        TCGA-CG-5723        TCGA-CG-5724        TCGA-CG-5725 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-CG-5726        TCGA-CG-5727        TCGA-CG-5728        TCGA-CG-5730 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-CG-5732        TCGA-CG-5733        TCGA-CG-5734        TCGA-D7-5577 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-D7-5578        TCGA-D7-5579        TCGA-D7-6518        TCGA-D7-6519 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-D7-6520        TCGA-D7-6521        TCGA-D7-6522        TCGA-D7-6524 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-D7-6525        TCGA-D7-6526        TCGA-D7-6527        TCGA-D7-6815 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-D7-6817        TCGA-D7-6818        TCGA-D7-6820        TCGA-D7-6822 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EQ-5647        TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-FP-7735        TCGA-FP-7829        TCGA-FP-7998        TCGA-HF-7131 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-HF-7132        TCGA-HF-7133        TCGA-HF-7134        TCGA-HF-7136 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-IN-7806        TCGA-IN-7808        TCGA-IP-7968 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
D50V6, multiclass
[1] "Remove cluster labels:" "8Q LOSS MUTATED"       
clus
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                2               138 
       TCGA-B7-5816        TCGA-B7-5818        TCGA-BR-4183        TCGA-BR-4184 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BR-4188        TCGA-BR-4190        TCGA-BR-4195        TCGA-BR-4199 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BR-4200        TCGA-BR-4253        TCGA-BR-4255        TCGA-BR-4256 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BR-4261        TCGA-BR-4267        TCGA-BR-4278        TCGA-BR-4279 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BR-4280        TCGA-BR-4281        TCGA-BR-4298        TCGA-BR-4361 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BR-4362        TCGA-BR-4367        TCGA-BR-4368        TCGA-BR-4376 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BR-6452        TCGA-BR-6453        TCGA-BR-6454        TCGA-BR-6455 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BR-6456        TCGA-BR-6457        TCGA-BR-6458        TCGA-BR-6563 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BR-6564        TCGA-BR-6565        TCGA-BR-6566        TCGA-BR-6705 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BR-6706        TCGA-BR-6707        TCGA-BR-6709        TCGA-BR-6710 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BR-6801        TCGA-BR-6802        TCGA-BR-6803        TCGA-BR-6852 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BR-7196        TCGA-BR-7197        TCGA-BR-7703        TCGA-BR-7704 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BR-7707        TCGA-BR-7715        TCGA-BR-7716        TCGA-BR-7717 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BR-7722        TCGA-BR-7723        TCGA-BR-7851        TCGA-BR-7901 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BR-7957        TCGA-CD-5798        TCGA-CD-5799        TCGA-CD-5800 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-CD-5801        TCGA-CD-5802        TCGA-CD-5803        TCGA-CD-5804 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-CG-4300        TCGA-CG-4301        TCGA-CG-4304        TCGA-CG-4305 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-CG-4306        TCGA-CG-4436        TCGA-CG-4437        TCGA-CG-4438 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-CG-4440        TCGA-CG-4441        TCGA-CG-4442        TCGA-CG-4443 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-CG-4444        TCGA-CG-4449        TCGA-CG-4455        TCGA-CG-4460 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-CG-4462        TCGA-CG-4465        TCGA-CG-4466        TCGA-CG-4469 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-CG-4472        TCGA-CG-4474        TCGA-CG-4475        TCGA-CG-4476 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-CG-4477        TCGA-CG-5716        TCGA-CG-5717        TCGA-CG-5718 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-CG-5719        TCGA-CG-5720        TCGA-CG-5721        TCGA-CG-5722 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-CG-5723        TCGA-CG-5724        TCGA-CG-5725        TCGA-CG-5726 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-CG-5727        TCGA-CG-5728        TCGA-CG-5730        TCGA-CG-5732 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-CG-5733        TCGA-CG-5734        TCGA-D7-5577        TCGA-D7-5578 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-D7-5579        TCGA-D7-6518        TCGA-D7-6519        TCGA-D7-6520 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-D7-6521        TCGA-D7-6522        TCGA-D7-6524        TCGA-D7-6525 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-D7-6526        TCGA-D7-6527        TCGA-D7-6815        TCGA-D7-6817 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-D7-6818        TCGA-D7-6820        TCGA-D7-6822        TCGA-EQ-5647 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875        TCGA-FP-7735 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-FP-7829        TCGA-FP-7998        TCGA-HF-7131        TCGA-HF-7132 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-HF-7133        TCGA-HF-7134        TCGA-HF-7136        TCGA-IN-7806 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-IN-7808        TCGA-IP-7968 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
D50V7, multiclass
    clus
vv   8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  M0               4               130
  M1               0                16
  MX               0                 8
D50V8, multiclass
[1] "Remove cluster labels:" "8Q LOSS MUTATED"       
clus
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                1               129 
       TCGA-B7-5816        TCGA-B7-5818        TCGA-BR-4183        TCGA-BR-4184 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BR-4190        TCGA-BR-4253        TCGA-BR-4255        TCGA-BR-4267 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BR-4278        TCGA-BR-4279        TCGA-BR-4280        TCGA-BR-4298 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BR-4361        TCGA-BR-4368        TCGA-BR-4376        TCGA-BR-6452 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BR-6453        TCGA-BR-6454        TCGA-BR-6455        TCGA-BR-6456 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BR-6457        TCGA-BR-6458        TCGA-BR-6563        TCGA-BR-6564 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BR-6565        TCGA-BR-6566        TCGA-BR-6705        TCGA-BR-6706 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BR-6707        TCGA-BR-6709        TCGA-BR-6710        TCGA-BR-6801 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BR-6802        TCGA-BR-6803        TCGA-BR-6852        TCGA-BR-7196 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BR-7197        TCGA-BR-7703        TCGA-BR-7704        TCGA-BR-7707 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BR-7715        TCGA-BR-7716        TCGA-BR-7717        TCGA-BR-7722 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BR-7723        TCGA-BR-7851        TCGA-BR-7901        TCGA-BR-7957 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-CD-5798        TCGA-CD-5799        TCGA-CD-5800        TCGA-CD-5801 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-CD-5802        TCGA-CD-5803        TCGA-CD-5804        TCGA-CG-4300 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-CG-4301        TCGA-CG-4304        TCGA-CG-4305        TCGA-CG-4306 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-CG-4436        TCGA-CG-4437        TCGA-CG-4438        TCGA-CG-4440 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-CG-4441        TCGA-CG-4442        TCGA-CG-4443        TCGA-CG-4444 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-CG-4449        TCGA-CG-4455        TCGA-CG-4460        TCGA-CG-4462 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-CG-4465        TCGA-CG-4466        TCGA-CG-4469        TCGA-CG-4472 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-CG-4474        TCGA-CG-4475        TCGA-CG-4476        TCGA-CG-4477 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-CG-5716        TCGA-CG-5717        TCGA-CG-5718        TCGA-CG-5719 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-CG-5720        TCGA-CG-5721        TCGA-CG-5722        TCGA-CG-5723 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-CG-5724        TCGA-CG-5725        TCGA-CG-5726        TCGA-CG-5727 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-CG-5728        TCGA-CG-5730        TCGA-CG-5732        TCGA-CG-5733 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-CG-5734        TCGA-D7-5577        TCGA-D7-5578        TCGA-D7-5579 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-D7-6518        TCGA-D7-6519        TCGA-D7-6520        TCGA-D7-6521 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-D7-6522        TCGA-D7-6524        TCGA-D7-6525        TCGA-D7-6526 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-D7-6527        TCGA-D7-6815        TCGA-D7-6817        TCGA-D7-6818 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-D7-6820        TCGA-D7-6822        TCGA-EQ-5647        TCGA-F1-6177 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-F1-6874        TCGA-F1-6875        TCGA-FP-7735        TCGA-FP-7829 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-FP-7998        TCGA-HF-7131        TCGA-HF-7132        TCGA-HF-7133 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-HF-7134        TCGA-HF-7136        TCGA-IN-7806        TCGA-IN-7808 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-IP-7968 
"8Q LOSS WILD-TYPE" 
D50V9, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED      0    4
  8Q LOSS WILD-TYPE    5  149
     clus
vv    8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  NO                0                 5
  YES               4               149
D50V10, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED      0    4
  8Q LOSS WILD-TYPE   10  144
     clus
vv    8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  NO                0                10
  YES               4               144

Clustering(51) Variable = 9p loss mutation analysis
D51V1, survival
                   sevent
clus2                0  1
  9P LOSS MUTATED   19  2
  9P LOSS WILD-TYPE 71 13
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               21                84 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
                2                13 
$`9P LOSS MUTATED`
TCGA-BR-7197 TCGA-BR-7723 TCGA-CD-5799 TCGA-CG-4301 TCGA-CG-4438 TCGA-CG-4449 
        1.48         4.54         0.69         3.02        54.05        19.07 
TCGA-CG-4466 TCGA-CG-4472 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5725 TCGA-CG-5730 
       18.94        12.00         1.02         1.02        15.02         4.01 
TCGA-CG-5732 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6525 TCGA-D7-6526 
       55.04        15.65         9.63         8.19         5.95         6.61 
TCGA-D7-6817 TCGA-F1-6875 TCGA-IN-7806 
        4.70        72.23         6.87 

$`9P LOSS WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-6452 TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6458 
        5.62         0.10         0.95         1.41         1.35         1.35 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
        0.85         0.82         0.62         0.62         1.71         2.17 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
        0.99         1.22         0.66         1.12         0.76         0.66 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
        0.26         1.22         0.46         1.25         0.13         1.05 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 
        0.82         0.69         0.16         0.99         0.95         0.69 
TCGA-CD-5798 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CG-4300 
        0.82         0.36         0.49         0.30         0.07        20.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4440 
       27.02        15.95         1.02        52.96         8.05         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4455 TCGA-CG-4460 TCGA-CG-4462 
       14.01        29.98        47.05        12.03        21.99         1.02 
TCGA-CG-4465 TCGA-CG-4469 TCGA-CG-4474 TCGA-CG-4477 TCGA-CG-5716 TCGA-CG-5717 
        8.98         7.07         1.02         1.02         1.02         6.94 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 
        0.99         5.98         0.95        70.06        12.03        28.96 
TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
       31.04        65.10        21.07         7.99         8.65         3.58 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6527 TCGA-D7-6528 
        4.54         9.80         6.90         0.69         4.14         1.68 
TCGA-D7-6815 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-EQ-5647 TCGA-F1-6177 
        3.65         4.04         2.93         4.27         0.62         6.54 
TCGA-F1-6874 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7998 TCGA-IN-7808 TCGA-IP-7968 
        2.01         0.39         0.20         3.58         3.55         2.53 

  9P LOSS MUTATED 9P LOSS WILD-TYPE 
             0.69              0.07 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
            72.23             70.06 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
             6.87              1.38 
[1] "0.7 - 72.2 (6.9)" "0.1 - 70.1 (1.4)"
       TCGA-B7-5816        TCGA-B7-5818        TCGA-BR-6452        TCGA-BR-6455 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-BR-6457        TCGA-BR-6458        TCGA-BR-6563        TCGA-BR-6564 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-BR-6565        TCGA-BR-6566        TCGA-BR-6705        TCGA-BR-6706 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-BR-6707        TCGA-BR-6709        TCGA-BR-6710        TCGA-BR-6801 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-BR-6802        TCGA-BR-6803        TCGA-BR-6852        TCGA-BR-7196 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-BR-7197        TCGA-BR-7703        TCGA-BR-7704        TCGA-BR-7707 
  "9P LOSS MUTATED" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-BR-7715        TCGA-BR-7716        TCGA-BR-7717        TCGA-BR-7722 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-BR-7723        TCGA-BR-7851        TCGA-BR-7901        TCGA-BR-7957 
  "9P LOSS MUTATED" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-CD-5798        TCGA-CD-5799        TCGA-CD-5800        TCGA-CD-5801 
"9P LOSS WILD-TYPE"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-CD-5802        TCGA-CD-5803        TCGA-CG-4300        TCGA-CG-4301 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" 
       TCGA-CG-4304        TCGA-CG-4305        TCGA-CG-4306        TCGA-CG-4436 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-CG-4437        TCGA-CG-4438        TCGA-CG-4440        TCGA-CG-4441 
"9P LOSS WILD-TYPE"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-CG-4443        TCGA-CG-4444        TCGA-CG-4449        TCGA-CG-4455 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" 
       TCGA-CG-4460        TCGA-CG-4462        TCGA-CG-4465        TCGA-CG-4466 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" 
       TCGA-CG-4469        TCGA-CG-4472        TCGA-CG-4474        TCGA-CG-4477 
"9P LOSS WILD-TYPE"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-CG-5716        TCGA-CG-5717        TCGA-CG-5718        TCGA-CG-5719 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED"   "9P LOSS MUTATED" 
       TCGA-CG-5720        TCGA-CG-5721        TCGA-CG-5722        TCGA-CG-5723 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-CG-5724        TCGA-CG-5725        TCGA-CG-5726        TCGA-CG-5727 
"9P LOSS WILD-TYPE"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-CG-5728        TCGA-CG-5730        TCGA-CG-5732        TCGA-CG-5733 
"9P LOSS WILD-TYPE"   "9P LOSS MUTATED"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" 
       TCGA-CG-5734        TCGA-D7-5577        TCGA-D7-5578        TCGA-D7-5579 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-D7-6518        TCGA-D7-6519        TCGA-D7-6520        TCGA-D7-6521 
"9P LOSS WILD-TYPE"   "9P LOSS MUTATED"   "9P LOSS MUTATED"   "9P LOSS MUTATED" 
       TCGA-D7-6522        TCGA-D7-6524        TCGA-D7-6525        TCGA-D7-6526 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED"   "9P LOSS MUTATED" 
       TCGA-D7-6527        TCGA-D7-6528        TCGA-D7-6815        TCGA-D7-6817 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" 
       TCGA-D7-6818        TCGA-D7-6820        TCGA-D7-6822        TCGA-EQ-5647 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875        TCGA-FP-7735 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" 
       TCGA-FP-7829        TCGA-FP-7998        TCGA-IN-7806        TCGA-IN-7808 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" 
       TCGA-IP-7968 
"9P LOSS WILD-TYPE" 
       TCGA-B7-5816        TCGA-B7-5818        TCGA-BR-6452        TCGA-BR-6455 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-BR-6457        TCGA-BR-6458        TCGA-BR-6563        TCGA-BR-6564 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-BR-6565        TCGA-BR-6566        TCGA-BR-6705        TCGA-BR-6706 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-BR-6707        TCGA-BR-6709        TCGA-BR-6710        TCGA-BR-6801 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-BR-6802        TCGA-BR-6803        TCGA-BR-6852        TCGA-BR-7196 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-BR-7197        TCGA-BR-7703        TCGA-BR-7704        TCGA-BR-7707 
  "9P LOSS MUTATED" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-BR-7715        TCGA-BR-7716        TCGA-BR-7717        TCGA-BR-7722 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-BR-7723        TCGA-BR-7851        TCGA-BR-7901        TCGA-BR-7957 
  "9P LOSS MUTATED" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-CD-5798        TCGA-CD-5799        TCGA-CD-5800        TCGA-CD-5801 
"9P LOSS WILD-TYPE"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-CD-5802        TCGA-CD-5803        TCGA-CG-4300        TCGA-CG-4301 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" 
       TCGA-CG-4304        TCGA-CG-4305        TCGA-CG-4306        TCGA-CG-4436 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-CG-4437        TCGA-CG-4438        TCGA-CG-4440        TCGA-CG-4441 
"9P LOSS WILD-TYPE"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-CG-4443        TCGA-CG-4444        TCGA-CG-4449        TCGA-CG-4455 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" 
       TCGA-CG-4460        TCGA-CG-4462        TCGA-CG-4465        TCGA-CG-4466 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" 
       TCGA-CG-4469        TCGA-CG-4472        TCGA-CG-4474        TCGA-CG-4477 
"9P LOSS WILD-TYPE"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-CG-5716        TCGA-CG-5717        TCGA-CG-5718        TCGA-CG-5719 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED"   "9P LOSS MUTATED" 
       TCGA-CG-5720        TCGA-CG-5721        TCGA-CG-5722        TCGA-CG-5723 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-CG-5724        TCGA-CG-5725        TCGA-CG-5726        TCGA-CG-5727 
"9P LOSS WILD-TYPE"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-CG-5728        TCGA-CG-5730        TCGA-CG-5732        TCGA-CG-5733 
"9P LOSS WILD-TYPE"   "9P LOSS MUTATED"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" 
       TCGA-CG-5734        TCGA-D7-5577        TCGA-D7-5578        TCGA-D7-5579 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-D7-6518        TCGA-D7-6519        TCGA-D7-6520        TCGA-D7-6521 
"9P LOSS WILD-TYPE"   "9P LOSS MUTATED"   "9P LOSS MUTATED"   "9P LOSS MUTATED" 
       TCGA-D7-6522        TCGA-D7-6524        TCGA-D7-6525        TCGA-D7-6526 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED"   "9P LOSS MUTATED" 
       TCGA-D7-6527        TCGA-D7-6528        TCGA-D7-6815        TCGA-D7-6817 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" 
       TCGA-D7-6818        TCGA-D7-6820        TCGA-D7-6822        TCGA-EQ-5647 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875        TCGA-FP-7735 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" 
       TCGA-FP-7829        TCGA-FP-7998        TCGA-IN-7806        TCGA-IN-7808 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" 
       TCGA-IP-7968 
"9P LOSS WILD-TYPE" 
       TCGA-B7-5816        TCGA-B7-5818        TCGA-BR-6452        TCGA-BR-6455 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-BR-6457        TCGA-BR-6458        TCGA-BR-6563        TCGA-BR-6564 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-BR-6565        TCGA-BR-6566        TCGA-BR-6705        TCGA-BR-6706 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-BR-6707        TCGA-BR-6709        TCGA-BR-6710        TCGA-BR-6801 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-BR-6802        TCGA-BR-6803        TCGA-BR-6852        TCGA-BR-7196 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-BR-7197        TCGA-BR-7703        TCGA-BR-7704        TCGA-BR-7707 
  "9P LOSS MUTATED" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-BR-7715        TCGA-BR-7716        TCGA-BR-7717        TCGA-BR-7722 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-BR-7723        TCGA-BR-7851        TCGA-BR-7901        TCGA-BR-7957 
  "9P LOSS MUTATED" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-CD-5798        TCGA-CD-5799        TCGA-CD-5800        TCGA-CD-5801 
"9P LOSS WILD-TYPE"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-CD-5802        TCGA-CD-5803        TCGA-CG-4300        TCGA-CG-4301 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" 
       TCGA-CG-4304        TCGA-CG-4305        TCGA-CG-4306        TCGA-CG-4436 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-CG-4437        TCGA-CG-4438        TCGA-CG-4440        TCGA-CG-4441 
"9P LOSS WILD-TYPE"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-CG-4443        TCGA-CG-4444        TCGA-CG-4449        TCGA-CG-4455 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" 
       TCGA-CG-4460        TCGA-CG-4462        TCGA-CG-4465        TCGA-CG-4466 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" 
       TCGA-CG-4469        TCGA-CG-4472        TCGA-CG-4474        TCGA-CG-4477 
"9P LOSS WILD-TYPE"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-CG-5716        TCGA-CG-5717        TCGA-CG-5718        TCGA-CG-5719 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED"   "9P LOSS MUTATED" 
       TCGA-CG-5720        TCGA-CG-5721        TCGA-CG-5722        TCGA-CG-5723 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-CG-5724        TCGA-CG-5725        TCGA-CG-5726        TCGA-CG-5727 
"9P LOSS WILD-TYPE"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-CG-5728        TCGA-CG-5730        TCGA-CG-5732        TCGA-CG-5733 
"9P LOSS WILD-TYPE"   "9P LOSS MUTATED"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" 
       TCGA-CG-5734        TCGA-D7-5577        TCGA-D7-5578        TCGA-D7-5579 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-D7-6518        TCGA-D7-6519        TCGA-D7-6520        TCGA-D7-6521 
"9P LOSS WILD-TYPE"   "9P LOSS MUTATED"   "9P LOSS MUTATED"   "9P LOSS MUTATED" 
       TCGA-D7-6522        TCGA-D7-6524        TCGA-D7-6525        TCGA-D7-6526 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED"   "9P LOSS MUTATED" 
       TCGA-D7-6527        TCGA-D7-6528        TCGA-D7-6815        TCGA-D7-6817 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" 
       TCGA-D7-6818        TCGA-D7-6820        TCGA-D7-6822        TCGA-EQ-5647 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875        TCGA-FP-7735 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" 
       TCGA-FP-7829        TCGA-FP-7998        TCGA-IN-7806        TCGA-IN-7808 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" 
       TCGA-IP-7968 
"9P LOSS WILD-TYPE" 
[1] "hr=" "5.7"
D51V2, continuous
D51V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED     10   18
  9P LOSS WILD-TYPE   50   80
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  FEMALE              10                50
  MALE                18                80
D51V4, multiclass
D51V5, multiclass
    clus
vv   9P LOSS MUTATED 9P LOSS WILD-TYPE
  T1               0                 6
  T2              14                38
  T3               5                56
  T4               4                14
D51V6, multiclass
    clus
vv   9P LOSS MUTATED 9P LOSS WILD-TYPE
  N0               5                39
  N1              11                46
  N2               6                18
  N3               3                12
D51V7, multiclass
    clus
vv   9P LOSS MUTATED 9P LOSS WILD-TYPE
  M0              25               109
  M1               3                13
  MX               0                 8
D51V8, multiclass
     clus
vv    9P LOSS MUTATED 9P LOSS WILD-TYPE
  I                 3                21
  II                5                32
  III               8                35
  IV                7                19
D51V9, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED      1   27
  9P LOSS WILD-TYPE    4  126
     clus
vv    9P LOSS MUTATED 9P LOSS WILD-TYPE
  NO                1                 4
  YES              27               126
D51V10, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED      4   24
  9P LOSS WILD-TYPE    6  124
     clus
vv    9P LOSS MUTATED 9P LOSS WILD-TYPE
  NO                4                 6
  YES              24               124

Clustering(52) Variable = 9q loss mutation analysis
D52V1, survival
                   sevent
clus2                0  1
  9Q LOSS MUTATED    7  1
  9Q LOSS WILD-TYPE 83 14
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
                8                97 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
                1                14 
$`9Q LOSS MUTATED`
TCGA-BR-7723 TCGA-CD-5799 TCGA-CG-4301 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6525 
        4.54         0.69         3.02        15.65         9.63         5.95 
TCGA-D7-6817 TCGA-F1-6875 
        4.70        72.23 

$`9Q LOSS WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-6452 TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6458 
        5.62         0.10         0.95         1.41         1.35         1.35 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
        0.85         0.82         0.62         0.62         1.71         2.17 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
        0.99         1.22         0.66         1.12         0.76         0.66 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
        0.26         1.22         1.48         0.46         1.25         0.13 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7851 TCGA-BR-7901 
        1.05         0.82         0.69         0.16         0.99         0.95 
TCGA-BR-7957 TCGA-CD-5798 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
        0.69         0.82         0.36         0.49         0.30         0.07 
TCGA-CG-4300 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
       20.02        27.02        15.95         1.02        52.96         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 
       54.05         4.01        14.01        29.98        47.05        19.07 
TCGA-CG-4455 TCGA-CG-4460 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       12.03        21.99         1.02         8.98        18.94         7.07 
TCGA-CG-4472 TCGA-CG-4474 TCGA-CG-4477 TCGA-CG-5716 TCGA-CG-5717 TCGA-CG-5718 
       12.00         1.02         1.02         1.02         6.94         1.02 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
        1.02         0.99         5.98         0.95        70.06        12.03 
TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       15.02        28.96        31.04        65.10         4.01        55.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99         8.65         3.58         4.54         9.80 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
        8.19         6.90         0.69         6.61         4.14         1.68 
TCGA-D7-6815 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-EQ-5647 TCGA-F1-6177 
        3.65         4.04         2.93         4.27         0.62         6.54 
TCGA-F1-6874 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7998 TCGA-IN-7806 TCGA-IN-7808 
        2.01         0.39         0.20         3.58         6.87         3.55 
TCGA-IP-7968 
        2.53 

  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
             0.69              0.07 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
            72.23             70.06 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
            5.325             2.010 
[1] "0.7 - 72.2 (5.3)" "0.1 - 70.1 (2.0)"
       TCGA-B7-5816        TCGA-B7-5818        TCGA-BR-6452        TCGA-BR-6455 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-BR-6457        TCGA-BR-6458        TCGA-BR-6563        TCGA-BR-6564 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-BR-6565        TCGA-BR-6566        TCGA-BR-6705        TCGA-BR-6706 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-BR-6707        TCGA-BR-6709        TCGA-BR-6710        TCGA-BR-6801 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-BR-6802        TCGA-BR-6803        TCGA-BR-6852        TCGA-BR-7196 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-BR-7197        TCGA-BR-7703        TCGA-BR-7704        TCGA-BR-7707 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-BR-7715        TCGA-BR-7716        TCGA-BR-7717        TCGA-BR-7722 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-BR-7723        TCGA-BR-7851        TCGA-BR-7901        TCGA-BR-7957 
  "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-CD-5798        TCGA-CD-5799        TCGA-CD-5800        TCGA-CD-5801 
"9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-CD-5802        TCGA-CD-5803        TCGA-CG-4300        TCGA-CG-4301 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" 
       TCGA-CG-4304        TCGA-CG-4305        TCGA-CG-4306        TCGA-CG-4436 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-CG-4437        TCGA-CG-4438        TCGA-CG-4440        TCGA-CG-4441 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-CG-4443        TCGA-CG-4444        TCGA-CG-4449        TCGA-CG-4455 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-CG-4460        TCGA-CG-4462        TCGA-CG-4465        TCGA-CG-4466 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-CG-4469        TCGA-CG-4472        TCGA-CG-4474        TCGA-CG-4477 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-CG-5716        TCGA-CG-5717        TCGA-CG-5718        TCGA-CG-5719 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-CG-5720        TCGA-CG-5721        TCGA-CG-5722        TCGA-CG-5723 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-CG-5724        TCGA-CG-5725        TCGA-CG-5726        TCGA-CG-5727 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-CG-5728        TCGA-CG-5730        TCGA-CG-5732        TCGA-CG-5733 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-CG-5734        TCGA-D7-5577        TCGA-D7-5578        TCGA-D7-5579 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-D7-6518        TCGA-D7-6519        TCGA-D7-6520        TCGA-D7-6521 
"9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" 
       TCGA-D7-6522        TCGA-D7-6524        TCGA-D7-6525        TCGA-D7-6526 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" 
       TCGA-D7-6527        TCGA-D7-6528        TCGA-D7-6815        TCGA-D7-6817 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" 
       TCGA-D7-6818        TCGA-D7-6820        TCGA-D7-6822        TCGA-EQ-5647 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875        TCGA-FP-7735 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" 
       TCGA-FP-7829        TCGA-FP-7998        TCGA-IN-7806        TCGA-IN-7808 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-IP-7968 
"9Q LOSS WILD-TYPE" 
       TCGA-B7-5816        TCGA-B7-5818        TCGA-BR-6452        TCGA-BR-6455 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-BR-6457        TCGA-BR-6458        TCGA-BR-6563        TCGA-BR-6564 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-BR-6565        TCGA-BR-6566        TCGA-BR-6705        TCGA-BR-6706 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-BR-6707        TCGA-BR-6709        TCGA-BR-6710        TCGA-BR-6801 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-BR-6802        TCGA-BR-6803        TCGA-BR-6852        TCGA-BR-7196 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-BR-7197        TCGA-BR-7703        TCGA-BR-7704        TCGA-BR-7707 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-BR-7715        TCGA-BR-7716        TCGA-BR-7717        TCGA-BR-7722 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-BR-7723        TCGA-BR-7851        TCGA-BR-7901        TCGA-BR-7957 
  "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-CD-5798        TCGA-CD-5799        TCGA-CD-5800        TCGA-CD-5801 
"9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-CD-5802        TCGA-CD-5803        TCGA-CG-4300        TCGA-CG-4301 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" 
       TCGA-CG-4304        TCGA-CG-4305        TCGA-CG-4306        TCGA-CG-4436 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-CG-4437        TCGA-CG-4438        TCGA-CG-4440        TCGA-CG-4441 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-CG-4443        TCGA-CG-4444        TCGA-CG-4449        TCGA-CG-4455 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-CG-4460        TCGA-CG-4462        TCGA-CG-4465        TCGA-CG-4466 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-CG-4469        TCGA-CG-4472        TCGA-CG-4474        TCGA-CG-4477 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-CG-5716        TCGA-CG-5717        TCGA-CG-5718        TCGA-CG-5719 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-CG-5720        TCGA-CG-5721        TCGA-CG-5722        TCGA-CG-5723 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-CG-5724        TCGA-CG-5725        TCGA-CG-5726        TCGA-CG-5727 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-CG-5728        TCGA-CG-5730        TCGA-CG-5732        TCGA-CG-5733 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-CG-5734        TCGA-D7-5577        TCGA-D7-5578        TCGA-D7-5579 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-D7-6518        TCGA-D7-6519        TCGA-D7-6520        TCGA-D7-6521 
"9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" 
       TCGA-D7-6522        TCGA-D7-6524        TCGA-D7-6525        TCGA-D7-6526 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" 
       TCGA-D7-6527        TCGA-D7-6528        TCGA-D7-6815        TCGA-D7-6817 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" 
       TCGA-D7-6818        TCGA-D7-6820        TCGA-D7-6822        TCGA-EQ-5647 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875        TCGA-FP-7735 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" 
       TCGA-FP-7829        TCGA-FP-7998        TCGA-IN-7806        TCGA-IN-7808 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-IP-7968 
"9Q LOSS WILD-TYPE" 
       TCGA-B7-5816        TCGA-B7-5818        TCGA-BR-6452        TCGA-BR-6455 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-BR-6457        TCGA-BR-6458        TCGA-BR-6563        TCGA-BR-6564 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-BR-6565        TCGA-BR-6566        TCGA-BR-6705        TCGA-BR-6706 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-BR-6707        TCGA-BR-6709        TCGA-BR-6710        TCGA-BR-6801 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-BR-6802        TCGA-BR-6803        TCGA-BR-6852        TCGA-BR-7196 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-BR-7197        TCGA-BR-7703        TCGA-BR-7704        TCGA-BR-7707 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-BR-7715        TCGA-BR-7716        TCGA-BR-7717        TCGA-BR-7722 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-BR-7723        TCGA-BR-7851        TCGA-BR-7901        TCGA-BR-7957 
  "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-CD-5798        TCGA-CD-5799        TCGA-CD-5800        TCGA-CD-5801 
"9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-CD-5802        TCGA-CD-5803        TCGA-CG-4300        TCGA-CG-4301 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" 
       TCGA-CG-4304        TCGA-CG-4305        TCGA-CG-4306        TCGA-CG-4436 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-CG-4437        TCGA-CG-4438        TCGA-CG-4440        TCGA-CG-4441 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-CG-4443        TCGA-CG-4444        TCGA-CG-4449        TCGA-CG-4455 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-CG-4460        TCGA-CG-4462        TCGA-CG-4465        TCGA-CG-4466 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-CG-4469        TCGA-CG-4472        TCGA-CG-4474        TCGA-CG-4477 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-CG-5716        TCGA-CG-5717        TCGA-CG-5718        TCGA-CG-5719 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-CG-5720        TCGA-CG-5721        TCGA-CG-5722        TCGA-CG-5723 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-CG-5724        TCGA-CG-5725        TCGA-CG-5726        TCGA-CG-5727 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-CG-5728        TCGA-CG-5730        TCGA-CG-5732        TCGA-CG-5733 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-CG-5734        TCGA-D7-5577        TCGA-D7-5578        TCGA-D7-5579 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-D7-6518        TCGA-D7-6519        TCGA-D7-6520        TCGA-D7-6521 
"9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" 
       TCGA-D7-6522        TCGA-D7-6524        TCGA-D7-6525        TCGA-D7-6526 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" 
       TCGA-D7-6527        TCGA-D7-6528        TCGA-D7-6815        TCGA-D7-6817 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" 
       TCGA-D7-6818        TCGA-D7-6820        TCGA-D7-6822        TCGA-EQ-5647 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875        TCGA-FP-7735 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" 
       TCGA-FP-7829        TCGA-FP-7998        TCGA-IN-7806        TCGA-IN-7808 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-IP-7968 
"9Q LOSS WILD-TYPE" 
[1] "hr="     "7.8e+07"
D52V2, continuous
D52V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED      4    8
  9Q LOSS WILD-TYPE   56   90
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  FEMALE               4                56
  MALE                 8                90
D52V4, multiclass
D52V5, multiclass
    clus
vv   9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  T1               0                 6
  T2               7                45
  T3               1                60
  T4               1                17
D52V6, multiclass
    clus
vv   9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  N0               1                43
  N1               4                53
  N2               3                21
  N3               2                13
D52V7, multiclass
    clus
vv   9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  M0              11               123
  M1               1                15
  MX               0                 8
D52V8, multiclass
     clus
vv    9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  I                 1                23
  II                2                35
  III               4                39
  IV                2                24
D52V9, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED      1   11
  9Q LOSS WILD-TYPE    4  142
     clus
vv    9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  NO                1                 4
  YES              11               142
D52V10, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED      2   10
  9Q LOSS WILD-TYPE    8  138
     clus
vv    9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  NO                2                 8
  YES              10               138

Clustering(53) Variable = 10p loss mutation analysis
D53V1, survival
                    sevent
clus2                 0  1
  10P LOSS MUTATED    6  0
  10P LOSS WILD-TYPE 84 15
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                 6                 99 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                 0                 15 
$`10P LOSS MUTATED`
TCGA-CG-4436 TCGA-CG-5732 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6820 TCGA-FP-7829 
       52.96        55.04         4.14         1.68         2.93         0.20 

$`10P LOSS WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-6452 TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6458 
        5.62         0.10         0.95         1.41         1.35         1.35 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
        0.85         0.82         0.62         0.62         1.71         2.17 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
        0.99         1.22         0.66         1.12         0.76         0.66 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
        0.26         1.22         1.48         0.46         1.25         0.13 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 
        1.05         0.82         0.69         0.16         4.54         0.99 
TCGA-BR-7901 TCGA-BR-7957 TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
        0.95         0.69         0.82         0.69         0.36         0.49 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
        0.30         0.07        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        1.02         8.05        54.05         4.01        14.01        29.98 
TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4460 TCGA-CG-4462 TCGA-CG-4465 
       47.05        19.07        12.03        21.99         1.02         8.98 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4474 TCGA-CG-4477 TCGA-CG-5716 
       18.94         7.07        12.00         1.02         1.02         1.02 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.94         1.02         1.02         0.99         5.98         0.95 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 
       70.06        12.03        15.02        28.96        31.04        65.10 
TCGA-CG-5730 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
        4.01        21.07         7.99         8.65         3.58         4.54 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
        9.80        15.65         9.63         8.19         6.90         0.69 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6822 
        5.95         6.61         3.65         4.70         4.04         4.27 
TCGA-EQ-5647 TCGA-F1-6177 TCGA-F1-6874 TCGA-F1-6875 TCGA-FP-7735 TCGA-FP-7998 
        0.62         6.54         2.01        72.23         0.39         3.58 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IP-7968 
        6.87         3.55         2.53 

  10P LOSS MUTATED 10P LOSS WILD-TYPE 
              0.20               0.07 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
             55.04              72.23 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
             3.535              2.530 
[1] "0.2 - 55.0 (3.5)" "0.1 - 72.2 (2.5)"
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-CD-5798 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-CD-5799         TCGA-CD-5800         TCGA-CD-5801 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-CD-5802         TCGA-CD-5803         TCGA-CG-4300 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-CG-4301         TCGA-CG-4304         TCGA-CG-4305 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-CG-4306         TCGA-CG-4436         TCGA-CG-4437 
"10P LOSS WILD-TYPE"   "10P LOSS MUTATED" "10P LOSS WILD-TYPE" 
        TCGA-CG-4438         TCGA-CG-4440         TCGA-CG-4441 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-CG-4443         TCGA-CG-4444         TCGA-CG-4449 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-CG-4455         TCGA-CG-4460         TCGA-CG-4462 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-CG-4465         TCGA-CG-4466         TCGA-CG-4469 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-CG-4472         TCGA-CG-4474         TCGA-CG-4477 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-CG-5716         TCGA-CG-5717         TCGA-CG-5718 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-CG-5719         TCGA-CG-5720         TCGA-CG-5721 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-CG-5722         TCGA-CG-5723         TCGA-CG-5724 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-CG-5725         TCGA-CG-5726         TCGA-CG-5727 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-CG-5728         TCGA-CG-5730         TCGA-CG-5732 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE"   "10P LOSS MUTATED" 
        TCGA-CG-5733         TCGA-CG-5734         TCGA-D7-5577 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-D7-5578         TCGA-D7-5579         TCGA-D7-6518 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-D7-6519         TCGA-D7-6520         TCGA-D7-6521 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-D7-6522         TCGA-D7-6524         TCGA-D7-6525 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-D7-6526         TCGA-D7-6527         TCGA-D7-6528 
"10P LOSS WILD-TYPE"   "10P LOSS MUTATED"   "10P LOSS MUTATED" 
        TCGA-D7-6815         TCGA-D7-6817         TCGA-D7-6818 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-D7-6820         TCGA-D7-6822         TCGA-EQ-5647 
  "10P LOSS MUTATED" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-F1-6177         TCGA-F1-6874         TCGA-F1-6875 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-FP-7735         TCGA-FP-7829         TCGA-FP-7998 
"10P LOSS WILD-TYPE"   "10P LOSS MUTATED" "10P LOSS WILD-TYPE" 
        TCGA-IN-7806         TCGA-IN-7808         TCGA-IP-7968 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-CD-5798 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-CD-5799         TCGA-CD-5800         TCGA-CD-5801 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-CD-5802         TCGA-CD-5803         TCGA-CG-4300 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-CG-4301         TCGA-CG-4304         TCGA-CG-4305 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-CG-4306         TCGA-CG-4436         TCGA-CG-4437 
"10P LOSS WILD-TYPE"   "10P LOSS MUTATED" "10P LOSS WILD-TYPE" 
        TCGA-CG-4438         TCGA-CG-4440         TCGA-CG-4441 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-CG-4443         TCGA-CG-4444         TCGA-CG-4449 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-CG-4455         TCGA-CG-4460         TCGA-CG-4462 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-CG-4465         TCGA-CG-4466         TCGA-CG-4469 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-CG-4472         TCGA-CG-4474         TCGA-CG-4477 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-CG-5716         TCGA-CG-5717         TCGA-CG-5718 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-CG-5719         TCGA-CG-5720         TCGA-CG-5721 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-CG-5722         TCGA-CG-5723         TCGA-CG-5724 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-CG-5725         TCGA-CG-5726         TCGA-CG-5727 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-CG-5728         TCGA-CG-5730         TCGA-CG-5732 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE"   "10P LOSS MUTATED" 
        TCGA-CG-5733         TCGA-CG-5734         TCGA-D7-5577 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-D7-5578         TCGA-D7-5579         TCGA-D7-6518 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-D7-6519         TCGA-D7-6520         TCGA-D7-6521 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-D7-6522         TCGA-D7-6524         TCGA-D7-6525 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-D7-6526         TCGA-D7-6527         TCGA-D7-6528 
"10P LOSS WILD-TYPE"   "10P LOSS MUTATED"   "10P LOSS MUTATED" 
        TCGA-D7-6815         TCGA-D7-6817         TCGA-D7-6818 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-D7-6820         TCGA-D7-6822         TCGA-EQ-5647 
  "10P LOSS MUTATED" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-F1-6177         TCGA-F1-6874         TCGA-F1-6875 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-FP-7735         TCGA-FP-7829         TCGA-FP-7998 
"10P LOSS WILD-TYPE"   "10P LOSS MUTATED" "10P LOSS WILD-TYPE" 
        TCGA-IN-7806         TCGA-IN-7808         TCGA-IP-7968 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-CD-5798 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-CD-5799         TCGA-CD-5800         TCGA-CD-5801 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-CD-5802         TCGA-CD-5803         TCGA-CG-4300 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-CG-4301         TCGA-CG-4304         TCGA-CG-4305 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-CG-4306         TCGA-CG-4436         TCGA-CG-4437 
"10P LOSS WILD-TYPE"   "10P LOSS MUTATED" "10P LOSS WILD-TYPE" 
        TCGA-CG-4438         TCGA-CG-4440         TCGA-CG-4441 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-CG-4443         TCGA-CG-4444         TCGA-CG-4449 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-CG-4455         TCGA-CG-4460         TCGA-CG-4462 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-CG-4465         TCGA-CG-4466         TCGA-CG-4469 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-CG-4472         TCGA-CG-4474         TCGA-CG-4477 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-CG-5716         TCGA-CG-5717         TCGA-CG-5718 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-CG-5719         TCGA-CG-5720         TCGA-CG-5721 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-CG-5722         TCGA-CG-5723         TCGA-CG-5724 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-CG-5725         TCGA-CG-5726         TCGA-CG-5727 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-CG-5728         TCGA-CG-5730         TCGA-CG-5732 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE"   "10P LOSS MUTATED" 
        TCGA-CG-5733         TCGA-CG-5734         TCGA-D7-5577 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-D7-5578         TCGA-D7-5579         TCGA-D7-6518 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-D7-6519         TCGA-D7-6520         TCGA-D7-6521 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-D7-6522         TCGA-D7-6524         TCGA-D7-6525 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-D7-6526         TCGA-D7-6527         TCGA-D7-6528 
"10P LOSS WILD-TYPE"   "10P LOSS MUTATED"   "10P LOSS MUTATED" 
        TCGA-D7-6815         TCGA-D7-6817         TCGA-D7-6818 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-D7-6820         TCGA-D7-6822         TCGA-EQ-5647 
  "10P LOSS MUTATED" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-F1-6177         TCGA-F1-6874         TCGA-F1-6875 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-FP-7735         TCGA-FP-7829         TCGA-FP-7998 
"10P LOSS WILD-TYPE"   "10P LOSS MUTATED" "10P LOSS WILD-TYPE" 
        TCGA-IN-7806         TCGA-IN-7808         TCGA-IP-7968 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
[1] "hr="   "8e+07"
D53V2, continuous
D53V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED      3    9
  10P LOSS WILD-TYPE   57   89
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  FEMALE                3                 57
  MALE                  9                 89
D53V4, multiclass
D53V5, multiclass
    clus
vv   10P LOSS MUTATED 10P LOSS WILD-TYPE
  T1                0                  6
  T2                7                 45
  T3                2                 59
  T4                0                 18
D53V6, multiclass
    clus
vv   10P LOSS MUTATED 10P LOSS WILD-TYPE
  N0                3                 41
  N1                5                 52
  N2                0                 24
  N3                2                 13
D53V7, multiclass
    clus
vv   10P LOSS MUTATED 10P LOSS WILD-TYPE
  M0               12                122
  M1                0                 16
  MX                0                  8
D53V8, multiclass
     clus
vv    10P LOSS MUTATED 10P LOSS WILD-TYPE
  I                  3                 21
  II                 3                 34
  III                1                 42
  IV                 2                 24
D53V9, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED      2   10
  10P LOSS WILD-TYPE    3  143
     clus
vv    10P LOSS MUTATED 10P LOSS WILD-TYPE
  NO                 2                  3
  YES               10                143
D53V10, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED      2   10
  10P LOSS WILD-TYPE    8  138
     clus
vv    10P LOSS MUTATED 10P LOSS WILD-TYPE
  NO                 2                  8
  YES               10                138

Clustering(54) Variable = 10q loss mutation analysis
D54V1, survival
                    sevent
clus2                 0  1
  10Q LOSS MUTATED    7  0
  10Q LOSS WILD-TYPE 83 15
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                 7                 98 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                 0                 15 
$`10Q LOSS MUTATED`
TCGA-BR-7704 TCGA-CG-4436 TCGA-CG-4466 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6817 
        1.25        52.96        18.94         4.14         1.68         4.70 
TCGA-FP-7829 
        0.20 

$`10Q LOSS WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-6452 TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6458 
        5.62         0.10         0.95         1.41         1.35         1.35 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
        0.85         0.82         0.62         0.62         1.71         2.17 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
        0.99         1.22         0.66         1.12         0.76         0.66 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 
        0.26         1.22         1.48         0.46         0.13         1.05 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 
        0.82         0.69         0.16         4.54         0.99         0.95 
TCGA-BR-7957 TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        0.69         0.82         0.69         0.36         0.49         0.30 
TCGA-CD-5803 TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
        0.07        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 
        8.05        54.05         4.01        14.01        29.98        47.05 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4460 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4469 
       19.07        12.03        21.99         1.02         8.98         7.07 
TCGA-CG-4472 TCGA-CG-4474 TCGA-CG-4477 TCGA-CG-5716 TCGA-CG-5717 TCGA-CG-5718 
       12.00         1.02         1.02         1.02         6.94         1.02 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
        1.02         0.99         5.98         0.95        70.06        12.03 
TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       15.02        28.96        31.04        65.10         4.01        55.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99         8.65         3.58         4.54         9.80 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       15.65         9.63         8.19         6.90         0.69         5.95 
TCGA-D7-6526 TCGA-D7-6815 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-EQ-5647 
        6.61         3.65         4.04         2.93         4.27         0.62 
TCGA-F1-6177 TCGA-F1-6874 TCGA-F1-6875 TCGA-FP-7735 TCGA-FP-7998 TCGA-IN-7806 
        6.54         2.01        72.23         0.39         3.58         6.87 
TCGA-IN-7808 TCGA-IP-7968 
        3.55         2.53 

  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
              0.20               0.07 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
             52.96              72.23 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
              4.14               2.73 
[1] "0.2 - 53.0 (4.1)" "0.1 - 72.2 (2.7)"
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-CD-5798 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-CD-5799         TCGA-CD-5800         TCGA-CD-5801 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-CD-5802         TCGA-CD-5803         TCGA-CG-4300 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-CG-4301         TCGA-CG-4304         TCGA-CG-4305 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-CG-4306         TCGA-CG-4436         TCGA-CG-4437 
"10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-CG-4438         TCGA-CG-4440         TCGA-CG-4441 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-CG-4443         TCGA-CG-4444         TCGA-CG-4449 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-CG-4455         TCGA-CG-4460         TCGA-CG-4462 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-CG-4465         TCGA-CG-4466         TCGA-CG-4469 
"10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-CG-4472         TCGA-CG-4474         TCGA-CG-4477 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-CG-5716         TCGA-CG-5717         TCGA-CG-5718 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-CG-5719         TCGA-CG-5720         TCGA-CG-5721 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-CG-5722         TCGA-CG-5723         TCGA-CG-5724 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-CG-5725         TCGA-CG-5726         TCGA-CG-5727 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-CG-5728         TCGA-CG-5730         TCGA-CG-5732 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-CG-5733         TCGA-CG-5734         TCGA-D7-5577 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-D7-5578         TCGA-D7-5579         TCGA-D7-6518 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-D7-6519         TCGA-D7-6520         TCGA-D7-6521 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-D7-6522         TCGA-D7-6524         TCGA-D7-6525 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-D7-6526         TCGA-D7-6527         TCGA-D7-6528 
"10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED"   "10Q LOSS MUTATED" 
        TCGA-D7-6815         TCGA-D7-6817         TCGA-D7-6818 
"10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-D7-6820         TCGA-D7-6822         TCGA-EQ-5647 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-F1-6177         TCGA-F1-6874         TCGA-F1-6875 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-FP-7735         TCGA-FP-7829         TCGA-FP-7998 
"10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-IN-7806         TCGA-IN-7808         TCGA-IP-7968 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-CD-5798 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-CD-5799         TCGA-CD-5800         TCGA-CD-5801 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-CD-5802         TCGA-CD-5803         TCGA-CG-4300 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-CG-4301         TCGA-CG-4304         TCGA-CG-4305 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-CG-4306         TCGA-CG-4436         TCGA-CG-4437 
"10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-CG-4438         TCGA-CG-4440         TCGA-CG-4441 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-CG-4443         TCGA-CG-4444         TCGA-CG-4449 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-CG-4455         TCGA-CG-4460         TCGA-CG-4462 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-CG-4465         TCGA-CG-4466         TCGA-CG-4469 
"10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-CG-4472         TCGA-CG-4474         TCGA-CG-4477 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-CG-5716         TCGA-CG-5717         TCGA-CG-5718 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-CG-5719         TCGA-CG-5720         TCGA-CG-5721 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-CG-5722         TCGA-CG-5723         TCGA-CG-5724 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-CG-5725         TCGA-CG-5726         TCGA-CG-5727 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-CG-5728         TCGA-CG-5730         TCGA-CG-5732 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-CG-5733         TCGA-CG-5734         TCGA-D7-5577 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-D7-5578         TCGA-D7-5579         TCGA-D7-6518 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-D7-6519         TCGA-D7-6520         TCGA-D7-6521 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-D7-6522         TCGA-D7-6524         TCGA-D7-6525 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-D7-6526         TCGA-D7-6527         TCGA-D7-6528 
"10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED"   "10Q LOSS MUTATED" 
        TCGA-D7-6815         TCGA-D7-6817         TCGA-D7-6818 
"10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-D7-6820         TCGA-D7-6822         TCGA-EQ-5647 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-F1-6177         TCGA-F1-6874         TCGA-F1-6875 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-FP-7735         TCGA-FP-7829         TCGA-FP-7998 
"10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-IN-7806         TCGA-IN-7808         TCGA-IP-7968 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-CD-5798 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-CD-5799         TCGA-CD-5800         TCGA-CD-5801 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-CD-5802         TCGA-CD-5803         TCGA-CG-4300 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-CG-4301         TCGA-CG-4304         TCGA-CG-4305 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-CG-4306         TCGA-CG-4436         TCGA-CG-4437 
"10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-CG-4438         TCGA-CG-4440         TCGA-CG-4441 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-CG-4443         TCGA-CG-4444         TCGA-CG-4449 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-CG-4455         TCGA-CG-4460         TCGA-CG-4462 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-CG-4465         TCGA-CG-4466         TCGA-CG-4469 
"10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-CG-4472         TCGA-CG-4474         TCGA-CG-4477 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-CG-5716         TCGA-CG-5717         TCGA-CG-5718 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-CG-5719         TCGA-CG-5720         TCGA-CG-5721 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-CG-5722         TCGA-CG-5723         TCGA-CG-5724 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-CG-5725         TCGA-CG-5726         TCGA-CG-5727 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-CG-5728         TCGA-CG-5730         TCGA-CG-5732 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-CG-5733         TCGA-CG-5734         TCGA-D7-5577 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-D7-5578         TCGA-D7-5579         TCGA-D7-6518 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-D7-6519         TCGA-D7-6520         TCGA-D7-6521 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-D7-6522         TCGA-D7-6524         TCGA-D7-6525 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-D7-6526         TCGA-D7-6527         TCGA-D7-6528 
"10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED"   "10Q LOSS MUTATED" 
        TCGA-D7-6815         TCGA-D7-6817         TCGA-D7-6818 
"10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-D7-6820         TCGA-D7-6822         TCGA-EQ-5647 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-F1-6177         TCGA-F1-6874         TCGA-F1-6875 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-FP-7735         TCGA-FP-7829         TCGA-FP-7998 
"10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-IN-7806         TCGA-IN-7808         TCGA-IP-7968 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
[1] "hr="     "7.5e+07"
D54V2, continuous
D54V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED      4    7
  10Q LOSS WILD-TYPE   56   91
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  FEMALE                4                 56
  MALE                  7                 91
D54V4, multiclass
D54V5, multiclass
    clus
vv   10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  T1                0                  6
  T2                5                 47
  T3                3                 58
  T4                0                 18
D54V6, multiclass
    clus
vv   10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  N0                4                 40
  N1                4                 53
  N2                0                 24
  N3                1                 14
D54V7, multiclass
    clus
vv   10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  M0               11                123
  M1                0                 16
  MX                0                  8
D54V8, multiclass
     clus
vv    10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  I                  3                 21
  II                 3                 34
  III                2                 41
  IV                 0                 26
D54V9, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED      1   10
  10Q LOSS WILD-TYPE    4  143
     clus
vv    10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  NO                 1                  4
  YES               10                143
D54V10, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED      1   10
  10Q LOSS WILD-TYPE    9  138
     clus
vv    10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  NO                 1                  9
  YES               10                138

Clustering(55) Variable = 11p loss mutation analysis
D55V1, survival
                    sevent
clus2                 0  1
  11P LOSS MUTATED    7  3
  11P LOSS WILD-TYPE 83 12
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                10                 95 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                 3                 12 
$`11P LOSS MUTATED`
TCGA-CD-5799 TCGA-CD-5802 TCGA-CG-4443 TCGA-CG-4460 TCGA-CG-4477 TCGA-CG-5724 
        0.69         0.30        29.98        21.99         1.02        12.03 
TCGA-CG-5730 TCGA-D7-6519 TCGA-D7-6815 TCGA-EQ-5647 
        4.01        15.65         3.65         0.62 

$`11P LOSS WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-6452 TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6458 
        5.62         0.10         0.95         1.41         1.35         1.35 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
        0.85         0.82         0.62         0.62         1.71         2.17 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
        0.99         1.22         0.66         1.12         0.76         0.66 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
        0.26         1.22         1.48         0.46         1.25         0.13 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 
        1.05         0.82         0.69         0.16         4.54         0.99 
TCGA-BR-7901 TCGA-BR-7957 TCGA-CD-5798 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5803 
        0.95         0.69         0.82         0.36         0.49         0.07 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02        52.96 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4444 TCGA-CG-4449 
        8.05        54.05         4.01        14.01        47.05        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 
       12.03         1.02         8.98        18.94         7.07        12.00 
TCGA-CG-4474 TCGA-CG-5716 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
        1.02         1.02         6.94         1.02         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5727 
        5.98         0.95        70.06        15.02        28.96        31.04 
TCGA-CG-5728 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
       65.10        55.04        21.07         7.99         8.65         3.58 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
        4.54         9.80         9.63         8.19         6.90         0.69 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6817 TCGA-D7-6818 
        5.95         6.61         4.14         1.68         4.70         4.04 
TCGA-D7-6820 TCGA-D7-6822 TCGA-F1-6177 TCGA-F1-6874 TCGA-F1-6875 TCGA-FP-7735 
        2.93         4.27         6.54         2.01        72.23         0.39 
TCGA-FP-7829 TCGA-FP-7998 TCGA-IN-7806 TCGA-IN-7808 TCGA-IP-7968 
        0.20         3.58         6.87         3.55         2.53 

  11P LOSS MUTATED 11P LOSS WILD-TYPE 
              0.30               0.07 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
             29.98              72.23 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
              3.83               2.53 
[1] "0.3 - 30.0 (3.8)" "0.1 - 72.2 (2.5)"
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-CD-5798 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-CD-5799         TCGA-CD-5800         TCGA-CD-5801 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-CD-5802         TCGA-CD-5803         TCGA-CG-4300 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-CG-4301         TCGA-CG-4304         TCGA-CG-4305 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-CG-4306         TCGA-CG-4436         TCGA-CG-4437 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-CG-4438         TCGA-CG-4440         TCGA-CG-4441 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-CG-4443         TCGA-CG-4444         TCGA-CG-4449 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-CG-4455         TCGA-CG-4460         TCGA-CG-4462 
"11P LOSS WILD-TYPE"   "11P LOSS MUTATED" "11P LOSS WILD-TYPE" 
        TCGA-CG-4465         TCGA-CG-4466         TCGA-CG-4469 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-CG-4472         TCGA-CG-4474         TCGA-CG-4477 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE"   "11P LOSS MUTATED" 
        TCGA-CG-5716         TCGA-CG-5717         TCGA-CG-5718 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-CG-5719         TCGA-CG-5720         TCGA-CG-5721 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-CG-5722         TCGA-CG-5723         TCGA-CG-5724 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE"   "11P LOSS MUTATED" 
        TCGA-CG-5725         TCGA-CG-5726         TCGA-CG-5727 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-CG-5728         TCGA-CG-5730         TCGA-CG-5732 
"11P LOSS WILD-TYPE"   "11P LOSS MUTATED" "11P LOSS WILD-TYPE" 
        TCGA-CG-5733         TCGA-CG-5734         TCGA-D7-5577 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-D7-5578         TCGA-D7-5579         TCGA-D7-6518 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-D7-6519         TCGA-D7-6520         TCGA-D7-6521 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-D7-6522         TCGA-D7-6524         TCGA-D7-6525 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-D7-6526         TCGA-D7-6527         TCGA-D7-6528 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-D7-6815         TCGA-D7-6817         TCGA-D7-6818 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-D7-6820         TCGA-D7-6822         TCGA-EQ-5647 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE"   "11P LOSS MUTATED" 
        TCGA-F1-6177         TCGA-F1-6874         TCGA-F1-6875 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-FP-7735         TCGA-FP-7829         TCGA-FP-7998 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-IN-7806         TCGA-IN-7808         TCGA-IP-7968 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-CD-5798 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-CD-5799         TCGA-CD-5800         TCGA-CD-5801 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-CD-5802         TCGA-CD-5803         TCGA-CG-4300 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-CG-4301         TCGA-CG-4304         TCGA-CG-4305 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-CG-4306         TCGA-CG-4436         TCGA-CG-4437 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-CG-4438         TCGA-CG-4440         TCGA-CG-4441 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-CG-4443         TCGA-CG-4444         TCGA-CG-4449 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-CG-4455         TCGA-CG-4460         TCGA-CG-4462 
"11P LOSS WILD-TYPE"   "11P LOSS MUTATED" "11P LOSS WILD-TYPE" 
        TCGA-CG-4465         TCGA-CG-4466         TCGA-CG-4469 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-CG-4472         TCGA-CG-4474         TCGA-CG-4477 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE"   "11P LOSS MUTATED" 
        TCGA-CG-5716         TCGA-CG-5717         TCGA-CG-5718 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-CG-5719         TCGA-CG-5720         TCGA-CG-5721 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-CG-5722         TCGA-CG-5723         TCGA-CG-5724 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE"   "11P LOSS MUTATED" 
        TCGA-CG-5725         TCGA-CG-5726         TCGA-CG-5727 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-CG-5728         TCGA-CG-5730         TCGA-CG-5732 
"11P LOSS WILD-TYPE"   "11P LOSS MUTATED" "11P LOSS WILD-TYPE" 
        TCGA-CG-5733         TCGA-CG-5734         TCGA-D7-5577 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-D7-5578         TCGA-D7-5579         TCGA-D7-6518 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-D7-6519         TCGA-D7-6520         TCGA-D7-6521 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-D7-6522         TCGA-D7-6524         TCGA-D7-6525 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-D7-6526         TCGA-D7-6527         TCGA-D7-6528 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-D7-6815         TCGA-D7-6817         TCGA-D7-6818 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-D7-6820         TCGA-D7-6822         TCGA-EQ-5647 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE"   "11P LOSS MUTATED" 
        TCGA-F1-6177         TCGA-F1-6874         TCGA-F1-6875 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-FP-7735         TCGA-FP-7829         TCGA-FP-7998 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-IN-7806         TCGA-IN-7808         TCGA-IP-7968 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-CD-5798 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-CD-5799         TCGA-CD-5800         TCGA-CD-5801 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-CD-5802         TCGA-CD-5803         TCGA-CG-4300 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-CG-4301         TCGA-CG-4304         TCGA-CG-4305 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-CG-4306         TCGA-CG-4436         TCGA-CG-4437 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-CG-4438         TCGA-CG-4440         TCGA-CG-4441 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-CG-4443         TCGA-CG-4444         TCGA-CG-4449 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-CG-4455         TCGA-CG-4460         TCGA-CG-4462 
"11P LOSS WILD-TYPE"   "11P LOSS MUTATED" "11P LOSS WILD-TYPE" 
        TCGA-CG-4465         TCGA-CG-4466         TCGA-CG-4469 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-CG-4472         TCGA-CG-4474         TCGA-CG-4477 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE"   "11P LOSS MUTATED" 
        TCGA-CG-5716         TCGA-CG-5717         TCGA-CG-5718 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-CG-5719         TCGA-CG-5720         TCGA-CG-5721 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-CG-5722         TCGA-CG-5723         TCGA-CG-5724 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE"   "11P LOSS MUTATED" 
        TCGA-CG-5725         TCGA-CG-5726         TCGA-CG-5727 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-CG-5728         TCGA-CG-5730         TCGA-CG-5732 
"11P LOSS WILD-TYPE"   "11P LOSS MUTATED" "11P LOSS WILD-TYPE" 
        TCGA-CG-5733         TCGA-CG-5734         TCGA-D7-5577 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-D7-5578         TCGA-D7-5579         TCGA-D7-6518 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-D7-6519         TCGA-D7-6520         TCGA-D7-6521 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-D7-6522         TCGA-D7-6524         TCGA-D7-6525 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-D7-6526         TCGA-D7-6527         TCGA-D7-6528 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-D7-6815         TCGA-D7-6817         TCGA-D7-6818 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-D7-6820         TCGA-D7-6822         TCGA-EQ-5647 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE"   "11P LOSS MUTATED" 
        TCGA-F1-6177         TCGA-F1-6874         TCGA-F1-6875 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-FP-7735         TCGA-FP-7829         TCGA-FP-7998 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-IN-7806         TCGA-IN-7808         TCGA-IP-7968 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
[1] "hr=" "1.8"
D55V2, continuous
D55V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED      7    6
  11P LOSS WILD-TYPE   53   92
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  FEMALE                7                 53
  MALE                  6                 92
D55V4, multiclass
D55V5, multiclass
    clus
vv   11P LOSS MUTATED 11P LOSS WILD-TYPE
  T1                1                  5
  T2                7                 45
  T3                2                 59
  T4                2                 16
D55V6, multiclass
    clus
vv   11P LOSS MUTATED 11P LOSS WILD-TYPE
  N0                3                 41
  N1                5                 52
  N2                1                 23
  N3                2                 13
D55V7, multiclass
    clus
vv   11P LOSS MUTATED 11P LOSS WILD-TYPE
  M0                9                125
  M1                4                 12
  MX                0                  8
D55V8, multiclass
     clus
vv    11P LOSS MUTATED 11P LOSS WILD-TYPE
  I                  2                 22
  II                 3                 34
  III                2                 41
  IV                 4                 22
D55V9, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED      0   13
  11P LOSS WILD-TYPE    5  140
     clus
vv    11P LOSS MUTATED 11P LOSS WILD-TYPE
  NO                 0                  5
  YES               13                140
D55V10, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED      0   13
  11P LOSS WILD-TYPE   10  135
     clus
vv    11P LOSS MUTATED 11P LOSS WILD-TYPE
  NO                 0                 10
  YES               13                135

Clustering(56) Variable = 11q loss mutation analysis
D56V1, survival
                    sevent
clus2                 0  1
  11Q LOSS MUTATED    5  2
  11Q LOSS WILD-TYPE 85 13
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                 7                 98 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                 2                 13 
$`11Q LOSS MUTATED`
TCGA-CD-5799 TCGA-CD-5802 TCGA-CG-4437 TCGA-CG-4443 TCGA-CG-5724 TCGA-D7-6815 
        0.69         0.30         8.05        29.98        12.03         3.65 
TCGA-EQ-5647 
        0.62 

$`11Q LOSS WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-6452 TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6458 
        5.62         0.10         0.95         1.41         1.35         1.35 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
        0.85         0.82         0.62         0.62         1.71         2.17 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
        0.99         1.22         0.66         1.12         0.76         0.66 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
        0.26         1.22         1.48         0.46         1.25         0.13 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 
        1.05         0.82         0.69         0.16         4.54         0.99 
TCGA-BR-7901 TCGA-BR-7957 TCGA-CD-5798 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5803 
        0.95         0.69         0.82         0.36         0.49         0.07 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02        52.96 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 
       54.05         4.01        14.01        47.05        19.07        12.03 
TCGA-CG-4460 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 
       21.99         1.02         8.98        18.94         7.07        12.00 
TCGA-CG-4474 TCGA-CG-4477 TCGA-CG-5716 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
        1.02         1.02         1.02         6.94         1.02         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5725 TCGA-CG-5726 
        0.99         5.98         0.95        70.06        15.02        28.96 
TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       31.04        65.10         4.01        55.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
        8.65         3.58         4.54         9.80        15.65         9.63 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
        8.19         6.90         0.69         5.95         6.61         4.14 
TCGA-D7-6528 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-F1-6177 
        1.68         4.70         4.04         2.93         4.27         6.54 
TCGA-F1-6874 TCGA-F1-6875 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7998 TCGA-IN-7806 
        2.01        72.23         0.39         0.20         3.58         6.87 
TCGA-IN-7808 TCGA-IP-7968 
        3.55         2.53 

  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
              0.30               0.07 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
             29.98              72.23 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
              3.65               2.73 
[1] "0.3 - 30.0 (3.6)" "0.1 - 72.2 (2.7)"
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-CD-5798 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-CD-5799         TCGA-CD-5800         TCGA-CD-5801 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-CD-5802         TCGA-CD-5803         TCGA-CG-4300 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-CG-4301         TCGA-CG-4304         TCGA-CG-4305 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-CG-4306         TCGA-CG-4436         TCGA-CG-4437 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" 
        TCGA-CG-4438         TCGA-CG-4440         TCGA-CG-4441 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-CG-4443         TCGA-CG-4444         TCGA-CG-4449 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-CG-4455         TCGA-CG-4460         TCGA-CG-4462 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-CG-4465         TCGA-CG-4466         TCGA-CG-4469 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-CG-4472         TCGA-CG-4474         TCGA-CG-4477 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-CG-5716         TCGA-CG-5717         TCGA-CG-5718 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-CG-5719         TCGA-CG-5720         TCGA-CG-5721 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-CG-5722         TCGA-CG-5723         TCGA-CG-5724 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" 
        TCGA-CG-5725         TCGA-CG-5726         TCGA-CG-5727 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-CG-5728         TCGA-CG-5730         TCGA-CG-5732 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-CG-5733         TCGA-CG-5734         TCGA-D7-5577 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-D7-5578         TCGA-D7-5579         TCGA-D7-6518 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-D7-6519         TCGA-D7-6520         TCGA-D7-6521 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-D7-6522         TCGA-D7-6524         TCGA-D7-6525 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-D7-6526         TCGA-D7-6527         TCGA-D7-6528 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-D7-6815         TCGA-D7-6817         TCGA-D7-6818 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-D7-6820         TCGA-D7-6822         TCGA-EQ-5647 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" 
        TCGA-F1-6177         TCGA-F1-6874         TCGA-F1-6875 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-FP-7735         TCGA-FP-7829         TCGA-FP-7998 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-IN-7806         TCGA-IN-7808         TCGA-IP-7968 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-CD-5798 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-CD-5799         TCGA-CD-5800         TCGA-CD-5801 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-CD-5802         TCGA-CD-5803         TCGA-CG-4300 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-CG-4301         TCGA-CG-4304         TCGA-CG-4305 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-CG-4306         TCGA-CG-4436         TCGA-CG-4437 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" 
        TCGA-CG-4438         TCGA-CG-4440         TCGA-CG-4441 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-CG-4443         TCGA-CG-4444         TCGA-CG-4449 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-CG-4455         TCGA-CG-4460         TCGA-CG-4462 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-CG-4465         TCGA-CG-4466         TCGA-CG-4469 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-CG-4472         TCGA-CG-4474         TCGA-CG-4477 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-CG-5716         TCGA-CG-5717         TCGA-CG-5718 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-CG-5719         TCGA-CG-5720         TCGA-CG-5721 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-CG-5722         TCGA-CG-5723         TCGA-CG-5724 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" 
        TCGA-CG-5725         TCGA-CG-5726         TCGA-CG-5727 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-CG-5728         TCGA-CG-5730         TCGA-CG-5732 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-CG-5733         TCGA-CG-5734         TCGA-D7-5577 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-D7-5578         TCGA-D7-5579         TCGA-D7-6518 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-D7-6519         TCGA-D7-6520         TCGA-D7-6521 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-D7-6522         TCGA-D7-6524         TCGA-D7-6525 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-D7-6526         TCGA-D7-6527         TCGA-D7-6528 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-D7-6815         TCGA-D7-6817         TCGA-D7-6818 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-D7-6820         TCGA-D7-6822         TCGA-EQ-5647 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" 
        TCGA-F1-6177         TCGA-F1-6874         TCGA-F1-6875 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-FP-7735         TCGA-FP-7829         TCGA-FP-7998 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-IN-7806         TCGA-IN-7808         TCGA-IP-7968 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-CD-5798 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-CD-5799         TCGA-CD-5800         TCGA-CD-5801 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-CD-5802         TCGA-CD-5803         TCGA-CG-4300 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-CG-4301         TCGA-CG-4304         TCGA-CG-4305 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-CG-4306         TCGA-CG-4436         TCGA-CG-4437 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" 
        TCGA-CG-4438         TCGA-CG-4440         TCGA-CG-4441 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-CG-4443         TCGA-CG-4444         TCGA-CG-4449 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-CG-4455         TCGA-CG-4460         TCGA-CG-4462 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-CG-4465         TCGA-CG-4466         TCGA-CG-4469 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-CG-4472         TCGA-CG-4474         TCGA-CG-4477 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-CG-5716         TCGA-CG-5717         TCGA-CG-5718 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-CG-5719         TCGA-CG-5720         TCGA-CG-5721 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-CG-5722         TCGA-CG-5723         TCGA-CG-5724 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" 
        TCGA-CG-5725         TCGA-CG-5726         TCGA-CG-5727 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-CG-5728         TCGA-CG-5730         TCGA-CG-5732 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-CG-5733         TCGA-CG-5734         TCGA-D7-5577 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-D7-5578         TCGA-D7-5579         TCGA-D7-6518 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-D7-6519         TCGA-D7-6520         TCGA-D7-6521 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-D7-6522         TCGA-D7-6524         TCGA-D7-6525 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-D7-6526         TCGA-D7-6527         TCGA-D7-6528 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-D7-6815         TCGA-D7-6817         TCGA-D7-6818 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-D7-6820         TCGA-D7-6822         TCGA-EQ-5647 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" 
        TCGA-F1-6177         TCGA-F1-6874         TCGA-F1-6875 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-FP-7735         TCGA-FP-7829         TCGA-FP-7998 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-IN-7806         TCGA-IN-7808         TCGA-IP-7968 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
[1] "hr=" "2.1"
D56V2, continuous
D56V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED      3    7
  11Q LOSS WILD-TYPE   57   91
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  FEMALE                3                 57
  MALE                  7                 91
D56V4, multiclass
D56V5, multiclass
    clus
vv   11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  T1                1                  5
  T2                5                 47
  T3                2                 59
  T4                1                 17
D56V6, multiclass
    clus
vv   11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  N0                2                 42
  N1                3                 54
  N2                1                 23
  N3                2                 13
D56V7, multiclass
    clus
vv   11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  M0                8                126
  M1                2                 14
  MX                0                  8
D56V8, multiclass
     clus
vv    11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  I                  1                 23
  II                 4                 33
  III                1                 42
  IV                 2                 24
D56V9, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED      0   10
  11Q LOSS WILD-TYPE    5  143
     clus
vv    11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  NO                 0                  5
  YES               10                143
D56V10, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED      0   10
  11Q LOSS WILD-TYPE   10  138
     clus
vv    11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  NO                 0                 10
  YES               10                138

Clustering(57) Variable = 12p loss mutation analysis
D57V1, survival
                    sevent
clus2                 0  1
  12P LOSS MUTATED    8  2
  12P LOSS WILD-TYPE 82 13
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                10                 95 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                 2                 13 
$`12P LOSS MUTATED`
TCGA-BR-7715 TCGA-CD-5800 TCGA-CD-5802 TCGA-CG-4436 TCGA-CG-4443 TCGA-CG-4477 
        1.05         0.36         0.30        52.96        29.98         1.02 
TCGA-CG-5725 TCGA-CG-5732 TCGA-D7-6822 TCGA-F1-6875 
       15.02        55.04         4.27        72.23 

$`12P LOSS WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-6452 TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6458 
        5.62         0.10         0.95         1.41         1.35         1.35 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
        0.85         0.82         0.62         0.62         1.71         2.17 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
        0.99         1.22         0.66         1.12         0.76         0.66 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
        0.26         1.22         1.48         0.46         1.25         0.13 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 
        0.82         0.69         0.16         4.54         0.99         0.95 
TCGA-BR-7957 TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5801 TCGA-CD-5803 TCGA-CG-4300 
        0.69         0.82         0.69         0.49         0.07        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4437 TCGA-CG-4438 
        3.02        27.02        15.95         1.02         8.05        54.05 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4460 
        4.01        14.01        47.05        19.07        12.03        21.99 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4474 
        1.02         8.98        18.94         7.07        12.00         1.02 
TCGA-CG-5716 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
        1.02         6.94         1.02         1.02         0.99         5.98 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 
        0.95        70.06        12.03        28.96        31.04        65.10 
TCGA-CG-5730 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
        4.01        21.07         7.99         8.65         3.58         4.54 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
        9.80        15.65         9.63         8.19         6.90         0.69 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
        5.95         6.61         4.14         1.68         3.65         4.70 
TCGA-D7-6818 TCGA-D7-6820 TCGA-EQ-5647 TCGA-F1-6177 TCGA-F1-6874 TCGA-FP-7735 
        4.04         2.93         0.62         6.54         2.01         0.39 
TCGA-FP-7829 TCGA-FP-7998 TCGA-IN-7806 TCGA-IN-7808 TCGA-IP-7968 
        0.20         3.58         6.87         3.55         2.53 

  12P LOSS MUTATED 12P LOSS WILD-TYPE 
              0.30               0.07 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
             72.23              70.06 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
             9.645              2.530 
[1] "0.3 - 72.2 (9.6)" "0.1 - 70.1 (2.5)"
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
  "12P LOSS MUTATED" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-CD-5798 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-CD-5799         TCGA-CD-5800         TCGA-CD-5801 
"12P LOSS WILD-TYPE"   "12P LOSS MUTATED" "12P LOSS WILD-TYPE" 
        TCGA-CD-5802         TCGA-CD-5803         TCGA-CG-4300 
  "12P LOSS MUTATED" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-CG-4301         TCGA-CG-4304         TCGA-CG-4305 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-CG-4306         TCGA-CG-4436         TCGA-CG-4437 
"12P LOSS WILD-TYPE"   "12P LOSS MUTATED" "12P LOSS WILD-TYPE" 
        TCGA-CG-4438         TCGA-CG-4440         TCGA-CG-4441 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-CG-4443         TCGA-CG-4444         TCGA-CG-4449 
  "12P LOSS MUTATED" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-CG-4455         TCGA-CG-4460         TCGA-CG-4462 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-CG-4465         TCGA-CG-4466         TCGA-CG-4469 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-CG-4472         TCGA-CG-4474         TCGA-CG-4477 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE"   "12P LOSS MUTATED" 
        TCGA-CG-5716         TCGA-CG-5717         TCGA-CG-5718 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-CG-5719         TCGA-CG-5720         TCGA-CG-5721 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-CG-5722         TCGA-CG-5723         TCGA-CG-5724 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-CG-5725         TCGA-CG-5726         TCGA-CG-5727 
  "12P LOSS MUTATED" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-CG-5728         TCGA-CG-5730         TCGA-CG-5732 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE"   "12P LOSS MUTATED" 
        TCGA-CG-5733         TCGA-CG-5734         TCGA-D7-5577 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-D7-5578         TCGA-D7-5579         TCGA-D7-6518 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-D7-6519         TCGA-D7-6520         TCGA-D7-6521 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-D7-6522         TCGA-D7-6524         TCGA-D7-6525 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-D7-6526         TCGA-D7-6527         TCGA-D7-6528 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-D7-6815         TCGA-D7-6817         TCGA-D7-6818 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-D7-6820         TCGA-D7-6822         TCGA-EQ-5647 
"12P LOSS WILD-TYPE"   "12P LOSS MUTATED" "12P LOSS WILD-TYPE" 
        TCGA-F1-6177         TCGA-F1-6874         TCGA-F1-6875 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE"   "12P LOSS MUTATED" 
        TCGA-FP-7735         TCGA-FP-7829         TCGA-FP-7998 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-IN-7806         TCGA-IN-7808         TCGA-IP-7968 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
  "12P LOSS MUTATED" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-CD-5798 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-CD-5799         TCGA-CD-5800         TCGA-CD-5801 
"12P LOSS WILD-TYPE"   "12P LOSS MUTATED" "12P LOSS WILD-TYPE" 
        TCGA-CD-5802         TCGA-CD-5803         TCGA-CG-4300 
  "12P LOSS MUTATED" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-CG-4301         TCGA-CG-4304         TCGA-CG-4305 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-CG-4306         TCGA-CG-4436         TCGA-CG-4437 
"12P LOSS WILD-TYPE"   "12P LOSS MUTATED" "12P LOSS WILD-TYPE" 
        TCGA-CG-4438         TCGA-CG-4440         TCGA-CG-4441 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-CG-4443         TCGA-CG-4444         TCGA-CG-4449 
  "12P LOSS MUTATED" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-CG-4455         TCGA-CG-4460         TCGA-CG-4462 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-CG-4465         TCGA-CG-4466         TCGA-CG-4469 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-CG-4472         TCGA-CG-4474         TCGA-CG-4477 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE"   "12P LOSS MUTATED" 
        TCGA-CG-5716         TCGA-CG-5717         TCGA-CG-5718 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-CG-5719         TCGA-CG-5720         TCGA-CG-5721 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-CG-5722         TCGA-CG-5723         TCGA-CG-5724 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-CG-5725         TCGA-CG-5726         TCGA-CG-5727 
  "12P LOSS MUTATED" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-CG-5728         TCGA-CG-5730         TCGA-CG-5732 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE"   "12P LOSS MUTATED" 
        TCGA-CG-5733         TCGA-CG-5734         TCGA-D7-5577 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-D7-5578         TCGA-D7-5579         TCGA-D7-6518 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-D7-6519         TCGA-D7-6520         TCGA-D7-6521 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-D7-6522         TCGA-D7-6524         TCGA-D7-6525 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-D7-6526         TCGA-D7-6527         TCGA-D7-6528 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-D7-6815         TCGA-D7-6817         TCGA-D7-6818 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-D7-6820         TCGA-D7-6822         TCGA-EQ-5647 
"12P LOSS WILD-TYPE"   "12P LOSS MUTATED" "12P LOSS WILD-TYPE" 
        TCGA-F1-6177         TCGA-F1-6874         TCGA-F1-6875 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE"   "12P LOSS MUTATED" 
        TCGA-FP-7735         TCGA-FP-7829         TCGA-FP-7998 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-IN-7806         TCGA-IN-7808         TCGA-IP-7968 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
  "12P LOSS MUTATED" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-CD-5798 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-CD-5799         TCGA-CD-5800         TCGA-CD-5801 
"12P LOSS WILD-TYPE"   "12P LOSS MUTATED" "12P LOSS WILD-TYPE" 
        TCGA-CD-5802         TCGA-CD-5803         TCGA-CG-4300 
  "12P LOSS MUTATED" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-CG-4301         TCGA-CG-4304         TCGA-CG-4305 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-CG-4306         TCGA-CG-4436         TCGA-CG-4437 
"12P LOSS WILD-TYPE"   "12P LOSS MUTATED" "12P LOSS WILD-TYPE" 
        TCGA-CG-4438         TCGA-CG-4440         TCGA-CG-4441 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-CG-4443         TCGA-CG-4444         TCGA-CG-4449 
  "12P LOSS MUTATED" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-CG-4455         TCGA-CG-4460         TCGA-CG-4462 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-CG-4465         TCGA-CG-4466         TCGA-CG-4469 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-CG-4472         TCGA-CG-4474         TCGA-CG-4477 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE"   "12P LOSS MUTATED" 
        TCGA-CG-5716         TCGA-CG-5717         TCGA-CG-5718 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-CG-5719         TCGA-CG-5720         TCGA-CG-5721 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-CG-5722         TCGA-CG-5723         TCGA-CG-5724 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-CG-5725         TCGA-CG-5726         TCGA-CG-5727 
  "12P LOSS MUTATED" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-CG-5728         TCGA-CG-5730         TCGA-CG-5732 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE"   "12P LOSS MUTATED" 
        TCGA-CG-5733         TCGA-CG-5734         TCGA-D7-5577 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-D7-5578         TCGA-D7-5579         TCGA-D7-6518 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-D7-6519         TCGA-D7-6520         TCGA-D7-6521 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-D7-6522         TCGA-D7-6524         TCGA-D7-6525 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-D7-6526         TCGA-D7-6527         TCGA-D7-6528 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-D7-6815         TCGA-D7-6817         TCGA-D7-6818 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-D7-6820         TCGA-D7-6822         TCGA-EQ-5647 
"12P LOSS WILD-TYPE"   "12P LOSS MUTATED" "12P LOSS WILD-TYPE" 
        TCGA-F1-6177         TCGA-F1-6874         TCGA-F1-6875 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE"   "12P LOSS MUTATED" 
        TCGA-FP-7735         TCGA-FP-7829         TCGA-FP-7998 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-IN-7806         TCGA-IN-7808         TCGA-IP-7968 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
[1] "hr=" "3.5"
D57V2, continuous
D57V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED      2   10
  12P LOSS WILD-TYPE   58   88
        clus
vv       12P LOSS MUTATED 12P LOSS WILD-TYPE
  FEMALE                2                 58
  MALE                 10                 88
D57V4, multiclass
D57V5, multiclass
    clus
vv   12P LOSS MUTATED 12P LOSS WILD-TYPE
  T1                1                  5
  T2                6                 46
  T3                3                 58
  T4                0                 18
D57V6, multiclass
    clus
vv   12P LOSS MUTATED 12P LOSS WILD-TYPE
  N0                9                 35
  N1                0                 57
  N2                0                 24
  N3                1                 14
D57V7, multiclass
    clus
vv   12P LOSS MUTATED 12P LOSS WILD-TYPE
  M0               12                122
  M1                0                 16
  MX                0                  8
D57V8, multiclass
     clus
vv    12P LOSS MUTATED 12P LOSS WILD-TYPE
  I                  6                 18
  II                 3                 34
  III                0                 43
  IV                 1                 25
D57V9, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED      0   12
  12P LOSS WILD-TYPE    5  141
     clus
vv    12P LOSS MUTATED 12P LOSS WILD-TYPE
  NO                 0                  5
  YES               12                141
D57V10, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED      0   12
  12P LOSS WILD-TYPE   10  136
     clus
vv    12P LOSS MUTATED 12P LOSS WILD-TYPE
  NO                 0                 10
  YES               12                136

Clustering(58) Variable = 12q loss mutation analysis
D58V1, survival
                    sevent
clus2                 0  1
  12Q LOSS MUTATED    5  1
  12Q LOSS WILD-TYPE 85 14
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                 6                 99 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                 1                 14 
$`12Q LOSS MUTATED`
TCGA-BR-7715 TCGA-CD-5802 TCGA-CG-4436 TCGA-CG-4443 TCGA-CG-5725 TCGA-CG-5732 
        1.05         0.30        52.96        29.98        15.02        55.04 

$`12Q LOSS WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-6452 TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6458 
        5.62         0.10         0.95         1.41         1.35         1.35 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
        0.85         0.82         0.62         0.62         1.71         2.17 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
        0.99         1.22         0.66         1.12         0.76         0.66 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
        0.26         1.22         1.48         0.46         1.25         0.13 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 
        0.82         0.69         0.16         4.54         0.99         0.95 
TCGA-BR-7957 TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5803 
        0.69         0.82         0.69         0.36         0.49         0.07 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4437 
       20.02         3.02        27.02        15.95         1.02         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 
       54.05         4.01        14.01        47.05        19.07        12.03 
TCGA-CG-4460 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 
       21.99         1.02         8.98        18.94         7.07        12.00 
TCGA-CG-4474 TCGA-CG-4477 TCGA-CG-5716 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
        1.02         1.02         1.02         6.94         1.02         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 
        0.99         5.98         0.95        70.06        12.03        28.96 
TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       31.04        65.10         4.01        21.07         7.99         8.65 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
        3.58         4.54         9.80        15.65         9.63         8.19 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
        6.90         0.69         5.95         6.61         4.14         1.68 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-EQ-5647 
        3.65         4.70         4.04         2.93         4.27         0.62 
TCGA-F1-6177 TCGA-F1-6874 TCGA-F1-6875 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7998 
        6.54         2.01        72.23         0.39         0.20         3.58 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IP-7968 
        6.87         3.55         2.53 

  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
              0.30               0.07 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
             55.04              72.23 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
             22.50               2.53 
[1] "0.3 - 55.0 (22.5)" "0.1 - 72.2 (2.5)" 
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
  "12Q LOSS MUTATED" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-CD-5798 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-CD-5799         TCGA-CD-5800         TCGA-CD-5801 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-CD-5802         TCGA-CD-5803         TCGA-CG-4300 
  "12Q LOSS MUTATED" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-CG-4301         TCGA-CG-4304         TCGA-CG-4305 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-CG-4306         TCGA-CG-4436         TCGA-CG-4437 
"12Q LOSS WILD-TYPE"   "12Q LOSS MUTATED" "12Q LOSS WILD-TYPE" 
        TCGA-CG-4438         TCGA-CG-4440         TCGA-CG-4441 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-CG-4443         TCGA-CG-4444         TCGA-CG-4449 
  "12Q LOSS MUTATED" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-CG-4455         TCGA-CG-4460         TCGA-CG-4462 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-CG-4465         TCGA-CG-4466         TCGA-CG-4469 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-CG-4472         TCGA-CG-4474         TCGA-CG-4477 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-CG-5716         TCGA-CG-5717         TCGA-CG-5718 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-CG-5719         TCGA-CG-5720         TCGA-CG-5721 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-CG-5722         TCGA-CG-5723         TCGA-CG-5724 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-CG-5725         TCGA-CG-5726         TCGA-CG-5727 
  "12Q LOSS MUTATED" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-CG-5728         TCGA-CG-5730         TCGA-CG-5732 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE"   "12Q LOSS MUTATED" 
        TCGA-CG-5733         TCGA-CG-5734         TCGA-D7-5577 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-D7-5578         TCGA-D7-5579         TCGA-D7-6518 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-D7-6519         TCGA-D7-6520         TCGA-D7-6521 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-D7-6522         TCGA-D7-6524         TCGA-D7-6525 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-D7-6526         TCGA-D7-6527         TCGA-D7-6528 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-D7-6815         TCGA-D7-6817         TCGA-D7-6818 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-D7-6820         TCGA-D7-6822         TCGA-EQ-5647 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-F1-6177         TCGA-F1-6874         TCGA-F1-6875 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-FP-7735         TCGA-FP-7829         TCGA-FP-7998 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-IN-7806         TCGA-IN-7808         TCGA-IP-7968 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
  "12Q LOSS MUTATED" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-CD-5798 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-CD-5799         TCGA-CD-5800         TCGA-CD-5801 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-CD-5802         TCGA-CD-5803         TCGA-CG-4300 
  "12Q LOSS MUTATED" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-CG-4301         TCGA-CG-4304         TCGA-CG-4305 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-CG-4306         TCGA-CG-4436         TCGA-CG-4437 
"12Q LOSS WILD-TYPE"   "12Q LOSS MUTATED" "12Q LOSS WILD-TYPE" 
        TCGA-CG-4438         TCGA-CG-4440         TCGA-CG-4441 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-CG-4443         TCGA-CG-4444         TCGA-CG-4449 
  "12Q LOSS MUTATED" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-CG-4455         TCGA-CG-4460         TCGA-CG-4462 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-CG-4465         TCGA-CG-4466         TCGA-CG-4469 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-CG-4472         TCGA-CG-4474         TCGA-CG-4477 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-CG-5716         TCGA-CG-5717         TCGA-CG-5718 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-CG-5719         TCGA-CG-5720         TCGA-CG-5721 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-CG-5722         TCGA-CG-5723         TCGA-CG-5724 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-CG-5725         TCGA-CG-5726         TCGA-CG-5727 
  "12Q LOSS MUTATED" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-CG-5728         TCGA-CG-5730         TCGA-CG-5732 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE"   "12Q LOSS MUTATED" 
        TCGA-CG-5733         TCGA-CG-5734         TCGA-D7-5577 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-D7-5578         TCGA-D7-5579         TCGA-D7-6518 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-D7-6519         TCGA-D7-6520         TCGA-D7-6521 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-D7-6522         TCGA-D7-6524         TCGA-D7-6525 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-D7-6526         TCGA-D7-6527         TCGA-D7-6528 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-D7-6815         TCGA-D7-6817         TCGA-D7-6818 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-D7-6820         TCGA-D7-6822         TCGA-EQ-5647 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-F1-6177         TCGA-F1-6874         TCGA-F1-6875 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-FP-7735         TCGA-FP-7829         TCGA-FP-7998 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-IN-7806         TCGA-IN-7808         TCGA-IP-7968 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
  "12Q LOSS MUTATED" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-CD-5798 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-CD-5799         TCGA-CD-5800         TCGA-CD-5801 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-CD-5802         TCGA-CD-5803         TCGA-CG-4300 
  "12Q LOSS MUTATED" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-CG-4301         TCGA-CG-4304         TCGA-CG-4305 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-CG-4306         TCGA-CG-4436         TCGA-CG-4437 
"12Q LOSS WILD-TYPE"   "12Q LOSS MUTATED" "12Q LOSS WILD-TYPE" 
        TCGA-CG-4438         TCGA-CG-4440         TCGA-CG-4441 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-CG-4443         TCGA-CG-4444         TCGA-CG-4449 
  "12Q LOSS MUTATED" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-CG-4455         TCGA-CG-4460         TCGA-CG-4462 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-CG-4465         TCGA-CG-4466         TCGA-CG-4469 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-CG-4472         TCGA-CG-4474         TCGA-CG-4477 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-CG-5716         TCGA-CG-5717         TCGA-CG-5718 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-CG-5719         TCGA-CG-5720         TCGA-CG-5721 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-CG-5722         TCGA-CG-5723         TCGA-CG-5724 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-CG-5725         TCGA-CG-5726         TCGA-CG-5727 
  "12Q LOSS MUTATED" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-CG-5728         TCGA-CG-5730         TCGA-CG-5732 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE"   "12Q LOSS MUTATED" 
        TCGA-CG-5733         TCGA-CG-5734         TCGA-D7-5577 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-D7-5578         TCGA-D7-5579         TCGA-D7-6518 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-D7-6519         TCGA-D7-6520         TCGA-D7-6521 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-D7-6522         TCGA-D7-6524         TCGA-D7-6525 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-D7-6526         TCGA-D7-6527         TCGA-D7-6528 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-D7-6815         TCGA-D7-6817         TCGA-D7-6818 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-D7-6820         TCGA-D7-6822         TCGA-EQ-5647 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-F1-6177         TCGA-F1-6874         TCGA-F1-6875 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-FP-7735         TCGA-FP-7829         TCGA-FP-7998 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-IN-7806         TCGA-IN-7808         TCGA-IP-7968 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
[1] "hr=" "2.5"
D58V2, continuous
D58V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED      0    8
  12Q LOSS WILD-TYPE   60   90
        clus
vv       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  FEMALE                0                 60
  MALE                  8                 90
D58V4, multiclass
D58V5, multiclass
    clus
vv   12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  T1                1                  5
  T2                3                 49
  T3                2                 59
  T4                0                 18
D58V6, multiclass
    clus
vv   12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  N0                5                 39
  N1                0                 57
  N2                0                 24
  N3                1                 14
D58V7, multiclass
    clus
vv   12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  M0                8                126
  M1                0                 16
  MX                0                  8
D58V8, multiclass
     clus
vv    12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  I                  3                 21
  II                 2                 35
  III                0                 43
  IV                 1                 25
D58V9, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED      0    8
  12Q LOSS WILD-TYPE    5  145
     clus
vv    12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  NO                 0                  5
  YES                8                145
D58V10, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED      0    8
  12Q LOSS WILD-TYPE   10  140
     clus
vv    12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  NO                 0                 10
  YES                8                140

Clustering(59) Variable = 13q loss mutation analysis
D59V1, survival
                    sevent
clus2                 0  1
  13Q LOSS MUTATED    2  0
  13Q LOSS WILD-TYPE 88 15
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                 2                103 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                 0                 15 
$`13Q LOSS MUTATED`
TCGA-CG-4301 TCGA-D7-6525 
        3.02         5.95 

$`13Q LOSS WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-6452 TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6458 
        5.62         0.10         0.95         1.41         1.35         1.35 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
        0.85         0.82         0.62         0.62         1.71         2.17 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
        0.99         1.22         0.66         1.12         0.76         0.66 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
        0.26         1.22         1.48         0.46         1.25         0.13 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 
        1.05         0.82         0.69         0.16         4.54         0.99 
TCGA-BR-7901 TCGA-BR-7957 TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
        0.95         0.69         0.82         0.69         0.36         0.49 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CG-4300 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
        0.30         0.07        20.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
       52.96         8.05        54.05         4.01        14.01        29.98 
TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4460 TCGA-CG-4462 TCGA-CG-4465 
       47.05        19.07        12.03        21.99         1.02         8.98 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4474 TCGA-CG-4477 TCGA-CG-5716 
       18.94         7.07        12.00         1.02         1.02         1.02 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.94         1.02         1.02         0.99         5.98         0.95 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 
       70.06        12.03        15.02        28.96        31.04        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        55.04        21.07         7.99         8.65         3.58 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
        4.54         9.80        15.65         9.63         8.19         6.90 
TCGA-D7-6524 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
        0.69         6.61         4.14         1.68         3.65         4.70 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-EQ-5647 TCGA-F1-6177 TCGA-F1-6874 
        4.04         2.93         4.27         0.62         6.54         2.01 
TCGA-F1-6875 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7998 TCGA-IN-7806 TCGA-IN-7808 
       72.23         0.39         0.20         3.58         6.87         3.55 
TCGA-IP-7968 
        2.53 

  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
              3.02               0.07 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
              5.95              72.23 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
             4.485              2.530 
[1] "3.0 - 6.0 (4.5)"  "0.1 - 72.2 (2.5)"
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-CD-5798 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CD-5799         TCGA-CD-5800         TCGA-CD-5801 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CD-5802         TCGA-CD-5803         TCGA-CG-4300 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CG-4301         TCGA-CG-4304         TCGA-CG-4305 
  "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CG-4306         TCGA-CG-4436         TCGA-CG-4437 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CG-4438         TCGA-CG-4440         TCGA-CG-4441 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CG-4443         TCGA-CG-4444         TCGA-CG-4449 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CG-4455         TCGA-CG-4460         TCGA-CG-4462 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CG-4465         TCGA-CG-4466         TCGA-CG-4469 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CG-4472         TCGA-CG-4474         TCGA-CG-4477 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CG-5716         TCGA-CG-5717         TCGA-CG-5718 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CG-5719         TCGA-CG-5720         TCGA-CG-5721 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CG-5722         TCGA-CG-5723         TCGA-CG-5724 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CG-5725         TCGA-CG-5726         TCGA-CG-5727 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CG-5728         TCGA-CG-5730         TCGA-CG-5732 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CG-5733         TCGA-CG-5734         TCGA-D7-5577 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-D7-5578         TCGA-D7-5579         TCGA-D7-6518 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-D7-6519         TCGA-D7-6520         TCGA-D7-6521 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-D7-6522         TCGA-D7-6524         TCGA-D7-6525 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" 
        TCGA-D7-6526         TCGA-D7-6527         TCGA-D7-6528 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-D7-6815         TCGA-D7-6817         TCGA-D7-6818 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-D7-6820         TCGA-D7-6822         TCGA-EQ-5647 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-F1-6177         TCGA-F1-6874         TCGA-F1-6875 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-FP-7735         TCGA-FP-7829         TCGA-FP-7998 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-IN-7806         TCGA-IN-7808         TCGA-IP-7968 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-CD-5798 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CD-5799         TCGA-CD-5800         TCGA-CD-5801 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CD-5802         TCGA-CD-5803         TCGA-CG-4300 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CG-4301         TCGA-CG-4304         TCGA-CG-4305 
  "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CG-4306         TCGA-CG-4436         TCGA-CG-4437 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CG-4438         TCGA-CG-4440         TCGA-CG-4441 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CG-4443         TCGA-CG-4444         TCGA-CG-4449 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CG-4455         TCGA-CG-4460         TCGA-CG-4462 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CG-4465         TCGA-CG-4466         TCGA-CG-4469 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CG-4472         TCGA-CG-4474         TCGA-CG-4477 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CG-5716         TCGA-CG-5717         TCGA-CG-5718 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CG-5719         TCGA-CG-5720         TCGA-CG-5721 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CG-5722         TCGA-CG-5723         TCGA-CG-5724 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CG-5725         TCGA-CG-5726         TCGA-CG-5727 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CG-5728         TCGA-CG-5730         TCGA-CG-5732 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CG-5733         TCGA-CG-5734         TCGA-D7-5577 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-D7-5578         TCGA-D7-5579         TCGA-D7-6518 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-D7-6519         TCGA-D7-6520         TCGA-D7-6521 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-D7-6522         TCGA-D7-6524         TCGA-D7-6525 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" 
        TCGA-D7-6526         TCGA-D7-6527         TCGA-D7-6528 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-D7-6815         TCGA-D7-6817         TCGA-D7-6818 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-D7-6820         TCGA-D7-6822         TCGA-EQ-5647 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-F1-6177         TCGA-F1-6874         TCGA-F1-6875 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-FP-7735         TCGA-FP-7829         TCGA-FP-7998 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-IN-7806         TCGA-IN-7808         TCGA-IP-7968 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-CD-5798 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CD-5799         TCGA-CD-5800         TCGA-CD-5801 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CD-5802         TCGA-CD-5803         TCGA-CG-4300 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CG-4301         TCGA-CG-4304         TCGA-CG-4305 
  "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CG-4306         TCGA-CG-4436         TCGA-CG-4437 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CG-4438         TCGA-CG-4440         TCGA-CG-4441 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CG-4443         TCGA-CG-4444         TCGA-CG-4449 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CG-4455         TCGA-CG-4460         TCGA-CG-4462 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CG-4465         TCGA-CG-4466         TCGA-CG-4469 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CG-4472         TCGA-CG-4474         TCGA-CG-4477 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CG-5716         TCGA-CG-5717         TCGA-CG-5718 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CG-5719         TCGA-CG-5720         TCGA-CG-5721 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CG-5722         TCGA-CG-5723         TCGA-CG-5724 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CG-5725         TCGA-CG-5726         TCGA-CG-5727 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CG-5728         TCGA-CG-5730         TCGA-CG-5732 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CG-5733         TCGA-CG-5734         TCGA-D7-5577 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-D7-5578         TCGA-D7-5579         TCGA-D7-6518 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-D7-6519         TCGA-D7-6520         TCGA-D7-6521 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-D7-6522         TCGA-D7-6524         TCGA-D7-6525 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" 
        TCGA-D7-6526         TCGA-D7-6527         TCGA-D7-6528 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-D7-6815         TCGA-D7-6817         TCGA-D7-6818 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-D7-6820         TCGA-D7-6822         TCGA-EQ-5647 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-F1-6177         TCGA-F1-6874         TCGA-F1-6875 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-FP-7735         TCGA-FP-7829         TCGA-FP-7998 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-IN-7806         TCGA-IN-7808         TCGA-IP-7968 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
[1] "Remove cluster labels:" "13Q LOSS MUTATED"      
clus
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                 2                103 
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-CD-5798 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CD-5799         TCGA-CD-5800         TCGA-CD-5801 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CD-5802         TCGA-CD-5803         TCGA-CG-4300 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CG-4304         TCGA-CG-4305         TCGA-CG-4306 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CG-4436         TCGA-CG-4437         TCGA-CG-4438 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CG-4440         TCGA-CG-4441         TCGA-CG-4443 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CG-4444         TCGA-CG-4449         TCGA-CG-4455 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CG-4460         TCGA-CG-4462         TCGA-CG-4465 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CG-4466         TCGA-CG-4469         TCGA-CG-4472 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CG-4474         TCGA-CG-4477         TCGA-CG-5716 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CG-5717         TCGA-CG-5718         TCGA-CG-5719 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CG-5720         TCGA-CG-5721         TCGA-CG-5722 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CG-5723         TCGA-CG-5724         TCGA-CG-5725 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CG-5726         TCGA-CG-5727         TCGA-CG-5728 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CG-5730         TCGA-CG-5732         TCGA-CG-5733 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CG-5734         TCGA-D7-5577         TCGA-D7-5578 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-D7-5579         TCGA-D7-6518         TCGA-D7-6519 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-D7-6520         TCGA-D7-6521         TCGA-D7-6522 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-D7-6524         TCGA-D7-6526         TCGA-D7-6527 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-D7-6528         TCGA-D7-6815         TCGA-D7-6817 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-D7-6818         TCGA-D7-6820         TCGA-D7-6822 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EQ-5647         TCGA-F1-6177         TCGA-F1-6874 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-F1-6875         TCGA-FP-7735         TCGA-FP-7829 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-FP-7998         TCGA-IN-7806         TCGA-IN-7808 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-IP-7968 
"13Q LOSS WILD-TYPE" 
D59V2, continuous
D59V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED      2    3
  13Q LOSS WILD-TYPE   58   95
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  FEMALE                2                 58
  MALE                  3                 95
D59V4, multiclass
D59V5, multiclass
    clus
vv   13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  T1                0                  6
  T2                3                 49
  T3                1                 60
  T4                1                 17
D59V6, multiclass
    clus
vv   13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  N0                0                 44
  N1                2                 55
  N2                1                 23
  N3                1                 14
D59V7, multiclass
    clus
vv   13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  M0                4                130
  M1                1                 15
  MX                0                  8
D59V8, multiclass
     clus
vv    13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  I                  0                 24
  II                 1                 36
  III                1                 42
  IV                 2                 24
D59V9, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED      1    4
  13Q LOSS WILD-TYPE    4  149
     clus
vv    13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  NO                 1                  4
  YES                4                149
D59V10, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED      2    3
  13Q LOSS WILD-TYPE    8  145
     clus
vv    13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  NO                 2                  8
  YES                3                145

Clustering(60) Variable = 14q loss mutation analysis
D60V1, survival
                    sevent
clus2                 0  1
  14Q LOSS MUTATED    7  0
  14Q LOSS WILD-TYPE 83 15
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                 7                 98 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                 0                 15 
$`14Q LOSS MUTATED`
TCGA-BR-6458 TCGA-BR-7715 TCGA-CG-4438 TCGA-CG-4477 TCGA-D7-6519 TCGA-D7-6520 
        1.35         1.05        54.05         1.02        15.65         9.63 
TCGA-IN-7806 
        6.87 

$`14Q LOSS WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-6452 TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6563 
        5.62         0.10         0.95         1.41         1.35         0.85 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
        0.82         0.62         0.62         1.71         2.17         0.99 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
        1.22         0.66         1.12         0.76         0.66         0.26 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7716 
        1.22         1.48         0.46         1.25         0.13         0.82 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 
        0.69         0.16         4.54         0.99         0.95         0.69 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
        0.82         0.69         0.36         0.49         0.30         0.07 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02        52.96 
TCGA-CG-4437 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 
        8.05         4.01        14.01        29.98        47.05        19.07 
TCGA-CG-4455 TCGA-CG-4460 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       12.03        21.99         1.02         8.98        18.94         7.07 
TCGA-CG-4472 TCGA-CG-4474 TCGA-CG-5716 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
       12.00         1.02         1.02         6.94         1.02         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 
        0.99         5.98         0.95        70.06        12.03        15.02 
TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       28.96        31.04        65.10         4.01        55.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6521 
        7.99         8.65         3.58         4.54         9.80         8.19 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
        6.90         0.69         5.95         6.61         4.14         1.68 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-EQ-5647 
        3.65         4.70         4.04         2.93         4.27         0.62 
TCGA-F1-6177 TCGA-F1-6874 TCGA-F1-6875 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7998 
        6.54         2.01        72.23         0.39         0.20         3.58 
TCGA-IN-7808 TCGA-IP-7968 
        3.55         2.53 

  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
              1.02               0.07 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
             54.05              72.23 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
              6.87               2.73 
[1] "1.0 - 54.0 (6.9)" "0.1 - 72.2 (2.7)"
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-CD-5798 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-CD-5799         TCGA-CD-5800         TCGA-CD-5801 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-CD-5802         TCGA-CD-5803         TCGA-CG-4300 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-CG-4301         TCGA-CG-4304         TCGA-CG-4305 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-CG-4306         TCGA-CG-4436         TCGA-CG-4437 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-CG-4438         TCGA-CG-4440         TCGA-CG-4441 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-CG-4443         TCGA-CG-4444         TCGA-CG-4449 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-CG-4455         TCGA-CG-4460         TCGA-CG-4462 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-CG-4465         TCGA-CG-4466         TCGA-CG-4469 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-CG-4472         TCGA-CG-4474         TCGA-CG-4477 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-CG-5716         TCGA-CG-5717         TCGA-CG-5718 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-CG-5719         TCGA-CG-5720         TCGA-CG-5721 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-CG-5722         TCGA-CG-5723         TCGA-CG-5724 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-CG-5725         TCGA-CG-5726         TCGA-CG-5727 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-CG-5728         TCGA-CG-5730         TCGA-CG-5732 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-CG-5733         TCGA-CG-5734         TCGA-D7-5577 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-D7-5578         TCGA-D7-5579         TCGA-D7-6518 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-D7-6519         TCGA-D7-6520         TCGA-D7-6521 
  "14Q LOSS MUTATED"   "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" 
        TCGA-D7-6522         TCGA-D7-6524         TCGA-D7-6525 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-D7-6526         TCGA-D7-6527         TCGA-D7-6528 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-D7-6815         TCGA-D7-6817         TCGA-D7-6818 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-D7-6820         TCGA-D7-6822         TCGA-EQ-5647 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-F1-6177         TCGA-F1-6874         TCGA-F1-6875 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-FP-7735         TCGA-FP-7829         TCGA-FP-7998 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-IN-7806         TCGA-IN-7808         TCGA-IP-7968 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-CD-5798 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-CD-5799         TCGA-CD-5800         TCGA-CD-5801 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-CD-5802         TCGA-CD-5803         TCGA-CG-4300 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-CG-4301         TCGA-CG-4304         TCGA-CG-4305 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-CG-4306         TCGA-CG-4436         TCGA-CG-4437 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-CG-4438         TCGA-CG-4440         TCGA-CG-4441 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-CG-4443         TCGA-CG-4444         TCGA-CG-4449 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-CG-4455         TCGA-CG-4460         TCGA-CG-4462 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-CG-4465         TCGA-CG-4466         TCGA-CG-4469 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-CG-4472         TCGA-CG-4474         TCGA-CG-4477 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-CG-5716         TCGA-CG-5717         TCGA-CG-5718 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-CG-5719         TCGA-CG-5720         TCGA-CG-5721 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-CG-5722         TCGA-CG-5723         TCGA-CG-5724 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-CG-5725         TCGA-CG-5726         TCGA-CG-5727 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-CG-5728         TCGA-CG-5730         TCGA-CG-5732 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-CG-5733         TCGA-CG-5734         TCGA-D7-5577 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-D7-5578         TCGA-D7-5579         TCGA-D7-6518 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-D7-6519         TCGA-D7-6520         TCGA-D7-6521 
  "14Q LOSS MUTATED"   "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" 
        TCGA-D7-6522         TCGA-D7-6524         TCGA-D7-6525 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-D7-6526         TCGA-D7-6527         TCGA-D7-6528 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-D7-6815         TCGA-D7-6817         TCGA-D7-6818 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-D7-6820         TCGA-D7-6822         TCGA-EQ-5647 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-F1-6177         TCGA-F1-6874         TCGA-F1-6875 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-FP-7735         TCGA-FP-7829         TCGA-FP-7998 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-IN-7806         TCGA-IN-7808         TCGA-IP-7968 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-CD-5798 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-CD-5799         TCGA-CD-5800         TCGA-CD-5801 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-CD-5802         TCGA-CD-5803         TCGA-CG-4300 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-CG-4301         TCGA-CG-4304         TCGA-CG-4305 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-CG-4306         TCGA-CG-4436         TCGA-CG-4437 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-CG-4438         TCGA-CG-4440         TCGA-CG-4441 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-CG-4443         TCGA-CG-4444         TCGA-CG-4449 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-CG-4455         TCGA-CG-4460         TCGA-CG-4462 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-CG-4465         TCGA-CG-4466         TCGA-CG-4469 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-CG-4472         TCGA-CG-4474         TCGA-CG-4477 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-CG-5716         TCGA-CG-5717         TCGA-CG-5718 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-CG-5719         TCGA-CG-5720         TCGA-CG-5721 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-CG-5722         TCGA-CG-5723         TCGA-CG-5724 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-CG-5725         TCGA-CG-5726         TCGA-CG-5727 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-CG-5728         TCGA-CG-5730         TCGA-CG-5732 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-CG-5733         TCGA-CG-5734         TCGA-D7-5577 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-D7-5578         TCGA-D7-5579         TCGA-D7-6518 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-D7-6519         TCGA-D7-6520         TCGA-D7-6521 
  "14Q LOSS MUTATED"   "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" 
        TCGA-D7-6522         TCGA-D7-6524         TCGA-D7-6525 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-D7-6526         TCGA-D7-6527         TCGA-D7-6528 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-D7-6815         TCGA-D7-6817         TCGA-D7-6818 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-D7-6820         TCGA-D7-6822         TCGA-EQ-5647 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-F1-6177         TCGA-F1-6874         TCGA-F1-6875 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-FP-7735         TCGA-FP-7829         TCGA-FP-7998 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-IN-7806         TCGA-IN-7808         TCGA-IP-7968 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
[1] "hr="     "7.7e+07"
D60V2, continuous
D60V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED      3    7
  14Q LOSS WILD-TYPE   57   91
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  FEMALE                3                 57
  MALE                  7                 91
D60V4, multiclass
D60V5, multiclass
    clus
vv   14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  T1                0                  6
  T2                4                 48
  T3                3                 58
  T4                1                 17
D60V6, multiclass
    clus
vv   14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  N0                2                 42
  N1                4                 53
  N2                2                 22
  N3                0                 15
D60V7, multiclass
    clus
vv   14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  M0               10                124
  M1                0                 16
  MX                0                  8
D60V8, multiclass
     clus
vv    14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  I                  1                 23
  II                 3                 34
  III                3                 40
  IV                 1                 25
D60V9, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED      0   10
  14Q LOSS WILD-TYPE    5  143
     clus
vv    14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  NO                 0                  5
  YES               10                143
D60V10, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED      0   10
  14Q LOSS WILD-TYPE   10  138
     clus
vv    14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  NO                 0                 10
  YES               10                138

Clustering(61) Variable = 15q loss mutation analysis
D61V1, survival
                    sevent
clus2                 0  1
  15Q LOSS MUTATED    6  1
  15Q LOSS WILD-TYPE 84 14
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                 7                 98 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                 1                 14 
$`15Q LOSS MUTATED`
TCGA-BR-7704 TCGA-CG-4436 TCGA-CG-4466 TCGA-CG-5724 TCGA-D7-6519 TCGA-D7-6527 
        1.25        52.96        18.94        12.03        15.65         4.14 
TCGA-D7-6817 
        4.70 

$`15Q LOSS WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-6452 TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6458 
        5.62         0.10         0.95         1.41         1.35         1.35 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
        0.85         0.82         0.62         0.62         1.71         2.17 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
        0.99         1.22         0.66         1.12         0.76         0.66 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 
        0.26         1.22         1.48         0.46         0.13         1.05 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 
        0.82         0.69         0.16         4.54         0.99         0.95 
TCGA-BR-7957 TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        0.69         0.82         0.69         0.36         0.49         0.30 
TCGA-CD-5803 TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
        0.07        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 
        8.05        54.05         4.01        14.01        29.98        47.05 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4460 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4469 
       19.07        12.03        21.99         1.02         8.98         7.07 
TCGA-CG-4472 TCGA-CG-4474 TCGA-CG-4477 TCGA-CG-5716 TCGA-CG-5717 TCGA-CG-5718 
       12.00         1.02         1.02         1.02         6.94         1.02 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5725 
        1.02         0.99         5.98         0.95        70.06        15.02 
TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       28.96        31.04        65.10         4.01        55.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6520 
        7.99         8.65         3.58         4.54         9.80         9.63 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6528 
        8.19         6.90         0.69         5.95         6.61         1.68 
TCGA-D7-6815 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-EQ-5647 TCGA-F1-6177 
        3.65         4.04         2.93         4.27         0.62         6.54 
TCGA-F1-6874 TCGA-F1-6875 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7998 TCGA-IN-7806 
        2.01        72.23         0.39         0.20         3.58         6.87 
TCGA-IN-7808 TCGA-IP-7968 
        3.55         2.53 

  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
              1.25               0.07 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
             52.96              72.23 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
             12.03               2.09 
[1] "1.2 - 53.0 (12.0)" "0.1 - 72.2 (2.1)" 
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-CD-5798 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-CD-5799         TCGA-CD-5800         TCGA-CD-5801 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-CD-5802         TCGA-CD-5803         TCGA-CG-4300 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-CG-4301         TCGA-CG-4304         TCGA-CG-4305 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-CG-4306         TCGA-CG-4436         TCGA-CG-4437 
"15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" 
        TCGA-CG-4438         TCGA-CG-4440         TCGA-CG-4441 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-CG-4443         TCGA-CG-4444         TCGA-CG-4449 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-CG-4455         TCGA-CG-4460         TCGA-CG-4462 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-CG-4465         TCGA-CG-4466         TCGA-CG-4469 
"15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" 
        TCGA-CG-4472         TCGA-CG-4474         TCGA-CG-4477 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-CG-5716         TCGA-CG-5717         TCGA-CG-5718 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-CG-5719         TCGA-CG-5720         TCGA-CG-5721 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-CG-5722         TCGA-CG-5723         TCGA-CG-5724 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" 
        TCGA-CG-5725         TCGA-CG-5726         TCGA-CG-5727 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-CG-5728         TCGA-CG-5730         TCGA-CG-5732 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-CG-5733         TCGA-CG-5734         TCGA-D7-5577 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-D7-5578         TCGA-D7-5579         TCGA-D7-6518 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-D7-6519         TCGA-D7-6520         TCGA-D7-6521 
  "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-D7-6522         TCGA-D7-6524         TCGA-D7-6525 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-D7-6526         TCGA-D7-6527         TCGA-D7-6528 
"15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" 
        TCGA-D7-6815         TCGA-D7-6817         TCGA-D7-6818 
"15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" 
        TCGA-D7-6820         TCGA-D7-6822         TCGA-EQ-5647 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-F1-6177         TCGA-F1-6874         TCGA-F1-6875 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-FP-7735         TCGA-FP-7829         TCGA-FP-7998 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-IN-7806         TCGA-IN-7808         TCGA-IP-7968 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-CD-5798 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-CD-5799         TCGA-CD-5800         TCGA-CD-5801 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-CD-5802         TCGA-CD-5803         TCGA-CG-4300 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-CG-4301         TCGA-CG-4304         TCGA-CG-4305 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-CG-4306         TCGA-CG-4436         TCGA-CG-4437 
"15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" 
        TCGA-CG-4438         TCGA-CG-4440         TCGA-CG-4441 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-CG-4443         TCGA-CG-4444         TCGA-CG-4449 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-CG-4455         TCGA-CG-4460         TCGA-CG-4462 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-CG-4465         TCGA-CG-4466         TCGA-CG-4469 
"15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" 
        TCGA-CG-4472         TCGA-CG-4474         TCGA-CG-4477 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-CG-5716         TCGA-CG-5717         TCGA-CG-5718 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-CG-5719         TCGA-CG-5720         TCGA-CG-5721 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-CG-5722         TCGA-CG-5723         TCGA-CG-5724 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" 
        TCGA-CG-5725         TCGA-CG-5726         TCGA-CG-5727 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-CG-5728         TCGA-CG-5730         TCGA-CG-5732 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-CG-5733         TCGA-CG-5734         TCGA-D7-5577 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-D7-5578         TCGA-D7-5579         TCGA-D7-6518 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-D7-6519         TCGA-D7-6520         TCGA-D7-6521 
  "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-D7-6522         TCGA-D7-6524         TCGA-D7-6525 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-D7-6526         TCGA-D7-6527         TCGA-D7-6528 
"15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" 
        TCGA-D7-6815         TCGA-D7-6817         TCGA-D7-6818 
"15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" 
        TCGA-D7-6820         TCGA-D7-6822         TCGA-EQ-5647 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-F1-6177         TCGA-F1-6874         TCGA-F1-6875 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-FP-7735         TCGA-FP-7829         TCGA-FP-7998 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-IN-7806         TCGA-IN-7808         TCGA-IP-7968 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-CD-5798 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-CD-5799         TCGA-CD-5800         TCGA-CD-5801 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-CD-5802         TCGA-CD-5803         TCGA-CG-4300 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-CG-4301         TCGA-CG-4304         TCGA-CG-4305 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-CG-4306         TCGA-CG-4436         TCGA-CG-4437 
"15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" 
        TCGA-CG-4438         TCGA-CG-4440         TCGA-CG-4441 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-CG-4443         TCGA-CG-4444         TCGA-CG-4449 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-CG-4455         TCGA-CG-4460         TCGA-CG-4462 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-CG-4465         TCGA-CG-4466         TCGA-CG-4469 
"15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" 
        TCGA-CG-4472         TCGA-CG-4474         TCGA-CG-4477 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-CG-5716         TCGA-CG-5717         TCGA-CG-5718 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-CG-5719         TCGA-CG-5720         TCGA-CG-5721 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-CG-5722         TCGA-CG-5723         TCGA-CG-5724 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" 
        TCGA-CG-5725         TCGA-CG-5726         TCGA-CG-5727 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-CG-5728         TCGA-CG-5730         TCGA-CG-5732 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-CG-5733         TCGA-CG-5734         TCGA-D7-5577 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-D7-5578         TCGA-D7-5579         TCGA-D7-6518 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-D7-6519         TCGA-D7-6520         TCGA-D7-6521 
  "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-D7-6522         TCGA-D7-6524         TCGA-D7-6525 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-D7-6526         TCGA-D7-6527         TCGA-D7-6528 
"15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" 
        TCGA-D7-6815         TCGA-D7-6817         TCGA-D7-6818 
"15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" 
        TCGA-D7-6820         TCGA-D7-6822         TCGA-EQ-5647 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-F1-6177         TCGA-F1-6874         TCGA-F1-6875 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-FP-7735         TCGA-FP-7829         TCGA-FP-7998 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-IN-7806         TCGA-IN-7808         TCGA-IP-7968 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
[1] "hr=" "1.8"
D61V2, continuous
D61V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED      5    6
  15Q LOSS WILD-TYPE   55   92
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  FEMALE                5                 55
  MALE                  6                 92
D61V4, multiclass
D61V5, multiclass
    clus
vv   15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  T1                0                  6
  T2                7                 45
  T3                3                 58
  T4                0                 18
D61V6, multiclass
    clus
vv   15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  N0                4                 40
  N1                3                 54
  N2                0                 24
  N3                2                 13
D61V7, multiclass
    clus
vv   15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  M0                9                125
  M1                1                 15
  MX                1                  7
D61V8, multiclass
     clus
vv    15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  I                  3                 21
  II                 2                 35
  III                3                 40
  IV                 1                 25
D61V9, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED      2    9
  15Q LOSS WILD-TYPE    3  144
     clus
vv    15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  NO                 2                  3
  YES                9                144
D61V10, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED      2    9
  15Q LOSS WILD-TYPE    8  139
     clus
vv    15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  NO                 2                  8
  YES                9                139

Clustering(62) Variable = 16p loss mutation analysis
D62V1, survival
                    sevent
clus2                 0  1
  16P LOSS MUTATED    5  1
  16P LOSS WILD-TYPE 85 14
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                 6                 99 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                 1                 14 
$`16P LOSS MUTATED`
TCGA-BR-7715 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-5724 TCGA-D7-6519 TCGA-D7-6822 
        1.05        29.98        19.07        12.03        15.65         4.27 

$`16P LOSS WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-6452 TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6458 
        5.62         0.10         0.95         1.41         1.35         1.35 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
        0.85         0.82         0.62         0.62         1.71         2.17 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
        0.99         1.22         0.66         1.12         0.76         0.66 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
        0.26         1.22         1.48         0.46         1.25         0.13 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 
        0.82         0.69         0.16         4.54         0.99         0.95 
TCGA-BR-7957 TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        0.69         0.82         0.69         0.36         0.49         0.30 
TCGA-CD-5803 TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
        0.07        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4444 
       52.96         8.05        54.05         4.01        14.01        47.05 
TCGA-CG-4455 TCGA-CG-4460 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       12.03        21.99         1.02         8.98        18.94         7.07 
TCGA-CG-4472 TCGA-CG-4474 TCGA-CG-4477 TCGA-CG-5716 TCGA-CG-5717 TCGA-CG-5718 
       12.00         1.02         1.02         1.02         6.94         1.02 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5725 
        1.02         0.99         5.98         0.95        70.06        15.02 
TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       28.96        31.04        65.10         4.01        55.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6520 
        7.99         8.65         3.58         4.54         9.80         9.63 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
        8.19         6.90         0.69         5.95         6.61         4.14 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-EQ-5647 
        1.68         3.65         4.70         4.04         2.93         0.62 
TCGA-F1-6177 TCGA-F1-6874 TCGA-F1-6875 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7998 
        6.54         2.01        72.23         0.39         0.20         3.58 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IP-7968 
        6.87         3.55         2.53 

  16P LOSS MUTATED 16P LOSS WILD-TYPE 
              1.05               0.07 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
             29.98              72.23 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
             13.84               2.17 
[1] "1.1 - 30.0 (13.8)" "0.1 - 72.2 (2.2)" 
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
  "16P LOSS MUTATED" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-CD-5798 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-CD-5799         TCGA-CD-5800         TCGA-CD-5801 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-CD-5802         TCGA-CD-5803         TCGA-CG-4300 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-CG-4301         TCGA-CG-4304         TCGA-CG-4305 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-CG-4306         TCGA-CG-4436         TCGA-CG-4437 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-CG-4438         TCGA-CG-4440         TCGA-CG-4441 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-CG-4443         TCGA-CG-4444         TCGA-CG-4449 
  "16P LOSS MUTATED" "16P LOSS WILD-TYPE"   "16P LOSS MUTATED" 
        TCGA-CG-4455         TCGA-CG-4460         TCGA-CG-4462 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-CG-4465         TCGA-CG-4466         TCGA-CG-4469 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-CG-4472         TCGA-CG-4474         TCGA-CG-4477 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-CG-5716         TCGA-CG-5717         TCGA-CG-5718 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-CG-5719         TCGA-CG-5720         TCGA-CG-5721 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-CG-5722         TCGA-CG-5723         TCGA-CG-5724 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE"   "16P LOSS MUTATED" 
        TCGA-CG-5725         TCGA-CG-5726         TCGA-CG-5727 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-CG-5728         TCGA-CG-5730         TCGA-CG-5732 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-CG-5733         TCGA-CG-5734         TCGA-D7-5577 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-D7-5578         TCGA-D7-5579         TCGA-D7-6518 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-D7-6519         TCGA-D7-6520         TCGA-D7-6521 
  "16P LOSS MUTATED" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-D7-6522         TCGA-D7-6524         TCGA-D7-6525 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-D7-6526         TCGA-D7-6527         TCGA-D7-6528 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-D7-6815         TCGA-D7-6817         TCGA-D7-6818 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-D7-6820         TCGA-D7-6822         TCGA-EQ-5647 
"16P LOSS WILD-TYPE"   "16P LOSS MUTATED" "16P LOSS WILD-TYPE" 
        TCGA-F1-6177         TCGA-F1-6874         TCGA-F1-6875 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-FP-7735         TCGA-FP-7829         TCGA-FP-7998 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-IN-7806         TCGA-IN-7808         TCGA-IP-7968 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
  "16P LOSS MUTATED" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-CD-5798 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-CD-5799         TCGA-CD-5800         TCGA-CD-5801 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-CD-5802         TCGA-CD-5803         TCGA-CG-4300 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-CG-4301         TCGA-CG-4304         TCGA-CG-4305 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-CG-4306         TCGA-CG-4436         TCGA-CG-4437 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-CG-4438         TCGA-CG-4440         TCGA-CG-4441 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-CG-4443         TCGA-CG-4444         TCGA-CG-4449 
  "16P LOSS MUTATED" "16P LOSS WILD-TYPE"   "16P LOSS MUTATED" 
        TCGA-CG-4455         TCGA-CG-4460         TCGA-CG-4462 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-CG-4465         TCGA-CG-4466         TCGA-CG-4469 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-CG-4472         TCGA-CG-4474         TCGA-CG-4477 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-CG-5716         TCGA-CG-5717         TCGA-CG-5718 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-CG-5719         TCGA-CG-5720         TCGA-CG-5721 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-CG-5722         TCGA-CG-5723         TCGA-CG-5724 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE"   "16P LOSS MUTATED" 
        TCGA-CG-5725         TCGA-CG-5726         TCGA-CG-5727 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-CG-5728         TCGA-CG-5730         TCGA-CG-5732 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-CG-5733         TCGA-CG-5734         TCGA-D7-5577 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-D7-5578         TCGA-D7-5579         TCGA-D7-6518 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-D7-6519         TCGA-D7-6520         TCGA-D7-6521 
  "16P LOSS MUTATED" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-D7-6522         TCGA-D7-6524         TCGA-D7-6525 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-D7-6526         TCGA-D7-6527         TCGA-D7-6528 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-D7-6815         TCGA-D7-6817         TCGA-D7-6818 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-D7-6820         TCGA-D7-6822         TCGA-EQ-5647 
"16P LOSS WILD-TYPE"   "16P LOSS MUTATED" "16P LOSS WILD-TYPE" 
        TCGA-F1-6177         TCGA-F1-6874         TCGA-F1-6875 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-FP-7735         TCGA-FP-7829         TCGA-FP-7998 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-IN-7806         TCGA-IN-7808         TCGA-IP-7968 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
  "16P LOSS MUTATED" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-CD-5798 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-CD-5799         TCGA-CD-5800         TCGA-CD-5801 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-CD-5802         TCGA-CD-5803         TCGA-CG-4300 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-CG-4301         TCGA-CG-4304         TCGA-CG-4305 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-CG-4306         TCGA-CG-4436         TCGA-CG-4437 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-CG-4438         TCGA-CG-4440         TCGA-CG-4441 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-CG-4443         TCGA-CG-4444         TCGA-CG-4449 
  "16P LOSS MUTATED" "16P LOSS WILD-TYPE"   "16P LOSS MUTATED" 
        TCGA-CG-4455         TCGA-CG-4460         TCGA-CG-4462 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-CG-4465         TCGA-CG-4466         TCGA-CG-4469 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-CG-4472         TCGA-CG-4474         TCGA-CG-4477 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-CG-5716         TCGA-CG-5717         TCGA-CG-5718 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-CG-5719         TCGA-CG-5720         TCGA-CG-5721 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-CG-5722         TCGA-CG-5723         TCGA-CG-5724 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE"   "16P LOSS MUTATED" 
        TCGA-CG-5725         TCGA-CG-5726         TCGA-CG-5727 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-CG-5728         TCGA-CG-5730         TCGA-CG-5732 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-CG-5733         TCGA-CG-5734         TCGA-D7-5577 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-D7-5578         TCGA-D7-5579         TCGA-D7-6518 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-D7-6519         TCGA-D7-6520         TCGA-D7-6521 
  "16P LOSS MUTATED" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-D7-6522         TCGA-D7-6524         TCGA-D7-6525 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-D7-6526         TCGA-D7-6527         TCGA-D7-6528 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-D7-6815         TCGA-D7-6817         TCGA-D7-6818 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-D7-6820         TCGA-D7-6822         TCGA-EQ-5647 
"16P LOSS WILD-TYPE"   "16P LOSS MUTATED" "16P LOSS WILD-TYPE" 
        TCGA-F1-6177         TCGA-F1-6874         TCGA-F1-6875 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-FP-7735         TCGA-FP-7829         TCGA-FP-7998 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-IN-7806         TCGA-IN-7808         TCGA-IP-7968 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
[1] "hr=" "1.7"
D62V2, continuous
D62V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED      1    9
  16P LOSS WILD-TYPE   59   89
        clus
vv       16P LOSS MUTATED 16P LOSS WILD-TYPE
  FEMALE                1                 59
  MALE                  9                 89
D62V4, multiclass
D62V5, multiclass
    clus
vv   16P LOSS MUTATED 16P LOSS WILD-TYPE
  T1                1                  5
  T2                4                 48
  T3                3                 58
  T4                0                 18
D62V6, multiclass
    clus
vv   16P LOSS MUTATED 16P LOSS WILD-TYPE
  N0                3                 41
  N1                3                 54
  N2                0                 24
  N3                1                 14
D62V7, multiclass
    clus
vv   16P LOSS MUTATED 16P LOSS WILD-TYPE
  M0                9                125
  M1                1                 15
  MX                0                  8
D62V8, multiclass
     clus
vv    16P LOSS MUTATED 16P LOSS WILD-TYPE
  I                  2                 22
  II                 2                 35
  III                2                 41
  IV                 1                 25
D62V9, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED      0   10
  16P LOSS WILD-TYPE    5  143
     clus
vv    16P LOSS MUTATED 16P LOSS WILD-TYPE
  NO                 0                  5
  YES               10                143
D62V10, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED      0   10
  16P LOSS WILD-TYPE   10  138
     clus
vv    16P LOSS MUTATED 16P LOSS WILD-TYPE
  NO                 0                 10
  YES               10                138

Clustering(63) Variable = 16q loss mutation analysis
D63V1, survival
                    sevent
clus2                 0  1
  16Q LOSS MUTATED    7  1
  16Q LOSS WILD-TYPE 83 14
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                 8                 97 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                 1                 14 
$`16Q LOSS MUTATED`
TCGA-BR-7715 TCGA-CD-5802 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4477 TCGA-CG-5724 
        1.05         0.30        29.98        19.07         1.02        12.03 
TCGA-D7-6519 TCGA-D7-6817 
       15.65         4.70 

$`16Q LOSS WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-6452 TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6458 
        5.62         0.10         0.95         1.41         1.35         1.35 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
        0.85         0.82         0.62         0.62         1.71         2.17 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
        0.99         1.22         0.66         1.12         0.76         0.66 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
        0.26         1.22         1.48         0.46         1.25         0.13 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 
        0.82         0.69         0.16         4.54         0.99         0.95 
TCGA-BR-7957 TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5803 
        0.69         0.82         0.69         0.36         0.49         0.07 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02        52.96 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4444 TCGA-CG-4455 
        8.05        54.05         4.01        14.01        47.05        12.03 
TCGA-CG-4460 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 
       21.99         1.02         8.98        18.94         7.07        12.00 
TCGA-CG-4474 TCGA-CG-5716 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
        1.02         1.02         6.94         1.02         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5727 
        5.98         0.95        70.06        15.02        28.96        31.04 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        55.04        21.07         7.99         8.65 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
        3.58         4.54         9.80         9.63         8.19         6.90 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
        0.69         5.95         6.61         4.14         1.68         3.65 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-EQ-5647 TCGA-F1-6177 TCGA-F1-6874 
        4.04         2.93         4.27         0.62         6.54         2.01 
TCGA-F1-6875 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7998 TCGA-IN-7806 TCGA-IN-7808 
       72.23         0.39         0.20         3.58         6.87         3.55 
TCGA-IP-7968 
        2.53 

  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
              0.30               0.07 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
             29.98              72.23 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
             8.365              2.530 
[1] "0.3 - 30.0 (8.4)" "0.1 - 72.2 (2.5)"
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
  "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-CD-5798 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CD-5799         TCGA-CD-5800         TCGA-CD-5801 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CD-5802         TCGA-CD-5803         TCGA-CG-4300 
  "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CG-4301         TCGA-CG-4304         TCGA-CG-4305 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CG-4306         TCGA-CG-4436         TCGA-CG-4437 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CG-4438         TCGA-CG-4440         TCGA-CG-4441 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CG-4443         TCGA-CG-4444         TCGA-CG-4449 
  "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" 
        TCGA-CG-4455         TCGA-CG-4460         TCGA-CG-4462 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CG-4465         TCGA-CG-4466         TCGA-CG-4469 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CG-4472         TCGA-CG-4474         TCGA-CG-4477 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" 
        TCGA-CG-5716         TCGA-CG-5717         TCGA-CG-5718 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CG-5719         TCGA-CG-5720         TCGA-CG-5721 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CG-5722         TCGA-CG-5723         TCGA-CG-5724 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" 
        TCGA-CG-5725         TCGA-CG-5726         TCGA-CG-5727 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CG-5728         TCGA-CG-5730         TCGA-CG-5732 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CG-5733         TCGA-CG-5734         TCGA-D7-5577 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-D7-5578         TCGA-D7-5579         TCGA-D7-6518 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-D7-6519         TCGA-D7-6520         TCGA-D7-6521 
  "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-D7-6522         TCGA-D7-6524         TCGA-D7-6525 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-D7-6526         TCGA-D7-6527         TCGA-D7-6528 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-D7-6815         TCGA-D7-6817         TCGA-D7-6818 
"16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" 
        TCGA-D7-6820         TCGA-D7-6822         TCGA-EQ-5647 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-F1-6177         TCGA-F1-6874         TCGA-F1-6875 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-FP-7735         TCGA-FP-7829         TCGA-FP-7998 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-IN-7806         TCGA-IN-7808         TCGA-IP-7968 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
  "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-CD-5798 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CD-5799         TCGA-CD-5800         TCGA-CD-5801 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CD-5802         TCGA-CD-5803         TCGA-CG-4300 
  "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CG-4301         TCGA-CG-4304         TCGA-CG-4305 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CG-4306         TCGA-CG-4436         TCGA-CG-4437 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CG-4438         TCGA-CG-4440         TCGA-CG-4441 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CG-4443         TCGA-CG-4444         TCGA-CG-4449 
  "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" 
        TCGA-CG-4455         TCGA-CG-4460         TCGA-CG-4462 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CG-4465         TCGA-CG-4466         TCGA-CG-4469 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CG-4472         TCGA-CG-4474         TCGA-CG-4477 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" 
        TCGA-CG-5716         TCGA-CG-5717         TCGA-CG-5718 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CG-5719         TCGA-CG-5720         TCGA-CG-5721 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CG-5722         TCGA-CG-5723         TCGA-CG-5724 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" 
        TCGA-CG-5725         TCGA-CG-5726         TCGA-CG-5727 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CG-5728         TCGA-CG-5730         TCGA-CG-5732 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CG-5733         TCGA-CG-5734         TCGA-D7-5577 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-D7-5578         TCGA-D7-5579         TCGA-D7-6518 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-D7-6519         TCGA-D7-6520         TCGA-D7-6521 
  "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-D7-6522         TCGA-D7-6524         TCGA-D7-6525 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-D7-6526         TCGA-D7-6527         TCGA-D7-6528 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-D7-6815         TCGA-D7-6817         TCGA-D7-6818 
"16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" 
        TCGA-D7-6820         TCGA-D7-6822         TCGA-EQ-5647 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-F1-6177         TCGA-F1-6874         TCGA-F1-6875 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-FP-7735         TCGA-FP-7829         TCGA-FP-7998 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-IN-7806         TCGA-IN-7808         TCGA-IP-7968 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
  "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-CD-5798 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CD-5799         TCGA-CD-5800         TCGA-CD-5801 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CD-5802         TCGA-CD-5803         TCGA-CG-4300 
  "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CG-4301         TCGA-CG-4304         TCGA-CG-4305 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CG-4306         TCGA-CG-4436         TCGA-CG-4437 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CG-4438         TCGA-CG-4440         TCGA-CG-4441 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CG-4443         TCGA-CG-4444         TCGA-CG-4449 
  "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" 
        TCGA-CG-4455         TCGA-CG-4460         TCGA-CG-4462 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CG-4465         TCGA-CG-4466         TCGA-CG-4469 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CG-4472         TCGA-CG-4474         TCGA-CG-4477 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" 
        TCGA-CG-5716         TCGA-CG-5717         TCGA-CG-5718 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CG-5719         TCGA-CG-5720         TCGA-CG-5721 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CG-5722         TCGA-CG-5723         TCGA-CG-5724 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" 
        TCGA-CG-5725         TCGA-CG-5726         TCGA-CG-5727 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CG-5728         TCGA-CG-5730         TCGA-CG-5732 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CG-5733         TCGA-CG-5734         TCGA-D7-5577 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-D7-5578         TCGA-D7-5579         TCGA-D7-6518 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-D7-6519         TCGA-D7-6520         TCGA-D7-6521 
  "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-D7-6522         TCGA-D7-6524         TCGA-D7-6525 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-D7-6526         TCGA-D7-6527         TCGA-D7-6528 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-D7-6815         TCGA-D7-6817         TCGA-D7-6818 
"16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" 
        TCGA-D7-6820         TCGA-D7-6822         TCGA-EQ-5647 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-F1-6177         TCGA-F1-6874         TCGA-F1-6875 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-FP-7735         TCGA-FP-7829         TCGA-FP-7998 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-IN-7806         TCGA-IN-7808         TCGA-IP-7968 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
[1] "hr=" "1.8"
D63V2, continuous
D63V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED      3   11
  16Q LOSS WILD-TYPE   57   87
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  FEMALE                3                 57
  MALE                 11                 87
D63V4, multiclass
D63V5, multiclass
    clus
vv   16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  T1                1                  5
  T2                6                 46
  T3                5                 56
  T4                0                 18
D63V6, multiclass
    clus
vv   16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  N0                4                 40
  N1                4                 53
  N2                0                 24
  N3                3                 12
D63V7, multiclass
    clus
vv   16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  M0               13                121
  M1                1                 15
  MX                0                  8
D63V8, multiclass
     clus
vv    16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  I                  2                 22
  II                 4                 33
  III                3                 40
  IV                 2                 24
D63V9, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED      1   13
  16Q LOSS WILD-TYPE    4  140
     clus
vv    16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  NO                 1                  4
  YES               13                140
D63V10, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED      1   13
  16Q LOSS WILD-TYPE    9  135
     clus
vv    16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  NO                 1                  9
  YES               13                135

Clustering(64) Variable = 17p loss mutation analysis
D64V1, survival
                    sevent
clus2                 0  1
  17P LOSS MUTATED   23  3
  17P LOSS WILD-TYPE 67 12
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                26                 79 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                 3                 12 
$`17P LOSS MUTATED`
TCGA-B7-5818 TCGA-BR-7197 TCGA-BR-7715 TCGA-CD-5799 TCGA-CD-5800 TCGA-CG-4300 
        0.10         1.48         1.05         0.69         0.36        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4443 
        3.02        27.02         8.05        54.05         4.01        29.98 
TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5719 TCGA-CG-5725 TCGA-CG-5727 TCGA-CG-5730 
        7.07         1.02         1.02        15.02        31.04         4.01 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6526 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6820 
        9.63         8.19         6.61         1.68         3.65         2.93 
TCGA-IN-7806 TCGA-IP-7968 
        6.87         2.53 

$`17P LOSS WILD-TYPE`
TCGA-B7-5816 TCGA-BR-6452 TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
        5.62         0.95         1.41         1.35         1.35         0.85 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
        0.82         0.62         0.62         1.71         2.17         0.99 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
        1.22         0.66         1.12         0.76         0.66         0.26 
TCGA-BR-7196 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7716 TCGA-BR-7717 
        1.22         0.46         1.25         0.13         0.82         0.69 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-CD-5798 
        0.16         4.54         0.99         0.95         0.69         0.82 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
        0.49         0.30         0.07        15.95         1.02        52.96 
TCGA-CG-4441 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4460 TCGA-CG-4462 
       14.01        47.05        19.07        12.03        21.99         1.02 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4472 TCGA-CG-4474 TCGA-CG-5716 TCGA-CG-5717 
        8.98        18.94        12.00         1.02         1.02         6.94 
TCGA-CG-5718 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
        1.02         0.99         5.98         0.95        70.06        12.03 
TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       28.96        65.10        55.04        21.07         7.99         8.65 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6522 TCGA-D7-6524 
        3.58         4.54         9.80        15.65         6.90         0.69 
TCGA-D7-6525 TCGA-D7-6527 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6822 TCGA-EQ-5647 
        5.95         4.14         4.70         4.04         4.27         0.62 
TCGA-F1-6177 TCGA-F1-6874 TCGA-F1-6875 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7998 
        6.54         2.01        72.23         0.39         0.20         3.58 
TCGA-IN-7808 
        3.55 

  17P LOSS MUTATED 17P LOSS WILD-TYPE 
              0.10               0.07 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
             54.05              72.23 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
              4.01               1.41 
[1] "0.1 - 54.0 (4.0)" "0.1 - 72.2 (1.4)"
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-CD-5798 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-CD-5799         TCGA-CD-5800         TCGA-CD-5801 
  "17P LOSS MUTATED"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-CD-5802         TCGA-CD-5803         TCGA-CG-4300 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-CG-4301         TCGA-CG-4304         TCGA-CG-4305 
  "17P LOSS MUTATED"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-CG-4306         TCGA-CG-4436         TCGA-CG-4437 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-CG-4438         TCGA-CG-4440         TCGA-CG-4441 
  "17P LOSS MUTATED"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-CG-4443         TCGA-CG-4444         TCGA-CG-4449 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-CG-4455         TCGA-CG-4460         TCGA-CG-4462 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-CG-4465         TCGA-CG-4466         TCGA-CG-4469 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-CG-4472         TCGA-CG-4474         TCGA-CG-4477 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-CG-5716         TCGA-CG-5717         TCGA-CG-5718 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-CG-5719         TCGA-CG-5720         TCGA-CG-5721 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-CG-5722         TCGA-CG-5723         TCGA-CG-5724 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-CG-5725         TCGA-CG-5726         TCGA-CG-5727 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-CG-5728         TCGA-CG-5730         TCGA-CG-5732 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-CG-5733         TCGA-CG-5734         TCGA-D7-5577 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-D7-5578         TCGA-D7-5579         TCGA-D7-6518 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-D7-6519         TCGA-D7-6520         TCGA-D7-6521 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED"   "17P LOSS MUTATED" 
        TCGA-D7-6522         TCGA-D7-6524         TCGA-D7-6525 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-D7-6526         TCGA-D7-6527         TCGA-D7-6528 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-D7-6815         TCGA-D7-6817         TCGA-D7-6818 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-D7-6820         TCGA-D7-6822         TCGA-EQ-5647 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-F1-6177         TCGA-F1-6874         TCGA-F1-6875 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-FP-7735         TCGA-FP-7829         TCGA-FP-7998 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-IN-7806         TCGA-IN-7808         TCGA-IP-7968 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-CD-5798 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-CD-5799         TCGA-CD-5800         TCGA-CD-5801 
  "17P LOSS MUTATED"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-CD-5802         TCGA-CD-5803         TCGA-CG-4300 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-CG-4301         TCGA-CG-4304         TCGA-CG-4305 
  "17P LOSS MUTATED"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-CG-4306         TCGA-CG-4436         TCGA-CG-4437 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-CG-4438         TCGA-CG-4440         TCGA-CG-4441 
  "17P LOSS MUTATED"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-CG-4443         TCGA-CG-4444         TCGA-CG-4449 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-CG-4455         TCGA-CG-4460         TCGA-CG-4462 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-CG-4465         TCGA-CG-4466         TCGA-CG-4469 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-CG-4472         TCGA-CG-4474         TCGA-CG-4477 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-CG-5716         TCGA-CG-5717         TCGA-CG-5718 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-CG-5719         TCGA-CG-5720         TCGA-CG-5721 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-CG-5722         TCGA-CG-5723         TCGA-CG-5724 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-CG-5725         TCGA-CG-5726         TCGA-CG-5727 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-CG-5728         TCGA-CG-5730         TCGA-CG-5732 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-CG-5733         TCGA-CG-5734         TCGA-D7-5577 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-D7-5578         TCGA-D7-5579         TCGA-D7-6518 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-D7-6519         TCGA-D7-6520         TCGA-D7-6521 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED"   "17P LOSS MUTATED" 
        TCGA-D7-6522         TCGA-D7-6524         TCGA-D7-6525 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-D7-6526         TCGA-D7-6527         TCGA-D7-6528 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-D7-6815         TCGA-D7-6817         TCGA-D7-6818 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-D7-6820         TCGA-D7-6822         TCGA-EQ-5647 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-F1-6177         TCGA-F1-6874         TCGA-F1-6875 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-FP-7735         TCGA-FP-7829         TCGA-FP-7998 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-IN-7806         TCGA-IN-7808         TCGA-IP-7968 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-CD-5798 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-CD-5799         TCGA-CD-5800         TCGA-CD-5801 
  "17P LOSS MUTATED"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-CD-5802         TCGA-CD-5803         TCGA-CG-4300 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-CG-4301         TCGA-CG-4304         TCGA-CG-4305 
  "17P LOSS MUTATED"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-CG-4306         TCGA-CG-4436         TCGA-CG-4437 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-CG-4438         TCGA-CG-4440         TCGA-CG-4441 
  "17P LOSS MUTATED"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-CG-4443         TCGA-CG-4444         TCGA-CG-4449 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-CG-4455         TCGA-CG-4460         TCGA-CG-4462 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-CG-4465         TCGA-CG-4466         TCGA-CG-4469 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-CG-4472         TCGA-CG-4474         TCGA-CG-4477 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-CG-5716         TCGA-CG-5717         TCGA-CG-5718 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-CG-5719         TCGA-CG-5720         TCGA-CG-5721 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-CG-5722         TCGA-CG-5723         TCGA-CG-5724 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-CG-5725         TCGA-CG-5726         TCGA-CG-5727 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-CG-5728         TCGA-CG-5730         TCGA-CG-5732 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-CG-5733         TCGA-CG-5734         TCGA-D7-5577 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-D7-5578         TCGA-D7-5579         TCGA-D7-6518 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-D7-6519         TCGA-D7-6520         TCGA-D7-6521 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED"   "17P LOSS MUTATED" 
        TCGA-D7-6522         TCGA-D7-6524         TCGA-D7-6525 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-D7-6526         TCGA-D7-6527         TCGA-D7-6528 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-D7-6815         TCGA-D7-6817         TCGA-D7-6818 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-D7-6820         TCGA-D7-6822         TCGA-EQ-5647 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-F1-6177         TCGA-F1-6874         TCGA-F1-6875 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-FP-7735         TCGA-FP-7829         TCGA-FP-7998 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-IN-7806         TCGA-IN-7808         TCGA-IP-7968 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
[1] "hr=" "1.6"
D64V2, continuous
D64V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED     12   23
  17P LOSS WILD-TYPE   48   75
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  FEMALE               12                 48
  MALE                 23                 75
D64V4, multiclass
D64V5, multiclass
    clus
vv   17P LOSS MUTATED 17P LOSS WILD-TYPE
  T1                1                  5
  T2               17                 35
  T3               12                 49
  T4                3                 15
D64V6, multiclass
    clus
vv   17P LOSS MUTATED 17P LOSS WILD-TYPE
  N0               13                 31
  N1                8                 49
  N2                7                 17
  N3                3                 12
D64V7, multiclass
    clus
vv   17P LOSS MUTATED 17P LOSS WILD-TYPE
  M0               29                105
  M1                4                 12
  MX                2                  6
D64V8, multiclass
     clus
vv    17P LOSS MUTATED 17P LOSS WILD-TYPE
  I                  8                 16
  II                 8                 29
  III                8                 35
  IV                 7                 19
D64V9, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED      3   32
  17P LOSS WILD-TYPE    2  121
     clus
vv    17P LOSS MUTATED 17P LOSS WILD-TYPE
  NO                 3                  2
  YES               32                121
D64V10, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED      5   30
  17P LOSS WILD-TYPE    5  118
     clus
vv    17P LOSS MUTATED 17P LOSS WILD-TYPE
  NO                 5                  5
  YES               30                118

Clustering(65) Variable = 17q loss mutation analysis
D65V1, survival
                    sevent
clus2                 0  1
  17Q LOSS MUTATED    5  1
  17Q LOSS WILD-TYPE 85 14
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                 6                 99 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                 1                 14 
$`17Q LOSS MUTATED`
TCGA-CG-4300 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4477 TCGA-D7-6526 TCGA-D7-6820 
       20.02        54.05         4.01         1.02         6.61         2.93 

$`17Q LOSS WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-6452 TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6458 
        5.62         0.10         0.95         1.41         1.35         1.35 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
        0.85         0.82         0.62         0.62         1.71         2.17 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
        0.99         1.22         0.66         1.12         0.76         0.66 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
        0.26         1.22         1.48         0.46         1.25         0.13 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 
        1.05         0.82         0.69         0.16         4.54         0.99 
TCGA-BR-7901 TCGA-BR-7957 TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
        0.95         0.69         0.82         0.69         0.36         0.49 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
        0.30         0.07         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 
       52.96         8.05        14.01        29.98        47.05        19.07 
TCGA-CG-4455 TCGA-CG-4460 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       12.03        21.99         1.02         8.98        18.94         7.07 
TCGA-CG-4472 TCGA-CG-4474 TCGA-CG-5716 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
       12.00         1.02         1.02         6.94         1.02         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 
        0.99         5.98         0.95        70.06        12.03        15.02 
TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       28.96        31.04        65.10         4.01        55.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99         8.65         3.58         4.54         9.80        15.65 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6527 
        9.63         8.19         6.90         0.69         5.95         4.14 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6822 TCGA-EQ-5647 
        1.68         3.65         4.70         4.04         4.27         0.62 
TCGA-F1-6177 TCGA-F1-6874 TCGA-F1-6875 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7998 
        6.54         2.01        72.23         0.39         0.20         3.58 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IP-7968 
        6.87         3.55         2.53 

  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
              1.02               0.07 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
             54.05              72.23 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
              5.31               2.17 
[1] "1.0 - 54.0 (5.3)" "0.1 - 72.2 (2.2)"
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-CD-5798 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-CD-5799         TCGA-CD-5800         TCGA-CD-5801 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-CD-5802         TCGA-CD-5803         TCGA-CG-4300 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE"   "17Q LOSS MUTATED" 
        TCGA-CG-4301         TCGA-CG-4304         TCGA-CG-4305 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-CG-4306         TCGA-CG-4436         TCGA-CG-4437 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-CG-4438         TCGA-CG-4440         TCGA-CG-4441 
  "17Q LOSS MUTATED"   "17Q LOSS MUTATED" "17Q LOSS WILD-TYPE" 
        TCGA-CG-4443         TCGA-CG-4444         TCGA-CG-4449 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-CG-4455         TCGA-CG-4460         TCGA-CG-4462 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-CG-4465         TCGA-CG-4466         TCGA-CG-4469 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-CG-4472         TCGA-CG-4474         TCGA-CG-4477 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE"   "17Q LOSS MUTATED" 
        TCGA-CG-5716         TCGA-CG-5717         TCGA-CG-5718 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-CG-5719         TCGA-CG-5720         TCGA-CG-5721 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-CG-5722         TCGA-CG-5723         TCGA-CG-5724 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-CG-5725         TCGA-CG-5726         TCGA-CG-5727 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-CG-5728         TCGA-CG-5730         TCGA-CG-5732 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-CG-5733         TCGA-CG-5734         TCGA-D7-5577 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-D7-5578         TCGA-D7-5579         TCGA-D7-6518 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-D7-6519         TCGA-D7-6520         TCGA-D7-6521 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-D7-6522         TCGA-D7-6524         TCGA-D7-6525 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-D7-6526         TCGA-D7-6527         TCGA-D7-6528 
  "17Q LOSS MUTATED" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-D7-6815         TCGA-D7-6817         TCGA-D7-6818 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-D7-6820         TCGA-D7-6822         TCGA-EQ-5647 
  "17Q LOSS MUTATED" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-F1-6177         TCGA-F1-6874         TCGA-F1-6875 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-FP-7735         TCGA-FP-7829         TCGA-FP-7998 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-IN-7806         TCGA-IN-7808         TCGA-IP-7968 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-CD-5798 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-CD-5799         TCGA-CD-5800         TCGA-CD-5801 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-CD-5802         TCGA-CD-5803         TCGA-CG-4300 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE"   "17Q LOSS MUTATED" 
        TCGA-CG-4301         TCGA-CG-4304         TCGA-CG-4305 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-CG-4306         TCGA-CG-4436         TCGA-CG-4437 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-CG-4438         TCGA-CG-4440         TCGA-CG-4441 
  "17Q LOSS MUTATED"   "17Q LOSS MUTATED" "17Q LOSS WILD-TYPE" 
        TCGA-CG-4443         TCGA-CG-4444         TCGA-CG-4449 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-CG-4455         TCGA-CG-4460         TCGA-CG-4462 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-CG-4465         TCGA-CG-4466         TCGA-CG-4469 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-CG-4472         TCGA-CG-4474         TCGA-CG-4477 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE"   "17Q LOSS MUTATED" 
        TCGA-CG-5716         TCGA-CG-5717         TCGA-CG-5718 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-CG-5719         TCGA-CG-5720         TCGA-CG-5721 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-CG-5722         TCGA-CG-5723         TCGA-CG-5724 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-CG-5725         TCGA-CG-5726         TCGA-CG-5727 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-CG-5728         TCGA-CG-5730         TCGA-CG-5732 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-CG-5733         TCGA-CG-5734         TCGA-D7-5577 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-D7-5578         TCGA-D7-5579         TCGA-D7-6518 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-D7-6519         TCGA-D7-6520         TCGA-D7-6521 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-D7-6522         TCGA-D7-6524         TCGA-D7-6525 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-D7-6526         TCGA-D7-6527         TCGA-D7-6528 
  "17Q LOSS MUTATED" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-D7-6815         TCGA-D7-6817         TCGA-D7-6818 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-D7-6820         TCGA-D7-6822         TCGA-EQ-5647 
  "17Q LOSS MUTATED" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-F1-6177         TCGA-F1-6874         TCGA-F1-6875 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-FP-7735         TCGA-FP-7829         TCGA-FP-7998 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-IN-7806         TCGA-IN-7808         TCGA-IP-7968 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-CD-5798 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-CD-5799         TCGA-CD-5800         TCGA-CD-5801 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-CD-5802         TCGA-CD-5803         TCGA-CG-4300 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE"   "17Q LOSS MUTATED" 
        TCGA-CG-4301         TCGA-CG-4304         TCGA-CG-4305 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-CG-4306         TCGA-CG-4436         TCGA-CG-4437 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-CG-4438         TCGA-CG-4440         TCGA-CG-4441 
  "17Q LOSS MUTATED"   "17Q LOSS MUTATED" "17Q LOSS WILD-TYPE" 
        TCGA-CG-4443         TCGA-CG-4444         TCGA-CG-4449 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-CG-4455         TCGA-CG-4460         TCGA-CG-4462 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-CG-4465         TCGA-CG-4466         TCGA-CG-4469 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-CG-4472         TCGA-CG-4474         TCGA-CG-4477 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE"   "17Q LOSS MUTATED" 
        TCGA-CG-5716         TCGA-CG-5717         TCGA-CG-5718 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-CG-5719         TCGA-CG-5720         TCGA-CG-5721 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-CG-5722         TCGA-CG-5723         TCGA-CG-5724 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-CG-5725         TCGA-CG-5726         TCGA-CG-5727 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-CG-5728         TCGA-CG-5730         TCGA-CG-5732 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-CG-5733         TCGA-CG-5734         TCGA-D7-5577 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-D7-5578         TCGA-D7-5579         TCGA-D7-6518 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-D7-6519         TCGA-D7-6520         TCGA-D7-6521 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-D7-6522         TCGA-D7-6524         TCGA-D7-6525 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-D7-6526         TCGA-D7-6527         TCGA-D7-6528 
  "17Q LOSS MUTATED" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-D7-6815         TCGA-D7-6817         TCGA-D7-6818 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-D7-6820         TCGA-D7-6822         TCGA-EQ-5647 
  "17Q LOSS MUTATED" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-F1-6177         TCGA-F1-6874         TCGA-F1-6875 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-FP-7735         TCGA-FP-7829         TCGA-FP-7998 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-IN-7806         TCGA-IN-7808         TCGA-IP-7968 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
[1] "hr=" "1.1"
D65V2, continuous
D65V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED      4    4
  17Q LOSS WILD-TYPE   56   94
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  FEMALE                4                 56
  MALE                  4                 94
D65V4, multiclass
D65V5, multiclass
    clus
vv   17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  T1                0                  6
  T2                4                 48
  T3                3                 58
  T4                1                 17
D65V6, multiclass
    clus
vv   17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  N0                2                 42
  N1                1                 56
  N2                3                 21
  N3                1                 14
D65V7, multiclass
    clus
vv   17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  M0                6                128
  M1                1                 15
  MX                1                  7
D65V8, multiclass
     clus
vv    17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  I                  2                 22
  II                 1                 36
  III                2                 41
  IV                 2                 24
D65V9, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED      1    7
  17Q LOSS WILD-TYPE    4  146
     clus
vv    17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  NO                 1                  4
  YES                7                146
D65V10, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED      2    6
  17Q LOSS WILD-TYPE    8  142
     clus
vv    17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  NO                 2                  8
  YES                6                142

Clustering(66) Variable = 18p loss mutation analysis
D66V1, survival
                    sevent
clus2                 0  1
  18P LOSS MUTATED    6  4
  18P LOSS WILD-TYPE 84 11
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                10                 95 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                 4                 11 
$`18P LOSS MUTATED`
TCGA-BR-7723 TCGA-CG-4440 TCGA-CG-4449 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5718 
        4.54         4.01        19.07         7.07         1.02         1.02 
TCGA-D7-6519 TCGA-D7-6525 TCGA-EQ-5647 TCGA-F1-6875 
       15.65         5.95         0.62        72.23 

$`18P LOSS WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-6452 TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6458 
        5.62         0.10         0.95         1.41         1.35         1.35 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
        0.85         0.82         0.62         0.62         1.71         2.17 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
        0.99         1.22         0.66         1.12         0.76         0.66 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
        0.26         1.22         1.48         0.46         1.25         0.13 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7851 TCGA-BR-7901 
        1.05         0.82         0.69         0.16         0.99         0.95 
TCGA-BR-7957 TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        0.69         0.82         0.69         0.36         0.49         0.30 
TCGA-CD-5803 TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
        0.07        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 
       52.96         8.05        54.05        14.01        29.98        47.05 
TCGA-CG-4455 TCGA-CG-4460 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4472 
       12.03        21.99         1.02         8.98        18.94        12.00 
TCGA-CG-4474 TCGA-CG-5716 TCGA-CG-5717 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
        1.02         1.02         6.94         1.02         0.99         5.98 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5727 
        0.95        70.06        12.03        15.02        28.96        31.04 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        55.04        21.07         7.99         8.65 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
        3.58         4.54         9.80         9.63         8.19         6.90 
TCGA-D7-6524 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
        0.69         6.61         4.14         1.68         3.65         4.70 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-F1-6177 TCGA-F1-6874 TCGA-FP-7735 
        4.04         2.93         4.27         6.54         2.01         0.39 
TCGA-FP-7829 TCGA-FP-7998 TCGA-IN-7806 TCGA-IN-7808 TCGA-IP-7968 
        0.20         3.58         6.87         3.55         2.53 

  18P LOSS MUTATED 18P LOSS WILD-TYPE 
              0.62               0.07 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
             72.23              70.06 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
             5.245              2.170 
[1] "0.6 - 72.2 (5.2)" "0.1 - 70.1 (2.2)"
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"18P LOSS WILD-TYPE"   "18P LOSS MUTATED" "18P LOSS WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-CD-5798 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-CD-5799         TCGA-CD-5800         TCGA-CD-5801 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-CD-5802         TCGA-CD-5803         TCGA-CG-4300 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-CG-4301         TCGA-CG-4304         TCGA-CG-4305 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-CG-4306         TCGA-CG-4436         TCGA-CG-4437 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-CG-4438         TCGA-CG-4440         TCGA-CG-4441 
"18P LOSS WILD-TYPE"   "18P LOSS MUTATED" "18P LOSS WILD-TYPE" 
        TCGA-CG-4443         TCGA-CG-4444         TCGA-CG-4449 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE"   "18P LOSS MUTATED" 
        TCGA-CG-4455         TCGA-CG-4460         TCGA-CG-4462 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-CG-4465         TCGA-CG-4466         TCGA-CG-4469 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE"   "18P LOSS MUTATED" 
        TCGA-CG-4472         TCGA-CG-4474         TCGA-CG-4477 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE"   "18P LOSS MUTATED" 
        TCGA-CG-5716         TCGA-CG-5717         TCGA-CG-5718 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE"   "18P LOSS MUTATED" 
        TCGA-CG-5719         TCGA-CG-5720         TCGA-CG-5721 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-CG-5722         TCGA-CG-5723         TCGA-CG-5724 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-CG-5725         TCGA-CG-5726         TCGA-CG-5727 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-CG-5728         TCGA-CG-5730         TCGA-CG-5732 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-CG-5733         TCGA-CG-5734         TCGA-D7-5577 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-D7-5578         TCGA-D7-5579         TCGA-D7-6518 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-D7-6519         TCGA-D7-6520         TCGA-D7-6521 
  "18P LOSS MUTATED" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-D7-6522         TCGA-D7-6524         TCGA-D7-6525 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE"   "18P LOSS MUTATED" 
        TCGA-D7-6526         TCGA-D7-6527         TCGA-D7-6528 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-D7-6815         TCGA-D7-6817         TCGA-D7-6818 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-D7-6820         TCGA-D7-6822         TCGA-EQ-5647 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE"   "18P LOSS MUTATED" 
        TCGA-F1-6177         TCGA-F1-6874         TCGA-F1-6875 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE"   "18P LOSS MUTATED" 
        TCGA-FP-7735         TCGA-FP-7829         TCGA-FP-7998 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-IN-7806         TCGA-IN-7808         TCGA-IP-7968 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"18P LOSS WILD-TYPE"   "18P LOSS MUTATED" "18P LOSS WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-CD-5798 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-CD-5799         TCGA-CD-5800         TCGA-CD-5801 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-CD-5802         TCGA-CD-5803         TCGA-CG-4300 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-CG-4301         TCGA-CG-4304         TCGA-CG-4305 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-CG-4306         TCGA-CG-4436         TCGA-CG-4437 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-CG-4438         TCGA-CG-4440         TCGA-CG-4441 
"18P LOSS WILD-TYPE"   "18P LOSS MUTATED" "18P LOSS WILD-TYPE" 
        TCGA-CG-4443         TCGA-CG-4444         TCGA-CG-4449 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE"   "18P LOSS MUTATED" 
        TCGA-CG-4455         TCGA-CG-4460         TCGA-CG-4462 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-CG-4465         TCGA-CG-4466         TCGA-CG-4469 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE"   "18P LOSS MUTATED" 
        TCGA-CG-4472         TCGA-CG-4474         TCGA-CG-4477 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE"   "18P LOSS MUTATED" 
        TCGA-CG-5716         TCGA-CG-5717         TCGA-CG-5718 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE"   "18P LOSS MUTATED" 
        TCGA-CG-5719         TCGA-CG-5720         TCGA-CG-5721 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-CG-5722         TCGA-CG-5723         TCGA-CG-5724 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-CG-5725         TCGA-CG-5726         TCGA-CG-5727 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-CG-5728         TCGA-CG-5730         TCGA-CG-5732 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-CG-5733         TCGA-CG-5734         TCGA-D7-5577 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-D7-5578         TCGA-D7-5579         TCGA-D7-6518 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-D7-6519         TCGA-D7-6520         TCGA-D7-6521 
  "18P LOSS MUTATED" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-D7-6522         TCGA-D7-6524         TCGA-D7-6525 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE"   "18P LOSS MUTATED" 
        TCGA-D7-6526         TCGA-D7-6527         TCGA-D7-6528 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-D7-6815         TCGA-D7-6817         TCGA-D7-6818 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-D7-6820         TCGA-D7-6822         TCGA-EQ-5647 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE"   "18P LOSS MUTATED" 
        TCGA-F1-6177         TCGA-F1-6874         TCGA-F1-6875 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE"   "18P LOSS MUTATED" 
        TCGA-FP-7735         TCGA-FP-7829         TCGA-FP-7998 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-IN-7806         TCGA-IN-7808         TCGA-IP-7968 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"18P LOSS WILD-TYPE"   "18P LOSS MUTATED" "18P LOSS WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-CD-5798 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-CD-5799         TCGA-CD-5800         TCGA-CD-5801 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-CD-5802         TCGA-CD-5803         TCGA-CG-4300 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-CG-4301         TCGA-CG-4304         TCGA-CG-4305 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-CG-4306         TCGA-CG-4436         TCGA-CG-4437 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-CG-4438         TCGA-CG-4440         TCGA-CG-4441 
"18P LOSS WILD-TYPE"   "18P LOSS MUTATED" "18P LOSS WILD-TYPE" 
        TCGA-CG-4443         TCGA-CG-4444         TCGA-CG-4449 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE"   "18P LOSS MUTATED" 
        TCGA-CG-4455         TCGA-CG-4460         TCGA-CG-4462 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-CG-4465         TCGA-CG-4466         TCGA-CG-4469 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE"   "18P LOSS MUTATED" 
        TCGA-CG-4472         TCGA-CG-4474         TCGA-CG-4477 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE"   "18P LOSS MUTATED" 
        TCGA-CG-5716         TCGA-CG-5717         TCGA-CG-5718 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE"   "18P LOSS MUTATED" 
        TCGA-CG-5719         TCGA-CG-5720         TCGA-CG-5721 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-CG-5722         TCGA-CG-5723         TCGA-CG-5724 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-CG-5725         TCGA-CG-5726         TCGA-CG-5727 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-CG-5728         TCGA-CG-5730         TCGA-CG-5732 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-CG-5733         TCGA-CG-5734         TCGA-D7-5577 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-D7-5578         TCGA-D7-5579         TCGA-D7-6518 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-D7-6519         TCGA-D7-6520         TCGA-D7-6521 
  "18P LOSS MUTATED" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-D7-6522         TCGA-D7-6524         TCGA-D7-6525 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE"   "18P LOSS MUTATED" 
        TCGA-D7-6526         TCGA-D7-6527         TCGA-D7-6528 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-D7-6815         TCGA-D7-6817         TCGA-D7-6818 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-D7-6820         TCGA-D7-6822         TCGA-EQ-5647 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE"   "18P LOSS MUTATED" 
        TCGA-F1-6177         TCGA-F1-6874         TCGA-F1-6875 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE"   "18P LOSS MUTATED" 
        TCGA-FP-7735         TCGA-FP-7829         TCGA-FP-7998 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-IN-7806         TCGA-IN-7808         TCGA-IP-7968 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
[1] "hr=" "2"  
D66V2, continuous
D66V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED      6    9
  18P LOSS WILD-TYPE   54   89
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  FEMALE                6                 54
  MALE                  9                 89
D66V4, multiclass
D66V5, multiclass
    clus
vv   18P LOSS MUTATED 18P LOSS WILD-TYPE
  T1                0                  6
  T2                8                 44
  T3                3                 58
  T4                1                 17
D66V6, multiclass
    clus
vv   18P LOSS MUTATED 18P LOSS WILD-TYPE
  N0                2                 42
  N1                4                 53
  N2                2                 22
  N3                3                 12
D66V7, multiclass
    clus
vv   18P LOSS MUTATED 18P LOSS WILD-TYPE
  M0               13                121
  M1                2                 14
  MX                0                  8
D66V8, multiclass
     clus
vv    18P LOSS MUTATED 18P LOSS WILD-TYPE
  I                  2                 22
  II                 4                 33
  III                2                 41
  IV                 3                 23
D66V9, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED      0   15
  18P LOSS WILD-TYPE    5  138
     clus
vv    18P LOSS MUTATED 18P LOSS WILD-TYPE
  NO                 0                  5
  YES               15                138
D66V10, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED      1   14
  18P LOSS WILD-TYPE    9  134
     clus
vv    18P LOSS MUTATED 18P LOSS WILD-TYPE
  NO                 1                  9
  YES               14                134

Clustering(67) Variable = 18q loss mutation analysis
D67V1, survival
                    sevent
clus2                 0  1
  18Q LOSS MUTATED   15  4
  18Q LOSS WILD-TYPE 75 11
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                19                 86 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                 4                 11 
$`18Q LOSS MUTATED`
TCGA-B7-5818 TCGA-BR-7723 TCGA-CD-5802 TCGA-CG-4301 TCGA-CG-4438 TCGA-CG-4440 
        0.10         4.54         0.30         3.02        54.05         4.01 
TCGA-CG-4449 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5718 TCGA-CG-5724 TCGA-CG-5730 
       19.07         7.07         1.02         1.02        12.03         4.01 
TCGA-D7-5577 TCGA-D7-6519 TCGA-D7-6521 TCGA-D7-6525 TCGA-D7-6526 TCGA-EQ-5647 
        8.65        15.65         8.19         5.95         6.61         0.62 
TCGA-FP-7829 
        0.20 

$`18Q LOSS WILD-TYPE`
TCGA-B7-5816 TCGA-BR-6452 TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
        5.62         0.95         1.41         1.35         1.35         0.85 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
        0.82         0.62         0.62         1.71         2.17         0.99 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
        1.22         0.66         1.12         0.76         0.66         0.26 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
        1.22         1.48         0.46         1.25         0.13         1.05 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 
        0.82         0.69         0.16         0.99         0.95         0.69 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5803 TCGA-CG-4300 
        0.82         0.69         0.36         0.49         0.07        20.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4441 
       27.02        15.95         1.02        52.96         8.05        14.01 
TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4455 TCGA-CG-4460 TCGA-CG-4462 TCGA-CG-4465 
       29.98        47.05        12.03        21.99         1.02         8.98 
TCGA-CG-4466 TCGA-CG-4472 TCGA-CG-4474 TCGA-CG-5716 TCGA-CG-5717 TCGA-CG-5719 
       18.94        12.00         1.02         1.02         6.94         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5725 TCGA-CG-5726 
        0.99         5.98         0.95        70.06        15.02        28.96 
TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5578 
       31.04        65.10        55.04        21.07         7.99         3.58 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6520 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6527 
        4.54         9.80         9.63         6.90         0.69         4.14 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
        1.68         3.65         4.70         4.04         2.93         4.27 
TCGA-F1-6177 TCGA-F1-6874 TCGA-F1-6875 TCGA-FP-7735 TCGA-FP-7998 TCGA-IN-7806 
        6.54         2.01        72.23         0.39         3.58         6.87 
TCGA-IN-7808 TCGA-IP-7968 
        3.55         2.53 

  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
              0.10               0.07 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
             54.05              72.23 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
              4.54               1.86 
[1] "0.1 - 54.0 (4.5)" "0.1 - 72.2 (1.9)"
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-CD-5798 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-CD-5799         TCGA-CD-5800         TCGA-CD-5801 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-CD-5802         TCGA-CD-5803         TCGA-CG-4300 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-CG-4301         TCGA-CG-4304         TCGA-CG-4305 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-CG-4306         TCGA-CG-4436         TCGA-CG-4437 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-CG-4438         TCGA-CG-4440         TCGA-CG-4441 
  "18Q LOSS MUTATED"   "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" 
        TCGA-CG-4443         TCGA-CG-4444         TCGA-CG-4449 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" 
        TCGA-CG-4455         TCGA-CG-4460         TCGA-CG-4462 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-CG-4465         TCGA-CG-4466         TCGA-CG-4469 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" 
        TCGA-CG-4472         TCGA-CG-4474         TCGA-CG-4477 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" 
        TCGA-CG-5716         TCGA-CG-5717         TCGA-CG-5718 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" 
        TCGA-CG-5719         TCGA-CG-5720         TCGA-CG-5721 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-CG-5722         TCGA-CG-5723         TCGA-CG-5724 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" 
        TCGA-CG-5725         TCGA-CG-5726         TCGA-CG-5727 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-CG-5728         TCGA-CG-5730         TCGA-CG-5732 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" 
        TCGA-CG-5733         TCGA-CG-5734         TCGA-D7-5577 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" 
        TCGA-D7-5578         TCGA-D7-5579         TCGA-D7-6518 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-D7-6519         TCGA-D7-6520         TCGA-D7-6521 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" 
        TCGA-D7-6522         TCGA-D7-6524         TCGA-D7-6525 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" 
        TCGA-D7-6526         TCGA-D7-6527         TCGA-D7-6528 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-D7-6815         TCGA-D7-6817         TCGA-D7-6818 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-D7-6820         TCGA-D7-6822         TCGA-EQ-5647 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" 
        TCGA-F1-6177         TCGA-F1-6874         TCGA-F1-6875 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-FP-7735         TCGA-FP-7829         TCGA-FP-7998 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" 
        TCGA-IN-7806         TCGA-IN-7808         TCGA-IP-7968 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-CD-5798 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-CD-5799         TCGA-CD-5800         TCGA-CD-5801 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-CD-5802         TCGA-CD-5803         TCGA-CG-4300 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-CG-4301         TCGA-CG-4304         TCGA-CG-4305 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-CG-4306         TCGA-CG-4436         TCGA-CG-4437 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-CG-4438         TCGA-CG-4440         TCGA-CG-4441 
  "18Q LOSS MUTATED"   "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" 
        TCGA-CG-4443         TCGA-CG-4444         TCGA-CG-4449 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" 
        TCGA-CG-4455         TCGA-CG-4460         TCGA-CG-4462 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-CG-4465         TCGA-CG-4466         TCGA-CG-4469 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" 
        TCGA-CG-4472         TCGA-CG-4474         TCGA-CG-4477 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" 
        TCGA-CG-5716         TCGA-CG-5717         TCGA-CG-5718 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" 
        TCGA-CG-5719         TCGA-CG-5720         TCGA-CG-5721 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-CG-5722         TCGA-CG-5723         TCGA-CG-5724 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" 
        TCGA-CG-5725         TCGA-CG-5726         TCGA-CG-5727 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-CG-5728         TCGA-CG-5730         TCGA-CG-5732 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" 
        TCGA-CG-5733         TCGA-CG-5734         TCGA-D7-5577 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" 
        TCGA-D7-5578         TCGA-D7-5579         TCGA-D7-6518 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-D7-6519         TCGA-D7-6520         TCGA-D7-6521 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" 
        TCGA-D7-6522         TCGA-D7-6524         TCGA-D7-6525 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" 
        TCGA-D7-6526         TCGA-D7-6527         TCGA-D7-6528 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-D7-6815         TCGA-D7-6817         TCGA-D7-6818 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-D7-6820         TCGA-D7-6822         TCGA-EQ-5647 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" 
        TCGA-F1-6177         TCGA-F1-6874         TCGA-F1-6875 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-FP-7735         TCGA-FP-7829         TCGA-FP-7998 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" 
        TCGA-IN-7806         TCGA-IN-7808         TCGA-IP-7968 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-CD-5798 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-CD-5799         TCGA-CD-5800         TCGA-CD-5801 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-CD-5802         TCGA-CD-5803         TCGA-CG-4300 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-CG-4301         TCGA-CG-4304         TCGA-CG-4305 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-CG-4306         TCGA-CG-4436         TCGA-CG-4437 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-CG-4438         TCGA-CG-4440         TCGA-CG-4441 
  "18Q LOSS MUTATED"   "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" 
        TCGA-CG-4443         TCGA-CG-4444         TCGA-CG-4449 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" 
        TCGA-CG-4455         TCGA-CG-4460         TCGA-CG-4462 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-CG-4465         TCGA-CG-4466         TCGA-CG-4469 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" 
        TCGA-CG-4472         TCGA-CG-4474         TCGA-CG-4477 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" 
        TCGA-CG-5716         TCGA-CG-5717         TCGA-CG-5718 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" 
        TCGA-CG-5719         TCGA-CG-5720         TCGA-CG-5721 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-CG-5722         TCGA-CG-5723         TCGA-CG-5724 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" 
        TCGA-CG-5725         TCGA-CG-5726         TCGA-CG-5727 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-CG-5728         TCGA-CG-5730         TCGA-CG-5732 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" 
        TCGA-CG-5733         TCGA-CG-5734         TCGA-D7-5577 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" 
        TCGA-D7-5578         TCGA-D7-5579         TCGA-D7-6518 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-D7-6519         TCGA-D7-6520         TCGA-D7-6521 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" 
        TCGA-D7-6522         TCGA-D7-6524         TCGA-D7-6525 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" 
        TCGA-D7-6526         TCGA-D7-6527         TCGA-D7-6528 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-D7-6815         TCGA-D7-6817         TCGA-D7-6818 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-D7-6820         TCGA-D7-6822         TCGA-EQ-5647 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" 
        TCGA-F1-6177         TCGA-F1-6874         TCGA-F1-6875 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-FP-7735         TCGA-FP-7829         TCGA-FP-7998 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" 
        TCGA-IN-7806         TCGA-IN-7808         TCGA-IP-7968 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
[1] "hr=" "2"  
D67V2, continuous
D67V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED     11   18
  18Q LOSS WILD-TYPE   49   80
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  FEMALE               11                 49
  MALE                 18                 80
D67V4, multiclass
D67V5, multiclass
    clus
vv   18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  T1                0                  6
  T2               12                 40
  T3               10                 51
  T4                3                 15
D67V6, multiclass
    clus
vv   18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  N0                4                 40
  N1               11                 46
  N2                5                 19
  N3                5                 10
D67V7, multiclass
    clus
vv   18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  M0               24                110
  M1                5                 11
  MX                0                  8
D67V8, multiclass
     clus
vv    18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  I                  3                 21
  II                 6                 31
  III                8                 35
  IV                 7                 19
D67V9, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED      0   29
  18Q LOSS WILD-TYPE    5  124
     clus
vv    18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  NO                 0                  5
  YES               29                124
D67V10, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED      4   25
  18Q LOSS WILD-TYPE    6  123
     clus
vv    18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  NO                 4                  6
  YES               25                123

Clustering(68) Variable = 19p loss mutation analysis
D68V1, survival
                    sevent
clus2                 0  1
  19P LOSS MUTATED   11  3
  19P LOSS WILD-TYPE 79 12
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                14                 91 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                 3                 12 
$`19P LOSS MUTATED`
TCGA-BR-6458 TCGA-BR-6565 TCGA-BR-7723 TCGA-CG-4436 TCGA-CG-4438 TCGA-CG-4440 
        1.35         0.62         4.54        52.96        54.05         4.01 
TCGA-CG-4443 TCGA-CG-4466 TCGA-CG-5725 TCGA-CG-5732 TCGA-D7-6520 TCGA-D7-6525 
       29.98        18.94        15.02        55.04         9.63         5.95 
TCGA-D7-6820 TCGA-EQ-5647 
        2.93         0.62 

$`19P LOSS WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-6452 TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6563 
        5.62         0.10         0.95         1.41         1.35         0.85 
TCGA-BR-6564 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
        0.82         0.62         1.71         2.17         0.99         1.22 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        0.66         1.12         0.76         0.66         0.26         1.22 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 
        1.48         0.46         1.25         0.13         1.05         0.82 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-CD-5798 
        0.69         0.16         0.99         0.95         0.69         0.82 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CG-4300 
        0.69         0.36         0.49         0.30         0.07        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4437 TCGA-CG-4441 
        3.02        27.02        15.95         1.02         8.05        14.01 
TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4460 TCGA-CG-4462 TCGA-CG-4465 
       47.05        19.07        12.03        21.99         1.02         8.98 
TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4474 TCGA-CG-4477 TCGA-CG-5716 TCGA-CG-5717 
        7.07        12.00         1.02         1.02         1.02         6.94 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
        1.02         1.02         0.99         5.98         0.95        70.06 
TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5733 
       12.03        28.96        31.04        65.10         4.01        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99         8.65         3.58         4.54         9.80        15.65 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
        8.19         6.90         0.69         6.61         4.14         1.68 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6822 TCGA-F1-6177 TCGA-F1-6874 
        3.65         4.70         4.04         4.27         6.54         2.01 
TCGA-F1-6875 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7998 TCGA-IN-7806 TCGA-IN-7808 
       72.23         0.39         0.20         3.58         6.87         3.55 
TCGA-IP-7968 
        2.53 

  19P LOSS MUTATED 19P LOSS WILD-TYPE 
              0.62               0.07 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
             55.04              72.23 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
              7.79               1.71 
[1] "0.6 - 55.0 (7.8)" "0.1 - 72.2 (1.7)"
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE"   "19P LOSS MUTATED" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE"   "19P LOSS MUTATED" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"19P LOSS WILD-TYPE"   "19P LOSS MUTATED" "19P LOSS WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-CD-5798 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-CD-5799         TCGA-CD-5800         TCGA-CD-5801 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-CD-5802         TCGA-CD-5803         TCGA-CG-4300 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-CG-4301         TCGA-CG-4304         TCGA-CG-4305 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-CG-4306         TCGA-CG-4436         TCGA-CG-4437 
"19P LOSS WILD-TYPE"   "19P LOSS MUTATED" "19P LOSS WILD-TYPE" 
        TCGA-CG-4438         TCGA-CG-4440         TCGA-CG-4441 
  "19P LOSS MUTATED"   "19P LOSS MUTATED" "19P LOSS WILD-TYPE" 
        TCGA-CG-4443         TCGA-CG-4444         TCGA-CG-4449 
  "19P LOSS MUTATED" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-CG-4455         TCGA-CG-4460         TCGA-CG-4462 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-CG-4465         TCGA-CG-4466         TCGA-CG-4469 
"19P LOSS WILD-TYPE"   "19P LOSS MUTATED" "19P LOSS WILD-TYPE" 
        TCGA-CG-4472         TCGA-CG-4474         TCGA-CG-4477 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-CG-5716         TCGA-CG-5717         TCGA-CG-5718 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-CG-5719         TCGA-CG-5720         TCGA-CG-5721 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-CG-5722         TCGA-CG-5723         TCGA-CG-5724 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-CG-5725         TCGA-CG-5726         TCGA-CG-5727 
  "19P LOSS MUTATED" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-CG-5728         TCGA-CG-5730         TCGA-CG-5732 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE"   "19P LOSS MUTATED" 
        TCGA-CG-5733         TCGA-CG-5734         TCGA-D7-5577 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-D7-5578         TCGA-D7-5579         TCGA-D7-6518 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-D7-6519         TCGA-D7-6520         TCGA-D7-6521 
"19P LOSS WILD-TYPE"   "19P LOSS MUTATED" "19P LOSS WILD-TYPE" 
        TCGA-D7-6522         TCGA-D7-6524         TCGA-D7-6525 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE"   "19P LOSS MUTATED" 
        TCGA-D7-6526         TCGA-D7-6527         TCGA-D7-6528 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-D7-6815         TCGA-D7-6817         TCGA-D7-6818 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-D7-6820         TCGA-D7-6822         TCGA-EQ-5647 
  "19P LOSS MUTATED" "19P LOSS WILD-TYPE"   "19P LOSS MUTATED" 
        TCGA-F1-6177         TCGA-F1-6874         TCGA-F1-6875 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-FP-7735         TCGA-FP-7829         TCGA-FP-7998 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-IN-7806         TCGA-IN-7808         TCGA-IP-7968 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE"   "19P LOSS MUTATED" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE"   "19P LOSS MUTATED" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"19P LOSS WILD-TYPE"   "19P LOSS MUTATED" "19P LOSS WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-CD-5798 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-CD-5799         TCGA-CD-5800         TCGA-CD-5801 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-CD-5802         TCGA-CD-5803         TCGA-CG-4300 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-CG-4301         TCGA-CG-4304         TCGA-CG-4305 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-CG-4306         TCGA-CG-4436         TCGA-CG-4437 
"19P LOSS WILD-TYPE"   "19P LOSS MUTATED" "19P LOSS WILD-TYPE" 
        TCGA-CG-4438         TCGA-CG-4440         TCGA-CG-4441 
  "19P LOSS MUTATED"   "19P LOSS MUTATED" "19P LOSS WILD-TYPE" 
        TCGA-CG-4443         TCGA-CG-4444         TCGA-CG-4449 
  "19P LOSS MUTATED" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-CG-4455         TCGA-CG-4460         TCGA-CG-4462 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-CG-4465         TCGA-CG-4466         TCGA-CG-4469 
"19P LOSS WILD-TYPE"   "19P LOSS MUTATED" "19P LOSS WILD-TYPE" 
        TCGA-CG-4472         TCGA-CG-4474         TCGA-CG-4477 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-CG-5716         TCGA-CG-5717         TCGA-CG-5718 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-CG-5719         TCGA-CG-5720         TCGA-CG-5721 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-CG-5722         TCGA-CG-5723         TCGA-CG-5724 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-CG-5725         TCGA-CG-5726         TCGA-CG-5727 
  "19P LOSS MUTATED" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-CG-5728         TCGA-CG-5730         TCGA-CG-5732 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE"   "19P LOSS MUTATED" 
        TCGA-CG-5733         TCGA-CG-5734         TCGA-D7-5577 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-D7-5578         TCGA-D7-5579         TCGA-D7-6518 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-D7-6519         TCGA-D7-6520         TCGA-D7-6521 
"19P LOSS WILD-TYPE"   "19P LOSS MUTATED" "19P LOSS WILD-TYPE" 
        TCGA-D7-6522         TCGA-D7-6524         TCGA-D7-6525 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE"   "19P LOSS MUTATED" 
        TCGA-D7-6526         TCGA-D7-6527         TCGA-D7-6528 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-D7-6815         TCGA-D7-6817         TCGA-D7-6818 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-D7-6820         TCGA-D7-6822         TCGA-EQ-5647 
  "19P LOSS MUTATED" "19P LOSS WILD-TYPE"   "19P LOSS MUTATED" 
        TCGA-F1-6177         TCGA-F1-6874         TCGA-F1-6875 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-FP-7735         TCGA-FP-7829         TCGA-FP-7998 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-IN-7806         TCGA-IN-7808         TCGA-IP-7968 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE"   "19P LOSS MUTATED" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE"   "19P LOSS MUTATED" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"19P LOSS WILD-TYPE"   "19P LOSS MUTATED" "19P LOSS WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-CD-5798 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-CD-5799         TCGA-CD-5800         TCGA-CD-5801 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-CD-5802         TCGA-CD-5803         TCGA-CG-4300 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-CG-4301         TCGA-CG-4304         TCGA-CG-4305 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-CG-4306         TCGA-CG-4436         TCGA-CG-4437 
"19P LOSS WILD-TYPE"   "19P LOSS MUTATED" "19P LOSS WILD-TYPE" 
        TCGA-CG-4438         TCGA-CG-4440         TCGA-CG-4441 
  "19P LOSS MUTATED"   "19P LOSS MUTATED" "19P LOSS WILD-TYPE" 
        TCGA-CG-4443         TCGA-CG-4444         TCGA-CG-4449 
  "19P LOSS MUTATED" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-CG-4455         TCGA-CG-4460         TCGA-CG-4462 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-CG-4465         TCGA-CG-4466         TCGA-CG-4469 
"19P LOSS WILD-TYPE"   "19P LOSS MUTATED" "19P LOSS WILD-TYPE" 
        TCGA-CG-4472         TCGA-CG-4474         TCGA-CG-4477 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-CG-5716         TCGA-CG-5717         TCGA-CG-5718 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-CG-5719         TCGA-CG-5720         TCGA-CG-5721 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-CG-5722         TCGA-CG-5723         TCGA-CG-5724 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-CG-5725         TCGA-CG-5726         TCGA-CG-5727 
  "19P LOSS MUTATED" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-CG-5728         TCGA-CG-5730         TCGA-CG-5732 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE"   "19P LOSS MUTATED" 
        TCGA-CG-5733         TCGA-CG-5734         TCGA-D7-5577 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-D7-5578         TCGA-D7-5579         TCGA-D7-6518 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-D7-6519         TCGA-D7-6520         TCGA-D7-6521 
"19P LOSS WILD-TYPE"   "19P LOSS MUTATED" "19P LOSS WILD-TYPE" 
        TCGA-D7-6522         TCGA-D7-6524         TCGA-D7-6525 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE"   "19P LOSS MUTATED" 
        TCGA-D7-6526         TCGA-D7-6527         TCGA-D7-6528 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-D7-6815         TCGA-D7-6817         TCGA-D7-6818 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-D7-6820         TCGA-D7-6822         TCGA-EQ-5647 
  "19P LOSS MUTATED" "19P LOSS WILD-TYPE"   "19P LOSS MUTATED" 
        TCGA-F1-6177         TCGA-F1-6874         TCGA-F1-6875 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-FP-7735         TCGA-FP-7829         TCGA-FP-7998 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-IN-7806         TCGA-IN-7808         TCGA-IP-7968 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
[1] "hr=" "1.3"
D68V2, continuous
D68V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED      4   12
  19P LOSS WILD-TYPE   56   86
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  FEMALE                4                 56
  MALE                 12                 86
D68V4, multiclass
D68V5, multiclass
    clus
vv   19P LOSS MUTATED 19P LOSS WILD-TYPE
  T1                1                  5
  T2                7                 45
  T3                5                 56
  T4                2                 16
D68V6, multiclass
    clus
vv   19P LOSS MUTATED 19P LOSS WILD-TYPE
  N0                5                 39
  N1                3                 54
  N2                4                 20
  N3                3                 12
D68V7, multiclass
    clus
vv   19P LOSS MUTATED 19P LOSS WILD-TYPE
  M0               14                120
  M1                2                 14
  MX                0                  8
D68V8, multiclass
     clus
vv    19P LOSS MUTATED 19P LOSS WILD-TYPE
  I                  4                 20
  II                 4                 33
  III                3                 40
  IV                 4                 22
D68V9, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED      0   16
  19P LOSS WILD-TYPE    5  137
     clus
vv    19P LOSS MUTATED 19P LOSS WILD-TYPE
  NO                 0                  5
  YES               16                137
D68V10, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED      1   15
  19P LOSS WILD-TYPE    9  133
     clus
vv    19P LOSS MUTATED 19P LOSS WILD-TYPE
  NO                 1                  9
  YES               15                133

Clustering(69) Variable = 19q loss mutation analysis
D69V1, survival
                    sevent
clus2                 0  1
  19Q LOSS MUTATED    7  3
  19Q LOSS WILD-TYPE 83 12
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                10                 95 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                 3                 12 
$`19Q LOSS MUTATED`
TCGA-BR-6565 TCGA-BR-7723 TCGA-CG-4436 TCGA-CG-4440 TCGA-CG-4443 TCGA-CG-4466 
        0.62         4.54        52.96         4.01        29.98        18.94 
TCGA-CG-5725 TCGA-CG-5732 TCGA-D7-6820 TCGA-EQ-5647 
       15.02        55.04         2.93         0.62 

$`19Q LOSS WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-6452 TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6458 
        5.62         0.10         0.95         1.41         1.35         1.35 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
        0.85         0.82         0.62         1.71         2.17         0.99 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
        1.22         0.66         1.12         0.76         0.66         0.26 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
        1.22         1.48         0.46         1.25         0.13         1.05 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 
        0.82         0.69         0.16         0.99         0.95         0.69 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
        0.82         0.69         0.36         0.49         0.30         0.07 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4437 
       20.02         3.02        27.02        15.95         1.02         8.05 
TCGA-CG-4438 TCGA-CG-4441 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4460 
       54.05        14.01        47.05        19.07        12.03        21.99 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4474 TCGA-CG-4477 
        1.02         8.98         7.07        12.00         1.02         1.02 
TCGA-CG-5716 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
        1.02         6.94         1.02         1.02         0.99         5.98 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 
        0.95        70.06        12.03        28.96        31.04        65.10 
TCGA-CG-5730 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
        4.01        21.07         7.99         8.65         3.58         4.54 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
        9.80        15.65         9.63         8.19         6.90         0.69 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
        5.95         6.61         4.14         1.68         3.65         4.70 
TCGA-D7-6818 TCGA-D7-6822 TCGA-F1-6177 TCGA-F1-6874 TCGA-F1-6875 TCGA-FP-7735 
        4.04         4.27         6.54         2.01        72.23         0.39 
TCGA-FP-7829 TCGA-FP-7998 TCGA-IN-7806 TCGA-IN-7808 TCGA-IP-7968 
        0.20         3.58         6.87         3.55         2.53 

  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
              0.62               0.07 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
             55.04              72.23 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
              9.78               2.01 
[1] "0.6 - 55.0 (9.8)" "0.1 - 72.2 (2.0)"
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE"   "19Q LOSS MUTATED" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"19Q LOSS WILD-TYPE"   "19Q LOSS MUTATED" "19Q LOSS WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-CD-5798 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-CD-5799         TCGA-CD-5800         TCGA-CD-5801 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-CD-5802         TCGA-CD-5803         TCGA-CG-4300 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-CG-4301         TCGA-CG-4304         TCGA-CG-4305 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-CG-4306         TCGA-CG-4436         TCGA-CG-4437 
"19Q LOSS WILD-TYPE"   "19Q LOSS MUTATED" "19Q LOSS WILD-TYPE" 
        TCGA-CG-4438         TCGA-CG-4440         TCGA-CG-4441 
"19Q LOSS WILD-TYPE"   "19Q LOSS MUTATED" "19Q LOSS WILD-TYPE" 
        TCGA-CG-4443         TCGA-CG-4444         TCGA-CG-4449 
  "19Q LOSS MUTATED" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-CG-4455         TCGA-CG-4460         TCGA-CG-4462 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-CG-4465         TCGA-CG-4466         TCGA-CG-4469 
"19Q LOSS WILD-TYPE"   "19Q LOSS MUTATED" "19Q LOSS WILD-TYPE" 
        TCGA-CG-4472         TCGA-CG-4474         TCGA-CG-4477 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-CG-5716         TCGA-CG-5717         TCGA-CG-5718 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-CG-5719         TCGA-CG-5720         TCGA-CG-5721 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-CG-5722         TCGA-CG-5723         TCGA-CG-5724 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-CG-5725         TCGA-CG-5726         TCGA-CG-5727 
  "19Q LOSS MUTATED" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-CG-5728         TCGA-CG-5730         TCGA-CG-5732 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE"   "19Q LOSS MUTATED" 
        TCGA-CG-5733         TCGA-CG-5734         TCGA-D7-5577 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-D7-5578         TCGA-D7-5579         TCGA-D7-6518 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-D7-6519         TCGA-D7-6520         TCGA-D7-6521 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-D7-6522         TCGA-D7-6524         TCGA-D7-6525 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-D7-6526         TCGA-D7-6527         TCGA-D7-6528 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-D7-6815         TCGA-D7-6817         TCGA-D7-6818 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-D7-6820         TCGA-D7-6822         TCGA-EQ-5647 
  "19Q LOSS MUTATED" "19Q LOSS WILD-TYPE"   "19Q LOSS MUTATED" 
        TCGA-F1-6177         TCGA-F1-6874         TCGA-F1-6875 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-FP-7735         TCGA-FP-7829         TCGA-FP-7998 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-IN-7806         TCGA-IN-7808         TCGA-IP-7968 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE"   "19Q LOSS MUTATED" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"19Q LOSS WILD-TYPE"   "19Q LOSS MUTATED" "19Q LOSS WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-CD-5798 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-CD-5799         TCGA-CD-5800         TCGA-CD-5801 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-CD-5802         TCGA-CD-5803         TCGA-CG-4300 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-CG-4301         TCGA-CG-4304         TCGA-CG-4305 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-CG-4306         TCGA-CG-4436         TCGA-CG-4437 
"19Q LOSS WILD-TYPE"   "19Q LOSS MUTATED" "19Q LOSS WILD-TYPE" 
        TCGA-CG-4438         TCGA-CG-4440         TCGA-CG-4441 
"19Q LOSS WILD-TYPE"   "19Q LOSS MUTATED" "19Q LOSS WILD-TYPE" 
        TCGA-CG-4443         TCGA-CG-4444         TCGA-CG-4449 
  "19Q LOSS MUTATED" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-CG-4455         TCGA-CG-4460         TCGA-CG-4462 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-CG-4465         TCGA-CG-4466         TCGA-CG-4469 
"19Q LOSS WILD-TYPE"   "19Q LOSS MUTATED" "19Q LOSS WILD-TYPE" 
        TCGA-CG-4472         TCGA-CG-4474         TCGA-CG-4477 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-CG-5716         TCGA-CG-5717         TCGA-CG-5718 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-CG-5719         TCGA-CG-5720         TCGA-CG-5721 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-CG-5722         TCGA-CG-5723         TCGA-CG-5724 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-CG-5725         TCGA-CG-5726         TCGA-CG-5727 
  "19Q LOSS MUTATED" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-CG-5728         TCGA-CG-5730         TCGA-CG-5732 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE"   "19Q LOSS MUTATED" 
        TCGA-CG-5733         TCGA-CG-5734         TCGA-D7-5577 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-D7-5578         TCGA-D7-5579         TCGA-D7-6518 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-D7-6519         TCGA-D7-6520         TCGA-D7-6521 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-D7-6522         TCGA-D7-6524         TCGA-D7-6525 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-D7-6526         TCGA-D7-6527         TCGA-D7-6528 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-D7-6815         TCGA-D7-6817         TCGA-D7-6818 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-D7-6820         TCGA-D7-6822         TCGA-EQ-5647 
  "19Q LOSS MUTATED" "19Q LOSS WILD-TYPE"   "19Q LOSS MUTATED" 
        TCGA-F1-6177         TCGA-F1-6874         TCGA-F1-6875 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-FP-7735         TCGA-FP-7829         TCGA-FP-7998 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-IN-7806         TCGA-IN-7808         TCGA-IP-7968 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE"   "19Q LOSS MUTATED" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"19Q LOSS WILD-TYPE"   "19Q LOSS MUTATED" "19Q LOSS WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-CD-5798 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-CD-5799         TCGA-CD-5800         TCGA-CD-5801 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-CD-5802         TCGA-CD-5803         TCGA-CG-4300 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-CG-4301         TCGA-CG-4304         TCGA-CG-4305 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-CG-4306         TCGA-CG-4436         TCGA-CG-4437 
"19Q LOSS WILD-TYPE"   "19Q LOSS MUTATED" "19Q LOSS WILD-TYPE" 
        TCGA-CG-4438         TCGA-CG-4440         TCGA-CG-4441 
"19Q LOSS WILD-TYPE"   "19Q LOSS MUTATED" "19Q LOSS WILD-TYPE" 
        TCGA-CG-4443         TCGA-CG-4444         TCGA-CG-4449 
  "19Q LOSS MUTATED" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-CG-4455         TCGA-CG-4460         TCGA-CG-4462 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-CG-4465         TCGA-CG-4466         TCGA-CG-4469 
"19Q LOSS WILD-TYPE"   "19Q LOSS MUTATED" "19Q LOSS WILD-TYPE" 
        TCGA-CG-4472         TCGA-CG-4474         TCGA-CG-4477 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-CG-5716         TCGA-CG-5717         TCGA-CG-5718 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-CG-5719         TCGA-CG-5720         TCGA-CG-5721 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-CG-5722         TCGA-CG-5723         TCGA-CG-5724 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-CG-5725         TCGA-CG-5726         TCGA-CG-5727 
  "19Q LOSS MUTATED" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-CG-5728         TCGA-CG-5730         TCGA-CG-5732 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE"   "19Q LOSS MUTATED" 
        TCGA-CG-5733         TCGA-CG-5734         TCGA-D7-5577 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-D7-5578         TCGA-D7-5579         TCGA-D7-6518 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-D7-6519         TCGA-D7-6520         TCGA-D7-6521 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-D7-6522         TCGA-D7-6524         TCGA-D7-6525 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-D7-6526         TCGA-D7-6527         TCGA-D7-6528 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-D7-6815         TCGA-D7-6817         TCGA-D7-6818 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-D7-6820         TCGA-D7-6822         TCGA-EQ-5647 
  "19Q LOSS MUTATED" "19Q LOSS WILD-TYPE"   "19Q LOSS MUTATED" 
        TCGA-F1-6177         TCGA-F1-6874         TCGA-F1-6875 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-FP-7735         TCGA-FP-7829         TCGA-FP-7998 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-IN-7806         TCGA-IN-7808         TCGA-IP-7968 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
[1] "hr=" "1.2"
D69V2, continuous
D69V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED      3    9
  19Q LOSS WILD-TYPE   57   89
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  FEMALE                3                 57
  MALE                  9                 89
D69V4, multiclass
D69V5, multiclass
    clus
vv   19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  T1                1                  5
  T2                5                 47
  T3                4                 57
  T4                1                 17
D69V6, multiclass
    clus
vv   19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  N0                5                 39
  N1                2                 55
  N2                1                 23
  N3                3                 12
D69V7, multiclass
    clus
vv   19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  M0               10                124
  M1                2                 14
  MX                0                  8
D69V8, multiclass
     clus
vv    19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  I                  4                 20
  II                 3                 34
  III                1                 42
  IV                 3                 23
D69V9, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED      0   12
  19Q LOSS WILD-TYPE    5  141
     clus
vv    19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  NO                 0                  5
  YES               12                141
D69V10, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED      0   12
  19Q LOSS WILD-TYPE   10  136
     clus
vv    19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  NO                 0                 10
  YES               12                136

Clustering(70) Variable = 20p loss mutation analysis
D70V1, survival
                    sevent
clus2                 0  1
  20P LOSS MUTATED    2  1
  20P LOSS WILD-TYPE 88 14
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                 3                102 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                 1                 14 
$`20P LOSS MUTATED`
TCGA-CG-4301 TCGA-D7-6519 TCGA-EQ-5647 
        3.02        15.65         0.62 

$`20P LOSS WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-6452 TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6458 
        5.62         0.10         0.95         1.41         1.35         1.35 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
        0.85         0.82         0.62         0.62         1.71         2.17 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
        0.99         1.22         0.66         1.12         0.76         0.66 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
        0.26         1.22         1.48         0.46         1.25         0.13 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 
        1.05         0.82         0.69         0.16         4.54         0.99 
TCGA-BR-7901 TCGA-BR-7957 TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
        0.95         0.69         0.82         0.69         0.36         0.49 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CG-4300 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
        0.30         0.07        20.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
       52.96         8.05        54.05         4.01        14.01        29.98 
TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4460 TCGA-CG-4462 TCGA-CG-4465 
       47.05        19.07        12.03        21.99         1.02         8.98 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4474 TCGA-CG-4477 TCGA-CG-5716 
       18.94         7.07        12.00         1.02         1.02         1.02 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.94         1.02         1.02         0.99         5.98         0.95 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 
       70.06        12.03        15.02        28.96        31.04        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        55.04        21.07         7.99         8.65         3.58 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
        4.54         9.80         9.63         8.19         6.90         0.69 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
        5.95         6.61         4.14         1.68         3.65         4.70 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-F1-6177 TCGA-F1-6874 TCGA-F1-6875 
        4.04         2.93         4.27         6.54         2.01        72.23 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7998 TCGA-IN-7806 TCGA-IN-7808 TCGA-IP-7968 
        0.39         0.20         3.58         6.87         3.55         2.53 

  20P LOSS MUTATED 20P LOSS WILD-TYPE 
              0.62               0.07 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
             15.65              72.23 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
              3.02               2.73 
[1] "0.6 - 15.7 (3.0)" "0.1 - 72.2 (2.7)"
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-CD-5798 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CD-5799         TCGA-CD-5800         TCGA-CD-5801 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CD-5802         TCGA-CD-5803         TCGA-CG-4300 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CG-4301         TCGA-CG-4304         TCGA-CG-4305 
  "20P LOSS MUTATED" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CG-4306         TCGA-CG-4436         TCGA-CG-4437 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CG-4438         TCGA-CG-4440         TCGA-CG-4441 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CG-4443         TCGA-CG-4444         TCGA-CG-4449 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CG-4455         TCGA-CG-4460         TCGA-CG-4462 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CG-4465         TCGA-CG-4466         TCGA-CG-4469 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CG-4472         TCGA-CG-4474         TCGA-CG-4477 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CG-5716         TCGA-CG-5717         TCGA-CG-5718 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CG-5719         TCGA-CG-5720         TCGA-CG-5721 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CG-5722         TCGA-CG-5723         TCGA-CG-5724 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CG-5725         TCGA-CG-5726         TCGA-CG-5727 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CG-5728         TCGA-CG-5730         TCGA-CG-5732 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CG-5733         TCGA-CG-5734         TCGA-D7-5577 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-D7-5578         TCGA-D7-5579         TCGA-D7-6518 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-D7-6519         TCGA-D7-6520         TCGA-D7-6521 
  "20P LOSS MUTATED" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-D7-6522         TCGA-D7-6524         TCGA-D7-6525 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-D7-6526         TCGA-D7-6527         TCGA-D7-6528 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-D7-6815         TCGA-D7-6817         TCGA-D7-6818 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-D7-6820         TCGA-D7-6822         TCGA-EQ-5647 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE"   "20P LOSS MUTATED" 
        TCGA-F1-6177         TCGA-F1-6874         TCGA-F1-6875 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-FP-7735         TCGA-FP-7829         TCGA-FP-7998 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-IN-7806         TCGA-IN-7808         TCGA-IP-7968 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-CD-5798 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CD-5799         TCGA-CD-5800         TCGA-CD-5801 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CD-5802         TCGA-CD-5803         TCGA-CG-4300 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CG-4301         TCGA-CG-4304         TCGA-CG-4305 
  "20P LOSS MUTATED" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CG-4306         TCGA-CG-4436         TCGA-CG-4437 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CG-4438         TCGA-CG-4440         TCGA-CG-4441 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CG-4443         TCGA-CG-4444         TCGA-CG-4449 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CG-4455         TCGA-CG-4460         TCGA-CG-4462 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CG-4465         TCGA-CG-4466         TCGA-CG-4469 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CG-4472         TCGA-CG-4474         TCGA-CG-4477 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CG-5716         TCGA-CG-5717         TCGA-CG-5718 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CG-5719         TCGA-CG-5720         TCGA-CG-5721 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CG-5722         TCGA-CG-5723         TCGA-CG-5724 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CG-5725         TCGA-CG-5726         TCGA-CG-5727 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CG-5728         TCGA-CG-5730         TCGA-CG-5732 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CG-5733         TCGA-CG-5734         TCGA-D7-5577 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-D7-5578         TCGA-D7-5579         TCGA-D7-6518 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-D7-6519         TCGA-D7-6520         TCGA-D7-6521 
  "20P LOSS MUTATED" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-D7-6522         TCGA-D7-6524         TCGA-D7-6525 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-D7-6526         TCGA-D7-6527         TCGA-D7-6528 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-D7-6815         TCGA-D7-6817         TCGA-D7-6818 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-D7-6820         TCGA-D7-6822         TCGA-EQ-5647 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE"   "20P LOSS MUTATED" 
        TCGA-F1-6177         TCGA-F1-6874         TCGA-F1-6875 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-FP-7735         TCGA-FP-7829         TCGA-FP-7998 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-IN-7806         TCGA-IN-7808         TCGA-IP-7968 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-CD-5798 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CD-5799         TCGA-CD-5800         TCGA-CD-5801 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CD-5802         TCGA-CD-5803         TCGA-CG-4300 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CG-4301         TCGA-CG-4304         TCGA-CG-4305 
  "20P LOSS MUTATED" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CG-4306         TCGA-CG-4436         TCGA-CG-4437 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CG-4438         TCGA-CG-4440         TCGA-CG-4441 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CG-4443         TCGA-CG-4444         TCGA-CG-4449 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CG-4455         TCGA-CG-4460         TCGA-CG-4462 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CG-4465         TCGA-CG-4466         TCGA-CG-4469 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CG-4472         TCGA-CG-4474         TCGA-CG-4477 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CG-5716         TCGA-CG-5717         TCGA-CG-5718 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CG-5719         TCGA-CG-5720         TCGA-CG-5721 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CG-5722         TCGA-CG-5723         TCGA-CG-5724 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CG-5725         TCGA-CG-5726         TCGA-CG-5727 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CG-5728         TCGA-CG-5730         TCGA-CG-5732 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CG-5733         TCGA-CG-5734         TCGA-D7-5577 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-D7-5578         TCGA-D7-5579         TCGA-D7-6518 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-D7-6519         TCGA-D7-6520         TCGA-D7-6521 
  "20P LOSS MUTATED" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-D7-6522         TCGA-D7-6524         TCGA-D7-6525 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-D7-6526         TCGA-D7-6527         TCGA-D7-6528 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-D7-6815         TCGA-D7-6817         TCGA-D7-6818 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-D7-6820         TCGA-D7-6822         TCGA-EQ-5647 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE"   "20P LOSS MUTATED" 
        TCGA-F1-6177         TCGA-F1-6874         TCGA-F1-6875 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-FP-7735         TCGA-FP-7829         TCGA-FP-7998 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-IN-7806         TCGA-IN-7808         TCGA-IP-7968 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
[1] "hr=" "2.7"
D70V2, continuous
D70V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED      3    1
  20P LOSS WILD-TYPE   57   97
        clus
vv       20P LOSS MUTATED 20P LOSS WILD-TYPE
  FEMALE                3                 57
  MALE                  1                 97
D70V4, multiclass
D70V5, multiclass
    clus
vv   20P LOSS MUTATED 20P LOSS WILD-TYPE
  T1                0                  6
  T2                2                 50
  T3                0                 61
  T4                2                 16
D70V6, multiclass
    clus
vv   20P LOSS MUTATED 20P LOSS WILD-TYPE
  N0                1                 43
  N1                2                 55
  N2                0                 24
  N3                1                 14
D70V7, multiclass
    clus
vv   20P LOSS MUTATED 20P LOSS WILD-TYPE
  M0                2                132
  M1                2                 14
  MX                0                  8
D70V8, multiclass
     clus
vv    20P LOSS MUTATED 20P LOSS WILD-TYPE
  I                  1                 23
  II                 0                 37
  III                1                 42
  IV                 2                 24
D70V9, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED      0    4
  20P LOSS WILD-TYPE    5  149
     clus
vv    20P LOSS MUTATED 20P LOSS WILD-TYPE
  NO                 0                  5
  YES                4                149
D70V10, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED      0    4
  20P LOSS WILD-TYPE   10  144
     clus
vv    20P LOSS MUTATED 20P LOSS WILD-TYPE
  NO                 0                 10
  YES                4                144

Clustering(71) Variable = 21q loss mutation analysis
D71V1, survival
                    sevent
clus2                 0  1
  21Q LOSS MUTATED   17  3
  21Q LOSS WILD-TYPE 73 12
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                20                 85 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                 3                 12 
$`21Q LOSS MUTATED`
TCGA-B7-5818 TCGA-BR-6458 TCGA-BR-7704 TCGA-BR-7715 TCGA-CG-4438 TCGA-CG-4466 
        0.10         1.35         1.25         1.05        54.05        18.94 
TCGA-CG-4477 TCGA-CG-5719 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5728 TCGA-CG-5730 
        1.02         1.02        12.03        15.02        65.10         4.01 
TCGA-D7-5579 TCGA-D7-6519 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6817 TCGA-EQ-5647 
        4.54        15.65         5.95         6.61         4.70         0.62 
TCGA-FP-7829 TCGA-IN-7806 
        0.20         6.87 

$`21Q LOSS WILD-TYPE`
TCGA-B7-5816 TCGA-BR-6452 TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6563 TCGA-BR-6564 
        5.62         0.95         1.41         1.35         0.85         0.82 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
        0.62         0.62         1.71         2.17         0.99         1.22 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        0.66         1.12         0.76         0.66         0.26         1.22 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
        1.48         0.46         0.13         0.82         0.69         0.16 
TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-CD-5798 TCGA-CD-5799 
        4.54         0.99         0.95         0.69         0.82         0.69 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CG-4300 TCGA-CG-4301 
        0.36         0.49         0.30         0.07        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4440 
       27.02        15.95         1.02        52.96         8.05         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4460 
       14.01        29.98        47.05        19.07        12.03        21.99 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4474 TCGA-CG-5716 
        1.02         8.98         7.07        12.00         1.02         1.02 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
        6.94         1.02         0.99         5.98         0.95        70.06 
TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       28.96        31.04        55.04        21.07         7.99         8.65 
TCGA-D7-5578 TCGA-D7-6518 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
        3.58         9.80         9.63         8.19         6.90         0.69 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
        4.14         1.68         3.65         4.04         2.93         4.27 
TCGA-F1-6177 TCGA-F1-6874 TCGA-F1-6875 TCGA-FP-7735 TCGA-FP-7998 TCGA-IN-7808 
        6.54         2.01        72.23         0.39         3.58         3.55 
TCGA-IP-7968 
        2.53 

  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
              0.10               0.07 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
             65.10              72.23 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
              4.62               2.17 
[1] "0.1 - 65.1 (4.6)" "0.1 - 72.2 (2.2)"
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
  "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-CD-5798 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-CD-5799         TCGA-CD-5800         TCGA-CD-5801 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-CD-5802         TCGA-CD-5803         TCGA-CG-4300 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-CG-4301         TCGA-CG-4304         TCGA-CG-4305 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-CG-4306         TCGA-CG-4436         TCGA-CG-4437 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-CG-4438         TCGA-CG-4440         TCGA-CG-4441 
  "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-CG-4443         TCGA-CG-4444         TCGA-CG-4449 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-CG-4455         TCGA-CG-4460         TCGA-CG-4462 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-CG-4465         TCGA-CG-4466         TCGA-CG-4469 
"21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-CG-4472         TCGA-CG-4474         TCGA-CG-4477 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" 
        TCGA-CG-5716         TCGA-CG-5717         TCGA-CG-5718 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-CG-5719         TCGA-CG-5720         TCGA-CG-5721 
  "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-CG-5722         TCGA-CG-5723         TCGA-CG-5724 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" 
        TCGA-CG-5725         TCGA-CG-5726         TCGA-CG-5727 
  "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-CG-5728         TCGA-CG-5730         TCGA-CG-5732 
  "21Q LOSS MUTATED"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-CG-5733         TCGA-CG-5734         TCGA-D7-5577 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-D7-5578         TCGA-D7-5579         TCGA-D7-6518 
"21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-D7-6519         TCGA-D7-6520         TCGA-D7-6521 
  "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-D7-6522         TCGA-D7-6524         TCGA-D7-6525 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" 
        TCGA-D7-6526         TCGA-D7-6527         TCGA-D7-6528 
  "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-D7-6815         TCGA-D7-6817         TCGA-D7-6818 
"21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-D7-6820         TCGA-D7-6822         TCGA-EQ-5647 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" 
        TCGA-F1-6177         TCGA-F1-6874         TCGA-F1-6875 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-FP-7735         TCGA-FP-7829         TCGA-FP-7998 
"21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-IN-7806         TCGA-IN-7808         TCGA-IP-7968 
  "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
  "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-CD-5798 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-CD-5799         TCGA-CD-5800         TCGA-CD-5801 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-CD-5802         TCGA-CD-5803         TCGA-CG-4300 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-CG-4301         TCGA-CG-4304         TCGA-CG-4305 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-CG-4306         TCGA-CG-4436         TCGA-CG-4437 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-CG-4438         TCGA-CG-4440         TCGA-CG-4441 
  "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-CG-4443         TCGA-CG-4444         TCGA-CG-4449 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-CG-4455         TCGA-CG-4460         TCGA-CG-4462 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-CG-4465         TCGA-CG-4466         TCGA-CG-4469 
"21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-CG-4472         TCGA-CG-4474         TCGA-CG-4477 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" 
        TCGA-CG-5716         TCGA-CG-5717         TCGA-CG-5718 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-CG-5719         TCGA-CG-5720         TCGA-CG-5721 
  "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-CG-5722         TCGA-CG-5723         TCGA-CG-5724 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" 
        TCGA-CG-5725         TCGA-CG-5726         TCGA-CG-5727 
  "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-CG-5728         TCGA-CG-5730         TCGA-CG-5732 
  "21Q LOSS MUTATED"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-CG-5733         TCGA-CG-5734         TCGA-D7-5577 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-D7-5578         TCGA-D7-5579         TCGA-D7-6518 
"21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-D7-6519         TCGA-D7-6520         TCGA-D7-6521 
  "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-D7-6522         TCGA-D7-6524         TCGA-D7-6525 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" 
        TCGA-D7-6526         TCGA-D7-6527         TCGA-D7-6528 
  "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-D7-6815         TCGA-D7-6817         TCGA-D7-6818 
"21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-D7-6820         TCGA-D7-6822         TCGA-EQ-5647 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" 
        TCGA-F1-6177         TCGA-F1-6874         TCGA-F1-6875 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-FP-7735         TCGA-FP-7829         TCGA-FP-7998 
"21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-IN-7806         TCGA-IN-7808         TCGA-IP-7968 
  "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
  "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-CD-5798 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-CD-5799         TCGA-CD-5800         TCGA-CD-5801 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-CD-5802         TCGA-CD-5803         TCGA-CG-4300 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-CG-4301         TCGA-CG-4304         TCGA-CG-4305 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-CG-4306         TCGA-CG-4436         TCGA-CG-4437 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-CG-4438         TCGA-CG-4440         TCGA-CG-4441 
  "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-CG-4443         TCGA-CG-4444         TCGA-CG-4449 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-CG-4455         TCGA-CG-4460         TCGA-CG-4462 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-CG-4465         TCGA-CG-4466         TCGA-CG-4469 
"21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-CG-4472         TCGA-CG-4474         TCGA-CG-4477 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" 
        TCGA-CG-5716         TCGA-CG-5717         TCGA-CG-5718 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-CG-5719         TCGA-CG-5720         TCGA-CG-5721 
  "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-CG-5722         TCGA-CG-5723         TCGA-CG-5724 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" 
        TCGA-CG-5725         TCGA-CG-5726         TCGA-CG-5727 
  "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-CG-5728         TCGA-CG-5730         TCGA-CG-5732 
  "21Q LOSS MUTATED"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-CG-5733         TCGA-CG-5734         TCGA-D7-5577 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-D7-5578         TCGA-D7-5579         TCGA-D7-6518 
"21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-D7-6519         TCGA-D7-6520         TCGA-D7-6521 
  "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-D7-6522         TCGA-D7-6524         TCGA-D7-6525 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" 
        TCGA-D7-6526         TCGA-D7-6527         TCGA-D7-6528 
  "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-D7-6815         TCGA-D7-6817         TCGA-D7-6818 
"21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-D7-6820         TCGA-D7-6822         TCGA-EQ-5647 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" 
        TCGA-F1-6177         TCGA-F1-6874         TCGA-F1-6875 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-FP-7735         TCGA-FP-7829         TCGA-FP-7998 
"21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-IN-7806         TCGA-IN-7808         TCGA-IP-7968 
  "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
[1] "hr=" "1"  
D71V2, continuous
D71V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED     13   18
  21Q LOSS WILD-TYPE   47   80
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  FEMALE               13                 47
  MALE                 18                 80
D71V4, multiclass
D71V5, multiclass
    clus
vv   21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  T1                0                  6
  T2               10                 42
  T3               12                 49
  T4                3                 15
D71V6, multiclass
    clus
vv   21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  N0                8                 36
  N1               10                 47
  N2                4                 20
  N3                4                 11
D71V7, multiclass
    clus
vv   21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  M0               25                109
  M1                4                 12
  MX                2                  6
D71V8, multiclass
     clus
vv    21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  I                  5                 19
  II                 5                 32
  III                8                 35
  IV                 6                 20
D71V9, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED      1   30
  21Q LOSS WILD-TYPE    4  123
     clus
vv    21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  NO                 1                  4
  YES               30                123
D71V10, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED      4   27
  21Q LOSS WILD-TYPE    6  121
     clus
vv    21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  NO                 4                  6
  YES               27                121

Clustering(72) Variable = 22q loss mutation analysis
D72V1, survival
                    sevent
clus2                 0  1
  22Q LOSS MUTATED   11  4
  22Q LOSS WILD-TYPE 79 11
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                15                 90 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                 4                 11 
$`22Q LOSS MUTATED`
TCGA-BR-6458 TCGA-BR-7715 TCGA-CD-5800 TCGA-CD-5802 TCGA-CG-4438 TCGA-CG-4460 
        1.35         1.05         0.36         0.30        54.05        21.99 
TCGA-CG-4466 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5732 TCGA-D7-5578 TCGA-D7-6519 
       18.94        12.03        15.02        55.04         3.58        15.65 
TCGA-D7-6817 TCGA-D7-6820 TCGA-EQ-5647 
        4.70         2.93         0.62 

$`22Q LOSS WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-6452 TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6563 
        5.62         0.10         0.95         1.41         1.35         0.85 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
        0.82         0.62         0.62         1.71         2.17         0.99 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
        1.22         0.66         1.12         0.76         0.66         0.26 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7716 
        1.22         1.48         0.46         1.25         0.13         0.82 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 
        0.69         0.16         4.54         0.99         0.95         0.69 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5801 TCGA-CD-5803 TCGA-CG-4300 TCGA-CG-4301 
        0.82         0.69         0.49         0.07        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4440 
       27.02        15.95         1.02        52.96         8.05         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
       14.01        29.98        47.05        19.07        12.03         1.02 
TCGA-CG-4465 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4474 TCGA-CG-4477 TCGA-CG-5716 
        8.98         7.07        12.00         1.02         1.02         1.02 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.94         1.02         1.02         0.99         5.98         0.95 
TCGA-CG-5723 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5733 
       70.06        28.96        31.04        65.10         4.01        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6520 TCGA-D7-6521 
        7.99         8.65         4.54         9.80         9.63         8.19 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
        6.90         0.69         5.95         6.61         4.14         1.68 
TCGA-D7-6815 TCGA-D7-6818 TCGA-D7-6822 TCGA-F1-6177 TCGA-F1-6874 TCGA-F1-6875 
        3.65         4.04         4.27         6.54         2.01        72.23 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7998 TCGA-IN-7806 TCGA-IN-7808 TCGA-IP-7968 
        0.39         0.20         3.58         6.87         3.55         2.53 

  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
              0.30               0.07 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
             55.04              72.23 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
              4.70               2.09 
[1] "0.3 - 55.0 (4.7)" "0.1 - 72.2 (2.1)"
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
  "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-CD-5798 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-CD-5799         TCGA-CD-5800         TCGA-CD-5801 
"22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" 
        TCGA-CD-5802         TCGA-CD-5803         TCGA-CG-4300 
  "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-CG-4301         TCGA-CG-4304         TCGA-CG-4305 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-CG-4306         TCGA-CG-4436         TCGA-CG-4437 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-CG-4438         TCGA-CG-4440         TCGA-CG-4441 
  "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-CG-4443         TCGA-CG-4444         TCGA-CG-4449 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-CG-4455         TCGA-CG-4460         TCGA-CG-4462 
"22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" 
        TCGA-CG-4465         TCGA-CG-4466         TCGA-CG-4469 
"22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" 
        TCGA-CG-4472         TCGA-CG-4474         TCGA-CG-4477 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-CG-5716         TCGA-CG-5717         TCGA-CG-5718 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-CG-5719         TCGA-CG-5720         TCGA-CG-5721 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-CG-5722         TCGA-CG-5723         TCGA-CG-5724 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" 
        TCGA-CG-5725         TCGA-CG-5726         TCGA-CG-5727 
  "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-CG-5728         TCGA-CG-5730         TCGA-CG-5732 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" 
        TCGA-CG-5733         TCGA-CG-5734         TCGA-D7-5577 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-D7-5578         TCGA-D7-5579         TCGA-D7-6518 
  "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-D7-6519         TCGA-D7-6520         TCGA-D7-6521 
  "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-D7-6522         TCGA-D7-6524         TCGA-D7-6525 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-D7-6526         TCGA-D7-6527         TCGA-D7-6528 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-D7-6815         TCGA-D7-6817         TCGA-D7-6818 
"22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" 
        TCGA-D7-6820         TCGA-D7-6822         TCGA-EQ-5647 
  "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" 
        TCGA-F1-6177         TCGA-F1-6874         TCGA-F1-6875 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-FP-7735         TCGA-FP-7829         TCGA-FP-7998 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-IN-7806         TCGA-IN-7808         TCGA-IP-7968 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
  "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-CD-5798 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-CD-5799         TCGA-CD-5800         TCGA-CD-5801 
"22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" 
        TCGA-CD-5802         TCGA-CD-5803         TCGA-CG-4300 
  "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-CG-4301         TCGA-CG-4304         TCGA-CG-4305 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-CG-4306         TCGA-CG-4436         TCGA-CG-4437 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-CG-4438         TCGA-CG-4440         TCGA-CG-4441 
  "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-CG-4443         TCGA-CG-4444         TCGA-CG-4449 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-CG-4455         TCGA-CG-4460         TCGA-CG-4462 
"22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" 
        TCGA-CG-4465         TCGA-CG-4466         TCGA-CG-4469 
"22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" 
        TCGA-CG-4472         TCGA-CG-4474         TCGA-CG-4477 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-CG-5716         TCGA-CG-5717         TCGA-CG-5718 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-CG-5719         TCGA-CG-5720         TCGA-CG-5721 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-CG-5722         TCGA-CG-5723         TCGA-CG-5724 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" 
        TCGA-CG-5725         TCGA-CG-5726         TCGA-CG-5727 
  "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-CG-5728         TCGA-CG-5730         TCGA-CG-5732 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" 
        TCGA-CG-5733         TCGA-CG-5734         TCGA-D7-5577 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-D7-5578         TCGA-D7-5579         TCGA-D7-6518 
  "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-D7-6519         TCGA-D7-6520         TCGA-D7-6521 
  "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-D7-6522         TCGA-D7-6524         TCGA-D7-6525 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-D7-6526         TCGA-D7-6527         TCGA-D7-6528 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-D7-6815         TCGA-D7-6817         TCGA-D7-6818 
"22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" 
        TCGA-D7-6820         TCGA-D7-6822         TCGA-EQ-5647 
  "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" 
        TCGA-F1-6177         TCGA-F1-6874         TCGA-F1-6875 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-FP-7735         TCGA-FP-7829         TCGA-FP-7998 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-IN-7806         TCGA-IN-7808         TCGA-IP-7968 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
  "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-CD-5798 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-CD-5799         TCGA-CD-5800         TCGA-CD-5801 
"22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" 
        TCGA-CD-5802         TCGA-CD-5803         TCGA-CG-4300 
  "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-CG-4301         TCGA-CG-4304         TCGA-CG-4305 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-CG-4306         TCGA-CG-4436         TCGA-CG-4437 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-CG-4438         TCGA-CG-4440         TCGA-CG-4441 
  "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-CG-4443         TCGA-CG-4444         TCGA-CG-4449 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-CG-4455         TCGA-CG-4460         TCGA-CG-4462 
"22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" 
        TCGA-CG-4465         TCGA-CG-4466         TCGA-CG-4469 
"22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" 
        TCGA-CG-4472         TCGA-CG-4474         TCGA-CG-4477 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-CG-5716         TCGA-CG-5717         TCGA-CG-5718 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-CG-5719         TCGA-CG-5720         TCGA-CG-5721 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-CG-5722         TCGA-CG-5723         TCGA-CG-5724 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" 
        TCGA-CG-5725         TCGA-CG-5726         TCGA-CG-5727 
  "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-CG-5728         TCGA-CG-5730         TCGA-CG-5732 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" 
        TCGA-CG-5733         TCGA-CG-5734         TCGA-D7-5577 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-D7-5578         TCGA-D7-5579         TCGA-D7-6518 
  "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-D7-6519         TCGA-D7-6520         TCGA-D7-6521 
  "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-D7-6522         TCGA-D7-6524         TCGA-D7-6525 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-D7-6526         TCGA-D7-6527         TCGA-D7-6528 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-D7-6815         TCGA-D7-6817         TCGA-D7-6818 
"22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" 
        TCGA-D7-6820         TCGA-D7-6822         TCGA-EQ-5647 
  "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" 
        TCGA-F1-6177         TCGA-F1-6874         TCGA-F1-6875 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-FP-7735         TCGA-FP-7829         TCGA-FP-7998 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-IN-7806         TCGA-IN-7808         TCGA-IP-7968 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
[1] "hr=" "1.4"
D72V2, continuous
D72V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED     10   14
  22Q LOSS WILD-TYPE   50   84
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  FEMALE               10                 50
  MALE                 14                 84
D72V4, multiclass
D72V5, multiclass
    clus
vv   22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  T1                0                  6
  T2                9                 43
  T3                8                 53
  T4                3                 15
D72V6, multiclass
    clus
vv   22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  N0                7                 37
  N1                7                 50
  N2                2                 22
  N3                4                 11
D72V7, multiclass
    clus
vv   22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  M0               20                114
  M1                3                 13
  MX                1                  7
D72V8, multiclass
     clus
vv    22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  I                  4                 20
  II                 6                 31
  III                4                 39
  IV                 5                 21
D72V9, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED      1   23
  22Q LOSS WILD-TYPE    4  130
     clus
vv    22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  NO                 1                  4
  YES               23                130
D72V10, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED      1   23
  22Q LOSS WILD-TYPE    9  125
     clus
vv    22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  NO                 1                  9
  YES               23                125

Clustering(73) Variable = Xq loss mutation analysis
D73V1, survival
                   sevent
clus2                0  1
  XQ LOSS MUTATED    1  2
  XQ LOSS WILD-TYPE 89 13
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
                3               102 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
                2                13 
$`XQ LOSS MUTATED`
TCGA-CG-4469 TCGA-CG-5725 TCGA-D7-6519 
        7.07        15.02        15.65 

$`XQ LOSS WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-6452 TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6458 
        5.62         0.10         0.95         1.41         1.35         1.35 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
        0.85         0.82         0.62         0.62         1.71         2.17 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
        0.99         1.22         0.66         1.12         0.76         0.66 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
        0.26         1.22         1.48         0.46         1.25         0.13 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 
        1.05         0.82         0.69         0.16         4.54         0.99 
TCGA-BR-7901 TCGA-BR-7957 TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
        0.95         0.69         0.82         0.69         0.36         0.49 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
        0.30         0.07        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02        52.96         8.05        54.05         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4460 TCGA-CG-4462 
       29.98        47.05        19.07        12.03        21.99         1.02 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4472 TCGA-CG-4474 TCGA-CG-4477 TCGA-CG-5716 
        8.98        18.94        12.00         1.02         1.02         1.02 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.94         1.02         1.02         0.99         5.98         0.95 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 
       70.06        12.03        28.96        31.04        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       55.04        21.07         7.99         8.65         3.58         4.54 
TCGA-D7-6518 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
        9.80         9.63         8.19         6.90         0.69         5.95 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
        6.61         4.14         1.68         3.65         4.70         4.04 
TCGA-D7-6820 TCGA-D7-6822 TCGA-EQ-5647 TCGA-F1-6177 TCGA-F1-6874 TCGA-F1-6875 
        2.93         4.27         0.62         6.54         2.01        72.23 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7998 TCGA-IN-7806 TCGA-IN-7808 TCGA-IP-7968 
        0.39         0.20         3.58         6.87         3.55         2.53 

  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
             7.07              0.07 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
            15.65             72.23 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
            15.02              2.35 
[1] "7.1 - 15.7 (15.0)" "0.1 - 72.2 (2.3)" 
       TCGA-B7-5816        TCGA-B7-5818        TCGA-BR-6452        TCGA-BR-6455 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BR-6457        TCGA-BR-6458        TCGA-BR-6563        TCGA-BR-6564 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BR-6565        TCGA-BR-6566        TCGA-BR-6705        TCGA-BR-6706 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BR-6707        TCGA-BR-6709        TCGA-BR-6710        TCGA-BR-6801 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BR-6802        TCGA-BR-6803        TCGA-BR-6852        TCGA-BR-7196 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BR-7197        TCGA-BR-7703        TCGA-BR-7704        TCGA-BR-7707 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BR-7715        TCGA-BR-7716        TCGA-BR-7717        TCGA-BR-7722 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BR-7723        TCGA-BR-7851        TCGA-BR-7901        TCGA-BR-7957 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-CD-5798        TCGA-CD-5799        TCGA-CD-5800        TCGA-CD-5801 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-CD-5802        TCGA-CD-5803        TCGA-CG-4300        TCGA-CG-4301 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-CG-4304        TCGA-CG-4305        TCGA-CG-4306        TCGA-CG-4436 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-CG-4437        TCGA-CG-4438        TCGA-CG-4440        TCGA-CG-4441 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-CG-4443        TCGA-CG-4444        TCGA-CG-4449        TCGA-CG-4455 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-CG-4460        TCGA-CG-4462        TCGA-CG-4465        TCGA-CG-4466 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-CG-4469        TCGA-CG-4472        TCGA-CG-4474        TCGA-CG-4477 
  "XQ LOSS MUTATED" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-CG-5716        TCGA-CG-5717        TCGA-CG-5718        TCGA-CG-5719 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-CG-5720        TCGA-CG-5721        TCGA-CG-5722        TCGA-CG-5723 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-CG-5724        TCGA-CG-5725        TCGA-CG-5726        TCGA-CG-5727 
"XQ LOSS WILD-TYPE"   "XQ LOSS MUTATED" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-CG-5728        TCGA-CG-5730        TCGA-CG-5732        TCGA-CG-5733 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-CG-5734        TCGA-D7-5577        TCGA-D7-5578        TCGA-D7-5579 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-D7-6518        TCGA-D7-6519        TCGA-D7-6520        TCGA-D7-6521 
"XQ LOSS WILD-TYPE"   "XQ LOSS MUTATED" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-D7-6522        TCGA-D7-6524        TCGA-D7-6525        TCGA-D7-6526 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-D7-6527        TCGA-D7-6528        TCGA-D7-6815        TCGA-D7-6817 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-D7-6818        TCGA-D7-6820        TCGA-D7-6822        TCGA-EQ-5647 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875        TCGA-FP-7735 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-FP-7829        TCGA-FP-7998        TCGA-IN-7806        TCGA-IN-7808 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-IP-7968 
"XQ LOSS WILD-TYPE" 
       TCGA-B7-5816        TCGA-B7-5818        TCGA-BR-6452        TCGA-BR-6455 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BR-6457        TCGA-BR-6458        TCGA-BR-6563        TCGA-BR-6564 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BR-6565        TCGA-BR-6566        TCGA-BR-6705        TCGA-BR-6706 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BR-6707        TCGA-BR-6709        TCGA-BR-6710        TCGA-BR-6801 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BR-6802        TCGA-BR-6803        TCGA-BR-6852        TCGA-BR-7196 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BR-7197        TCGA-BR-7703        TCGA-BR-7704        TCGA-BR-7707 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BR-7715        TCGA-BR-7716        TCGA-BR-7717        TCGA-BR-7722 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BR-7723        TCGA-BR-7851        TCGA-BR-7901        TCGA-BR-7957 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-CD-5798        TCGA-CD-5799        TCGA-CD-5800        TCGA-CD-5801 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-CD-5802        TCGA-CD-5803        TCGA-CG-4300        TCGA-CG-4301 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-CG-4304        TCGA-CG-4305        TCGA-CG-4306        TCGA-CG-4436 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-CG-4437        TCGA-CG-4438        TCGA-CG-4440        TCGA-CG-4441 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-CG-4443        TCGA-CG-4444        TCGA-CG-4449        TCGA-CG-4455 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-CG-4460        TCGA-CG-4462        TCGA-CG-4465        TCGA-CG-4466 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-CG-4469        TCGA-CG-4472        TCGA-CG-4474        TCGA-CG-4477 
  "XQ LOSS MUTATED" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-CG-5716        TCGA-CG-5717        TCGA-CG-5718        TCGA-CG-5719 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-CG-5720        TCGA-CG-5721        TCGA-CG-5722        TCGA-CG-5723 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-CG-5724        TCGA-CG-5725        TCGA-CG-5726        TCGA-CG-5727 
"XQ LOSS WILD-TYPE"   "XQ LOSS MUTATED" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-CG-5728        TCGA-CG-5730        TCGA-CG-5732        TCGA-CG-5733 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-CG-5734        TCGA-D7-5577        TCGA-D7-5578        TCGA-D7-5579 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-D7-6518        TCGA-D7-6519        TCGA-D7-6520        TCGA-D7-6521 
"XQ LOSS WILD-TYPE"   "XQ LOSS MUTATED" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-D7-6522        TCGA-D7-6524        TCGA-D7-6525        TCGA-D7-6526 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-D7-6527        TCGA-D7-6528        TCGA-D7-6815        TCGA-D7-6817 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-D7-6818        TCGA-D7-6820        TCGA-D7-6822        TCGA-EQ-5647 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875        TCGA-FP-7735 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-FP-7829        TCGA-FP-7998        TCGA-IN-7806        TCGA-IN-7808 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-IP-7968 
"XQ LOSS WILD-TYPE" 
       TCGA-B7-5816        TCGA-B7-5818        TCGA-BR-6452        TCGA-BR-6455 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BR-6457        TCGA-BR-6458        TCGA-BR-6563        TCGA-BR-6564 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BR-6565        TCGA-BR-6566        TCGA-BR-6705        TCGA-BR-6706 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BR-6707        TCGA-BR-6709        TCGA-BR-6710        TCGA-BR-6801 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BR-6802        TCGA-BR-6803        TCGA-BR-6852        TCGA-BR-7196 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BR-7197        TCGA-BR-7703        TCGA-BR-7704        TCGA-BR-7707 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BR-7715        TCGA-BR-7716        TCGA-BR-7717        TCGA-BR-7722 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BR-7723        TCGA-BR-7851        TCGA-BR-7901        TCGA-BR-7957 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-CD-5798        TCGA-CD-5799        TCGA-CD-5800        TCGA-CD-5801 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-CD-5802        TCGA-CD-5803        TCGA-CG-4300        TCGA-CG-4301 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-CG-4304        TCGA-CG-4305        TCGA-CG-4306        TCGA-CG-4436 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-CG-4437        TCGA-CG-4438        TCGA-CG-4440        TCGA-CG-4441 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-CG-4443        TCGA-CG-4444        TCGA-CG-4449        TCGA-CG-4455 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-CG-4460        TCGA-CG-4462        TCGA-CG-4465        TCGA-CG-4466 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-CG-4469        TCGA-CG-4472        TCGA-CG-4474        TCGA-CG-4477 
  "XQ LOSS MUTATED" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-CG-5716        TCGA-CG-5717        TCGA-CG-5718        TCGA-CG-5719 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-CG-5720        TCGA-CG-5721        TCGA-CG-5722        TCGA-CG-5723 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-CG-5724        TCGA-CG-5725        TCGA-CG-5726        TCGA-CG-5727 
"XQ LOSS WILD-TYPE"   "XQ LOSS MUTATED" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-CG-5728        TCGA-CG-5730        TCGA-CG-5732        TCGA-CG-5733 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-CG-5734        TCGA-D7-5577        TCGA-D7-5578        TCGA-D7-5579 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-D7-6518        TCGA-D7-6519        TCGA-D7-6520        TCGA-D7-6521 
"XQ LOSS WILD-TYPE"   "XQ LOSS MUTATED" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-D7-6522        TCGA-D7-6524        TCGA-D7-6525        TCGA-D7-6526 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-D7-6527        TCGA-D7-6528        TCGA-D7-6815        TCGA-D7-6817 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-D7-6818        TCGA-D7-6820        TCGA-D7-6822        TCGA-EQ-5647 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875        TCGA-FP-7735 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-FP-7829        TCGA-FP-7998        TCGA-IN-7806        TCGA-IN-7808 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-IP-7968 
"XQ LOSS WILD-TYPE" 
[1] "hr=" "2.9"
D73V2, continuous
D73V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED      2    5
  XQ LOSS WILD-TYPE   58   93
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  FEMALE               2                58
  MALE                 5                93
D73V4, multiclass
D73V5, multiclass
    clus
vv   XQ LOSS MUTATED XQ LOSS WILD-TYPE
  T1               0                 6
  T2               4                48
  T3               1                60
  T4               0                18
D73V6, multiclass
    clus
vv   XQ LOSS MUTATED XQ LOSS WILD-TYPE
  N0               1                43
  N1               3                54
  N2               0                24
  N3               2                13
D73V7, multiclass
    clus
vv   XQ LOSS MUTATED XQ LOSS WILD-TYPE
  M0               7               127
  M1               0                16
  MX               0                 8
D73V8, multiclass
     clus
vv    XQ LOSS MUTATED XQ LOSS WILD-TYPE
  I                 1                23
  II                0                37
  III               1                42
  IV                2                24
D73V9, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED      1    6
  XQ LOSS WILD-TYPE    4  147
     clus
vv    XQ LOSS MUTATED XQ LOSS WILD-TYPE
  NO                1                 4
  YES               6               147
D73V10, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED      1    6
  XQ LOSS WILD-TYPE    9  142
     clus
vv    XQ LOSS MUTATED XQ LOSS WILD-TYPE
  NO                1                 9
  YES               6               142
                                    V1.D 
                         "Time to Death" 
                                      V2 
                                   "AGE" 
                                      V3 
                                "GENDER" 
                                      V4 
                     "HISTOLOGICAL.TYPE" 
                                      V5 
                           "PATHOLOGY.T" 
                                      V6 
                           "PATHOLOGY.N" 
                                      V7 
                   "PATHOLOGICSPREAD(M)" 
                                      V8 
                           "TUMOR.STAGE" 
                                      V9 
"RADIATIONS.RADIATION.REGIMENINDICATION" 
                                     V10 
                   "NEOADJUVANT.THERAPY" 
> q(save="no")
