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

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> source("/xchip/tcga/gdac_prod/applications/process_mgmt/firehose_task_registry/tcga-gdac/Correlate_Clinical_Cnvsarms_onlysig/broadinstitute.org/cancer.genome.analysis/00498/18/CNV2ClinicalAnalysis_nozzle_onlysig_arm.R")
> result <- main("/xchip/tcga/gdac_prod/applications/process_mgmt/firehose_task_registry/tcga-gdac/Correlate_Clinical_Cnvsarms_onlysig/broadinstitute.org/cancer.genome.analysis/00498/18/", "-nF=/xchip/tcga/Tools/Nozzle/v1.current", "-iD=/xchip/cga/gdac-prod/tcga-gdac/jobResults/cnvarms2cluster/STAD-TP/2735928/broad_values_by_arm.mutsig.cluster.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPickerPipeline/STAD-TP/2589043/1.GDAC_clinicalDataPicker.Finished/STAD-TP.clin.merged.picked.txt", "-fF=", "-fC=3", "-fH=5", "-fW=9", "-fP=OUT", "-cP=1", "-cQ=0.25", "-MF=ONLYSIG", "-oT=STAD-TP", "-nV=Nozzle.R1", "-OP=", "-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-TP"
[1] "opt"  "-OP="
[1] "tl"   "-iT="
[1] "dx"   "-iX="
[1] "opt" ""   
[1] "dx" ""  

nPatients in clinical file=162, in cluster file=237, common to both=161
[1] "Reduce the number of clustering variables from 80 to 74."
[1]  74 161
[1] "1p gain mutation analysis"
[1] 3
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
                6               155 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
                6               155 
[1] "1q gain mutation analysis"
[1] 3
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               19               142 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               19               142 
[1] "2p gain mutation analysis"
[1] 3
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               10               151 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               10               151 
[1] "2q gain mutation analysis"
[1] 3
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               11               150 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               11               150 
[1] "3p gain mutation analysis"
[1] 3
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
                4               157 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
                4               157 
[1] "3q gain mutation analysis"
[1] 3
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               13               148 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               13               148 
[1] "4p gain mutation analysis"
[1] 3
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                3               158 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                3               158 
[1] "5p gain mutation analysis"
[1] 3
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               26               135 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               26               135 
[1] "5q gain mutation analysis"
[1] 3
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
                6               155 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
                6               155 
[1] "6p gain mutation analysis"
[1] 3
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               11               150 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               11               150 
[1] "6q gain mutation analysis"
[1] 3
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               10               151 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               10               151 
[1] "7p gain mutation analysis"
[1] 3
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               49               112 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               49               112 
[1] "7q gain mutation analysis"
[1] 3
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               44               117 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               44               117 
[1] "8p gain mutation analysis"
[1] 3
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               50               111 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               50               111 
[1] "8q gain mutation analysis"
[1] 3
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               68                93 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               68                93 
[1] "9p gain mutation analysis"
[1] 3
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               11               150 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               11               150 
[1] "9q gain mutation analysis"
[1] 3
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               15               146 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               15               146 
[1] "10p gain mutation analysis"
[1] 3
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                23                138 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                23                138 
[1] "10q gain mutation analysis"
[1] 3
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                10                151 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                10                151 
[1] "11p gain mutation analysis"
[1] 3
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 4                157 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 4                157 
[1] "11q gain mutation analysis"
[1] 3
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 8                153 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 8                153 
[1] "12p gain mutation analysis"
[1] 3
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                15                146 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                15                146 
[1] "12q gain mutation analysis"
[1] 3
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                10                151 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                10                151 
[1] "13q gain mutation analysis"
[1] 3
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                30                131 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                30                131 
[1] "15q gain mutation analysis"
[1] 3
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                 7                154 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                 7                154 
[1] "16p gain mutation analysis"
[1] 3
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                12                149 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                12                149 
[1] "16q gain mutation analysis"
[1] 3
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                 8                153 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                 8                153 
[1] "17p gain mutation analysis"
[1] 3
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                 6                155 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                 6                155 
[1] "17q gain mutation analysis"
[1] 3
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                 9                152 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                 9                152 
[1] "18p gain mutation analysis"
[1] 3
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                13                148 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                13                148 
[1] "18q gain mutation analysis"
[1] 3
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 7                154 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 7                154 
[1] "19p gain mutation analysis"
[1] 3
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                10                151 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                10                151 
[1] "19q gain mutation analysis"
[1] 3
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                17                144 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                17                144 
[1] "20p gain mutation analysis"
[1] 3
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                61                100 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                61                100 
[1] "20q gain mutation analysis"
[1] 3
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                75                 86 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                75                 86 
[1] "22q gain mutation analysis"
[1] 3
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                 3                158 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                 3                158 
[1] "1p loss mutation analysis"
[1] 3
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
                6               155 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
                6               155 
[1] "2p loss mutation analysis"
[1] 3
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
                3               158 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
                3               158 
[1] "2q loss mutation analysis"
[1] 3
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
                4               157 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
                4               157 
[1] "3p loss mutation analysis"
[1] 3
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               10               151 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               10               151 
[1] "3q loss mutation analysis"
[1] 3
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
                6               155 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
                6               155 
[1] "4p loss mutation analysis"
[1] 3
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               24               137 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               24               137 
[1] "4q loss mutation analysis"
[1] 3
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               20               141 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               20               141 
[1] "5p loss mutation analysis"
[1] 3
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
                7               154 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
                7               154 
[1] "5q loss mutation analysis"
[1] 3
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               15               146 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               15               146 
[1] "6p loss mutation analysis"
[1] 3
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
                8               153 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
                8               153 
[1] "6q loss mutation analysis"
[1] 3
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               12               149 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               12               149 
[1] "7p loss mutation analysis"
[1] 3
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
                3               158 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
                3               158 
[1] "7q loss mutation analysis"
[1] 3
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
                5               156 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
                5               156 
[1] "8p loss mutation analysis"
[1] 3
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               10               151 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               10               151 
[1] "8q loss mutation analysis"
[1] 3
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                3               158 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                3               158 
[1] "9p loss mutation analysis"
[1] 3
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               26               135 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               26               135 
[1] "9q loss mutation analysis"
[1] 3
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               11               150 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               11               150 
[1] "10p loss mutation analysis"
[1] 3
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                10                151 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                10                151 
[1] "10q loss mutation analysis"
[1] 3
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                 9                152 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                 9                152 
[1] "11p loss mutation analysis"
[1] 3
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                12                149 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                12                149 
[1] "11q loss mutation analysis"
[1] 3
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                 9                152 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                 9                152 
[1] "12p loss mutation analysis"
[1] 3
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                11                150 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                11                150 
[1] "12q loss mutation analysis"
[1] 3
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                 6                155 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                 6                155 
[1] "13q loss mutation analysis"
[1] 3
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                 5                156 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                 5                156 
[1] "14q loss mutation analysis"
[1] 3
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                10                151 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                10                151 
[1] "15q loss mutation analysis"
[1] 3
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                10                151 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                10                151 
[1] "16p loss mutation analysis"
[1] 3
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                 9                152 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                 9                152 
[1] "16q loss mutation analysis"
[1] 3
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                14                147 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                14                147 
[1] "17p loss mutation analysis"
[1] 3
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                32                129 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                32                129 
[1] "17q loss mutation analysis"
[1] 3
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                 9                152 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                 9                152 
[1] "18p loss mutation analysis"
[1] 3
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                12                149 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                12                149 
[1] "18q loss mutation analysis"
[1] 3
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                24                137 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                24                137 
[1] "19p loss mutation analysis"
[1] 3
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                16                145 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                16                145 
[1] "19q loss mutation analysis"
[1] 3
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                12                149 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                12                149 
[1] "20p loss mutation analysis"
[1] 3
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                 4                157 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                 4                157 
[1] "21q loss mutation analysis"
[1] 3
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                29                132 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                29                132 
[1] "22q loss mutation analysis"
[1] 3
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                22                139 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                22                139 
[1] "Xq loss mutation analysis"
[1] 3
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
                7               154 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
                7               154 
[1] "data2feature, selection="
 [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] "BATCHNUMBER"                           

Input Data has 15 rows and 161 columns.

[1] "Batch" "15"   
[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-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 
          NA           NA           NA           NA           NA           NA 
TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-4292 TCGA-BR-4294 TCGA-BR-4357 
          NA           NA           NA           NA           NA           NA 
TCGA-BR-4361 TCGA-BR-4362 TCGA-BR-4363 TCGA-BR-4366 TCGA-BR-4367 TCGA-BR-4368 
          NA           NA           NA           NA           NA           NA 
TCGA-BR-4369 TCGA-BR-4370 TCGA-BR-4371 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6454 
          NA           NA           NA           29           NA           NA 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
          43           NA           41           41           26           25 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
          19           19           52           66           30           37 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
          20           34           23           20            8           37 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 
          45           14           38            4           32           25 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 
          21            5          138           30           29           21 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 
           5           33           25           40           21           29 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
          15           14           22            8           13            8 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-CD-5798 TCGA-CD-5799 
          36           47           45           23           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-EQ-8122 TCGA-F1-6177 TCGA-F1-6874 TCGA-F1-6875 TCGA-FP-7735 TCGA-FP-7829 
         237          199           61           NA           12            6 
TCGA-FP-7916 TCGA-FP-7998 TCGA-HF-7131 TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 
          92          109           NA           NA           NA           NA 
TCGA-HF-7136 TCGA-HJ-7597 TCGA-IN-7806 TCGA-IN-7808 TCGA-IP-7968 
          NA           NA          209          108           77 
Variable 1:'AGE':	nDistinctValues=44,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'DAYSTODEATH':	nDistinctValues=16,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 3:'DAYSTOLASTFOLLOWUP':	nDistinctValues=88,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 5:'DCCUPLOADDAY':	nDistinctValues=5,	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=11,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 9:'HISTOLOGICAL.TYPE':	nDistinctValues=7,	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:'BATCH.NUMBER':	nDistinctValues=9,	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"
[1] "TUMOR.?STAGE" "7"           
[1] "stage2"
vv
 1  2  3  4 
25 43 48 29 
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T" "4"          
[1] "PATHOLOGY.N" "5"          
Output Data has 161 columns, 1 survival variables, and 8 non-survival variables.
AGE, nv=44, binary=FALSE, numeric=TRUE
GENDER, nv=2, binary=FALSE, numeric=FALSE
HISTOLOGICAL.TYPE, nv=7, binary=FALSE, numeric=FALSE
PATHOLOGY.T, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.T',vnm)"
vv
T1 T2 T3 T4 
 6 53 59 33 
[1] "table(vv)"
vv
T1 T2 T3 T4 
 6 53 59 33 
$ClinVariableName
[1] "PATHOLOGY.T"

$Table
vv
T1 T2 T3 T4 
 6 53 59 33 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


T1 T2 T3 T4 
 6 53 59 33 
PATHOLOGY.N, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.N',vnm)"
vv
N0 N1 N2 N3 
50 57 24 19 
[1] "table(vv)"
vv
N0 N1 N2 N3 
50 57 24 19 
$ClinVariableName
[1] "PATHOLOGY.N"

$Table
vv
N0 N1 N2 N3 
50 57 24 19 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


N0 N1 N2 N3 
50 57 24 19 
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 
 25  43  48  29 
[1] "table(vv)"
vv
  I  II III  IV 
 25  43  48  29 
$ClinVariableName
[1] "TUMOR.STAGE"

$Table
vv
  I  II III  IV 
 25  43  48  29 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


  I  II III  IV 
 25  43  48  29 
RADIATIONS.RADIATION.REGIMENINDICATION, nv=2, binary=FALSE, numeric=FALSE

Clustering(1) Variable = 1p gain mutation analysis
D1V1, survival
                   sevent
clus2                 0   1
  1P GAIN MUTATED     2   0
  1P GAIN WILD-TYPE 106  16
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
                2               122 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
                0                16 
$`1P GAIN MUTATED`
TCGA-BR-7717 TCGA-D7-6521 
        0.69         8.19 

$`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-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 
        1.05         0.82         0.16         4.54         0.99         0.95 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
        0.69         0.16         1.08         0.82         1.32         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
        0.95         0.49         0.46         0.72         0.26         0.43 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-CD-5798 
        0.26         1.18         1.55         1.48         0.76         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-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       15.65         9.63         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-EQ-8122 TCGA-F1-6177 TCGA-F1-6874 TCGA-F1-6875 
        4.27         0.62         7.79         6.54         2.01        72.23 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-HJ-7597 TCGA-IN-7806 
        0.39         0.20         3.02         3.58        26.43         6.87 
TCGA-IN-7808 TCGA-IP-7968 
        3.55         2.53 

  1P GAIN MUTATED 1P GAIN WILD-TYPE 
             0.69              0.07 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
             8.19             72.23 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
            4.440             1.515 
[1] "0.7 - 8.2 (4.4)"  "0.1 - 72.2 (1.5)"
       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 MUTATED" "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-BR-7958        TCGA-BR-7959        TCGA-BR-8059        TCGA-BR-8060 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-BR-8077        TCGA-BR-8078        TCGA-BR-8080        TCGA-BR-8081 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-BR-8284        TCGA-BR-8285        TCGA-BR-8286        TCGA-BR-8289 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-BR-8291        TCGA-BR-8295        TCGA-BR-8296        TCGA-BR-8297 
"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 MUTATED" 
       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-EQ-8122        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-7916        TCGA-FP-7998 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-HJ-7597        TCGA-IN-7806        TCGA-IN-7808        TCGA-IP-7968 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "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 MUTATED" "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-BR-7958        TCGA-BR-7959        TCGA-BR-8059        TCGA-BR-8060 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-BR-8077        TCGA-BR-8078        TCGA-BR-8080        TCGA-BR-8081 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-BR-8284        TCGA-BR-8285        TCGA-BR-8286        TCGA-BR-8289 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-BR-8291        TCGA-BR-8295        TCGA-BR-8296        TCGA-BR-8297 
"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 MUTATED" 
       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-EQ-8122        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-7916        TCGA-FP-7998 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-HJ-7597        TCGA-IN-7806        TCGA-IN-7808        TCGA-IP-7968 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "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 MUTATED" "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-BR-7958        TCGA-BR-7959        TCGA-BR-8059        TCGA-BR-8060 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-BR-8077        TCGA-BR-8078        TCGA-BR-8080        TCGA-BR-8081 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-BR-8284        TCGA-BR-8285        TCGA-BR-8286        TCGA-BR-8289 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-BR-8291        TCGA-BR-8295        TCGA-BR-8296        TCGA-BR-8297 
"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 MUTATED" 
       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-EQ-8122        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-7916        TCGA-FP-7998 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-HJ-7597        TCGA-IN-7806        TCGA-IN-7808        TCGA-IP-7968 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
[1] "Remove cluster labels:" "1P GAIN MUTATED"       
clus
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
                2               122 
       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-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-BR-7958 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-BR-7959        TCGA-BR-8059        TCGA-BR-8060        TCGA-BR-8077 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-BR-8078        TCGA-BR-8080        TCGA-BR-8081        TCGA-BR-8284 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-BR-8285        TCGA-BR-8286        TCGA-BR-8289        TCGA-BR-8291 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-BR-8295        TCGA-BR-8296        TCGA-BR-8297        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-CG-4300        TCGA-CG-4301        TCGA-CG-4304 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CG-4305        TCGA-CG-4306        TCGA-CG-4436        TCGA-CG-4437 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CG-4438        TCGA-CG-4440        TCGA-CG-4441        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-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-D7-6522        TCGA-D7-6524 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-D7-6525        TCGA-D7-6526        TCGA-D7-6527        TCGA-D7-6528 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-D7-6815        TCGA-D7-6817        TCGA-D7-6818        TCGA-D7-6820 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-D7-6822        TCGA-EQ-5647        TCGA-EQ-8122        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-7916        TCGA-FP-7998        TCGA-HJ-7597        TCGA-IN-7806 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-IN-7808        TCGA-IP-7968 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
D1V2, continuous
D1V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED      1    5
  1P GAIN WILD-TYPE   64   91
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  FEMALE               1                64
  MALE                 5                91
                   vv
clus                STOMACH ADENOCARCINOMA - DIFFUSE TYPE
  1P GAIN MUTATED                                       1
  1P GAIN WILD-TYPE                                    18
                   vv
clus                STOMACH ADENOCARCINOMA - NOT OTHERWISE SPECIFIED (NOS)
  1P GAIN MUTATED                                                        5
  1P GAIN WILD-TYPE                                                     74
                   vv
clus                STOMACH ADENOCARCINOMA - SIGNET RING TYPE
  1P GAIN MUTATED                                           0
  1P GAIN WILD-TYPE                                         1
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - MUCINOUS TYPE
  1P GAIN MUTATED                                                   0
  1P GAIN WILD-TYPE                                                 9
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - PAPILLARY TYPE
  1P GAIN MUTATED                                                    0
  1P GAIN WILD-TYPE                                                  3
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - TUBULAR TYPE
  1P GAIN MUTATED                                                  0
  1P GAIN WILD-TYPE                                               10
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - TYPE NOT OTHERWISE SPECIFIED (NOS)
  1P GAIN MUTATED                                                                        0
  1P GAIN WILD-TYPE                                                                     35
D1V4, multiclass
                   vv
clus                T1 T2 T3 T4
  1P GAIN MUTATED    0  2  2  1
  1P GAIN WILD-TYPE  6 51 57 32
D1V5, multiclass
                   vv
clus                N0 N1 N2 N3
  1P GAIN MUTATED    2  1  1  0
  1P GAIN WILD-TYPE 48 56 23 19
D1V6, multiclass
                   vv
clus                 M0  M1  MX
  1P GAIN MUTATED     5   0   1
  1P GAIN WILD-TYPE 127  18  10
D1V7, multiclass
                   vv
clus                 I II III IV
  1P GAIN MUTATED    1  1   1  1
  1P GAIN WILD-TYPE 24 42  47 28
D1V8, multiclass
D1V9, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED      0    6
  1P GAIN WILD-TYPE    5  150
     clus
vv    1P GAIN MUTATED 1P GAIN WILD-TYPE
  NO                0                 5
  YES               6               150

Clustering(2) Variable = 1q gain mutation analysis
D2V1, survival
                   sevent
clus2                0  1
  1Q GAIN MUTATED   10  3
  1Q GAIN WILD-TYPE 98 13
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               13               111 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
                3                13 
$`1Q GAIN MUTATED`
TCGA-BR-7717 TCGA-BR-7723 TCGA-CG-4460 TCGA-D7-6521 TCGA-D7-6526 TCGA-D7-6527 
        0.69         4.54        21.99         8.19         6.61         4.14 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6822 TCGA-EQ-5647 TCGA-F1-6875 TCGA-FP-7735 
        4.70         4.04         4.27         0.62        72.23         0.39 
TCGA-IN-7808 
        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-BR-7958 TCGA-BR-7959 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 
        0.16         1.08         0.82         1.32         0.69         0.95 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
        0.49         0.46         0.72         0.26         0.43         0.26 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-CD-5798 TCGA-CD-5799 
        1.18         1.55         1.48         0.76         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-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-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-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6820 
        6.90         0.69         5.95         1.68         3.65         2.93 
TCGA-EQ-8122 TCGA-F1-6177 TCGA-F1-6874 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
        7.79         6.54         2.01         0.20         3.02         3.58 
TCGA-HJ-7597 TCGA-IN-7806 TCGA-IP-7968 
       26.43         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 
             4.27              1.35 
[1] "0.4 - 72.2 (4.3)" "0.1 - 70.1 (1.4)"
       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-BR-7958        TCGA-BR-7959        TCGA-BR-8059        TCGA-BR-8060 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-BR-8077        TCGA-BR-8078        TCGA-BR-8080        TCGA-BR-8081 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-BR-8284        TCGA-BR-8285        TCGA-BR-8286        TCGA-BR-8289 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-BR-8291        TCGA-BR-8295        TCGA-BR-8296        TCGA-BR-8297 
"1Q GAIN WILD-TYPE" "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 MUTATED" 
       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-EQ-8122        TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" 
       TCGA-FP-7735        TCGA-FP-7829        TCGA-FP-7916        TCGA-FP-7998 
  "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-HJ-7597        TCGA-IN-7806        TCGA-IN-7808        TCGA-IP-7968 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" "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-BR-7958        TCGA-BR-7959        TCGA-BR-8059        TCGA-BR-8060 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-BR-8077        TCGA-BR-8078        TCGA-BR-8080        TCGA-BR-8081 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-BR-8284        TCGA-BR-8285        TCGA-BR-8286        TCGA-BR-8289 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-BR-8291        TCGA-BR-8295        TCGA-BR-8296        TCGA-BR-8297 
"1Q GAIN WILD-TYPE" "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 MUTATED" 
       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-EQ-8122        TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" 
       TCGA-FP-7735        TCGA-FP-7829        TCGA-FP-7916        TCGA-FP-7998 
  "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-HJ-7597        TCGA-IN-7806        TCGA-IN-7808        TCGA-IP-7968 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" "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-BR-7958        TCGA-BR-7959        TCGA-BR-8059        TCGA-BR-8060 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-BR-8077        TCGA-BR-8078        TCGA-BR-8080        TCGA-BR-8081 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-BR-8284        TCGA-BR-8285        TCGA-BR-8286        TCGA-BR-8289 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-BR-8291        TCGA-BR-8295        TCGA-BR-8296        TCGA-BR-8297 
"1Q GAIN WILD-TYPE" "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 MUTATED" 
       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-EQ-8122        TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" 
       TCGA-FP-7735        TCGA-FP-7829        TCGA-FP-7916        TCGA-FP-7998 
  "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-HJ-7597        TCGA-IN-7806        TCGA-IN-7808        TCGA-IP-7968 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" 
[1] "hr=" "1.2"
D2V2, continuous
D2V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED      5   14
  1Q GAIN WILD-TYPE   60   82
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  FEMALE               5                60
  MALE                14                82
                   vv
clus                STOMACH ADENOCARCINOMA - DIFFUSE TYPE
  1Q GAIN MUTATED                                       3
  1Q GAIN WILD-TYPE                                    16
                   vv
clus                STOMACH ADENOCARCINOMA - NOT OTHERWISE SPECIFIED (NOS)
  1Q GAIN MUTATED                                                       10
  1Q GAIN WILD-TYPE                                                     69
                   vv
clus                STOMACH ADENOCARCINOMA - SIGNET RING TYPE
  1Q GAIN MUTATED                                           0
  1Q GAIN WILD-TYPE                                         1
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - MUCINOUS TYPE
  1Q GAIN MUTATED                                                   0
  1Q GAIN WILD-TYPE                                                 9
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - PAPILLARY TYPE
  1Q GAIN MUTATED                                                    1
  1Q GAIN WILD-TYPE                                                  2
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - TUBULAR TYPE
  1Q GAIN MUTATED                                                  3
  1Q GAIN WILD-TYPE                                                7
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - TYPE NOT OTHERWISE SPECIFIED (NOS)
  1Q GAIN MUTATED                                                                        2
  1Q GAIN WILD-TYPE                                                                     33
D2V4, multiclass
                   vv
clus                T1 T2 T3 T4
  1Q GAIN MUTATED    1  9  5  3
  1Q GAIN WILD-TYPE  5 44 54 30
D2V5, multiclass
                   vv
clus                N0 N1 N2 N3
  1Q GAIN MUTATED    6  3  3  4
  1Q GAIN WILD-TYPE 44 54 21 15
D2V6, multiclass
                   vv
clus                 M0  M1  MX
  1Q GAIN MUTATED    14   3   2
  1Q GAIN WILD-TYPE 118  15   9
D2V7, multiclass
                   vv
clus                 I II III IV
  1Q GAIN MUTATED    5  3   4  4
  1Q GAIN WILD-TYPE 20 40  44 25
D2V8, multiclass
D2V9, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED      2   17
  1Q GAIN WILD-TYPE    3  139
     clus
vv    1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  NO                2                 3
  YES              17               139

Clustering(3) Variable = 2p gain mutation analysis
D3V1, survival
                   sevent
clus2                0  1
  2P GAIN MUTATED    9  1
  2P GAIN WILD-TYPE 99 15
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               10               114 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
                1                15 
$`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-BR-7958 TCGA-BR-7959 
        4.54         0.99         0.95         0.69         0.16         1.08 
TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
        0.82         1.32         0.69         0.95         0.49         0.46 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
        0.72         0.26         0.43         0.26         1.18         1.55 
TCGA-BR-8296 TCGA-BR-8297 TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5803 
        1.48         0.76         0.82         0.69         0.36         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-4474 TCGA-CG-4477 TCGA-CG-5716 TCGA-CG-5717 TCGA-CG-5719 TCGA-CG-5720 
        1.02         1.02         1.02         6.94         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-D7-6527 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-EQ-8122 TCGA-F1-6177 TCGA-F1-6874 TCGA-F1-6875 TCGA-FP-7735 TCGA-FP-7829 
        7.79         6.54         2.01        72.23         0.39         0.20 
TCGA-FP-7916 TCGA-FP-7998 TCGA-HJ-7597 TCGA-IN-7806 TCGA-IN-7808 TCGA-IP-7968 
        3.02         3.58        26.43         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 
            1.150             1.695 
[1] "0.3 - 31.0 (1.1)" "0.1 - 72.2 (1.7)"
       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-BR-7958        TCGA-BR-7959        TCGA-BR-8059        TCGA-BR-8060 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-BR-8077        TCGA-BR-8078        TCGA-BR-8080        TCGA-BR-8081 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-BR-8284        TCGA-BR-8285        TCGA-BR-8286        TCGA-BR-8289 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-BR-8291        TCGA-BR-8295        TCGA-BR-8296        TCGA-BR-8297 
"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-EQ-8122        TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-FP-7735        TCGA-FP-7829        TCGA-FP-7916        TCGA-FP-7998 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-HJ-7597        TCGA-IN-7806        TCGA-IN-7808        TCGA-IP-7968 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "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-BR-7958        TCGA-BR-7959        TCGA-BR-8059        TCGA-BR-8060 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-BR-8077        TCGA-BR-8078        TCGA-BR-8080        TCGA-BR-8081 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-BR-8284        TCGA-BR-8285        TCGA-BR-8286        TCGA-BR-8289 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-BR-8291        TCGA-BR-8295        TCGA-BR-8296        TCGA-BR-8297 
"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-EQ-8122        TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-FP-7735        TCGA-FP-7829        TCGA-FP-7916        TCGA-FP-7998 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-HJ-7597        TCGA-IN-7806        TCGA-IN-7808        TCGA-IP-7968 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "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-BR-7958        TCGA-BR-7959        TCGA-BR-8059        TCGA-BR-8060 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-BR-8077        TCGA-BR-8078        TCGA-BR-8080        TCGA-BR-8081 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-BR-8284        TCGA-BR-8285        TCGA-BR-8286        TCGA-BR-8289 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-BR-8291        TCGA-BR-8295        TCGA-BR-8296        TCGA-BR-8297 
"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-EQ-8122        TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-FP-7735        TCGA-FP-7829        TCGA-FP-7916        TCGA-FP-7998 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-HJ-7597        TCGA-IN-7806        TCGA-IN-7808        TCGA-IP-7968 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
[1] "hr=" "1.5"
D3V2, continuous
D3V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED      3    7
  2P GAIN WILD-TYPE   62   89
        clus
vv       2P GAIN MUTATED 2P GAIN WILD-TYPE
  FEMALE               3                62
  MALE                 7                89
                   vv
clus                STOMACH ADENOCARCINOMA - DIFFUSE TYPE
  2P GAIN MUTATED                                       0
  2P GAIN WILD-TYPE                                    19
                   vv
clus                STOMACH ADENOCARCINOMA - NOT OTHERWISE SPECIFIED (NOS)
  2P GAIN MUTATED                                                        5
  2P GAIN WILD-TYPE                                                     74
                   vv
clus                STOMACH ADENOCARCINOMA - SIGNET RING TYPE
  2P GAIN MUTATED                                           0
  2P GAIN WILD-TYPE                                         1
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - MUCINOUS TYPE
  2P GAIN MUTATED                                                   0
  2P GAIN WILD-TYPE                                                 9
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - PAPILLARY TYPE
  2P GAIN MUTATED                                                    0
  2P GAIN WILD-TYPE                                                  3
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - TUBULAR TYPE
  2P GAIN MUTATED                                                  0
  2P GAIN WILD-TYPE                                               10
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - TYPE NOT OTHERWISE SPECIFIED (NOS)
  2P GAIN MUTATED                                                                        4
  2P GAIN WILD-TYPE                                                                     31
D3V4, multiclass
                   vv
clus                T1 T2 T3 T4
  2P GAIN MUTATED    0  1  6  3
  2P GAIN WILD-TYPE  6 52 53 30
D3V5, multiclass
                   vv
clus                N0 N1 N2 N3
  2P GAIN MUTATED    5  5  0  0
  2P GAIN WILD-TYPE 45 52 24 19
D3V6, multiclass
                   vv
clus                 M0  M1  MX
  2P GAIN MUTATED     9   1   0
  2P GAIN WILD-TYPE 123  17  11
D3V7, multiclass
                   vv
clus                 I II III IV
  2P GAIN MUTATED    0  6   1  3
  2P GAIN WILD-TYPE 25 37  47 26
D3V8, multiclass
D3V9, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED      0   10
  2P GAIN WILD-TYPE    5  146
     clus
vv    2P GAIN MUTATED 2P GAIN WILD-TYPE
  NO                0                 5
  YES              10               146

Clustering(4) Variable = 2q gain mutation analysis
D4V1, survival
                   sevent
clus2                 0   1
  2Q GAIN MUTATED     8   2
  2Q GAIN WILD-TYPE 100  14
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               10               114 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
                2                14 
$`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-BR-7958 TCGA-BR-7959 
        4.54         0.99         0.95         0.69         0.16         1.08 
TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
        0.82         1.32         0.69         0.95         0.49         0.46 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
        0.72         0.26         0.43         0.26         1.18         1.55 
TCGA-BR-8296 TCGA-BR-8297 TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5802 
        1.48         0.76         0.82         0.69         0.36         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-4474 TCGA-CG-4477 TCGA-CG-5716 TCGA-CG-5717 TCGA-CG-5719 
        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-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       28.96        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-D7-6822 
        1.68         3.65         4.70         4.04         2.93         4.27 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6177 TCGA-F1-6874 TCGA-FP-7735 TCGA-FP-7829 
        0.62         7.79         6.54         2.01         0.39         0.20 
TCGA-FP-7916 TCGA-FP-7998 TCGA-HJ-7597 TCGA-IN-7806 TCGA-IN-7808 TCGA-IP-7968 
        3.02         3.58        26.43         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             1.615 
[1] "0.5 - 72.2 (1.4)" "0.1 - 70.1 (1.6)"
       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-BR-7958        TCGA-BR-7959        TCGA-BR-8059        TCGA-BR-8060 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-BR-8077        TCGA-BR-8078        TCGA-BR-8080        TCGA-BR-8081 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-BR-8284        TCGA-BR-8285        TCGA-BR-8286        TCGA-BR-8289 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-BR-8291        TCGA-BR-8295        TCGA-BR-8296        TCGA-BR-8297 
"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-EQ-8122        TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" 
       TCGA-FP-7735        TCGA-FP-7829        TCGA-FP-7916        TCGA-FP-7998 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-HJ-7597        TCGA-IN-7806        TCGA-IN-7808        TCGA-IP-7968 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "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-BR-7958        TCGA-BR-7959        TCGA-BR-8059        TCGA-BR-8060 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-BR-8077        TCGA-BR-8078        TCGA-BR-8080        TCGA-BR-8081 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-BR-8284        TCGA-BR-8285        TCGA-BR-8286        TCGA-BR-8289 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-BR-8291        TCGA-BR-8295        TCGA-BR-8296        TCGA-BR-8297 
"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-EQ-8122        TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" 
       TCGA-FP-7735        TCGA-FP-7829        TCGA-FP-7916        TCGA-FP-7998 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-HJ-7597        TCGA-IN-7806        TCGA-IN-7808        TCGA-IP-7968 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "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-BR-7958        TCGA-BR-7959        TCGA-BR-8059        TCGA-BR-8060 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-BR-8077        TCGA-BR-8078        TCGA-BR-8080        TCGA-BR-8081 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-BR-8284        TCGA-BR-8285        TCGA-BR-8286        TCGA-BR-8289 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-BR-8291        TCGA-BR-8295        TCGA-BR-8296        TCGA-BR-8297 
"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-EQ-8122        TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" 
       TCGA-FP-7735        TCGA-FP-7829        TCGA-FP-7916        TCGA-FP-7998 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-HJ-7597        TCGA-IN-7806        TCGA-IN-7808        TCGA-IP-7968 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
[1] "hr=" "2.3"
D4V2, continuous
D4V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED      3    8
  2Q GAIN WILD-TYPE   62   88
        clus
vv       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  FEMALE               3                62
  MALE                 8                88
                   vv
clus                STOMACH ADENOCARCINOMA - DIFFUSE TYPE
  2Q GAIN MUTATED                                       0
  2Q GAIN WILD-TYPE                                    19
                   vv
clus                STOMACH ADENOCARCINOMA - NOT OTHERWISE SPECIFIED (NOS)
  2Q GAIN MUTATED                                                        6
  2Q GAIN WILD-TYPE                                                     73
                   vv
clus                STOMACH ADENOCARCINOMA - SIGNET RING TYPE
  2Q GAIN MUTATED                                           0
  2Q GAIN WILD-TYPE                                         1
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - MUCINOUS TYPE
  2Q GAIN MUTATED                                                   0
  2Q GAIN WILD-TYPE                                                 9
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - PAPILLARY TYPE
  2Q GAIN MUTATED                                                    0
  2Q GAIN WILD-TYPE                                                  3
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - TUBULAR TYPE
  2Q GAIN MUTATED                                                  0
  2Q GAIN WILD-TYPE                                               10
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - TYPE NOT OTHERWISE SPECIFIED (NOS)
  2Q GAIN MUTATED                                                                        4
  2Q GAIN WILD-TYPE                                                                     31
D4V4, multiclass
                   vv
clus                T1 T2 T3 T4
  2Q GAIN MUTATED    0  2  6  3
  2Q GAIN WILD-TYPE  6 51 53 30
D4V5, multiclass
                   vv
clus                N0 N1 N2 N3
  2Q GAIN MUTATED    5  5  0  0
  2Q GAIN WILD-TYPE 45 52 24 19
D4V6, multiclass
                   vv
clus                 M0  M1  MX
  2Q GAIN MUTATED     9   1   1
  2Q GAIN WILD-TYPE 123  17  10
D4V7, multiclass
                   vv
clus                 I II III IV
  2Q GAIN MUTATED    1  5   1  3
  2Q GAIN WILD-TYPE 24 38  47 26
D4V8, multiclass
D4V9, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED      0   11
  2Q GAIN WILD-TYPE    5  145
     clus
vv    2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  NO                0                 5
  YES              11               145

Clustering(5) Variable = 3p gain mutation analysis
D5V1, survival
                   sevent
clus2                 0   1
  3P GAIN MUTATED     2   0
  3P GAIN WILD-TYPE 106  16
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
                2               122 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
                0                16 
$`3P GAIN MUTATED`
TCGA-BR-7722 TCGA-D7-6521 
        0.16         8.19 

$`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-BR-7958 TCGA-BR-7959 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
        0.69         0.16         1.08         0.82         1.32         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
        0.95         0.49         0.46         0.72         0.26         0.43 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-CD-5798 
        0.26         1.18         1.55         1.48         0.76         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-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       15.65         9.63         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-EQ-8122 TCGA-F1-6177 TCGA-F1-6874 TCGA-F1-6875 
        4.27         0.62         7.79         6.54         2.01        72.23 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-HJ-7597 TCGA-IN-7806 
        0.39         0.20         3.02         3.58        26.43         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 
             8.19             72.23 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
            4.175             1.515 
[1] "0.2 - 8.2 (4.2)"  "0.1 - 72.2 (1.5)"
       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-BR-7958        TCGA-BR-7959        TCGA-BR-8059        TCGA-BR-8060 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BR-8077        TCGA-BR-8078        TCGA-BR-8080        TCGA-BR-8081 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BR-8284        TCGA-BR-8285        TCGA-BR-8286        TCGA-BR-8289 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BR-8291        TCGA-BR-8295        TCGA-BR-8296        TCGA-BR-8297 
"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 MUTATED" 
       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-EQ-8122        TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-FP-7735        TCGA-FP-7829        TCGA-FP-7916        TCGA-FP-7998 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-HJ-7597        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" 
       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-BR-7958        TCGA-BR-7959        TCGA-BR-8059        TCGA-BR-8060 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BR-8077        TCGA-BR-8078        TCGA-BR-8080        TCGA-BR-8081 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BR-8284        TCGA-BR-8285        TCGA-BR-8286        TCGA-BR-8289 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BR-8291        TCGA-BR-8295        TCGA-BR-8296        TCGA-BR-8297 
"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 MUTATED" 
       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-EQ-8122        TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-FP-7735        TCGA-FP-7829        TCGA-FP-7916        TCGA-FP-7998 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-HJ-7597        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" 
       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-BR-7958        TCGA-BR-7959        TCGA-BR-8059        TCGA-BR-8060 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BR-8077        TCGA-BR-8078        TCGA-BR-8080        TCGA-BR-8081 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BR-8284        TCGA-BR-8285        TCGA-BR-8286        TCGA-BR-8289 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BR-8291        TCGA-BR-8295        TCGA-BR-8296        TCGA-BR-8297 
"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 MUTATED" 
       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-EQ-8122        TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-FP-7735        TCGA-FP-7829        TCGA-FP-7916        TCGA-FP-7998 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-HJ-7597        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" 
[1] "Remove cluster labels:" "3P GAIN MUTATED"       
clus
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
                2               122 
       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-BR-7958 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BR-7959        TCGA-BR-8059        TCGA-BR-8060        TCGA-BR-8077 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BR-8078        TCGA-BR-8080        TCGA-BR-8081        TCGA-BR-8284 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BR-8285        TCGA-BR-8286        TCGA-BR-8289        TCGA-BR-8291 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BR-8295        TCGA-BR-8296        TCGA-BR-8297        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-D7-6522        TCGA-D7-6524 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-D7-6525        TCGA-D7-6526        TCGA-D7-6527        TCGA-D7-6528 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-D7-6815        TCGA-D7-6817        TCGA-D7-6818        TCGA-D7-6820 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-D7-6822        TCGA-EQ-5647        TCGA-EQ-8122        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-7916        TCGA-FP-7998        TCGA-HJ-7597        TCGA-IN-7806 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-IN-7808        TCGA-IP-7968 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
D5V2, continuous
D5V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED      1    3
  3P GAIN WILD-TYPE   64   93
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  FEMALE               1                64
  MALE                 3                93
                   vv
clus                STOMACH ADENOCARCINOMA - DIFFUSE TYPE
  3P GAIN MUTATED                                       1
  3P GAIN WILD-TYPE                                    18
                   vv
clus                STOMACH ADENOCARCINOMA - NOT OTHERWISE SPECIFIED (NOS)
  3P GAIN MUTATED                                                        3
  3P GAIN WILD-TYPE                                                     76
                   vv
clus                STOMACH ADENOCARCINOMA - SIGNET RING TYPE
  3P GAIN MUTATED                                           0
  3P GAIN WILD-TYPE                                         1
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - MUCINOUS TYPE
  3P GAIN MUTATED                                                   0
  3P GAIN WILD-TYPE                                                 9
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - PAPILLARY TYPE
  3P GAIN MUTATED                                                    0
  3P GAIN WILD-TYPE                                                  3
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - TUBULAR TYPE
  3P GAIN MUTATED                                                  0
  3P GAIN WILD-TYPE                                               10
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - TYPE NOT OTHERWISE SPECIFIED (NOS)
  3P GAIN MUTATED                                                                        0
  3P GAIN WILD-TYPE                                                                     35
D5V4, multiclass
                   vv
clus                T1 T2 T3 T4
  3P GAIN MUTATED    0  2  1  1
  3P GAIN WILD-TYPE  6 51 58 32
D5V5, multiclass
                   vv
clus                N0 N1 N2 N3
  3P GAIN MUTATED    1  1  2  0
  3P GAIN WILD-TYPE 49 56 22 19
D5V6, multiclass
                   vv
clus                 M0  M1  MX
  3P GAIN MUTATED     4   0   0
  3P GAIN WILD-TYPE 128  18  11
D5V7, multiclass
                   vv
clus                 I II III IV
  3P GAIN MUTATED    1  0   2  1
  3P GAIN WILD-TYPE 24 43  46 28
D5V8, multiclass
D5V9, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED      0    4
  3P GAIN WILD-TYPE    5  152
     clus
vv    3P GAIN MUTATED 3P GAIN WILD-TYPE
  NO                0                 5
  YES               4               152

Clustering(6) Variable = 3q gain mutation analysis
D6V1, survival
                   sevent
clus2                0  1
  3Q GAIN MUTATED    9  0
  3Q GAIN WILD-TYPE 99 16
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
                9               115 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
                0                16 
$`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-BR-7958 TCGA-BR-7959 
        0.69         0.99         0.95         0.69         0.16         1.08 
TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
        0.82         1.32         0.69         0.95         0.49         0.46 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
        0.72         0.26         0.43         0.26         1.18         1.55 
TCGA-BR-8296 TCGA-BR-8297 TCGA-CD-5798 TCGA-CD-5800 TCGA-CD-5802 TCGA-CD-5803 
        1.48         0.76         0.82         0.36         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-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-D7-6522 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-EQ-8122 TCGA-F1-6177 TCGA-F1-6874 TCGA-F1-6875 TCGA-FP-7735 
        0.62         7.79         6.54         2.01        72.23         0.39 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-HJ-7597 TCGA-IN-7806 TCGA-IN-7808 
        0.20         3.02         3.58        26.43         6.87         3.55 
TCGA-IP-7968 
        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 
             0.69              1.55 
[1] "0.1 - 15.9 (0.7)" "0.1 - 72.2 (1.6)"
       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-BR-7958        TCGA-BR-7959        TCGA-BR-8059        TCGA-BR-8060 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-BR-8077        TCGA-BR-8078        TCGA-BR-8080        TCGA-BR-8081 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-BR-8284        TCGA-BR-8285        TCGA-BR-8286        TCGA-BR-8289 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-BR-8291        TCGA-BR-8295        TCGA-BR-8296        TCGA-BR-8297 
"3Q GAIN WILD-TYPE" "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-EQ-8122        TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-FP-7735        TCGA-FP-7829        TCGA-FP-7916        TCGA-FP-7998 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-HJ-7597        TCGA-IN-7806        TCGA-IN-7808        TCGA-IP-7968 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "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-BR-7958        TCGA-BR-7959        TCGA-BR-8059        TCGA-BR-8060 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-BR-8077        TCGA-BR-8078        TCGA-BR-8080        TCGA-BR-8081 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-BR-8284        TCGA-BR-8285        TCGA-BR-8286        TCGA-BR-8289 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-BR-8291        TCGA-BR-8295        TCGA-BR-8296        TCGA-BR-8297 
"3Q GAIN WILD-TYPE" "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-EQ-8122        TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-FP-7735        TCGA-FP-7829        TCGA-FP-7916        TCGA-FP-7998 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-HJ-7597        TCGA-IN-7806        TCGA-IN-7808        TCGA-IP-7968 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "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-BR-7958        TCGA-BR-7959        TCGA-BR-8059        TCGA-BR-8060 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-BR-8077        TCGA-BR-8078        TCGA-BR-8080        TCGA-BR-8081 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-BR-8284        TCGA-BR-8285        TCGA-BR-8286        TCGA-BR-8289 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-BR-8291        TCGA-BR-8295        TCGA-BR-8296        TCGA-BR-8297 
"3Q GAIN WILD-TYPE" "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-EQ-8122        TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-FP-7735        TCGA-FP-7829        TCGA-FP-7916        TCGA-FP-7998 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-HJ-7597        TCGA-IN-7806        TCGA-IN-7808        TCGA-IP-7968 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
[1] "hr="     "2.7e+07"
D6V2, continuous
D6V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED      1   12
  3Q GAIN WILD-TYPE   64   84
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  FEMALE               1                64
  MALE                12                84
                   vv
clus                STOMACH ADENOCARCINOMA - DIFFUSE TYPE
  3Q GAIN MUTATED                                       3
  3Q GAIN WILD-TYPE                                    16
                   vv
clus                STOMACH ADENOCARCINOMA - NOT OTHERWISE SPECIFIED (NOS)
  3Q GAIN MUTATED                                                        8
  3Q GAIN WILD-TYPE                                                     71
                   vv
clus                STOMACH ADENOCARCINOMA - SIGNET RING TYPE
  3Q GAIN MUTATED                                           0
  3Q GAIN WILD-TYPE                                         1
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - MUCINOUS TYPE
  3Q GAIN MUTATED                                                   0
  3Q GAIN WILD-TYPE                                                 9
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - PAPILLARY TYPE
  3Q GAIN MUTATED                                                    0
  3Q GAIN WILD-TYPE                                                  3
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - TUBULAR TYPE
  3Q GAIN MUTATED                                                  0
  3Q GAIN WILD-TYPE                                               10
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - TYPE NOT OTHERWISE SPECIFIED (NOS)
  3Q GAIN MUTATED                                                                        1
  3Q GAIN WILD-TYPE                                                                     34
D6V4, multiclass
                   vv
clus                T1 T2 T3 T4
  3Q GAIN MUTATED    0  5  5  3
  3Q GAIN WILD-TYPE  6 48 54 30
D6V5, multiclass
                   vv
clus                N0 N1 N2 N3
  3Q GAIN MUTATED    3  5  3  1
  3Q GAIN WILD-TYPE 47 52 21 18
D6V6, multiclass
                   vv
clus                 M0  M1  MX
  3Q GAIN MUTATED    12   0   1
  3Q GAIN WILD-TYPE 120  18  10
D6V7, multiclass
                   vv
clus                 I II III IV
  3Q GAIN MUTATED    2  4   4  2
  3Q GAIN WILD-TYPE 23 39  44 27
D6V8, multiclass
D6V9, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED      0   13
  3Q GAIN WILD-TYPE    5  143
     clus
vv    3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  NO                0                 5
  YES              13               143

Clustering(7) Variable = 4p gain mutation analysis
D7V1, survival
                   sevent
clus2                 0   1
  4P GAIN MUTATED     2   0
  4P GAIN WILD-TYPE 106  16
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                2               122 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                0                16 
$`4P GAIN MUTATED`
TCGA-CG-4443 TCGA-D7-5579 
       29.98         4.54 

$`4P 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-BR-7958 TCGA-BR-7959 TCGA-BR-8059 TCGA-BR-8060 
        0.95         0.69         0.16         1.08         0.82         1.32 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
        0.69         0.95         0.49         0.46         0.72         0.26 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
        0.43         0.26         1.18         1.55         1.48         0.76 
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-4444 TCGA-CG-4449 
        8.05        54.05         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-D7-6518 TCGA-D7-6519 
       21.07         7.99         8.65         3.58         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-EQ-8122 TCGA-F1-6177 TCGA-F1-6874 TCGA-F1-6875 
        4.27         0.62         7.79         6.54         2.01        72.23 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-HJ-7597 TCGA-IN-7806 
        0.39         0.20         3.02         3.58        26.43         6.87 
TCGA-IN-7808 TCGA-IP-7968 
        3.55         2.53 

  4P GAIN MUTATED 4P GAIN WILD-TYPE 
             4.54              0.07 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
            29.98             72.23 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
            17.26              1.48 
[1] "4.5 - 30.0 (17.3)" "0.1 - 72.2 (1.5)" 
       TCGA-B7-5816        TCGA-B7-5818        TCGA-BR-6452        TCGA-BR-6455 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BR-6457        TCGA-BR-6458        TCGA-BR-6563        TCGA-BR-6564 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BR-6565        TCGA-BR-6566        TCGA-BR-6705        TCGA-BR-6706 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BR-6707        TCGA-BR-6709        TCGA-BR-6710        TCGA-BR-6801 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BR-6802        TCGA-BR-6803        TCGA-BR-6852        TCGA-BR-7196 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BR-7197        TCGA-BR-7703        TCGA-BR-7704        TCGA-BR-7707 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BR-7715        TCGA-BR-7716        TCGA-BR-7717        TCGA-BR-7722 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BR-7723        TCGA-BR-7851        TCGA-BR-7901        TCGA-BR-7957 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BR-7958        TCGA-BR-7959        TCGA-BR-8059        TCGA-BR-8060 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BR-8077        TCGA-BR-8078        TCGA-BR-8080        TCGA-BR-8081 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BR-8284        TCGA-BR-8285        TCGA-BR-8286        TCGA-BR-8289 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BR-8291        TCGA-BR-8295        TCGA-BR-8296        TCGA-BR-8297 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-CD-5798        TCGA-CD-5799        TCGA-CD-5800        TCGA-CD-5801 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-CD-5802        TCGA-CD-5803        TCGA-CG-4300        TCGA-CG-4301 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-CG-4304        TCGA-CG-4305        TCGA-CG-4306        TCGA-CG-4436 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-CG-4437        TCGA-CG-4438        TCGA-CG-4440        TCGA-CG-4441 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-CG-4443        TCGA-CG-4444        TCGA-CG-4449        TCGA-CG-4455 
  "4P GAIN MUTATED" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-CG-4460        TCGA-CG-4462        TCGA-CG-4465        TCGA-CG-4466 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-CG-4469        TCGA-CG-4472        TCGA-CG-4474        TCGA-CG-4477 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-CG-5716        TCGA-CG-5717        TCGA-CG-5718        TCGA-CG-5719 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-CG-5720        TCGA-CG-5721        TCGA-CG-5722        TCGA-CG-5723 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-CG-5724        TCGA-CG-5725        TCGA-CG-5726        TCGA-CG-5727 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-CG-5728        TCGA-CG-5730        TCGA-CG-5732        TCGA-CG-5733 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-CG-5734        TCGA-D7-5577        TCGA-D7-5578        TCGA-D7-5579 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE"   "4P GAIN MUTATED" 
       TCGA-D7-6518        TCGA-D7-6519        TCGA-D7-6520        TCGA-D7-6521 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-D7-6522        TCGA-D7-6524        TCGA-D7-6525        TCGA-D7-6526 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-D7-6527        TCGA-D7-6528        TCGA-D7-6815        TCGA-D7-6817 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-D7-6818        TCGA-D7-6820        TCGA-D7-6822        TCGA-EQ-5647 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EQ-8122        TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-FP-7735        TCGA-FP-7829        TCGA-FP-7916        TCGA-FP-7998 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-HJ-7597        TCGA-IN-7806        TCGA-IN-7808        TCGA-IP-7968 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-B7-5816        TCGA-B7-5818        TCGA-BR-6452        TCGA-BR-6455 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BR-6457        TCGA-BR-6458        TCGA-BR-6563        TCGA-BR-6564 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BR-6565        TCGA-BR-6566        TCGA-BR-6705        TCGA-BR-6706 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BR-6707        TCGA-BR-6709        TCGA-BR-6710        TCGA-BR-6801 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BR-6802        TCGA-BR-6803        TCGA-BR-6852        TCGA-BR-7196 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BR-7197        TCGA-BR-7703        TCGA-BR-7704        TCGA-BR-7707 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BR-7715        TCGA-BR-7716        TCGA-BR-7717        TCGA-BR-7722 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BR-7723        TCGA-BR-7851        TCGA-BR-7901        TCGA-BR-7957 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BR-7958        TCGA-BR-7959        TCGA-BR-8059        TCGA-BR-8060 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BR-8077        TCGA-BR-8078        TCGA-BR-8080        TCGA-BR-8081 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BR-8284        TCGA-BR-8285        TCGA-BR-8286        TCGA-BR-8289 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BR-8291        TCGA-BR-8295        TCGA-BR-8296        TCGA-BR-8297 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-CD-5798        TCGA-CD-5799        TCGA-CD-5800        TCGA-CD-5801 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-CD-5802        TCGA-CD-5803        TCGA-CG-4300        TCGA-CG-4301 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-CG-4304        TCGA-CG-4305        TCGA-CG-4306        TCGA-CG-4436 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-CG-4437        TCGA-CG-4438        TCGA-CG-4440        TCGA-CG-4441 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-CG-4443        TCGA-CG-4444        TCGA-CG-4449        TCGA-CG-4455 
  "4P GAIN MUTATED" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-CG-4460        TCGA-CG-4462        TCGA-CG-4465        TCGA-CG-4466 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-CG-4469        TCGA-CG-4472        TCGA-CG-4474        TCGA-CG-4477 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-CG-5716        TCGA-CG-5717        TCGA-CG-5718        TCGA-CG-5719 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-CG-5720        TCGA-CG-5721        TCGA-CG-5722        TCGA-CG-5723 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-CG-5724        TCGA-CG-5725        TCGA-CG-5726        TCGA-CG-5727 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-CG-5728        TCGA-CG-5730        TCGA-CG-5732        TCGA-CG-5733 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-CG-5734        TCGA-D7-5577        TCGA-D7-5578        TCGA-D7-5579 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE"   "4P GAIN MUTATED" 
       TCGA-D7-6518        TCGA-D7-6519        TCGA-D7-6520        TCGA-D7-6521 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-D7-6522        TCGA-D7-6524        TCGA-D7-6525        TCGA-D7-6526 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-D7-6527        TCGA-D7-6528        TCGA-D7-6815        TCGA-D7-6817 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-D7-6818        TCGA-D7-6820        TCGA-D7-6822        TCGA-EQ-5647 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EQ-8122        TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-FP-7735        TCGA-FP-7829        TCGA-FP-7916        TCGA-FP-7998 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-HJ-7597        TCGA-IN-7806        TCGA-IN-7808        TCGA-IP-7968 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-B7-5816        TCGA-B7-5818        TCGA-BR-6452        TCGA-BR-6455 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BR-6457        TCGA-BR-6458        TCGA-BR-6563        TCGA-BR-6564 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BR-6565        TCGA-BR-6566        TCGA-BR-6705        TCGA-BR-6706 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BR-6707        TCGA-BR-6709        TCGA-BR-6710        TCGA-BR-6801 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BR-6802        TCGA-BR-6803        TCGA-BR-6852        TCGA-BR-7196 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BR-7197        TCGA-BR-7703        TCGA-BR-7704        TCGA-BR-7707 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BR-7715        TCGA-BR-7716        TCGA-BR-7717        TCGA-BR-7722 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BR-7723        TCGA-BR-7851        TCGA-BR-7901        TCGA-BR-7957 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BR-7958        TCGA-BR-7959        TCGA-BR-8059        TCGA-BR-8060 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BR-8077        TCGA-BR-8078        TCGA-BR-8080        TCGA-BR-8081 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BR-8284        TCGA-BR-8285        TCGA-BR-8286        TCGA-BR-8289 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BR-8291        TCGA-BR-8295        TCGA-BR-8296        TCGA-BR-8297 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-CD-5798        TCGA-CD-5799        TCGA-CD-5800        TCGA-CD-5801 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-CD-5802        TCGA-CD-5803        TCGA-CG-4300        TCGA-CG-4301 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-CG-4304        TCGA-CG-4305        TCGA-CG-4306        TCGA-CG-4436 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-CG-4437        TCGA-CG-4438        TCGA-CG-4440        TCGA-CG-4441 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-CG-4443        TCGA-CG-4444        TCGA-CG-4449        TCGA-CG-4455 
  "4P GAIN MUTATED" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-CG-4460        TCGA-CG-4462        TCGA-CG-4465        TCGA-CG-4466 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-CG-4469        TCGA-CG-4472        TCGA-CG-4474        TCGA-CG-4477 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-CG-5716        TCGA-CG-5717        TCGA-CG-5718        TCGA-CG-5719 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-CG-5720        TCGA-CG-5721        TCGA-CG-5722        TCGA-CG-5723 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-CG-5724        TCGA-CG-5725        TCGA-CG-5726        TCGA-CG-5727 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-CG-5728        TCGA-CG-5730        TCGA-CG-5732        TCGA-CG-5733 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-CG-5734        TCGA-D7-5577        TCGA-D7-5578        TCGA-D7-5579 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE"   "4P GAIN MUTATED" 
       TCGA-D7-6518        TCGA-D7-6519        TCGA-D7-6520        TCGA-D7-6521 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-D7-6522        TCGA-D7-6524        TCGA-D7-6525        TCGA-D7-6526 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-D7-6527        TCGA-D7-6528        TCGA-D7-6815        TCGA-D7-6817 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-D7-6818        TCGA-D7-6820        TCGA-D7-6822        TCGA-EQ-5647 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EQ-8122        TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-FP-7735        TCGA-FP-7829        TCGA-FP-7916        TCGA-FP-7998 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-HJ-7597        TCGA-IN-7806        TCGA-IN-7808        TCGA-IP-7968 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
[1] "Remove cluster labels:" "4P GAIN MUTATED"       
clus
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                2               122 
       TCGA-B7-5816        TCGA-B7-5818        TCGA-BR-6452        TCGA-BR-6455 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BR-6457        TCGA-BR-6458        TCGA-BR-6563        TCGA-BR-6564 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BR-6565        TCGA-BR-6566        TCGA-BR-6705        TCGA-BR-6706 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BR-6707        TCGA-BR-6709        TCGA-BR-6710        TCGA-BR-6801 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BR-6802        TCGA-BR-6803        TCGA-BR-6852        TCGA-BR-7196 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BR-7197        TCGA-BR-7703        TCGA-BR-7704        TCGA-BR-7707 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BR-7715        TCGA-BR-7716        TCGA-BR-7717        TCGA-BR-7722 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BR-7723        TCGA-BR-7851        TCGA-BR-7901        TCGA-BR-7957 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BR-7958        TCGA-BR-7959        TCGA-BR-8059        TCGA-BR-8060 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BR-8077        TCGA-BR-8078        TCGA-BR-8080        TCGA-BR-8081 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BR-8284        TCGA-BR-8285        TCGA-BR-8286        TCGA-BR-8289 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BR-8291        TCGA-BR-8295        TCGA-BR-8296        TCGA-BR-8297 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-CD-5798        TCGA-CD-5799        TCGA-CD-5800        TCGA-CD-5801 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-CD-5802        TCGA-CD-5803        TCGA-CG-4300        TCGA-CG-4301 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-CG-4304        TCGA-CG-4305        TCGA-CG-4306        TCGA-CG-4436 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-CG-4437        TCGA-CG-4438        TCGA-CG-4440        TCGA-CG-4441 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-CG-4444        TCGA-CG-4449        TCGA-CG-4455        TCGA-CG-4460 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-CG-4462        TCGA-CG-4465        TCGA-CG-4466        TCGA-CG-4469 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-CG-4472        TCGA-CG-4474        TCGA-CG-4477        TCGA-CG-5716 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-CG-5717        TCGA-CG-5718        TCGA-CG-5719        TCGA-CG-5720 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-CG-5721        TCGA-CG-5722        TCGA-CG-5723        TCGA-CG-5724 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-CG-5725        TCGA-CG-5726        TCGA-CG-5727        TCGA-CG-5728 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-CG-5730        TCGA-CG-5732        TCGA-CG-5733        TCGA-CG-5734 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-D7-5577        TCGA-D7-5578        TCGA-D7-6518        TCGA-D7-6519 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-D7-6520        TCGA-D7-6521        TCGA-D7-6522        TCGA-D7-6524 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-D7-6525        TCGA-D7-6526        TCGA-D7-6527        TCGA-D7-6528 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-D7-6815        TCGA-D7-6817        TCGA-D7-6818        TCGA-D7-6820 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-D7-6822        TCGA-EQ-5647        TCGA-EQ-8122        TCGA-F1-6177 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-F1-6874        TCGA-F1-6875        TCGA-FP-7735        TCGA-FP-7829 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-FP-7916        TCGA-FP-7998        TCGA-HJ-7597        TCGA-IN-7806 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-IN-7808        TCGA-IP-7968 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
D7V2, continuous
D7V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED      0    3
  4P GAIN WILD-TYPE   65   93
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  FEMALE               0                65
  MALE                 3                93
                   vv
clus                STOMACH ADENOCARCINOMA - DIFFUSE TYPE
  4P GAIN MUTATED                                       0
  4P GAIN WILD-TYPE                                    19
                   vv
clus                STOMACH ADENOCARCINOMA - NOT OTHERWISE SPECIFIED (NOS)
  4P GAIN MUTATED                                                        0
  4P GAIN WILD-TYPE                                                     79
                   vv
clus                STOMACH ADENOCARCINOMA - SIGNET RING TYPE
  4P GAIN MUTATED                                           0
  4P GAIN WILD-TYPE                                         1
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - MUCINOUS TYPE
  4P GAIN MUTATED                                                   1
  4P GAIN WILD-TYPE                                                 8
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - PAPILLARY TYPE
  4P GAIN MUTATED                                                    0
  4P GAIN WILD-TYPE                                                  3
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - TUBULAR TYPE
  4P GAIN MUTATED                                                  0
  4P GAIN WILD-TYPE                                               10
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - TYPE NOT OTHERWISE SPECIFIED (NOS)
  4P GAIN MUTATED                                                                        1
  4P GAIN WILD-TYPE                                                                     34
D7V4, multiclass
[1] "Remove cluster labels:" "4P GAIN MUTATED"       
clus
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                2               154 
       TCGA-B7-5816        TCGA-B7-5818        TCGA-BR-4183        TCGA-BR-4184 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BR-4187        TCGA-BR-4188        TCGA-BR-4191        TCGA-BR-4201 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BR-4253        TCGA-BR-4255        TCGA-BR-4256        TCGA-BR-4257 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BR-4267        TCGA-BR-4279        TCGA-BR-4280        TCGA-BR-4292 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BR-4294        TCGA-BR-4357        TCGA-BR-4361        TCGA-BR-4362 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BR-4363        TCGA-BR-4366        TCGA-BR-4367        TCGA-BR-4368 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BR-4369        TCGA-BR-4370        TCGA-BR-4371        TCGA-BR-6452 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BR-6453        TCGA-BR-6454        TCGA-BR-6455        TCGA-BR-6456 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BR-6457        TCGA-BR-6458        TCGA-BR-6563        TCGA-BR-6564 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BR-6565        TCGA-BR-6566        TCGA-BR-6705        TCGA-BR-6706 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BR-6707        TCGA-BR-6709        TCGA-BR-6710        TCGA-BR-6801 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BR-6802        TCGA-BR-6803        TCGA-BR-6852        TCGA-BR-7196 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BR-7197        TCGA-BR-7703        TCGA-BR-7704        TCGA-BR-7707 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BR-7715        TCGA-BR-7716        TCGA-BR-7717        TCGA-BR-7722 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BR-7723        TCGA-BR-7851        TCGA-BR-7901        TCGA-BR-7957 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BR-7958        TCGA-BR-7959        TCGA-BR-8059        TCGA-BR-8060 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BR-8077        TCGA-BR-8078        TCGA-BR-8080        TCGA-BR-8081 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BR-8284        TCGA-BR-8285        TCGA-BR-8286        TCGA-BR-8289 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BR-8291        TCGA-BR-8295        TCGA-BR-8296        TCGA-BR-8297 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-CD-5798        TCGA-CD-5799        TCGA-CD-5800        TCGA-CD-5801 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-CD-5802        TCGA-CD-5803        TCGA-CD-5804        TCGA-CG-4300 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-CG-4301        TCGA-CG-4304        TCGA-CG-4305        TCGA-CG-4306 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-CG-4436        TCGA-CG-4437        TCGA-CG-4438        TCGA-CG-4440 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-CG-4441        TCGA-CG-4442        TCGA-CG-4449        TCGA-CG-4455 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-CG-4460        TCGA-CG-4466        TCGA-CG-4469        TCGA-CG-4474 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-CG-4476        TCGA-CG-4477        TCGA-CG-5716        TCGA-CG-5717 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-CG-5718        TCGA-CG-5719        TCGA-CG-5720        TCGA-CG-5721 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-CG-5722        TCGA-CG-5723        TCGA-CG-5724        TCGA-CG-5725 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-CG-5726        TCGA-CG-5727        TCGA-CG-5728        TCGA-CG-5730 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-CG-5732        TCGA-CG-5733        TCGA-CG-5734        TCGA-D7-5577 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-D7-5578        TCGA-D7-6518        TCGA-D7-6519        TCGA-D7-6520 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-D7-6521        TCGA-D7-6522        TCGA-D7-6524        TCGA-D7-6525 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-D7-6526        TCGA-D7-6527        TCGA-D7-6528        TCGA-D7-6815 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-D7-6817        TCGA-D7-6818        TCGA-D7-6820        TCGA-D7-6822 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EQ-5647        TCGA-EQ-8122        TCGA-F1-6177        TCGA-F1-6874 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-F1-6875        TCGA-FP-7735        TCGA-FP-7829        TCGA-FP-7916 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-FP-7998        TCGA-HF-7131        TCGA-HF-7132        TCGA-HF-7133 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-HF-7134        TCGA-HF-7136        TCGA-HJ-7597        TCGA-IN-7806 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-IN-7808        TCGA-IP-7968 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
                   vv
clus                T1 T2 T3 T4
  4P GAIN MUTATED    1  0  2  0
  4P GAIN WILD-TYPE  5 53 57 33
D7V5, multiclass
                   vv
clus                N0 N1 N2 N3
  4P GAIN MUTATED    1  1  1  0
  4P GAIN WILD-TYPE 49 56 23 19
D7V6, multiclass
                   vv
clus                 M0  M1  MX
  4P GAIN MUTATED     3   0   0
  4P GAIN WILD-TYPE 129  18  11
D7V7, multiclass
                   vv
clus                 I II III IV
  4P GAIN MUTATED    1  2   0  0
  4P GAIN WILD-TYPE 24 41  48 29
D7V8, multiclass
D7V9, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED      0    3
  4P GAIN WILD-TYPE    5  153
     clus
vv    4P GAIN MUTATED 4P GAIN WILD-TYPE
  NO                0                 5
  YES               3               153

Clustering(8) Variable = 5p gain mutation analysis
D8V1, survival
                   sevent
clus2                0  1
  5P GAIN MUTATED   18  4
  5P GAIN WILD-TYPE 90 12
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               22               102 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
                4                12 
$`5P GAIN MUTATED`
TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7717 TCGA-BR-7901 TCGA-CD-5801 TCGA-CG-4436 
        1.25         1.05         0.69         0.95         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-D7-6527 
        1.02         0.95        12.03        15.02         4.54         4.14 
TCGA-D7-6818 TCGA-D7-6820 TCGA-EQ-5647 TCGA-FP-7829 
        4.04         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-7716 
        0.26         1.22         1.48         0.46         0.13         0.82 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
        0.16         4.54         0.99         0.69         0.16         1.08 
TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
        0.82         1.32         0.69         0.95         0.49         0.46 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
        0.72         0.26         0.43         0.26         1.18         1.55 
TCGA-BR-8296 TCGA-BR-8297 TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5802 
        1.48         0.76         0.82         0.69         0.36         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-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4462 
        8.05         4.01        14.01        29.98        19.07         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-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5723 TCGA-CG-5726 TCGA-CG-5727 
        1.02         0.99         5.98        70.06        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-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
        3.58         9.80        15.65         9.63         8.19         6.90 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
        0.69         5.95         6.61         1.68         3.65         4.70 
TCGA-D7-6822 TCGA-EQ-8122 TCGA-F1-6177 TCGA-F1-6874 TCGA-F1-6875 TCGA-FP-7735 
        4.27         7.79         6.54         2.01        72.23         0.39 
TCGA-FP-7916 TCGA-FP-7998 TCGA-HJ-7597 TCGA-IN-7806 TCGA-IN-7808 TCGA-IP-7968 
        3.02         3.58        26.43         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 
            4.090             1.445 
[1] "0.2 - 54.0 (4.1)" "0.1 - 72.2 (1.4)"
       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 WILD-TYPE"   "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 MUTATED" "5P GAIN WILD-TYPE" 
       TCGA-BR-7958        TCGA-BR-7959        TCGA-BR-8059        TCGA-BR-8060 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-BR-8077        TCGA-BR-8078        TCGA-BR-8080        TCGA-BR-8081 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-BR-8284        TCGA-BR-8285        TCGA-BR-8286        TCGA-BR-8289 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-BR-8291        TCGA-BR-8295        TCGA-BR-8296        TCGA-BR-8297 
"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 MUTATED" "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-EQ-8122        TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-FP-7735        TCGA-FP-7829        TCGA-FP-7916        TCGA-FP-7998 
"5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-HJ-7597        TCGA-IN-7806        TCGA-IN-7808        TCGA-IP-7968 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "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 WILD-TYPE"   "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 MUTATED" "5P GAIN WILD-TYPE" 
       TCGA-BR-7958        TCGA-BR-7959        TCGA-BR-8059        TCGA-BR-8060 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-BR-8077        TCGA-BR-8078        TCGA-BR-8080        TCGA-BR-8081 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-BR-8284        TCGA-BR-8285        TCGA-BR-8286        TCGA-BR-8289 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-BR-8291        TCGA-BR-8295        TCGA-BR-8296        TCGA-BR-8297 
"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 MUTATED" "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-EQ-8122        TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-FP-7735        TCGA-FP-7829        TCGA-FP-7916        TCGA-FP-7998 
"5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-HJ-7597        TCGA-IN-7806        TCGA-IN-7808        TCGA-IP-7968 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "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 WILD-TYPE"   "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 MUTATED" "5P GAIN WILD-TYPE" 
       TCGA-BR-7958        TCGA-BR-7959        TCGA-BR-8059        TCGA-BR-8060 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-BR-8077        TCGA-BR-8078        TCGA-BR-8080        TCGA-BR-8081 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-BR-8284        TCGA-BR-8285        TCGA-BR-8286        TCGA-BR-8289 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-BR-8291        TCGA-BR-8295        TCGA-BR-8296        TCGA-BR-8297 
"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 MUTATED" "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-EQ-8122        TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-FP-7735        TCGA-FP-7829        TCGA-FP-7916        TCGA-FP-7998 
"5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-HJ-7597        TCGA-IN-7806        TCGA-IN-7808        TCGA-IP-7968 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
[1] "hr=" "1"  
D8V2, continuous
D8V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED      7   19
  5P GAIN WILD-TYPE   58   77
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  FEMALE               7                58
  MALE                19                77
                   vv
clus                STOMACH ADENOCARCINOMA - DIFFUSE TYPE
  5P GAIN MUTATED                                       2
  5P GAIN WILD-TYPE                                    17
                   vv
clus                STOMACH ADENOCARCINOMA - NOT OTHERWISE SPECIFIED (NOS)
  5P GAIN MUTATED                                                        9
  5P GAIN WILD-TYPE                                                     70
                   vv
clus                STOMACH ADENOCARCINOMA - SIGNET RING TYPE
  5P GAIN MUTATED                                           0
  5P GAIN WILD-TYPE                                         1
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - MUCINOUS TYPE
  5P GAIN MUTATED                                                   3
  5P GAIN WILD-TYPE                                                 6
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - PAPILLARY TYPE
  5P GAIN MUTATED                                                    1
  5P GAIN WILD-TYPE                                                  2
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - TUBULAR TYPE
  5P GAIN MUTATED                                                  1
  5P GAIN WILD-TYPE                                                9
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - TYPE NOT OTHERWISE SPECIFIED (NOS)
  5P GAIN MUTATED                                                                        7
  5P GAIN WILD-TYPE                                                                     28
D8V4, multiclass
                   vv
clus                T1 T2 T3 T4
  5P GAIN MUTATED    0  9 10  5
  5P GAIN WILD-TYPE  6 44 49 28
D8V5, multiclass
                   vv
clus                N0 N1 N2 N3
  5P GAIN MUTATED    6 12  4  3
  5P GAIN WILD-TYPE 44 45 20 16
D8V6, multiclass
                   vv
clus                 M0  M1  MX
  5P GAIN MUTATED    22   4   0
  5P GAIN WILD-TYPE 110  14  11
D8V7, multiclass
                   vv
clus                 I II III IV
  5P GAIN MUTATED    3  9   4  8
  5P GAIN WILD-TYPE 22 34  44 21
D8V8, multiclass
D8V9, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED      2   24
  5P GAIN WILD-TYPE    3  132
     clus
vv    5P GAIN MUTATED 5P GAIN WILD-TYPE
  NO                2                 3
  YES              24               132

Clustering(9) Variable = 5q gain mutation analysis
D9V1, survival
                   sevent
clus2                 0   1
  5Q GAIN MUTATED     6   0
  5Q GAIN WILD-TYPE 102  16
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
                6               118 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
                0                16 
$`5Q GAIN MUTATED`
TCGA-BR-7715 TCGA-CG-4436 TCGA-CG-4438 TCGA-CG-4455 TCGA-CG-4466 TCGA-FP-7829 
        1.05        52.96        54.05        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-BR-7958 TCGA-BR-7959 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
        0.69         0.16         1.08         0.82         1.32         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
        0.95         0.49         0.46         0.72         0.26         0.43 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-CD-5798 
        0.26         1.18         1.55         1.48         0.76         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-4440 
        3.02        27.02        15.95         1.02         8.05         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4460 TCGA-CG-4462 
       14.01        29.98        47.05        19.07        21.99         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-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-EQ-8122 
        4.70         4.04         2.93         4.27         0.62         7.79 
TCGA-F1-6177 TCGA-F1-6874 TCGA-F1-6875 TCGA-FP-7735 TCGA-FP-7916 TCGA-FP-7998 
        6.54         2.01        72.23         0.39         3.02         3.58 
TCGA-HJ-7597 TCGA-IN-7806 TCGA-IN-7808 TCGA-IP-7968 
       26.43         6.87         3.55         2.53 

  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
             0.20              0.07 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
            54.05             72.23 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
           15.485             1.480 
[1] "0.2 - 54.0 (15.5)" "0.1 - 72.2 (1.5)" 
       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-BR-7958        TCGA-BR-7959        TCGA-BR-8059        TCGA-BR-8060 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-BR-8077        TCGA-BR-8078        TCGA-BR-8080        TCGA-BR-8081 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-BR-8284        TCGA-BR-8285        TCGA-BR-8286        TCGA-BR-8289 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-BR-8291        TCGA-BR-8295        TCGA-BR-8296        TCGA-BR-8297 
"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 MUTATED" "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-EQ-8122        TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-FP-7735        TCGA-FP-7829        TCGA-FP-7916        TCGA-FP-7998 
"5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-HJ-7597        TCGA-IN-7806        TCGA-IN-7808        TCGA-IP-7968 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "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-BR-7958        TCGA-BR-7959        TCGA-BR-8059        TCGA-BR-8060 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-BR-8077        TCGA-BR-8078        TCGA-BR-8080        TCGA-BR-8081 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-BR-8284        TCGA-BR-8285        TCGA-BR-8286        TCGA-BR-8289 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-BR-8291        TCGA-BR-8295        TCGA-BR-8296        TCGA-BR-8297 
"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 MUTATED" "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-EQ-8122        TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-FP-7735        TCGA-FP-7829        TCGA-FP-7916        TCGA-FP-7998 
"5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-HJ-7597        TCGA-IN-7806        TCGA-IN-7808        TCGA-IP-7968 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "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-BR-7958        TCGA-BR-7959        TCGA-BR-8059        TCGA-BR-8060 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-BR-8077        TCGA-BR-8078        TCGA-BR-8080        TCGA-BR-8081 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-BR-8284        TCGA-BR-8285        TCGA-BR-8286        TCGA-BR-8289 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-BR-8291        TCGA-BR-8295        TCGA-BR-8296        TCGA-BR-8297 
"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 MUTATED" "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-EQ-8122        TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-FP-7735        TCGA-FP-7829        TCGA-FP-7916        TCGA-FP-7998 
"5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-HJ-7597        TCGA-IN-7806        TCGA-IN-7808        TCGA-IP-7968 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
[1] "hr="     "8.4e+07"
D9V2, continuous
D9V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED      1    5
  5Q GAIN WILD-TYPE   64   91
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  FEMALE               1                64
  MALE                 5                91
                   vv
clus                STOMACH ADENOCARCINOMA - DIFFUSE TYPE
  5Q GAIN MUTATED                                       0
  5Q GAIN WILD-TYPE                                    19
                   vv
clus                STOMACH ADENOCARCINOMA - NOT OTHERWISE SPECIFIED (NOS)
  5Q GAIN MUTATED                                                        1
  5Q GAIN WILD-TYPE                                                     78
                   vv
clus                STOMACH ADENOCARCINOMA - SIGNET RING TYPE
  5Q GAIN MUTATED                                           0
  5Q GAIN WILD-TYPE                                         1
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - MUCINOUS TYPE
  5Q GAIN MUTATED                                                   2
  5Q GAIN WILD-TYPE                                                 7
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - PAPILLARY TYPE
  5Q GAIN MUTATED                                                    0
  5Q GAIN WILD-TYPE                                                  3
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - TUBULAR TYPE
  5Q GAIN MUTATED                                                  0
  5Q GAIN WILD-TYPE                                               10
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - TYPE NOT OTHERWISE SPECIFIED (NOS)
  5Q GAIN MUTATED                                                                        3
  5Q GAIN WILD-TYPE                                                                     32
D9V4, multiclass
                   vv
clus                T1 T2 T3 T4
  5Q GAIN MUTATED    0  3  2  1
  5Q GAIN WILD-TYPE  6 50 57 32
D9V5, multiclass
                   vv
clus                N0 N1 N2 N3
  5Q GAIN MUTATED    3  2  1  0
  5Q GAIN WILD-TYPE 47 55 23 19
D9V6, multiclass
                   vv
clus                 M0  M1  MX
  5Q GAIN MUTATED     6   0   0
  5Q GAIN WILD-TYPE 126  18  11
D9V7, multiclass
                   vv
clus                 I II III IV
  5Q GAIN MUTATED    2  2   1  1
  5Q GAIN WILD-TYPE 23 41  47 28
D9V8, multiclass
D9V9, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED      0    6
  5Q GAIN WILD-TYPE    5  150
     clus
vv    5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  NO                0                 5
  YES               6               150

Clustering(10) Variable = 6p gain mutation analysis
D10V1, survival
                   sevent
clus2                 0   1
  6P GAIN MUTATED     6   1
  6P GAIN WILD-TYPE 102  15
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
                7               117 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
                1                15 
$`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-BR-7958 TCGA-BR-7959 
        4.54         0.99         0.95         0.69         0.16         1.08 
TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
        0.82         1.32         0.69         0.95         0.49         0.46 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
        0.72         0.26         0.43         0.26         1.18         1.55 
TCGA-BR-8296 TCGA-BR-8297 TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
        1.48         0.76         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-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-EQ-5647 TCGA-EQ-8122 TCGA-F1-6177 TCGA-F1-6874 
        4.04         2.93         0.62         7.79         6.54         2.01 
TCGA-F1-6875 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-HJ-7597 
       72.23         0.39         0.20         3.02         3.58        26.43 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IP-7968 
        6.87         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 
             1.48              1.55 
[1] "0.7 - 54.0 (1.5)" "0.1 - 72.2 (1.6)"
       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-BR-7958        TCGA-BR-7959        TCGA-BR-8059        TCGA-BR-8060 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-BR-8077        TCGA-BR-8078        TCGA-BR-8080        TCGA-BR-8081 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-BR-8284        TCGA-BR-8285        TCGA-BR-8286        TCGA-BR-8289 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-BR-8291        TCGA-BR-8295        TCGA-BR-8296        TCGA-BR-8297 
"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-EQ-8122        TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-FP-7735        TCGA-FP-7829        TCGA-FP-7916        TCGA-FP-7998 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-HJ-7597        TCGA-IN-7806        TCGA-IN-7808        TCGA-IP-7968 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "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-BR-7958        TCGA-BR-7959        TCGA-BR-8059        TCGA-BR-8060 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-BR-8077        TCGA-BR-8078        TCGA-BR-8080        TCGA-BR-8081 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-BR-8284        TCGA-BR-8285        TCGA-BR-8286        TCGA-BR-8289 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-BR-8291        TCGA-BR-8295        TCGA-BR-8296        TCGA-BR-8297 
"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-EQ-8122        TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-FP-7735        TCGA-FP-7829        TCGA-FP-7916        TCGA-FP-7998 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-HJ-7597        TCGA-IN-7806        TCGA-IN-7808        TCGA-IP-7968 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "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-BR-7958        TCGA-BR-7959        TCGA-BR-8059        TCGA-BR-8060 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-BR-8077        TCGA-BR-8078        TCGA-BR-8080        TCGA-BR-8081 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-BR-8284        TCGA-BR-8285        TCGA-BR-8286        TCGA-BR-8289 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-BR-8291        TCGA-BR-8295        TCGA-BR-8296        TCGA-BR-8297 
"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-EQ-8122        TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-FP-7735        TCGA-FP-7829        TCGA-FP-7916        TCGA-FP-7998 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-HJ-7597        TCGA-IN-7806        TCGA-IN-7808        TCGA-IP-7968 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
[1] "hr=" "1.3"
D10V2, continuous
D10V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED      5    6
  6P GAIN WILD-TYPE   60   90
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  FEMALE               5                60
  MALE                 6                90
                   vv
clus                STOMACH ADENOCARCINOMA - DIFFUSE TYPE
  6P GAIN MUTATED                                       0
  6P GAIN WILD-TYPE                                    19
                   vv
clus                STOMACH ADENOCARCINOMA - NOT OTHERWISE SPECIFIED (NOS)
  6P GAIN MUTATED                                                        7
  6P GAIN WILD-TYPE                                                     72
                   vv
clus                STOMACH ADENOCARCINOMA - SIGNET RING TYPE
  6P GAIN MUTATED                                           0
  6P GAIN WILD-TYPE                                         1
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - MUCINOUS TYPE
  6P GAIN MUTATED                                                   0
  6P GAIN WILD-TYPE                                                 9
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - PAPILLARY TYPE
  6P GAIN MUTATED                                                    0
  6P GAIN WILD-TYPE                                                  3
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - TUBULAR TYPE
  6P GAIN MUTATED                                                  1
  6P GAIN WILD-TYPE                                                9
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - TYPE NOT OTHERWISE SPECIFIED (NOS)
  6P GAIN MUTATED                                                                        3
  6P GAIN WILD-TYPE                                                                     32
D10V4, multiclass
                   vv
clus                T1 T2 T3 T4
  6P GAIN MUTATED    0  1  5  4
  6P GAIN WILD-TYPE  6 52 54 29
D10V5, multiclass
                   vv
clus                N0 N1 N2 N3
  6P GAIN MUTATED    4  5  2  0
  6P GAIN WILD-TYPE 46 52 22 19
D10V6, multiclass
                   vv
clus                 M0  M1  MX
  6P GAIN MUTATED    10   1   0
  6P GAIN WILD-TYPE 122  17  11
D10V7, multiclass
                   vv
clus                 I II III IV
  6P GAIN MUTATED    1  3   2  4
  6P GAIN WILD-TYPE 24 40  46 25
D10V8, multiclass
D10V9, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED      0   11
  6P GAIN WILD-TYPE    5  145
     clus
vv    6P GAIN MUTATED 6P GAIN WILD-TYPE
  NO                0                 5
  YES              11               145

Clustering(11) Variable = 6q gain mutation analysis
D11V1, survival
                   sevent
clus2                 0   1
  6Q GAIN MUTATED     6   0
  6Q GAIN WILD-TYPE 102  16
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
                6               118 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
                0                16 
$`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-BR-7958 TCGA-BR-7959 
        4.54         0.99         0.95         0.69         0.16         1.08 
TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
        0.82         1.32         0.69         0.95         0.49         0.46 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
        0.72         0.26         0.43         0.26         1.18         1.55 
TCGA-BR-8296 TCGA-BR-8297 TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
        1.48         0.76         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-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-EQ-5647 TCGA-EQ-8122 TCGA-F1-6177 
        4.70         4.04         2.93         0.62         7.79         6.54 
TCGA-F1-6874 TCGA-F1-6875 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
        2.01        72.23         0.39         0.20         3.02         3.58 
TCGA-HJ-7597 TCGA-IN-7806 TCGA-IN-7808 TCGA-IP-7968 
       26.43         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             1.615 
[1] "0.7 - 54.0 (1.4)" "0.1 - 72.2 (1.6)"
       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-BR-7958        TCGA-BR-7959        TCGA-BR-8059        TCGA-BR-8060 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-BR-8077        TCGA-BR-8078        TCGA-BR-8080        TCGA-BR-8081 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-BR-8284        TCGA-BR-8285        TCGA-BR-8286        TCGA-BR-8289 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-BR-8291        TCGA-BR-8295        TCGA-BR-8296        TCGA-BR-8297 
"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-EQ-8122        TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-FP-7735        TCGA-FP-7829        TCGA-FP-7916        TCGA-FP-7998 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-HJ-7597        TCGA-IN-7806        TCGA-IN-7808        TCGA-IP-7968 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "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-BR-7958        TCGA-BR-7959        TCGA-BR-8059        TCGA-BR-8060 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-BR-8077        TCGA-BR-8078        TCGA-BR-8080        TCGA-BR-8081 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-BR-8284        TCGA-BR-8285        TCGA-BR-8286        TCGA-BR-8289 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-BR-8291        TCGA-BR-8295        TCGA-BR-8296        TCGA-BR-8297 
"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-EQ-8122        TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-FP-7735        TCGA-FP-7829        TCGA-FP-7916        TCGA-FP-7998 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-HJ-7597        TCGA-IN-7806        TCGA-IN-7808        TCGA-IP-7968 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "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-BR-7958        TCGA-BR-7959        TCGA-BR-8059        TCGA-BR-8060 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-BR-8077        TCGA-BR-8078        TCGA-BR-8080        TCGA-BR-8081 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-BR-8284        TCGA-BR-8285        TCGA-BR-8286        TCGA-BR-8289 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-BR-8291        TCGA-BR-8295        TCGA-BR-8296        TCGA-BR-8297 
"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-EQ-8122        TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-FP-7735        TCGA-FP-7829        TCGA-FP-7916        TCGA-FP-7998 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-HJ-7597        TCGA-IN-7806        TCGA-IN-7808        TCGA-IP-7968 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
[1] "hr="     "7.3e+07"
D11V2, continuous
D11V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED      4    6
  6Q GAIN WILD-TYPE   61   90
        clus
vv       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  FEMALE               4                61
  MALE                 6                90
                   vv
clus                STOMACH ADENOCARCINOMA - DIFFUSE TYPE
  6Q GAIN MUTATED                                       0
  6Q GAIN WILD-TYPE                                    19
                   vv
clus                STOMACH ADENOCARCINOMA - NOT OTHERWISE SPECIFIED (NOS)
  6Q GAIN MUTATED                                                        7
  6Q GAIN WILD-TYPE                                                     72
                   vv
clus                STOMACH ADENOCARCINOMA - SIGNET RING TYPE
  6Q GAIN MUTATED                                           0
  6Q GAIN WILD-TYPE                                         1
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - MUCINOUS TYPE
  6Q GAIN MUTATED                                                   0
  6Q GAIN WILD-TYPE                                                 9
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - PAPILLARY TYPE
  6Q GAIN MUTATED                                                    0
  6Q GAIN WILD-TYPE                                                  3
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - TUBULAR TYPE
  6Q GAIN MUTATED                                                  1
  6Q GAIN WILD-TYPE                                                9
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - TYPE NOT OTHERWISE SPECIFIED (NOS)
  6Q GAIN MUTATED                                                                        2
  6Q GAIN WILD-TYPE                                                                     33
D11V4, multiclass
                   vv
clus                T1 T2 T3 T4
  6Q GAIN MUTATED    0  1  5  3
  6Q GAIN WILD-TYPE  6 52 54 30
D11V5, multiclass
                   vv
clus                N0 N1 N2 N3
  6Q GAIN MUTATED    4  4  2  0
  6Q GAIN WILD-TYPE 46 53 22 19
D11V6, multiclass
                   vv
clus                 M0  M1  MX
  6Q GAIN MUTATED    10   0   0
  6Q GAIN WILD-TYPE 122  18  11
D11V7, multiclass
                   vv
clus                 I II III IV
  6Q GAIN MUTATED    1  3   2  3
  6Q GAIN WILD-TYPE 24 40  46 26
D11V8, multiclass
D11V9, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED      0   10
  6Q GAIN WILD-TYPE    5  146
     clus
vv    6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  NO                0                 5
  YES              10               146

Clustering(12) Variable = 7p gain mutation analysis
D12V1, survival
                   sevent
clus2                0  1
  7P GAIN MUTATED   29  6
  7P GAIN WILD-TYPE 79 10
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               35                89 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
                6                10 
$`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-EQ-8122 
        8.19         6.61         1.68         4.04         4.27         7.79 
TCGA-F1-6177 TCGA-F1-6874 TCGA-F1-6875 TCGA-FP-7735 TCGA-IN-7808 
        6.54         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-BR-7958 
        0.82         0.16         4.54         0.99         0.69         0.16 
TCGA-BR-7959 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
        1.08         0.82         1.32         0.69         0.95         0.49 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
        0.46         0.72         0.26         0.43         0.26         1.18 
TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
        1.55         1.48         0.76         0.82         0.69         0.36 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CG-4301 TCGA-CG-4306 TCGA-CG-4437 TCGA-CG-4438 
        0.30         0.07         3.02         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-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4477 TCGA-CG-5716 TCGA-CG-5717 
        1.02         8.98        18.94         1.02         1.02         6.94 
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-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
       65.10         4.01        55.04         7.99         8.65         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-D7-6527 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6820 TCGA-EQ-5647 TCGA-FP-7829 
        4.14         3.65         4.70         2.93         0.62         0.20 
TCGA-FP-7916 TCGA-FP-7998 TCGA-HJ-7597 TCGA-IN-7806 TCGA-IP-7968 
        3.02         3.58        26.43         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 
             4.27              1.32 
[1] "0.1 - 72.2 (4.3)" "0.1 - 70.1 (1.3)"
       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-BR-7958        TCGA-BR-7959        TCGA-BR-8059        TCGA-BR-8060 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-BR-8077        TCGA-BR-8078        TCGA-BR-8080        TCGA-BR-8081 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-BR-8284        TCGA-BR-8285        TCGA-BR-8286        TCGA-BR-8289 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-BR-8291        TCGA-BR-8295        TCGA-BR-8296        TCGA-BR-8297 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "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-EQ-8122        TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875 
  "7P GAIN MUTATED"   "7P GAIN MUTATED"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-FP-7735        TCGA-FP-7829        TCGA-FP-7916        TCGA-FP-7998 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-HJ-7597        TCGA-IN-7806        TCGA-IN-7808        TCGA-IP-7968 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "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-BR-7958        TCGA-BR-7959        TCGA-BR-8059        TCGA-BR-8060 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-BR-8077        TCGA-BR-8078        TCGA-BR-8080        TCGA-BR-8081 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-BR-8284        TCGA-BR-8285        TCGA-BR-8286        TCGA-BR-8289 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-BR-8291        TCGA-BR-8295        TCGA-BR-8296        TCGA-BR-8297 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "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-EQ-8122        TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875 
  "7P GAIN MUTATED"   "7P GAIN MUTATED"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-FP-7735        TCGA-FP-7829        TCGA-FP-7916        TCGA-FP-7998 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-HJ-7597        TCGA-IN-7806        TCGA-IN-7808        TCGA-IP-7968 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "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-BR-7958        TCGA-BR-7959        TCGA-BR-8059        TCGA-BR-8060 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-BR-8077        TCGA-BR-8078        TCGA-BR-8080        TCGA-BR-8081 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-BR-8284        TCGA-BR-8285        TCGA-BR-8286        TCGA-BR-8289 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-BR-8291        TCGA-BR-8295        TCGA-BR-8296        TCGA-BR-8297 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "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-EQ-8122        TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875 
  "7P GAIN MUTATED"   "7P GAIN MUTATED"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-FP-7735        TCGA-FP-7829        TCGA-FP-7916        TCGA-FP-7998 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-HJ-7597        TCGA-IN-7806        TCGA-IN-7808        TCGA-IP-7968 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
[1] "hr=" "1.4"
D12V2, continuous
D12V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED     15   34
  7P GAIN WILD-TYPE   50   62
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  FEMALE              15                50
  MALE                34                62
                   vv
clus                STOMACH ADENOCARCINOMA - DIFFUSE TYPE
  7P GAIN MUTATED                                       8
  7P GAIN WILD-TYPE                                    11
                   vv
clus                STOMACH ADENOCARCINOMA - NOT OTHERWISE SPECIFIED (NOS)
  7P GAIN MUTATED                                                       25
  7P GAIN WILD-TYPE                                                     54
                   vv
clus                STOMACH ADENOCARCINOMA - SIGNET RING TYPE
  7P GAIN MUTATED                                           0
  7P GAIN WILD-TYPE                                         1
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - MUCINOUS TYPE
  7P GAIN MUTATED                                                   0
  7P GAIN WILD-TYPE                                                 9
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - PAPILLARY TYPE
  7P GAIN MUTATED                                                    0
  7P GAIN WILD-TYPE                                                  3
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - TUBULAR TYPE
  7P GAIN MUTATED                                                  3
  7P GAIN WILD-TYPE                                                7
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - TYPE NOT OTHERWISE SPECIFIED (NOS)
  7P GAIN MUTATED                                                                       11
  7P GAIN WILD-TYPE                                                                     24
D12V4, multiclass
                   vv
clus                T1 T2 T3 T4
  7P GAIN MUTATED    3 16 19  7
  7P GAIN WILD-TYPE  3 37 40 26
D12V5, multiclass
                   vv
clus                N0 N1 N2 N3
  7P GAIN MUTATED   19 15  6  6
  7P GAIN WILD-TYPE 31 42 18 13
D12V6, multiclass
                   vv
clus                M0 M1 MX
  7P GAIN MUTATED   41  4  4
  7P GAIN WILD-TYPE 91 14  7
D12V7, multiclass
                   vv
clus                 I II III IV
  7P GAIN MUTATED   12 12  11  9
  7P GAIN WILD-TYPE 13 31  37 20
D12V8, multiclass
D12V9, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED      2   47
  7P GAIN WILD-TYPE    3  109
     clus
vv    7P GAIN MUTATED 7P GAIN WILD-TYPE
  NO                2                 3
  YES              47               109

Clustering(13) Variable = 7q gain mutation analysis
D13V1, survival
                   sevent
clus2                0  1
  7Q GAIN MUTATED   24  6
  7Q GAIN WILD-TYPE 84 10
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               30                94 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
                6                10 
$`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-EQ-8122 TCGA-F1-6177 TCGA-F1-6874 TCGA-F1-6875 TCGA-FP-7735 
        1.68         7.79         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-BR-7958 TCGA-BR-7959 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
        0.69         0.16         1.08         0.82         1.32         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
        0.95         0.49         0.46         0.72         0.26         0.43 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-CD-5798 
        0.26         1.18         1.55         1.48         0.76         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-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 
        8.05        54.05        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-4477 
       12.03        21.99         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-D7-6818 
        0.69         5.95         4.14         3.65         4.70         4.04 
TCGA-D7-6820 TCGA-D7-6822 TCGA-EQ-5647 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
        2.93         4.27         0.62         0.20         3.02         3.58 
TCGA-HJ-7597 TCGA-IN-7806 TCGA-IN-7808 TCGA-IP-7968 
       26.43         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 
            6.575             1.335 
[1] "0.1 - 72.2 (6.6)" "0.1 - 70.1 (1.3)"
       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-BR-7958        TCGA-BR-7959        TCGA-BR-8059        TCGA-BR-8060 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-BR-8077        TCGA-BR-8078        TCGA-BR-8080        TCGA-BR-8081 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-BR-8284        TCGA-BR-8285        TCGA-BR-8286        TCGA-BR-8289 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-BR-8291        TCGA-BR-8295        TCGA-BR-8296        TCGA-BR-8297 
"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-EQ-8122        TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875 
  "7Q GAIN MUTATED"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" 
       TCGA-FP-7735        TCGA-FP-7829        TCGA-FP-7916        TCGA-FP-7998 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-HJ-7597        TCGA-IN-7806        TCGA-IN-7808        TCGA-IP-7968 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "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-BR-7958        TCGA-BR-7959        TCGA-BR-8059        TCGA-BR-8060 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-BR-8077        TCGA-BR-8078        TCGA-BR-8080        TCGA-BR-8081 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-BR-8284        TCGA-BR-8285        TCGA-BR-8286        TCGA-BR-8289 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-BR-8291        TCGA-BR-8295        TCGA-BR-8296        TCGA-BR-8297 
"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-EQ-8122        TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875 
  "7Q GAIN MUTATED"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" 
       TCGA-FP-7735        TCGA-FP-7829        TCGA-FP-7916        TCGA-FP-7998 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-HJ-7597        TCGA-IN-7806        TCGA-IN-7808        TCGA-IP-7968 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "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-BR-7958        TCGA-BR-7959        TCGA-BR-8059        TCGA-BR-8060 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-BR-8077        TCGA-BR-8078        TCGA-BR-8080        TCGA-BR-8081 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-BR-8284        TCGA-BR-8285        TCGA-BR-8286        TCGA-BR-8289 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-BR-8291        TCGA-BR-8295        TCGA-BR-8296        TCGA-BR-8297 
"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-EQ-8122        TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875 
  "7Q GAIN MUTATED"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" 
       TCGA-FP-7735        TCGA-FP-7829        TCGA-FP-7916        TCGA-FP-7998 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-HJ-7597        TCGA-IN-7806        TCGA-IN-7808        TCGA-IP-7968 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
[1] "hr=" "1.2"
D13V2, continuous
D13V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED     15   29
  7Q GAIN WILD-TYPE   50   67
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  FEMALE              15                50
  MALE                29                67
                   vv
clus                STOMACH ADENOCARCINOMA - DIFFUSE TYPE
  7Q GAIN MUTATED                                       6
  7Q GAIN WILD-TYPE                                    13
                   vv
clus                STOMACH ADENOCARCINOMA - NOT OTHERWISE SPECIFIED (NOS)
  7Q GAIN MUTATED                                                       23
  7Q GAIN WILD-TYPE                                                     56
                   vv
clus                STOMACH ADENOCARCINOMA - SIGNET RING TYPE
  7Q GAIN MUTATED                                           0
  7Q GAIN WILD-TYPE                                         1
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - MUCINOUS TYPE
  7Q GAIN MUTATED                                                   0
  7Q GAIN WILD-TYPE                                                 9
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - PAPILLARY TYPE
  7Q GAIN MUTATED                                                    0
  7Q GAIN WILD-TYPE                                                  3
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - TUBULAR TYPE
  7Q GAIN MUTATED                                                  2
  7Q GAIN WILD-TYPE                                                8
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - TYPE NOT OTHERWISE SPECIFIED (NOS)
  7Q GAIN MUTATED                                                                       11
  7Q GAIN WILD-TYPE                                                                     24
D13V4, multiclass
                   vv
clus                T1 T2 T3 T4
  7Q GAIN MUTATED    3 14 18  5
  7Q GAIN WILD-TYPE  3 39 41 28
D13V5, multiclass
                   vv
clus                N0 N1 N2 N3
  7Q GAIN MUTATED   17 13  6  5
  7Q GAIN WILD-TYPE 33 44 18 14
D13V6, multiclass
                   vv
clus                M0 M1 MX
  7Q GAIN MUTATED   36  3  5
  7Q GAIN WILD-TYPE 96 15  6
D13V7, multiclass
                   vv
clus                 I II III IV
  7Q GAIN MUTATED   11 11   9  7
  7Q GAIN WILD-TYPE 14 32  39 22
D13V8, multiclass
D13V9, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED      1   43
  7Q GAIN WILD-TYPE    4  113
     clus
vv    7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  NO                1                 4
  YES              43               113

Clustering(14) Variable = 8p gain mutation analysis
D14V1, survival
                   sevent
clus2                0  1
  8P GAIN MUTATED   26  7
  8P GAIN WILD-TYPE 82  9
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               33                91 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
                7                 9 
$`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-4444 TCGA-CG-4455 
        0.13         1.05        15.95        14.01        47.05        12.03 
TCGA-CG-4460 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-5718 TCGA-CG-5725 
       21.99        18.94         7.07        12.00         1.02        15.02 
TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5733 TCGA-D7-5578 TCGA-D7-5579 
       28.96        31.04        65.10        21.07         3.58         4.54 
TCGA-D7-6520 TCGA-D7-6524 TCGA-D7-6526 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6822 
        9.63         0.69         6.61         4.70         4.04         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-BR-7958 TCGA-BR-7959 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 
        0.16         1.08         0.82         1.32         0.69         0.95 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
        0.49         0.46         0.72         0.26         0.43         0.26 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-CD-5798 TCGA-CD-5799 
        1.18         1.55         1.48         0.76         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-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       27.02         1.02        52.96         8.05        54.05         4.01 
TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4474 TCGA-CG-4477 
       29.98        19.07         1.02         8.98         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-5730 TCGA-CG-5732 TCGA-CG-5734 TCGA-D7-5577 
       70.06        12.03         4.01        55.04         7.99         8.65 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6525 TCGA-D7-6527 
        9.80        15.65         8.19         6.90         5.95         4.14 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6820 TCGA-EQ-8122 TCGA-F1-6177 TCGA-F1-6874 
        1.68         3.65         2.93         7.79         6.54         2.01 
TCGA-F1-6875 TCGA-FP-7735 TCGA-FP-7916 TCGA-FP-7998 TCGA-HJ-7597 TCGA-IN-7806 
       72.23         0.39         3.02         3.58        26.43         6.87 
TCGA-IP-7968 
        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 
             4.70              1.22 
[1] "0.1 - 65.1 (4.7)" "0.1 - 72.2 (1.2)"
       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-BR-7958        TCGA-BR-7959        TCGA-BR-8059        TCGA-BR-8060 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-BR-8077        TCGA-BR-8078        TCGA-BR-8080        TCGA-BR-8081 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-BR-8284        TCGA-BR-8285        TCGA-BR-8286        TCGA-BR-8289 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-BR-8291        TCGA-BR-8295        TCGA-BR-8296        TCGA-BR-8297 
"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 MUTATED" "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 WILD-TYPE"   "8P GAIN MUTATED"   "8P GAIN MUTATED" 
       TCGA-EQ-8122        TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-FP-7735        TCGA-FP-7829        TCGA-FP-7916        TCGA-FP-7998 
"8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-HJ-7597        TCGA-IN-7806        TCGA-IN-7808        TCGA-IP-7968 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "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-BR-7958        TCGA-BR-7959        TCGA-BR-8059        TCGA-BR-8060 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-BR-8077        TCGA-BR-8078        TCGA-BR-8080        TCGA-BR-8081 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-BR-8284        TCGA-BR-8285        TCGA-BR-8286        TCGA-BR-8289 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-BR-8291        TCGA-BR-8295        TCGA-BR-8296        TCGA-BR-8297 
"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 MUTATED" "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 WILD-TYPE"   "8P GAIN MUTATED"   "8P GAIN MUTATED" 
       TCGA-EQ-8122        TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-FP-7735        TCGA-FP-7829        TCGA-FP-7916        TCGA-FP-7998 
"8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-HJ-7597        TCGA-IN-7806        TCGA-IN-7808        TCGA-IP-7968 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "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-BR-7958        TCGA-BR-7959        TCGA-BR-8059        TCGA-BR-8060 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-BR-8077        TCGA-BR-8078        TCGA-BR-8080        TCGA-BR-8081 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-BR-8284        TCGA-BR-8285        TCGA-BR-8286        TCGA-BR-8289 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-BR-8291        TCGA-BR-8295        TCGA-BR-8296        TCGA-BR-8297 
"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 MUTATED" "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 WILD-TYPE"   "8P GAIN MUTATED"   "8P GAIN MUTATED" 
       TCGA-EQ-8122        TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-FP-7735        TCGA-FP-7829        TCGA-FP-7916        TCGA-FP-7998 
"8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-HJ-7597        TCGA-IN-7806        TCGA-IN-7808        TCGA-IP-7968 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" 
[1] "hr=" "1.3"
D14V2, continuous
D14V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED     23   27
  8P GAIN WILD-TYPE   42   69
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  FEMALE              23                42
  MALE                27                69
                   vv
clus                STOMACH ADENOCARCINOMA - DIFFUSE TYPE
  8P GAIN MUTATED                                       4
  8P GAIN WILD-TYPE                                    15
                   vv
clus                STOMACH ADENOCARCINOMA - NOT OTHERWISE SPECIFIED (NOS)
  8P GAIN MUTATED                                                       23
  8P GAIN WILD-TYPE                                                     56
                   vv
clus                STOMACH ADENOCARCINOMA - SIGNET RING TYPE
  8P GAIN MUTATED                                           0
  8P GAIN WILD-TYPE                                         1
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - MUCINOUS TYPE
  8P GAIN MUTATED                                                   4
  8P GAIN WILD-TYPE                                                 5
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - PAPILLARY TYPE
  8P GAIN MUTATED                                                    0
  8P GAIN WILD-TYPE                                                  3
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - TUBULAR TYPE
  8P GAIN MUTATED                                                  5
  8P GAIN WILD-TYPE                                                5
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - TYPE NOT OTHERWISE SPECIFIED (NOS)
  8P GAIN MUTATED                                                                       12
  8P GAIN WILD-TYPE                                                                     23
D14V4, multiclass
                   vv
clus                T1 T2 T3 T4
  8P GAIN MUTATED    3 21 15  6
  8P GAIN WILD-TYPE  3 32 44 27
D14V5, multiclass
                   vv
clus                N0 N1 N2 N3
  8P GAIN MUTATED   17 13  8  5
  8P GAIN WILD-TYPE 33 44 16 14
D14V6, multiclass
                   vv
clus                M0 M1 MX
  8P GAIN MUTATED   46  3  1
  8P GAIN WILD-TYPE 86 15 10
D14V7, multiclass
                   vv
clus                 I II III IV
  8P GAIN MUTATED    9 14  13  6
  8P GAIN WILD-TYPE 16 29  35 23
D14V8, multiclass
D14V9, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED      3   47
  8P GAIN WILD-TYPE    2  109
     clus
vv    8P GAIN MUTATED 8P GAIN WILD-TYPE
  NO                3                 2
  YES              47               109

Clustering(15) Variable = 8q gain mutation analysis
D15V1, survival
                   sevent
clus2                0  1
  8Q GAIN MUTATED   39  8
  8Q GAIN WILD-TYPE 69  8
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               47                77 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
                8                 8 
$`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-4444 TCGA-CG-4455 TCGA-CG-4460 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 
       47.05        12.03        21.99        18.94         7.07        12.00 
TCGA-CG-5718 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 
        1.02        15.02        28.96        31.04        65.10         4.01 
TCGA-CG-5733 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6520 TCGA-D7-6524 TCGA-D7-6525 
       21.07         3.58         4.54         9.63         0.69         5.95 
TCGA-D7-6526 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6822 TCGA-EQ-5647 
        6.61         3.65         4.70         4.04         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-BR-7958 TCGA-BR-7959 TCGA-BR-8059 TCGA-BR-8060 
        0.95         0.69         0.16         1.08         0.82         1.32 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
        0.69         0.95         0.49         0.46         0.72         0.26 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
        0.43         0.26         1.18         1.55         1.48         0.76 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CG-4300 
        0.82         0.69         0.49         0.30         0.07        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4306 TCGA-CG-4437 TCGA-CG-4440 TCGA-CG-4449 
        3.02        27.02         1.02         8.05         4.01        19.07 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4474 TCGA-CG-4477 TCGA-CG-5716 TCGA-CG-5717 
        1.02         8.98         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-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-D7-6527 TCGA-D7-6528 TCGA-D7-6820 TCGA-EQ-8122 TCGA-F1-6874 
        6.90         4.14         1.68         2.93         7.79         2.01 
TCGA-FP-7916 TCGA-FP-7998 TCGA-HJ-7597 TCGA-IN-7806 TCGA-IP-7968 
        3.02         3.58        26.43         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 
             4.54              1.12 
[1] "0.1 - 72.2 (4.5)" "0.1 - 70.1 (1.1)"
       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-BR-7958        TCGA-BR-7959        TCGA-BR-8059        TCGA-BR-8060 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-BR-8077        TCGA-BR-8078        TCGA-BR-8080        TCGA-BR-8081 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-BR-8284        TCGA-BR-8285        TCGA-BR-8286        TCGA-BR-8289 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-BR-8291        TCGA-BR-8295        TCGA-BR-8296        TCGA-BR-8297 
"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 MUTATED" "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 WILD-TYPE"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" 
       TCGA-EQ-8122        TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875 
"8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
       TCGA-FP-7735        TCGA-FP-7829        TCGA-FP-7916        TCGA-FP-7998 
  "8Q GAIN MUTATED"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-HJ-7597        TCGA-IN-7806        TCGA-IN-7808        TCGA-IP-7968 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "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-BR-7958        TCGA-BR-7959        TCGA-BR-8059        TCGA-BR-8060 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-BR-8077        TCGA-BR-8078        TCGA-BR-8080        TCGA-BR-8081 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-BR-8284        TCGA-BR-8285        TCGA-BR-8286        TCGA-BR-8289 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-BR-8291        TCGA-BR-8295        TCGA-BR-8296        TCGA-BR-8297 
"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 MUTATED" "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 WILD-TYPE"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" 
       TCGA-EQ-8122        TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875 
"8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
       TCGA-FP-7735        TCGA-FP-7829        TCGA-FP-7916        TCGA-FP-7998 
  "8Q GAIN MUTATED"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-HJ-7597        TCGA-IN-7806        TCGA-IN-7808        TCGA-IP-7968 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "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-BR-7958        TCGA-BR-7959        TCGA-BR-8059        TCGA-BR-8060 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-BR-8077        TCGA-BR-8078        TCGA-BR-8080        TCGA-BR-8081 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-BR-8284        TCGA-BR-8285        TCGA-BR-8286        TCGA-BR-8289 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-BR-8291        TCGA-BR-8295        TCGA-BR-8296        TCGA-BR-8297 
"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 MUTATED" "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 WILD-TYPE"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" 
       TCGA-EQ-8122        TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875 
"8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
       TCGA-FP-7735        TCGA-FP-7829        TCGA-FP-7916        TCGA-FP-7998 
  "8Q GAIN MUTATED"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-HJ-7597        TCGA-IN-7806        TCGA-IN-7808        TCGA-IP-7968 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
[1] "hr=" "1.7"
D15V2, continuous
D15V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED     30   38
  8Q GAIN WILD-TYPE   35   58
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  FEMALE              30                35
  MALE                38                58
                   vv
clus                STOMACH ADENOCARCINOMA - DIFFUSE TYPE
  8Q GAIN MUTATED                                       5
  8Q GAIN WILD-TYPE                                    14
                   vv
clus                STOMACH ADENOCARCINOMA - NOT OTHERWISE SPECIFIED (NOS)
  8Q GAIN MUTATED                                                       34
  8Q GAIN WILD-TYPE                                                     45
                   vv
clus                STOMACH ADENOCARCINOMA - SIGNET RING TYPE
  8Q GAIN MUTATED                                           0
  8Q GAIN WILD-TYPE                                         1
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - MUCINOUS TYPE
  8Q GAIN MUTATED                                                   4
  8Q GAIN WILD-TYPE                                                 5
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - PAPILLARY TYPE
  8Q GAIN MUTATED                                                    1
  8Q GAIN WILD-TYPE                                                  2
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - TUBULAR TYPE
  8Q GAIN MUTATED                                                  6
  8Q GAIN WILD-TYPE                                                4
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - TYPE NOT OTHERWISE SPECIFIED (NOS)
  8Q GAIN MUTATED                                                                       16
  8Q GAIN WILD-TYPE                                                                     19
D15V4, multiclass
                   vv
clus                T1 T2 T3 T4
  8Q GAIN MUTATED    5 27 22  8
  8Q GAIN WILD-TYPE  1 26 37 25
D15V5, multiclass
                   vv
clus                N0 N1 N2 N3
  8Q GAIN MUTATED   24 19 12  5
  8Q GAIN WILD-TYPE 26 38 12 14
D15V6, multiclass
                   vv
clus                M0 M1 MX
  8Q GAIN MUTATED   60  4  4
  8Q GAIN WILD-TYPE 72 14  7
D15V7, multiclass
                   vv
clus                 I II III IV
  8Q GAIN MUTATED   14 18  17  9
  8Q GAIN WILD-TYPE 11 25  31 20
D15V8, multiclass
D15V9, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED      3   65
  8Q GAIN WILD-TYPE    2   91
     clus
vv    8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  NO                3                 2
  YES              65                91

Clustering(16) Variable = 9p gain mutation analysis
D16V1, survival
                   sevent
clus2                 0   1
  9P GAIN MUTATED     6   1
  9P GAIN WILD-TYPE 102  15
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
                7               117 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
                1                15 
$`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-BR-7958 TCGA-BR-7959 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 
        0.16         1.08         0.82         1.32         0.69         0.95 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
        0.49         0.46         0.72         0.26         0.43         0.26 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-CD-5798 TCGA-CD-5799 
        1.18         1.55         1.48         0.76         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-4437 TCGA-CG-4438 TCGA-CG-4440 
       27.02        15.95         1.02         8.05        54.05         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-D7-6815 TCGA-D7-6817 TCGA-D7-6820 TCGA-EQ-8122 TCGA-F1-6177 TCGA-F1-6874 
        3.65         4.70         2.93         7.79         6.54         2.01 
TCGA-F1-6875 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-HJ-7597 
       72.23         0.39         0.20         3.02         3.58        26.43 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IP-7968 
        6.87         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 
             1.68              1.48 
[1] "0.1 - 53.0 (1.7)" "0.1 - 72.2 (1.5)"
       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-BR-7958        TCGA-BR-7959        TCGA-BR-8059        TCGA-BR-8060 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-BR-8077        TCGA-BR-8078        TCGA-BR-8080        TCGA-BR-8081 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-BR-8284        TCGA-BR-8285        TCGA-BR-8286        TCGA-BR-8289 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-BR-8291        TCGA-BR-8295        TCGA-BR-8296        TCGA-BR-8297 
"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-EQ-8122        TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-FP-7735        TCGA-FP-7829        TCGA-FP-7916        TCGA-FP-7998 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-HJ-7597        TCGA-IN-7806        TCGA-IN-7808        TCGA-IP-7968 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "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-BR-7958        TCGA-BR-7959        TCGA-BR-8059        TCGA-BR-8060 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-BR-8077        TCGA-BR-8078        TCGA-BR-8080        TCGA-BR-8081 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-BR-8284        TCGA-BR-8285        TCGA-BR-8286        TCGA-BR-8289 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-BR-8291        TCGA-BR-8295        TCGA-BR-8296        TCGA-BR-8297 
"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-EQ-8122        TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-FP-7735        TCGA-FP-7829        TCGA-FP-7916        TCGA-FP-7998 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-HJ-7597        TCGA-IN-7806        TCGA-IN-7808        TCGA-IP-7968 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "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-BR-7958        TCGA-BR-7959        TCGA-BR-8059        TCGA-BR-8060 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-BR-8077        TCGA-BR-8078        TCGA-BR-8080        TCGA-BR-8081 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-BR-8284        TCGA-BR-8285        TCGA-BR-8286        TCGA-BR-8289 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-BR-8291        TCGA-BR-8295        TCGA-BR-8296        TCGA-BR-8297 
"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-EQ-8122        TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-FP-7735        TCGA-FP-7829        TCGA-FP-7916        TCGA-FP-7998 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-HJ-7597        TCGA-IN-7806        TCGA-IN-7808        TCGA-IP-7968 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
[1] "hr=" "1.2"
D16V2, continuous
D16V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED      6    5
  9P GAIN WILD-TYPE   59   91
        clus
vv       9P GAIN MUTATED 9P GAIN WILD-TYPE
  FEMALE               6                59
  MALE                 5                91
                   vv
clus                STOMACH ADENOCARCINOMA - DIFFUSE TYPE
  9P GAIN MUTATED                                       1
  9P GAIN WILD-TYPE                                    18
                   vv
clus                STOMACH ADENOCARCINOMA - NOT OTHERWISE SPECIFIED (NOS)
  9P GAIN MUTATED                                                        6
  9P GAIN WILD-TYPE                                                     73
                   vv
clus                STOMACH ADENOCARCINOMA - SIGNET RING TYPE
  9P GAIN MUTATED                                           0
  9P GAIN WILD-TYPE                                         1
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - MUCINOUS TYPE
  9P GAIN MUTATED                                                   0
  9P GAIN WILD-TYPE                                                 9
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - PAPILLARY TYPE
  9P GAIN MUTATED                                                    0
  9P GAIN WILD-TYPE                                                  3
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - TUBULAR TYPE
  9P GAIN MUTATED                                                  2
  9P GAIN WILD-TYPE                                                8
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - TYPE NOT OTHERWISE SPECIFIED (NOS)
  9P GAIN MUTATED                                                                        2
  9P GAIN WILD-TYPE                                                                     33
D16V4, multiclass
                   vv
clus                T1 T2 T3 T4
  9P GAIN MUTATED    2  5  2  1
  9P GAIN WILD-TYPE  4 48 57 32
D16V5, multiclass
                   vv
clus                N0 N1 N2 N3
  9P GAIN MUTATED    6  2  0  2
  9P GAIN WILD-TYPE 44 55 24 17
D16V6, multiclass
                   vv
clus                 M0  M1  MX
  9P GAIN MUTATED    10   1   0
  9P GAIN WILD-TYPE 122  17  11
D16V7, multiclass
                   vv
clus                 I II III IV
  9P GAIN MUTATED    5  2   0  2
  9P GAIN WILD-TYPE 20 41  48 27
D16V8, multiclass
D16V9, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED      1   10
  9P GAIN WILD-TYPE    4  146
     clus
vv    9P GAIN MUTATED 9P GAIN WILD-TYPE
  NO                1                 4
  YES              10               146

Clustering(17) Variable = 9q gain mutation analysis
D17V1, survival
                   sevent
clus2                 0   1
  9Q GAIN MUTATED     8   1
  9Q GAIN WILD-TYPE 100  15
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
                9               115 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
                1                15 
$`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-BR-7958 
        0.16         4.54         0.99         0.95         0.69         0.16 
TCGA-BR-7959 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
        1.08         0.82         1.32         0.69         0.95         0.49 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
        0.46         0.72         0.26         0.43         0.26         1.18 
TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
        1.55         1.48         0.76         0.82         0.69         0.36 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
        0.49         0.30         0.07        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
       15.95         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-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-D7-6820 TCGA-D7-6822 TCGA-EQ-8122 TCGA-F1-6177 TCGA-F1-6874 
        4.70         2.93         4.27         7.79         6.54         2.01 
TCGA-F1-6875 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-HJ-7597 TCGA-IN-7806 
       72.23         0.20         3.02         3.58        26.43         6.87 
TCGA-IP-7968 
        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              1.55 
[1] "0.1 - 53.0 (1.2)" "0.1 - 72.2 (1.6)"
       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-BR-7958        TCGA-BR-7959        TCGA-BR-8059        TCGA-BR-8060 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-BR-8077        TCGA-BR-8078        TCGA-BR-8080        TCGA-BR-8081 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-BR-8284        TCGA-BR-8285        TCGA-BR-8286        TCGA-BR-8289 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-BR-8291        TCGA-BR-8295        TCGA-BR-8296        TCGA-BR-8297 
"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-EQ-8122        TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-FP-7735        TCGA-FP-7829        TCGA-FP-7916        TCGA-FP-7998 
  "9Q GAIN MUTATED" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-HJ-7597        TCGA-IN-7806        TCGA-IN-7808        TCGA-IP-7968 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE"   "9Q GAIN MUTATED" "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-BR-7958        TCGA-BR-7959        TCGA-BR-8059        TCGA-BR-8060 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-BR-8077        TCGA-BR-8078        TCGA-BR-8080        TCGA-BR-8081 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-BR-8284        TCGA-BR-8285        TCGA-BR-8286        TCGA-BR-8289 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-BR-8291        TCGA-BR-8295        TCGA-BR-8296        TCGA-BR-8297 
"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-EQ-8122        TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-FP-7735        TCGA-FP-7829        TCGA-FP-7916        TCGA-FP-7998 
  "9Q GAIN MUTATED" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-HJ-7597        TCGA-IN-7806        TCGA-IN-7808        TCGA-IP-7968 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE"   "9Q GAIN MUTATED" "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-BR-7958        TCGA-BR-7959        TCGA-BR-8059        TCGA-BR-8060 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-BR-8077        TCGA-BR-8078        TCGA-BR-8080        TCGA-BR-8081 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-BR-8284        TCGA-BR-8285        TCGA-BR-8286        TCGA-BR-8289 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-BR-8291        TCGA-BR-8295        TCGA-BR-8296        TCGA-BR-8297 
"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-EQ-8122        TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-FP-7735        TCGA-FP-7829        TCGA-FP-7916        TCGA-FP-7998 
  "9Q GAIN MUTATED" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-HJ-7597        TCGA-IN-7806        TCGA-IN-7808        TCGA-IP-7968 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE"   "9Q GAIN MUTATED" "9Q GAIN WILD-TYPE" 
[1] "hr=" "1.2"
D17V2, continuous
D17V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED      7    8
  9Q GAIN WILD-TYPE   58   88
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  FEMALE               7                58
  MALE                 8                88
                   vv
clus                STOMACH ADENOCARCINOMA - DIFFUSE TYPE
  9Q GAIN MUTATED                                       2
  9Q GAIN WILD-TYPE                                    17
                   vv
clus                STOMACH ADENOCARCINOMA - NOT OTHERWISE SPECIFIED (NOS)
  9Q GAIN MUTATED                                                        9
  9Q GAIN WILD-TYPE                                                     70
                   vv
clus                STOMACH ADENOCARCINOMA - SIGNET RING TYPE
  9Q GAIN MUTATED                                           0
  9Q GAIN WILD-TYPE                                         1
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - MUCINOUS TYPE
  9Q GAIN MUTATED                                                   0
  9Q GAIN WILD-TYPE                                                 9
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - PAPILLARY TYPE
  9Q GAIN MUTATED                                                    0
  9Q GAIN WILD-TYPE                                                  3
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - TUBULAR TYPE
  9Q GAIN MUTATED                                                  1
  9Q GAIN WILD-TYPE                                                9
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - TYPE NOT OTHERWISE SPECIFIED (NOS)
  9Q GAIN MUTATED                                                                        3
  9Q GAIN WILD-TYPE                                                                     32
D17V4, multiclass
                   vv
clus                T1 T2 T3 T4
  9Q GAIN MUTATED    2  5  5  1
  9Q GAIN WILD-TYPE  4 48 54 32
D17V5, multiclass
                   vv
clus                N0 N1 N2 N3
  9Q GAIN MUTATED    7  4  0  3
  9Q GAIN WILD-TYPE 43 53 24 16
D17V6, multiclass
                   vv
clus                 M0  M1  MX
  9Q GAIN MUTATED    12   2   1
  9Q GAIN WILD-TYPE 120  16  10
D17V7, multiclass
                   vv
clus                 I II III IV
  9Q GAIN MUTATED    5  3   2  2
  9Q GAIN WILD-TYPE 20 40  46 27
D17V8, multiclass
D17V9, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED      1   14
  9Q GAIN WILD-TYPE    4  142
     clus
vv    9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  NO                1                 4
  YES              14               142

Clustering(18) Variable = 10p gain mutation analysis
D18V1, survival
                    sevent
clus2                 0  1
  10P GAIN MUTATED   15  4
  10P GAIN WILD-TYPE 93 12
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                19                105 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                 4                 12 
$`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 
TCGA-FP-7735 
        0.39 

$`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-BR-7958 TCGA-BR-7959 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
        0.69         0.16         1.08         0.82         1.32         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
        0.95         0.49         0.46         0.72         0.26         0.43 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-CD-5798 
        0.26         1.18         1.55         1.48         0.76         0.82 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5802 TCGA-CD-5803 TCGA-CG-4301 TCGA-CG-4304 
        0.69         0.36         0.30         0.07         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4441 
       15.95         1.02        52.96         8.05        54.05        14.01 
TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       29.98        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-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-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-D7-6519 TCGA-D7-6521 
        7.99         8.65         3.58         4.54        15.65         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-8122 
        3.65         4.70         4.04         2.93         4.27         7.79 
TCGA-F1-6177 TCGA-F1-6874 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-HJ-7597 
        6.54         2.01         0.20         3.02         3.58        26.43 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IP-7968 
        6.87         3.55         2.53 

  10P GAIN MUTATED 10P GAIN WILD-TYPE 
              0.39               0.07 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
             72.23              70.06 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
              4.01               1.48 
[1] "0.4 - 72.2 (4.0)" "0.1 - 70.1 (1.5)"
        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-BR-7958 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BR-7959         TCGA-BR-8059         TCGA-BR-8060 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BR-8077         TCGA-BR-8078         TCGA-BR-8080 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BR-8081         TCGA-BR-8284         TCGA-BR-8285 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BR-8286         TCGA-BR-8289         TCGA-BR-8291 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BR-8295         TCGA-BR-8296         TCGA-BR-8297 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-CD-5798         TCGA-CD-5799         TCGA-CD-5800 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-CD-5801         TCGA-CD-5802         TCGA-CD-5803 
  "10P GAIN MUTATED" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-CG-4300         TCGA-CG-4301         TCGA-CG-4304 
  "10P GAIN MUTATED" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-CG-4305         TCGA-CG-4306         TCGA-CG-4436 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-CG-4437         TCGA-CG-4438         TCGA-CG-4440 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE"   "10P GAIN MUTATED" 
        TCGA-CG-4441         TCGA-CG-4443         TCGA-CG-4444 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE"   "10P GAIN MUTATED" 
        TCGA-CG-4449         TCGA-CG-4455         TCGA-CG-4460 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE"   "10P GAIN MUTATED" 
        TCGA-CG-4462         TCGA-CG-4465         TCGA-CG-4466 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-CG-4469         TCGA-CG-4472         TCGA-CG-4474 
"10P GAIN WILD-TYPE"   "10P GAIN MUTATED" "10P GAIN WILD-TYPE" 
        TCGA-CG-4477         TCGA-CG-5716         TCGA-CG-5717 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-CG-5718         TCGA-CG-5719         TCGA-CG-5720 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-CG-5721         TCGA-CG-5722         TCGA-CG-5723 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-CG-5724         TCGA-CG-5725         TCGA-CG-5726 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-CG-5727         TCGA-CG-5728         TCGA-CG-5730 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE"   "10P GAIN MUTATED" 
        TCGA-CG-5732         TCGA-CG-5733         TCGA-CG-5734 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-D7-5577         TCGA-D7-5578         TCGA-D7-5579 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-D7-6518         TCGA-D7-6519         TCGA-D7-6520 
  "10P GAIN MUTATED" "10P GAIN WILD-TYPE"   "10P GAIN MUTATED" 
        TCGA-D7-6521         TCGA-D7-6522         TCGA-D7-6524 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-D7-6525         TCGA-D7-6526         TCGA-D7-6527 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-D7-6528         TCGA-D7-6815         TCGA-D7-6817 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-D7-6818         TCGA-D7-6820         TCGA-D7-6822 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-EQ-5647         TCGA-EQ-8122         TCGA-F1-6177 
  "10P GAIN MUTATED" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-F1-6874         TCGA-F1-6875         TCGA-FP-7735 
"10P GAIN WILD-TYPE"   "10P GAIN MUTATED"   "10P GAIN MUTATED" 
        TCGA-FP-7829         TCGA-FP-7916         TCGA-FP-7998 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-HJ-7597         TCGA-IN-7806         TCGA-IN-7808 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-IP-7968 
"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-BR-7958 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BR-7959         TCGA-BR-8059         TCGA-BR-8060 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BR-8077         TCGA-BR-8078         TCGA-BR-8080 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BR-8081         TCGA-BR-8284         TCGA-BR-8285 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BR-8286         TCGA-BR-8289         TCGA-BR-8291 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BR-8295         TCGA-BR-8296         TCGA-BR-8297 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-CD-5798         TCGA-CD-5799         TCGA-CD-5800 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-CD-5801         TCGA-CD-5802         TCGA-CD-5803 
  "10P GAIN MUTATED" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-CG-4300         TCGA-CG-4301         TCGA-CG-4304 
  "10P GAIN MUTATED" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-CG-4305         TCGA-CG-4306         TCGA-CG-4436 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-CG-4437         TCGA-CG-4438         TCGA-CG-4440 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE"   "10P GAIN MUTATED" 
        TCGA-CG-4441         TCGA-CG-4443         TCGA-CG-4444 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE"   "10P GAIN MUTATED" 
        TCGA-CG-4449         TCGA-CG-4455         TCGA-CG-4460 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE"   "10P GAIN MUTATED" 
        TCGA-CG-4462         TCGA-CG-4465         TCGA-CG-4466 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-CG-4469         TCGA-CG-4472         TCGA-CG-4474 
"10P GAIN WILD-TYPE"   "10P GAIN MUTATED" "10P GAIN WILD-TYPE" 
        TCGA-CG-4477         TCGA-CG-5716         TCGA-CG-5717 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-CG-5718         TCGA-CG-5719         TCGA-CG-5720 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-CG-5721         TCGA-CG-5722         TCGA-CG-5723 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-CG-5724         TCGA-CG-5725         TCGA-CG-5726 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-CG-5727         TCGA-CG-5728         TCGA-CG-5730 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE"   "10P GAIN MUTATED" 
        TCGA-CG-5732         TCGA-CG-5733         TCGA-CG-5734 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-D7-5577         TCGA-D7-5578         TCGA-D7-5579 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-D7-6518         TCGA-D7-6519         TCGA-D7-6520 
  "10P GAIN MUTATED" "10P GAIN WILD-TYPE"   "10P GAIN MUTATED" 
        TCGA-D7-6521         TCGA-D7-6522         TCGA-D7-6524 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-D7-6525         TCGA-D7-6526         TCGA-D7-6527 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-D7-6528         TCGA-D7-6815         TCGA-D7-6817 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-D7-6818         TCGA-D7-6820         TCGA-D7-6822 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-EQ-5647         TCGA-EQ-8122         TCGA-F1-6177 
  "10P GAIN MUTATED" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-F1-6874         TCGA-F1-6875         TCGA-FP-7735 
"10P GAIN WILD-TYPE"   "10P GAIN MUTATED"   "10P GAIN MUTATED" 
        TCGA-FP-7829         TCGA-FP-7916         TCGA-FP-7998 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-HJ-7597         TCGA-IN-7806         TCGA-IN-7808 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-IP-7968 
"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-BR-7958 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BR-7959         TCGA-BR-8059         TCGA-BR-8060 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BR-8077         TCGA-BR-8078         TCGA-BR-8080 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BR-8081         TCGA-BR-8284         TCGA-BR-8285 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BR-8286         TCGA-BR-8289         TCGA-BR-8291 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BR-8295         TCGA-BR-8296         TCGA-BR-8297 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-CD-5798         TCGA-CD-5799         TCGA-CD-5800 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-CD-5801         TCGA-CD-5802         TCGA-CD-5803 
  "10P GAIN MUTATED" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-CG-4300         TCGA-CG-4301         TCGA-CG-4304 
  "10P GAIN MUTATED" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-CG-4305         TCGA-CG-4306         TCGA-CG-4436 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-CG-4437         TCGA-CG-4438         TCGA-CG-4440 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE"   "10P GAIN MUTATED" 
        TCGA-CG-4441         TCGA-CG-4443         TCGA-CG-4444 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE"   "10P GAIN MUTATED" 
        TCGA-CG-4449         TCGA-CG-4455         TCGA-CG-4460 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE"   "10P GAIN MUTATED" 
        TCGA-CG-4462         TCGA-CG-4465         TCGA-CG-4466 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-CG-4469         TCGA-CG-4472         TCGA-CG-4474 
"10P GAIN WILD-TYPE"   "10P GAIN MUTATED" "10P GAIN WILD-TYPE" 
        TCGA-CG-4477         TCGA-CG-5716         TCGA-CG-5717 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-CG-5718         TCGA-CG-5719         TCGA-CG-5720 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-CG-5721         TCGA-CG-5722         TCGA-CG-5723 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-CG-5724         TCGA-CG-5725         TCGA-CG-5726 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-CG-5727         TCGA-CG-5728         TCGA-CG-5730 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE"   "10P GAIN MUTATED" 
        TCGA-CG-5732         TCGA-CG-5733         TCGA-CG-5734 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-D7-5577         TCGA-D7-5578         TCGA-D7-5579 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-D7-6518         TCGA-D7-6519         TCGA-D7-6520 
  "10P GAIN MUTATED" "10P GAIN WILD-TYPE"   "10P GAIN MUTATED" 
        TCGA-D7-6521         TCGA-D7-6522         TCGA-D7-6524 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-D7-6525         TCGA-D7-6526         TCGA-D7-6527 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-D7-6528         TCGA-D7-6815         TCGA-D7-6817 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-D7-6818         TCGA-D7-6820         TCGA-D7-6822 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-EQ-5647         TCGA-EQ-8122         TCGA-F1-6177 
  "10P GAIN MUTATED" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-F1-6874         TCGA-F1-6875         TCGA-FP-7735 
"10P GAIN WILD-TYPE"   "10P GAIN MUTATED"   "10P GAIN MUTATED" 
        TCGA-FP-7829         TCGA-FP-7916         TCGA-FP-7998 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-HJ-7597         TCGA-IN-7806         TCGA-IN-7808 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-IP-7968 
"10P GAIN WILD-TYPE" 
[1] "hr=" "1"  
D18V2, continuous
D18V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED      7   16
  10P GAIN WILD-TYPE   58   80
        clus
vv       10P GAIN MUTATED 10P GAIN WILD-TYPE
  FEMALE                7                 58
  MALE                 16                 80
                    vv
clus                 STOMACH ADENOCARCINOMA - DIFFUSE TYPE
  10P GAIN MUTATED                                       1
  10P GAIN WILD-TYPE                                    18
                    vv
clus                 STOMACH ADENOCARCINOMA - NOT OTHERWISE SPECIFIED (NOS)
  10P GAIN MUTATED                                                       16
  10P GAIN WILD-TYPE                                                     63
                    vv
clus                 STOMACH ADENOCARCINOMA - SIGNET RING TYPE
  10P GAIN MUTATED                                           0
  10P GAIN WILD-TYPE                                         1
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - MUCINOUS TYPE
  10P GAIN MUTATED                                                   0
  10P GAIN WILD-TYPE                                                 9
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - PAPILLARY TYPE
  10P GAIN MUTATED                                                    0
  10P GAIN WILD-TYPE                                                  3
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - TUBULAR TYPE
  10P GAIN MUTATED                                                  1
  10P GAIN WILD-TYPE                                                9
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - TYPE NOT OTHERWISE SPECIFIED (NOS)
  10P GAIN MUTATED                                                                        3
  10P GAIN WILD-TYPE                                                                     32
D18V4, multiclass
                    vv
clus                 T1 T2 T3 T4
  10P GAIN MUTATED    0  6  9  7
  10P GAIN WILD-TYPE  6 47 50 26
D18V5, multiclass
                    vv
clus                 N0 N1 N2 N3
  10P GAIN MUTATED    6  8  5  3
  10P GAIN WILD-TYPE 44 49 19 16
D18V6, multiclass
                    vv
clus                  M0  M1  MX
  10P GAIN MUTATED    17   4   2
  10P GAIN WILD-TYPE 115  14   9
D18V7, multiclass
                    vv
clus                  I II III IV
  10P GAIN MUTATED    2  5   5  9
  10P GAIN WILD-TYPE 23 38  43 20
D18V8, multiclass
D18V9, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED      0   23
  10P GAIN WILD-TYPE    5  133
     clus
vv    10P GAIN MUTATED 10P GAIN WILD-TYPE
  NO                 0                  5
  YES               23                133

Clustering(19) Variable = 10q gain mutation analysis
D19V1, survival
                    sevent
clus2                  0   1
  10Q GAIN MUTATED     6   2
  10Q GAIN WILD-TYPE 102  14
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                 8                116 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                 2                 14 
$`10Q GAIN MUTATED`
TCGA-BR-7197 TCGA-BR-7715 TCGA-CD-5801 TCGA-CG-4460 TCGA-CG-4472 TCGA-D7-6520 
        1.48         1.05         0.49        21.99        12.00         9.63 
TCGA-F1-6875 TCGA-FP-7735 
       72.23         0.39 

$`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-BR-7958 TCGA-BR-7959 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 
        0.16         1.08         0.82         1.32         0.69         0.95 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
        0.49         0.46         0.72         0.26         0.43         0.26 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-CD-5798 TCGA-CD-5799 
        1.18         1.55         1.48         0.76         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-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-D7-6521 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-D7-6527 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-EQ-8122 TCGA-F1-6177 
        4.04         2.93         4.27         0.62         7.79         6.54 
TCGA-F1-6874 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-HJ-7597 TCGA-IN-7806 
        2.01         0.20         3.02         3.58        26.43         6.87 
TCGA-IN-7808 TCGA-IP-7968 
        3.55         2.53 

  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
              0.39               0.07 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
             72.23              70.06 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
             5.555              1.515 
[1] "0.4 - 72.2 (5.6)" "0.1 - 70.1 (1.5)"
        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-BR-7958 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BR-7959         TCGA-BR-8059         TCGA-BR-8060 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BR-8077         TCGA-BR-8078         TCGA-BR-8080 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BR-8081         TCGA-BR-8284         TCGA-BR-8285 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BR-8286         TCGA-BR-8289         TCGA-BR-8291 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BR-8295         TCGA-BR-8296         TCGA-BR-8297 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CD-5798         TCGA-CD-5799         TCGA-CD-5800 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CD-5801         TCGA-CD-5802         TCGA-CD-5803 
  "10Q GAIN MUTATED" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CG-4300         TCGA-CG-4301         TCGA-CG-4304 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CG-4305         TCGA-CG-4306         TCGA-CG-4436 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CG-4437         TCGA-CG-4438         TCGA-CG-4440 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CG-4441         TCGA-CG-4443         TCGA-CG-4444 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CG-4449         TCGA-CG-4455         TCGA-CG-4460 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE"   "10Q GAIN MUTATED" 
        TCGA-CG-4462         TCGA-CG-4465         TCGA-CG-4466 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CG-4469         TCGA-CG-4472         TCGA-CG-4474 
"10Q GAIN WILD-TYPE"   "10Q GAIN MUTATED" "10Q GAIN WILD-TYPE" 
        TCGA-CG-4477         TCGA-CG-5716         TCGA-CG-5717 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CG-5718         TCGA-CG-5719         TCGA-CG-5720 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CG-5721         TCGA-CG-5722         TCGA-CG-5723 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CG-5724         TCGA-CG-5725         TCGA-CG-5726 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CG-5727         TCGA-CG-5728         TCGA-CG-5730 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CG-5732         TCGA-CG-5733         TCGA-CG-5734 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-D7-5577         TCGA-D7-5578         TCGA-D7-5579 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-D7-6518         TCGA-D7-6519         TCGA-D7-6520 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE"   "10Q GAIN MUTATED" 
        TCGA-D7-6521         TCGA-D7-6522         TCGA-D7-6524 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-D7-6525         TCGA-D7-6526         TCGA-D7-6527 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-D7-6528         TCGA-D7-6815         TCGA-D7-6817 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-D7-6818         TCGA-D7-6820         TCGA-D7-6822 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-EQ-5647         TCGA-EQ-8122         TCGA-F1-6177 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-F1-6874         TCGA-F1-6875         TCGA-FP-7735 
"10Q GAIN WILD-TYPE"   "10Q GAIN MUTATED"   "10Q GAIN MUTATED" 
        TCGA-FP-7829         TCGA-FP-7916         TCGA-FP-7998 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-HJ-7597         TCGA-IN-7806         TCGA-IN-7808 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-IP-7968 
"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-BR-7958 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BR-7959         TCGA-BR-8059         TCGA-BR-8060 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BR-8077         TCGA-BR-8078         TCGA-BR-8080 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BR-8081         TCGA-BR-8284         TCGA-BR-8285 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BR-8286         TCGA-BR-8289         TCGA-BR-8291 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BR-8295         TCGA-BR-8296         TCGA-BR-8297 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CD-5798         TCGA-CD-5799         TCGA-CD-5800 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CD-5801         TCGA-CD-5802         TCGA-CD-5803 
  "10Q GAIN MUTATED" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CG-4300         TCGA-CG-4301         TCGA-CG-4304 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CG-4305         TCGA-CG-4306         TCGA-CG-4436 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CG-4437         TCGA-CG-4438         TCGA-CG-4440 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CG-4441         TCGA-CG-4443         TCGA-CG-4444 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CG-4449         TCGA-CG-4455         TCGA-CG-4460 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE"   "10Q GAIN MUTATED" 
        TCGA-CG-4462         TCGA-CG-4465         TCGA-CG-4466 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CG-4469         TCGA-CG-4472         TCGA-CG-4474 
"10Q GAIN WILD-TYPE"   "10Q GAIN MUTATED" "10Q GAIN WILD-TYPE" 
        TCGA-CG-4477         TCGA-CG-5716         TCGA-CG-5717 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CG-5718         TCGA-CG-5719         TCGA-CG-5720 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CG-5721         TCGA-CG-5722         TCGA-CG-5723 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CG-5724         TCGA-CG-5725         TCGA-CG-5726 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CG-5727         TCGA-CG-5728         TCGA-CG-5730 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CG-5732         TCGA-CG-5733         TCGA-CG-5734 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-D7-5577         TCGA-D7-5578         TCGA-D7-5579 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-D7-6518         TCGA-D7-6519         TCGA-D7-6520 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE"   "10Q GAIN MUTATED" 
        TCGA-D7-6521         TCGA-D7-6522         TCGA-D7-6524 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-D7-6525         TCGA-D7-6526         TCGA-D7-6527 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-D7-6528         TCGA-D7-6815         TCGA-D7-6817 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-D7-6818         TCGA-D7-6820         TCGA-D7-6822 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-EQ-5647         TCGA-EQ-8122         TCGA-F1-6177 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-F1-6874         TCGA-F1-6875         TCGA-FP-7735 
"10Q GAIN WILD-TYPE"   "10Q GAIN MUTATED"   "10Q GAIN MUTATED" 
        TCGA-FP-7829         TCGA-FP-7916         TCGA-FP-7998 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-HJ-7597         TCGA-IN-7806         TCGA-IN-7808 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-IP-7968 
"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-BR-7958 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BR-7959         TCGA-BR-8059         TCGA-BR-8060 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BR-8077         TCGA-BR-8078         TCGA-BR-8080 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BR-8081         TCGA-BR-8284         TCGA-BR-8285 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BR-8286         TCGA-BR-8289         TCGA-BR-8291 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BR-8295         TCGA-BR-8296         TCGA-BR-8297 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CD-5798         TCGA-CD-5799         TCGA-CD-5800 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CD-5801         TCGA-CD-5802         TCGA-CD-5803 
  "10Q GAIN MUTATED" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CG-4300         TCGA-CG-4301         TCGA-CG-4304 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CG-4305         TCGA-CG-4306         TCGA-CG-4436 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CG-4437         TCGA-CG-4438         TCGA-CG-4440 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CG-4441         TCGA-CG-4443         TCGA-CG-4444 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CG-4449         TCGA-CG-4455         TCGA-CG-4460 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE"   "10Q GAIN MUTATED" 
        TCGA-CG-4462         TCGA-CG-4465         TCGA-CG-4466 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CG-4469         TCGA-CG-4472         TCGA-CG-4474 
"10Q GAIN WILD-TYPE"   "10Q GAIN MUTATED" "10Q GAIN WILD-TYPE" 
        TCGA-CG-4477         TCGA-CG-5716         TCGA-CG-5717 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CG-5718         TCGA-CG-5719         TCGA-CG-5720 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CG-5721         TCGA-CG-5722         TCGA-CG-5723 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CG-5724         TCGA-CG-5725         TCGA-CG-5726 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CG-5727         TCGA-CG-5728         TCGA-CG-5730 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CG-5732         TCGA-CG-5733         TCGA-CG-5734 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-D7-5577         TCGA-D7-5578         TCGA-D7-5579 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-D7-6518         TCGA-D7-6519         TCGA-D7-6520 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE"   "10Q GAIN MUTATED" 
        TCGA-D7-6521         TCGA-D7-6522         TCGA-D7-6524 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-D7-6525         TCGA-D7-6526         TCGA-D7-6527 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-D7-6528         TCGA-D7-6815         TCGA-D7-6817 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-D7-6818         TCGA-D7-6820         TCGA-D7-6822 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-EQ-5647         TCGA-EQ-8122         TCGA-F1-6177 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-F1-6874         TCGA-F1-6875         TCGA-FP-7735 
"10Q GAIN WILD-TYPE"   "10Q GAIN MUTATED"   "10Q GAIN MUTATED" 
        TCGA-FP-7829         TCGA-FP-7916         TCGA-FP-7998 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-HJ-7597         TCGA-IN-7806         TCGA-IN-7808 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-IP-7968 
"10Q GAIN WILD-TYPE" 
[1] "hr=" "1.6"
D19V2, continuous
D19V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED      3    7
  10Q GAIN WILD-TYPE   62   89
        clus
vv       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  FEMALE                3                 62
  MALE                  7                 89
                    vv
clus                 STOMACH ADENOCARCINOMA - DIFFUSE TYPE
  10Q GAIN MUTATED                                       0
  10Q GAIN WILD-TYPE                                    19
                    vv
clus                 STOMACH ADENOCARCINOMA - NOT OTHERWISE SPECIFIED (NOS)
  10Q GAIN MUTATED                                                        7
  10Q GAIN WILD-TYPE                                                     72
                    vv
clus                 STOMACH ADENOCARCINOMA - SIGNET RING TYPE
  10Q GAIN MUTATED                                           0
  10Q GAIN WILD-TYPE                                         1
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - MUCINOUS TYPE
  10Q GAIN MUTATED                                                   0
  10Q GAIN WILD-TYPE                                                 9
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - PAPILLARY TYPE
  10Q GAIN MUTATED                                                    0
  10Q GAIN WILD-TYPE                                                  3
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - TUBULAR TYPE
  10Q GAIN MUTATED                                                  1
  10Q GAIN WILD-TYPE                                                9
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - TYPE NOT OTHERWISE SPECIFIED (NOS)
  10Q GAIN MUTATED                                                                        1
  10Q GAIN WILD-TYPE                                                                     34
D19V4, multiclass
                    vv
clus                 T1 T2 T3 T4
  10Q GAIN MUTATED    0  3  4  3
  10Q GAIN WILD-TYPE  6 50 55 30
D19V5, multiclass
                    vv
clus                 N0 N1 N2 N3
  10Q GAIN MUTATED    4  4  2  0
  10Q GAIN WILD-TYPE 46 53 22 19
D19V6, multiclass
                    vv
clus                  M0  M1  MX
  10Q GAIN MUTATED     8   1   1
  10Q GAIN WILD-TYPE 124  17  10
D19V7, multiclass
                    vv
clus                  I II III IV
  10Q GAIN MUTATED    2  3   2  3
  10Q GAIN WILD-TYPE 23 40  46 26
D19V8, multiclass
D19V9, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED      0   10
  10Q GAIN WILD-TYPE    5  146
     clus
vv    10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  NO                 0                  5
  YES               10                146

Clustering(20) Variable = 11p gain mutation analysis
D20V1, survival
                    sevent
clus2                  0   1
  11P GAIN MUTATED     2   0
  11P GAIN WILD-TYPE 106  16
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 2                122 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 0                 16 
$`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-BR-7958 TCGA-BR-7959 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
        0.69         0.16         1.08         0.82         1.32         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
        0.95         0.49         0.46         0.72         0.26         0.43 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-CD-5798 
        0.26         1.18         1.55         1.48         0.76         0.82 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CG-4301 
        0.69         0.36         0.49         0.30         0.07         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-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-D7-6528 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-EQ-8122 TCGA-F1-6177 TCGA-F1-6874 TCGA-F1-6875 
        4.27         0.62         7.79         6.54         2.01        72.23 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-HJ-7597 TCGA-IN-7806 
        0.39         0.20         3.02         3.58        26.43         6.87 
TCGA-IN-7808 TCGA-IP-7968 
        3.55         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              1.515 
[1] "1.4 - 20.0 (10.7)" "0.1 - 72.2 (1.5)" 
        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-BR-7958 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-BR-7959         TCGA-BR-8059         TCGA-BR-8060 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-BR-8077         TCGA-BR-8078         TCGA-BR-8080 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-BR-8081         TCGA-BR-8284         TCGA-BR-8285 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-BR-8286         TCGA-BR-8289         TCGA-BR-8291 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-BR-8295         TCGA-BR-8296         TCGA-BR-8297 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-CD-5798         TCGA-CD-5799         TCGA-CD-5800 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-CD-5801         TCGA-CD-5802         TCGA-CD-5803 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-CG-4300         TCGA-CG-4301         TCGA-CG-4304 
  "11P GAIN MUTATED" "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-EQ-8122         TCGA-F1-6177 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-F1-6874         TCGA-F1-6875         TCGA-FP-7735 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-FP-7829         TCGA-FP-7916         TCGA-FP-7998 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-HJ-7597         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" 
        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-BR-7958 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-BR-7959         TCGA-BR-8059         TCGA-BR-8060 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-BR-8077         TCGA-BR-8078         TCGA-BR-8080 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-BR-8081         TCGA-BR-8284         TCGA-BR-8285 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-BR-8286         TCGA-BR-8289         TCGA-BR-8291 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-BR-8295         TCGA-BR-8296         TCGA-BR-8297 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-CD-5798         TCGA-CD-5799         TCGA-CD-5800 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-CD-5801         TCGA-CD-5802         TCGA-CD-5803 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-CG-4300         TCGA-CG-4301         TCGA-CG-4304 
  "11P GAIN MUTATED" "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-EQ-8122         TCGA-F1-6177 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-F1-6874         TCGA-F1-6875         TCGA-FP-7735 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-FP-7829         TCGA-FP-7916         TCGA-FP-7998 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-HJ-7597         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" 
        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-BR-7958 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-BR-7959         TCGA-BR-8059         TCGA-BR-8060 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-BR-8077         TCGA-BR-8078         TCGA-BR-8080 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-BR-8081         TCGA-BR-8284         TCGA-BR-8285 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-BR-8286         TCGA-BR-8289         TCGA-BR-8291 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-BR-8295         TCGA-BR-8296         TCGA-BR-8297 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-CD-5798         TCGA-CD-5799         TCGA-CD-5800 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-CD-5801         TCGA-CD-5802         TCGA-CD-5803 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-CG-4300         TCGA-CG-4301         TCGA-CG-4304 
  "11P GAIN MUTATED" "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-EQ-8122         TCGA-F1-6177 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-F1-6874         TCGA-F1-6875         TCGA-FP-7735 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-FP-7829         TCGA-FP-7916         TCGA-FP-7998 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-HJ-7597         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" 
[1] "Remove cluster labels:" "11P GAIN MUTATED"      
clus
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 2                122 
        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-BR-7958         TCGA-BR-7959 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-BR-8059         TCGA-BR-8060         TCGA-BR-8077 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-BR-8078         TCGA-BR-8080         TCGA-BR-8081 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-BR-8284         TCGA-BR-8285         TCGA-BR-8286 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-BR-8289         TCGA-BR-8291         TCGA-BR-8295 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-BR-8296         TCGA-BR-8297         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-4301 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-CG-4304         TCGA-CG-4305         TCGA-CG-4306 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-CG-4436         TCGA-CG-4437         TCGA-CG-4438 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-CG-4440         TCGA-CG-4441         TCGA-CG-4443 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-CG-4444         TCGA-CG-4449         TCGA-CG-4455 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-CG-4460         TCGA-CG-4462         TCGA-CG-4465 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-CG-4466         TCGA-CG-4469         TCGA-CG-4472 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-CG-4474         TCGA-CG-4477         TCGA-CG-5716 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-CG-5717         TCGA-CG-5718         TCGA-CG-5719 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-CG-5720         TCGA-CG-5721         TCGA-CG-5722 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-CG-5723         TCGA-CG-5724         TCGA-CG-5725 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-CG-5726         TCGA-CG-5727         TCGA-CG-5728 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-CG-5730         TCGA-CG-5732         TCGA-CG-5733 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-CG-5734         TCGA-D7-5577         TCGA-D7-5578 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-D7-5579         TCGA-D7-6518         TCGA-D7-6519 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-D7-6520         TCGA-D7-6521         TCGA-D7-6522 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-D7-6524         TCGA-D7-6525         TCGA-D7-6526 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-D7-6527         TCGA-D7-6528         TCGA-D7-6815 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-D7-6817         TCGA-D7-6818         TCGA-D7-6820 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-D7-6822         TCGA-EQ-5647         TCGA-EQ-8122 
"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-7916 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-FP-7998         TCGA-HJ-7597         TCGA-IN-7806 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-IN-7808         TCGA-IP-7968 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
D20V2, continuous
D20V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED      1    3
  11P GAIN WILD-TYPE   64   93
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  FEMALE                1                 64
  MALE                  3                 93
                    vv
clus                 STOMACH ADENOCARCINOMA - DIFFUSE TYPE
  11P GAIN MUTATED                                       0
  11P GAIN WILD-TYPE                                    19
                    vv
clus                 STOMACH ADENOCARCINOMA - NOT OTHERWISE SPECIFIED (NOS)
  11P GAIN MUTATED                                                        4
  11P GAIN WILD-TYPE                                                     75
                    vv
clus                 STOMACH ADENOCARCINOMA - SIGNET RING TYPE
  11P GAIN MUTATED                                           0
  11P GAIN WILD-TYPE                                         1
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - MUCINOUS TYPE
  11P GAIN MUTATED                                                   0
  11P GAIN WILD-TYPE                                                 9
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - PAPILLARY TYPE
  11P GAIN MUTATED                                                    0
  11P GAIN WILD-TYPE                                                  3
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - TUBULAR TYPE
  11P GAIN MUTATED                                                  0
  11P GAIN WILD-TYPE                                               10
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - TYPE NOT OTHERWISE SPECIFIED (NOS)
  11P GAIN MUTATED                                                                        0
  11P GAIN WILD-TYPE                                                                     35
D20V4, multiclass
                    vv
clus                 T1 T2 T3 T4
  11P GAIN MUTATED    0  0  3  1
  11P GAIN WILD-TYPE  6 53 56 32
D20V5, multiclass
                    vv
clus                 N0 N1 N2 N3
  11P GAIN MUTATED    0  2  2  0
  11P GAIN WILD-TYPE 50 55 22 19
D20V6, multiclass
                    vv
clus                  M0  M1  MX
  11P GAIN MUTATED     4   0   0
  11P GAIN WILD-TYPE 128  18  11
D20V7, multiclass
                    vv
clus                  I II III IV
  11P GAIN MUTATED    0  0   3  1
  11P GAIN WILD-TYPE 25 43  45 28
D20V8, multiclass
D20V9, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED      0    4
  11P GAIN WILD-TYPE    5  152
     clus
vv    11P GAIN MUTATED 11P GAIN WILD-TYPE
  NO                 0                  5
  YES                4                152

Clustering(21) Variable = 11q gain mutation analysis
D21V1, survival
                    sevent
clus2                  0   1
  11Q GAIN MUTATED     5   1
  11Q GAIN WILD-TYPE 103  15
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 6                118 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 1                 15 
$`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-BR-7958 TCGA-BR-7959 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 
        0.16         1.08         0.82         1.32         0.69         0.95 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
        0.49         0.46         0.72         0.26         0.43         0.26 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-CD-5798 TCGA-CD-5799 
        1.18         1.55         1.48         0.76         0.82         0.69 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CG-4301 TCGA-CG-4304 
        0.36         0.49         0.30         0.07         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-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-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-D7-6520 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-EQ-8122 
        4.70         4.04         2.93         4.27         0.62         7.79 
TCGA-F1-6177 TCGA-F1-6874 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
        6.54         2.01         0.39         0.20         3.02         3.58 
TCGA-HJ-7597 TCGA-IN-7806 TCGA-IN-7808 TCGA-IP-7968 
       26.43         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               1.48 
[1] "1.2 - 72.2 (6.8)" "0.1 - 70.1 (1.5)"
        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-BR-7958 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-BR-7959         TCGA-BR-8059         TCGA-BR-8060 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-BR-8077         TCGA-BR-8078         TCGA-BR-8080 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-BR-8081         TCGA-BR-8284         TCGA-BR-8285 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-BR-8286         TCGA-BR-8289         TCGA-BR-8291 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-BR-8295         TCGA-BR-8296         TCGA-BR-8297 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-CD-5798         TCGA-CD-5799         TCGA-CD-5800 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-CD-5801         TCGA-CD-5802         TCGA-CD-5803 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-CG-4300         TCGA-CG-4301         TCGA-CG-4304 
  "11Q GAIN MUTATED" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-CG-4305         TCGA-CG-4306         TCGA-CG-4436 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-CG-4437         TCGA-CG-4438         TCGA-CG-4440 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-CG-4441         TCGA-CG-4443         TCGA-CG-4444 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-CG-4449         TCGA-CG-4455         TCGA-CG-4460 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-CG-4462         TCGA-CG-4465         TCGA-CG-4466 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-CG-4469         TCGA-CG-4472         TCGA-CG-4474 
"11Q GAIN WILD-TYPE"   "11Q GAIN MUTATED" "11Q GAIN WILD-TYPE" 
        TCGA-CG-4477         TCGA-CG-5716         TCGA-CG-5717 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-CG-5718         TCGA-CG-5719         TCGA-CG-5720 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-CG-5721         TCGA-CG-5722         TCGA-CG-5723 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-CG-5724         TCGA-CG-5725         TCGA-CG-5726 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-CG-5727         TCGA-CG-5728         TCGA-CG-5730 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-CG-5732         TCGA-CG-5733         TCGA-CG-5734 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-D7-5577         TCGA-D7-5578         TCGA-D7-5579 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-D7-6518         TCGA-D7-6519         TCGA-D7-6520 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-D7-6521         TCGA-D7-6522         TCGA-D7-6524 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-D7-6525         TCGA-D7-6526         TCGA-D7-6527 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-D7-6528         TCGA-D7-6815         TCGA-D7-6817 
  "11Q GAIN MUTATED" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-D7-6818         TCGA-D7-6820         TCGA-D7-6822 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EQ-5647         TCGA-EQ-8122         TCGA-F1-6177 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-F1-6874         TCGA-F1-6875         TCGA-FP-7735 
"11Q GAIN WILD-TYPE"   "11Q GAIN MUTATED" "11Q GAIN WILD-TYPE" 
        TCGA-FP-7829         TCGA-FP-7916         TCGA-FP-7998 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-HJ-7597         TCGA-IN-7806         TCGA-IN-7808 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-IP-7968 
"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-BR-7958 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-BR-7959         TCGA-BR-8059         TCGA-BR-8060 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-BR-8077         TCGA-BR-8078         TCGA-BR-8080 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-BR-8081         TCGA-BR-8284         TCGA-BR-8285 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-BR-8286         TCGA-BR-8289         TCGA-BR-8291 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-BR-8295         TCGA-BR-8296         TCGA-BR-8297 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-CD-5798         TCGA-CD-5799         TCGA-CD-5800 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-CD-5801         TCGA-CD-5802         TCGA-CD-5803 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-CG-4300         TCGA-CG-4301         TCGA-CG-4304 
  "11Q GAIN MUTATED" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-CG-4305         TCGA-CG-4306         TCGA-CG-4436 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-CG-4437         TCGA-CG-4438         TCGA-CG-4440 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-CG-4441         TCGA-CG-4443         TCGA-CG-4444 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-CG-4449         TCGA-CG-4455         TCGA-CG-4460 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-CG-4462         TCGA-CG-4465         TCGA-CG-4466 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-CG-4469         TCGA-CG-4472         TCGA-CG-4474 
"11Q GAIN WILD-TYPE"   "11Q GAIN MUTATED" "11Q GAIN WILD-TYPE" 
        TCGA-CG-4477         TCGA-CG-5716         TCGA-CG-5717 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-CG-5718         TCGA-CG-5719         TCGA-CG-5720 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-CG-5721         TCGA-CG-5722         TCGA-CG-5723 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-CG-5724         TCGA-CG-5725         TCGA-CG-5726 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-CG-5727         TCGA-CG-5728         TCGA-CG-5730 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-CG-5732         TCGA-CG-5733         TCGA-CG-5734 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-D7-5577         TCGA-D7-5578         TCGA-D7-5579 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-D7-6518         TCGA-D7-6519         TCGA-D7-6520 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-D7-6521         TCGA-D7-6522         TCGA-D7-6524 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-D7-6525         TCGA-D7-6526         TCGA-D7-6527 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-D7-6528         TCGA-D7-6815         TCGA-D7-6817 
  "11Q GAIN MUTATED" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-D7-6818         TCGA-D7-6820         TCGA-D7-6822 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EQ-5647         TCGA-EQ-8122         TCGA-F1-6177 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-F1-6874         TCGA-F1-6875         TCGA-FP-7735 
"11Q GAIN WILD-TYPE"   "11Q GAIN MUTATED" "11Q GAIN WILD-TYPE" 
        TCGA-FP-7829         TCGA-FP-7916         TCGA-FP-7998 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-HJ-7597         TCGA-IN-7806         TCGA-IN-7808 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-IP-7968 
"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-BR-7958 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-BR-7959         TCGA-BR-8059         TCGA-BR-8060 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-BR-8077         TCGA-BR-8078         TCGA-BR-8080 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-BR-8081         TCGA-BR-8284         TCGA-BR-8285 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-BR-8286         TCGA-BR-8289         TCGA-BR-8291 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-BR-8295         TCGA-BR-8296         TCGA-BR-8297 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-CD-5798         TCGA-CD-5799         TCGA-CD-5800 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-CD-5801         TCGA-CD-5802         TCGA-CD-5803 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-CG-4300         TCGA-CG-4301         TCGA-CG-4304 
  "11Q GAIN MUTATED" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-CG-4305         TCGA-CG-4306         TCGA-CG-4436 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-CG-4437         TCGA-CG-4438         TCGA-CG-4440 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-CG-4441         TCGA-CG-4443         TCGA-CG-4444 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-CG-4449         TCGA-CG-4455         TCGA-CG-4460 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-CG-4462         TCGA-CG-4465         TCGA-CG-4466 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-CG-4469         TCGA-CG-4472         TCGA-CG-4474 
"11Q GAIN WILD-TYPE"   "11Q GAIN MUTATED" "11Q GAIN WILD-TYPE" 
        TCGA-CG-4477         TCGA-CG-5716         TCGA-CG-5717 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-CG-5718         TCGA-CG-5719         TCGA-CG-5720 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-CG-5721         TCGA-CG-5722         TCGA-CG-5723 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-CG-5724         TCGA-CG-5725         TCGA-CG-5726 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-CG-5727         TCGA-CG-5728         TCGA-CG-5730 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-CG-5732         TCGA-CG-5733         TCGA-CG-5734 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-D7-5577         TCGA-D7-5578         TCGA-D7-5579 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-D7-6518         TCGA-D7-6519         TCGA-D7-6520 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-D7-6521         TCGA-D7-6522         TCGA-D7-6524 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-D7-6525         TCGA-D7-6526         TCGA-D7-6527 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-D7-6528         TCGA-D7-6815         TCGA-D7-6817 
  "11Q GAIN MUTATED" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-D7-6818         TCGA-D7-6820         TCGA-D7-6822 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EQ-5647         TCGA-EQ-8122         TCGA-F1-6177 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-F1-6874         TCGA-F1-6875         TCGA-FP-7735 
"11Q GAIN WILD-TYPE"   "11Q GAIN MUTATED" "11Q GAIN WILD-TYPE" 
        TCGA-FP-7829         TCGA-FP-7916         TCGA-FP-7998 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-HJ-7597         TCGA-IN-7806         TCGA-IN-7808 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-IP-7968 
"11Q GAIN WILD-TYPE" 
[1] "hr="     "7.6e+07"
D21V2, continuous
D21V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED      3    5
  11Q GAIN WILD-TYPE   62   91
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  FEMALE                3                 62
  MALE                  5                 91
                    vv
clus                 STOMACH ADENOCARCINOMA - DIFFUSE TYPE
  11Q GAIN MUTATED                                       0
  11Q GAIN WILD-TYPE                                    19
                    vv
clus                 STOMACH ADENOCARCINOMA - NOT OTHERWISE SPECIFIED (NOS)
  11Q GAIN MUTATED                                                        5
  11Q GAIN WILD-TYPE                                                     74
                    vv
clus                 STOMACH ADENOCARCINOMA - SIGNET RING TYPE
  11Q GAIN MUTATED                                           0
  11Q GAIN WILD-TYPE                                         1
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - MUCINOUS TYPE
  11Q GAIN MUTATED                                                   0
  11Q GAIN WILD-TYPE                                                 9
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - PAPILLARY TYPE
  11Q GAIN MUTATED                                                    0
  11Q GAIN WILD-TYPE                                                  3
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - TUBULAR TYPE
  11Q GAIN MUTATED                                                  1
  11Q GAIN WILD-TYPE                                                9
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - TYPE NOT OTHERWISE SPECIFIED (NOS)
  11Q GAIN MUTATED                                                                        1
  11Q GAIN WILD-TYPE                                                                     34
D21V4, multiclass
                    vv
clus                 T1 T2 T3 T4
  11Q GAIN MUTATED    0  2  4  2
  11Q GAIN WILD-TYPE  6 51 55 31
D21V5, multiclass
                    vv
clus                 N0 N1 N2 N3
  11Q GAIN MUTATED    3  3  2  0
  11Q GAIN WILD-TYPE 47 54 22 19
D21V6, multiclass
                    vv
clus                  M0  M1  MX
  11Q GAIN MUTATED     8   0   0
  11Q GAIN WILD-TYPE 124  18  11
D21V7, multiclass
                    vv
clus                  I II III IV
  11Q GAIN MUTATED    2  1   3  2
  11Q GAIN WILD-TYPE 23 42  45 27
D21V8, multiclass
D21V9, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED      0    8
  11Q GAIN WILD-TYPE    5  148
     clus
vv    11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  NO                 0                  5
  YES                8                148

Clustering(22) Variable = 12p gain mutation analysis
D22V1, survival
                    sevent
clus2                 0  1
  12P GAIN MUTATED   10  2
  12P GAIN WILD-TYPE 98 14
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                12                112 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                 2                 14 
$`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-BR-7958 
        0.69         0.16         0.99         0.95         0.69         0.16 
TCGA-BR-7959 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
        1.08         0.82         1.32         0.69         0.95         0.49 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
        0.46         0.72         0.26         0.43         0.26         1.18 
TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-CD-5798 TCGA-CD-5800 TCGA-CD-5801 
        1.55         1.48         0.76         0.82         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-5728 TCGA-CG-5730 TCGA-CG-5732 
       70.06        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-D7-6822 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6177 TCGA-F1-6874 TCGA-F1-6875 
        4.27         0.62         7.79         6.54         2.01        72.23 
TCGA-FP-7916 TCGA-FP-7998 TCGA-HJ-7597 TCGA-IN-7806 
        3.02         3.58        26.43         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               1.48 
[1] "0.2 - 31.0 (2.7)" "0.1 - 72.2 (1.5)"
        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-BR-7958 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-BR-7959         TCGA-BR-8059         TCGA-BR-8060 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-BR-8077         TCGA-BR-8078         TCGA-BR-8080 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-BR-8081         TCGA-BR-8284         TCGA-BR-8285 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-BR-8286         TCGA-BR-8289         TCGA-BR-8291 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-BR-8295         TCGA-BR-8296         TCGA-BR-8297 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-CD-5798         TCGA-CD-5799         TCGA-CD-5800 
"12P GAIN WILD-TYPE"   "12P GAIN MUTATED" "12P GAIN WILD-TYPE" 
        TCGA-CD-5801         TCGA-CD-5802         TCGA-CD-5803 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-CG-4300         TCGA-CG-4301         TCGA-CG-4304 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-CG-4305         TCGA-CG-4306         TCGA-CG-4436 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-CG-4437         TCGA-CG-4438         TCGA-CG-4440 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-CG-4441         TCGA-CG-4443         TCGA-CG-4444 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-CG-4449         TCGA-CG-4455         TCGA-CG-4460 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE"   "12P GAIN MUTATED" 
        TCGA-CG-4462         TCGA-CG-4465         TCGA-CG-4466 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-CG-4469         TCGA-CG-4472         TCGA-CG-4474 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-CG-4477         TCGA-CG-5716         TCGA-CG-5717 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-CG-5718         TCGA-CG-5719         TCGA-CG-5720 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-CG-5721         TCGA-CG-5722         TCGA-CG-5723 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-CG-5724         TCGA-CG-5725         TCGA-CG-5726 
  "12P GAIN MUTATED" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-CG-5727         TCGA-CG-5728         TCGA-CG-5730 
  "12P GAIN MUTATED" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-CG-5732         TCGA-CG-5733         TCGA-CG-5734 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-D7-5577         TCGA-D7-5578         TCGA-D7-5579 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-D7-6518         TCGA-D7-6519         TCGA-D7-6520 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-D7-6521         TCGA-D7-6522         TCGA-D7-6524 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-D7-6525         TCGA-D7-6526         TCGA-D7-6527 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-D7-6528         TCGA-D7-6815         TCGA-D7-6817 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-D7-6818         TCGA-D7-6820         TCGA-D7-6822 
"12P GAIN WILD-TYPE"   "12P GAIN MUTATED" "12P GAIN WILD-TYPE" 
        TCGA-EQ-5647         TCGA-EQ-8122         TCGA-F1-6177 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-F1-6874         TCGA-F1-6875         TCGA-FP-7735 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE"   "12P GAIN MUTATED" 
        TCGA-FP-7829         TCGA-FP-7916         TCGA-FP-7998 
  "12P GAIN MUTATED" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-HJ-7597         TCGA-IN-7806         TCGA-IN-7808 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE"   "12P GAIN MUTATED" 
        TCGA-IP-7968 
  "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-BR-7958 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-BR-7959         TCGA-BR-8059         TCGA-BR-8060 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-BR-8077         TCGA-BR-8078         TCGA-BR-8080 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-BR-8081         TCGA-BR-8284         TCGA-BR-8285 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-BR-8286         TCGA-BR-8289         TCGA-BR-8291 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-BR-8295         TCGA-BR-8296         TCGA-BR-8297 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-CD-5798         TCGA-CD-5799         TCGA-CD-5800 
"12P GAIN WILD-TYPE"   "12P GAIN MUTATED" "12P GAIN WILD-TYPE" 
        TCGA-CD-5801         TCGA-CD-5802         TCGA-CD-5803 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-CG-4300         TCGA-CG-4301         TCGA-CG-4304 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-CG-4305         TCGA-CG-4306         TCGA-CG-4436 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-CG-4437         TCGA-CG-4438         TCGA-CG-4440 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-CG-4441         TCGA-CG-4443         TCGA-CG-4444 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-CG-4449         TCGA-CG-4455         TCGA-CG-4460 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE"   "12P GAIN MUTATED" 
        TCGA-CG-4462         TCGA-CG-4465         TCGA-CG-4466 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-CG-4469         TCGA-CG-4472         TCGA-CG-4474 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-CG-4477         TCGA-CG-5716         TCGA-CG-5717 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-CG-5718         TCGA-CG-5719         TCGA-CG-5720 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-CG-5721         TCGA-CG-5722         TCGA-CG-5723 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-CG-5724         TCGA-CG-5725         TCGA-CG-5726 
  "12P GAIN MUTATED" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-CG-5727         TCGA-CG-5728         TCGA-CG-5730 
  "12P GAIN MUTATED" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-CG-5732         TCGA-CG-5733         TCGA-CG-5734 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-D7-5577         TCGA-D7-5578         TCGA-D7-5579 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-D7-6518         TCGA-D7-6519         TCGA-D7-6520 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-D7-6521         TCGA-D7-6522         TCGA-D7-6524 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-D7-6525         TCGA-D7-6526         TCGA-D7-6527 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-D7-6528         TCGA-D7-6815         TCGA-D7-6817 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-D7-6818         TCGA-D7-6820         TCGA-D7-6822 
"12P GAIN WILD-TYPE"   "12P GAIN MUTATED" "12P GAIN WILD-TYPE" 
        TCGA-EQ-5647         TCGA-EQ-8122         TCGA-F1-6177 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-F1-6874         TCGA-F1-6875         TCGA-FP-7735 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE"   "12P GAIN MUTATED" 
        TCGA-FP-7829         TCGA-FP-7916         TCGA-FP-7998 
  "12P GAIN MUTATED" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-HJ-7597         TCGA-IN-7806         TCGA-IN-7808 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE"   "12P GAIN MUTATED" 
        TCGA-IP-7968 
  "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-BR-7958 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-BR-7959         TCGA-BR-8059         TCGA-BR-8060 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-BR-8077         TCGA-BR-8078         TCGA-BR-8080 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-BR-8081         TCGA-BR-8284         TCGA-BR-8285 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-BR-8286         TCGA-BR-8289         TCGA-BR-8291 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-BR-8295         TCGA-BR-8296         TCGA-BR-8297 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-CD-5798         TCGA-CD-5799         TCGA-CD-5800 
"12P GAIN WILD-TYPE"   "12P GAIN MUTATED" "12P GAIN WILD-TYPE" 
        TCGA-CD-5801         TCGA-CD-5802         TCGA-CD-5803 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-CG-4300         TCGA-CG-4301         TCGA-CG-4304 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-CG-4305         TCGA-CG-4306         TCGA-CG-4436 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-CG-4437         TCGA-CG-4438         TCGA-CG-4440 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-CG-4441         TCGA-CG-4443         TCGA-CG-4444 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-CG-4449         TCGA-CG-4455         TCGA-CG-4460 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE"   "12P GAIN MUTATED" 
        TCGA-CG-4462         TCGA-CG-4465         TCGA-CG-4466 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-CG-4469         TCGA-CG-4472         TCGA-CG-4474 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-CG-4477         TCGA-CG-5716         TCGA-CG-5717 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-CG-5718         TCGA-CG-5719         TCGA-CG-5720 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-CG-5721         TCGA-CG-5722         TCGA-CG-5723 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-CG-5724         TCGA-CG-5725         TCGA-CG-5726 
  "12P GAIN MUTATED" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-CG-5727         TCGA-CG-5728         TCGA-CG-5730 
  "12P GAIN MUTATED" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-CG-5732         TCGA-CG-5733         TCGA-CG-5734 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-D7-5577         TCGA-D7-5578         TCGA-D7-5579 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-D7-6518         TCGA-D7-6519         TCGA-D7-6520 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-D7-6521         TCGA-D7-6522         TCGA-D7-6524 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-D7-6525         TCGA-D7-6526         TCGA-D7-6527 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-D7-6528         TCGA-D7-6815         TCGA-D7-6817 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-D7-6818         TCGA-D7-6820         TCGA-D7-6822 
"12P GAIN WILD-TYPE"   "12P GAIN MUTATED" "12P GAIN WILD-TYPE" 
        TCGA-EQ-5647         TCGA-EQ-8122         TCGA-F1-6177 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-F1-6874         TCGA-F1-6875         TCGA-FP-7735 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE"   "12P GAIN MUTATED" 
        TCGA-FP-7829         TCGA-FP-7916         TCGA-FP-7998 
  "12P GAIN MUTATED" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-HJ-7597         TCGA-IN-7806         TCGA-IN-7808 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE"   "12P GAIN MUTATED" 
        TCGA-IP-7968 
  "12P GAIN MUTATED" 
[1] "hr=" "1.3"
D22V2, continuous
D22V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED      3   12
  12P GAIN WILD-TYPE   62   84
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  FEMALE                3                 62
  MALE                 12                 84
                    vv
clus                 STOMACH ADENOCARCINOMA - DIFFUSE TYPE
  12P GAIN MUTATED                                       2
  12P GAIN WILD-TYPE                                    17
                    vv
clus                 STOMACH ADENOCARCINOMA - NOT OTHERWISE SPECIFIED (NOS)
  12P GAIN MUTATED                                                        7
  12P GAIN WILD-TYPE                                                     72
                    vv
clus                 STOMACH ADENOCARCINOMA - SIGNET RING TYPE
  12P GAIN MUTATED                                           0
  12P GAIN WILD-TYPE                                         1
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - MUCINOUS TYPE
  12P GAIN MUTATED                                                   1
  12P GAIN WILD-TYPE                                                 8
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - PAPILLARY TYPE
  12P GAIN MUTATED                                                    0
  12P GAIN WILD-TYPE                                                  3
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - TUBULAR TYPE
  12P GAIN MUTATED                                                  1
  12P GAIN WILD-TYPE                                                9
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - TYPE NOT OTHERWISE SPECIFIED (NOS)
  12P GAIN MUTATED                                                                        3
  12P GAIN WILD-TYPE                                                                     32
D22V4, multiclass
                    vv
clus                 T1 T2 T3 T4
  12P GAIN MUTATED    0  3  9  3
  12P GAIN WILD-TYPE  6 50 50 30
D22V5, multiclass
                    vv
clus                 N0 N1 N2 N3
  12P GAIN MUTATED    4  5  4  2
  12P GAIN WILD-TYPE 46 52 20 17
D22V6, multiclass
                    vv
clus                  M0  M1  MX
  12P GAIN MUTATED    10   3   2
  12P GAIN WILD-TYPE 122  15   9
D22V7, multiclass
                    vv
clus                  I II III IV
  12P GAIN MUTATED    1  6   5  3
  12P GAIN WILD-TYPE 24 37  43 26
D22V8, multiclass
D22V9, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED      0   15
  12P GAIN WILD-TYPE    5  141
     clus
vv    12P GAIN MUTATED 12P GAIN WILD-TYPE
  NO                 0                  5
  YES               15                141

Clustering(23) Variable = 12q gain mutation analysis
D23V1, survival
                    sevent
clus2                  0   1
  12Q GAIN MUTATED     7   1
  12Q GAIN WILD-TYPE 101  15
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                 8                116 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                 1                 15 
$`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-BR-7958 TCGA-BR-7959 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 
        0.16         1.08         0.82         1.32         0.69         0.95 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
        0.49         0.46         0.72         0.26         0.43         0.26 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-CD-5798 TCGA-CD-5800 
        1.18         1.55         1.48         0.76         0.82         0.36 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
        0.49         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-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-D7-6520 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-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
        5.95         6.61         1.68         3.65         4.70         4.04 
TCGA-D7-6820 TCGA-D7-6822 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6177 TCGA-F1-6874 
        2.93         4.27         0.62         7.79         6.54         2.01 
TCGA-F1-6875 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-HJ-7597 
       72.23         0.39         0.20         3.02         3.58        26.43 
TCGA-IN-7806 TCGA-IN-7808 
        6.87         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 
             4.340              1.445 
[1] "0.7 - 31.0 (4.3)" "0.1 - 72.2 (1.4)"
        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-BR-7958 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-BR-7959         TCGA-BR-8059         TCGA-BR-8060 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-BR-8077         TCGA-BR-8078         TCGA-BR-8080 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-BR-8081         TCGA-BR-8284         TCGA-BR-8285 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-BR-8286         TCGA-BR-8289         TCGA-BR-8291 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-BR-8295         TCGA-BR-8296         TCGA-BR-8297 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-CD-5798         TCGA-CD-5799         TCGA-CD-5800 
"12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" 
        TCGA-CD-5801         TCGA-CD-5802         TCGA-CD-5803 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-CG-4300         TCGA-CG-4301         TCGA-CG-4304 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-CG-4305         TCGA-CG-4306         TCGA-CG-4436 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-CG-4437         TCGA-CG-4438         TCGA-CG-4440 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-CG-4441         TCGA-CG-4443         TCGA-CG-4444 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-CG-4449         TCGA-CG-4455         TCGA-CG-4460 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" 
        TCGA-CG-4462         TCGA-CG-4465         TCGA-CG-4466 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-CG-4469         TCGA-CG-4472         TCGA-CG-4474 
"12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" 
        TCGA-CG-4477         TCGA-CG-5716         TCGA-CG-5717 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-CG-5718         TCGA-CG-5719         TCGA-CG-5720 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-CG-5721         TCGA-CG-5722         TCGA-CG-5723 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-CG-5724         TCGA-CG-5725         TCGA-CG-5726 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-CG-5727         TCGA-CG-5728         TCGA-CG-5730 
  "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-CG-5732         TCGA-CG-5733         TCGA-CG-5734 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-D7-5577         TCGA-D7-5578         TCGA-D7-5579 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-D7-6518         TCGA-D7-6519         TCGA-D7-6520 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-D7-6521         TCGA-D7-6522         TCGA-D7-6524 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-D7-6525         TCGA-D7-6526         TCGA-D7-6527 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" 
        TCGA-D7-6528         TCGA-D7-6815         TCGA-D7-6817 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-D7-6818         TCGA-D7-6820         TCGA-D7-6822 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EQ-5647         TCGA-EQ-8122         TCGA-F1-6177 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-F1-6874         TCGA-F1-6875         TCGA-FP-7735 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-FP-7829         TCGA-FP-7916         TCGA-FP-7998 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-HJ-7597         TCGA-IN-7806         TCGA-IN-7808 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-IP-7968 
  "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-BR-7958 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-BR-7959         TCGA-BR-8059         TCGA-BR-8060 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-BR-8077         TCGA-BR-8078         TCGA-BR-8080 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-BR-8081         TCGA-BR-8284         TCGA-BR-8285 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-BR-8286         TCGA-BR-8289         TCGA-BR-8291 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-BR-8295         TCGA-BR-8296         TCGA-BR-8297 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-CD-5798         TCGA-CD-5799         TCGA-CD-5800 
"12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" 
        TCGA-CD-5801         TCGA-CD-5802         TCGA-CD-5803 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-CG-4300         TCGA-CG-4301         TCGA-CG-4304 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-CG-4305         TCGA-CG-4306         TCGA-CG-4436 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-CG-4437         TCGA-CG-4438         TCGA-CG-4440 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-CG-4441         TCGA-CG-4443         TCGA-CG-4444 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-CG-4449         TCGA-CG-4455         TCGA-CG-4460 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" 
        TCGA-CG-4462         TCGA-CG-4465         TCGA-CG-4466 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-CG-4469         TCGA-CG-4472         TCGA-CG-4474 
"12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" 
        TCGA-CG-4477         TCGA-CG-5716         TCGA-CG-5717 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-CG-5718         TCGA-CG-5719         TCGA-CG-5720 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-CG-5721         TCGA-CG-5722         TCGA-CG-5723 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-CG-5724         TCGA-CG-5725         TCGA-CG-5726 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-CG-5727         TCGA-CG-5728         TCGA-CG-5730 
  "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-CG-5732         TCGA-CG-5733         TCGA-CG-5734 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-D7-5577         TCGA-D7-5578         TCGA-D7-5579 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-D7-6518         TCGA-D7-6519         TCGA-D7-6520 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-D7-6521         TCGA-D7-6522         TCGA-D7-6524 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-D7-6525         TCGA-D7-6526         TCGA-D7-6527 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" 
        TCGA-D7-6528         TCGA-D7-6815         TCGA-D7-6817 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-D7-6818         TCGA-D7-6820         TCGA-D7-6822 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EQ-5647         TCGA-EQ-8122         TCGA-F1-6177 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-F1-6874         TCGA-F1-6875         TCGA-FP-7735 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-FP-7829         TCGA-FP-7916         TCGA-FP-7998 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-HJ-7597         TCGA-IN-7806         TCGA-IN-7808 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-IP-7968 
  "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-BR-7958 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-BR-7959         TCGA-BR-8059         TCGA-BR-8060 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-BR-8077         TCGA-BR-8078         TCGA-BR-8080 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-BR-8081         TCGA-BR-8284         TCGA-BR-8285 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-BR-8286         TCGA-BR-8289         TCGA-BR-8291 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-BR-8295         TCGA-BR-8296         TCGA-BR-8297 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-CD-5798         TCGA-CD-5799         TCGA-CD-5800 
"12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" 
        TCGA-CD-5801         TCGA-CD-5802         TCGA-CD-5803 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-CG-4300         TCGA-CG-4301         TCGA-CG-4304 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-CG-4305         TCGA-CG-4306         TCGA-CG-4436 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-CG-4437         TCGA-CG-4438         TCGA-CG-4440 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-CG-4441         TCGA-CG-4443         TCGA-CG-4444 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-CG-4449         TCGA-CG-4455         TCGA-CG-4460 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" 
        TCGA-CG-4462         TCGA-CG-4465         TCGA-CG-4466 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-CG-4469         TCGA-CG-4472         TCGA-CG-4474 
"12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" 
        TCGA-CG-4477         TCGA-CG-5716         TCGA-CG-5717 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-CG-5718         TCGA-CG-5719         TCGA-CG-5720 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-CG-5721         TCGA-CG-5722         TCGA-CG-5723 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-CG-5724         TCGA-CG-5725         TCGA-CG-5726 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-CG-5727         TCGA-CG-5728         TCGA-CG-5730 
  "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-CG-5732         TCGA-CG-5733         TCGA-CG-5734 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-D7-5577         TCGA-D7-5578         TCGA-D7-5579 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-D7-6518         TCGA-D7-6519         TCGA-D7-6520 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-D7-6521         TCGA-D7-6522         TCGA-D7-6524 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-D7-6525         TCGA-D7-6526         TCGA-D7-6527 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" 
        TCGA-D7-6528         TCGA-D7-6815         TCGA-D7-6817 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-D7-6818         TCGA-D7-6820         TCGA-D7-6822 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EQ-5647         TCGA-EQ-8122         TCGA-F1-6177 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-F1-6874         TCGA-F1-6875         TCGA-FP-7735 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-FP-7829         TCGA-FP-7916         TCGA-FP-7998 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-HJ-7597         TCGA-IN-7806         TCGA-IN-7808 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-IP-7968 
  "12Q GAIN MUTATED" 
[1] "hr=" "1.6"
D23V2, continuous
D23V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED      3    7
  12Q GAIN WILD-TYPE   62   89
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  FEMALE                3                 62
  MALE                  7                 89
                    vv
clus                 STOMACH ADENOCARCINOMA - DIFFUSE TYPE
  12Q GAIN MUTATED                                       0
  12Q GAIN WILD-TYPE                                    19
                    vv
clus                 STOMACH ADENOCARCINOMA - NOT OTHERWISE SPECIFIED (NOS)
  12Q GAIN MUTATED                                                        5
  12Q GAIN WILD-TYPE                                                     74
                    vv
clus                 STOMACH ADENOCARCINOMA - SIGNET RING TYPE
  12Q GAIN MUTATED                                           0
  12Q GAIN WILD-TYPE                                         1
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - MUCINOUS TYPE
  12Q GAIN MUTATED                                                   0
  12Q GAIN WILD-TYPE                                                 9
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - PAPILLARY TYPE
  12Q GAIN MUTATED                                                    1
  12Q GAIN WILD-TYPE                                                  2
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - TUBULAR TYPE
  12Q GAIN MUTATED                                                  0
  12Q GAIN WILD-TYPE                                               10
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - TYPE NOT OTHERWISE SPECIFIED (NOS)
  12Q GAIN MUTATED                                                                        3
  12Q GAIN WILD-TYPE                                                                     32
D23V4, multiclass
                    vv
clus                 T1 T2 T3 T4
  12Q GAIN MUTATED    0  3  4  3
  12Q GAIN WILD-TYPE  6 50 55 30
D23V5, multiclass
                    vv
clus                 N0 N1 N2 N3
  12Q GAIN MUTATED    2  4  4  0
  12Q GAIN WILD-TYPE 48 53 20 19
D23V6, multiclass
                    vv
clus                  M0  M1  MX
  12Q GAIN MUTATED     8   1   1
  12Q GAIN WILD-TYPE 124  17  10
D23V7, multiclass
                    vv
clus                  I II III IV
  12Q GAIN MUTATED    1  4   2  3
  12Q GAIN WILD-TYPE 24 39  46 26
D23V8, multiclass
D23V9, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED      1    9
  12Q GAIN WILD-TYPE    4  147
     clus
vv    12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  NO                 1                  4
  YES                9                147

Clustering(24) Variable = 13q gain mutation analysis
D24V1, survival
                    sevent
clus2                 0  1
  13Q GAIN MUTATED   21  3
  13Q GAIN WILD-TYPE 87 13
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                24                100 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                 3                 13 
$`13Q GAIN MUTATED`
TCGA-B7-5818 TCGA-BR-6565 TCGA-BR-6705 TCGA-BR-6801 TCGA-BR-7197 TCGA-BR-7704 
        0.10         0.62         1.71         1.12         1.48         1.25 
TCGA-BR-7717 TCGA-BR-7723 TCGA-CD-5799 TCGA-CD-5800 TCGA-CG-4300 TCGA-CG-4305 
        0.69         4.54         0.69         0.36        20.02        15.95 
TCGA-CG-4436 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-5730 TCGA-CG-5732 TCGA-D7-5577 
       52.96         7.07        12.00         4.01        55.04         8.65 
TCGA-D7-6518 TCGA-D7-6527 TCGA-D7-6820 TCGA-EQ-5647 TCGA-F1-6875 TCGA-FP-7829 
        9.80         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-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 
        0.82         0.62         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-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-BR-7958 TCGA-BR-7959 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 
        0.16         1.08         0.82         1.32         0.69         0.95 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
        0.49         0.46         0.72         0.26         0.43         0.26 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-CD-5798 TCGA-CD-5801 
        1.18         1.55         1.48         0.76         0.82         0.49 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4306 TCGA-CG-4437 
        0.30         0.07         3.02        27.02         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-4474 
       12.03        21.99         1.02         8.98        18.94         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-5733 TCGA-CG-5734 TCGA-D7-5578 TCGA-D7-5579 
       31.04        65.10        21.07         7.99         3.58         4.54 
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-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6822 
        6.61         1.68         3.65         4.70         4.04         4.27 
TCGA-EQ-8122 TCGA-F1-6177 TCGA-F1-6874 TCGA-FP-7735 TCGA-FP-7916 TCGA-FP-7998 
        7.79         6.54         2.01         0.39         3.02         3.58 
TCGA-HJ-7597 TCGA-IN-7806 TCGA-IN-7808 TCGA-IP-7968 
       26.43         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 
              3.47               1.38 
[1] "0.1 - 72.2 (3.5)" "0.1 - 70.1 (1.4)"
        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 MUTATED" "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-BR-7958 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-BR-7959         TCGA-BR-8059         TCGA-BR-8060 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-BR-8077         TCGA-BR-8078         TCGA-BR-8080 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-BR-8081         TCGA-BR-8284         TCGA-BR-8285 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-BR-8286         TCGA-BR-8289         TCGA-BR-8291 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-BR-8295         TCGA-BR-8296         TCGA-BR-8297 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-CD-5798         TCGA-CD-5799         TCGA-CD-5800 
"13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED"   "13Q GAIN MUTATED" 
        TCGA-CD-5801         TCGA-CD-5802         TCGA-CD-5803 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-CG-4300         TCGA-CG-4301         TCGA-CG-4304 
  "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-CG-4305         TCGA-CG-4306         TCGA-CG-4436 
  "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" 
        TCGA-CG-4437         TCGA-CG-4438         TCGA-CG-4440 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-CG-4441         TCGA-CG-4443         TCGA-CG-4444 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-CG-4449         TCGA-CG-4455         TCGA-CG-4460 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-CG-4462         TCGA-CG-4465         TCGA-CG-4466 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-CG-4469         TCGA-CG-4472         TCGA-CG-4474 
  "13Q GAIN MUTATED"   "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" 
        TCGA-CG-4477         TCGA-CG-5716         TCGA-CG-5717 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-CG-5718         TCGA-CG-5719         TCGA-CG-5720 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-CG-5721         TCGA-CG-5722         TCGA-CG-5723 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-CG-5724         TCGA-CG-5725         TCGA-CG-5726 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-CG-5727         TCGA-CG-5728         TCGA-CG-5730 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" 
        TCGA-CG-5732         TCGA-CG-5733         TCGA-CG-5734 
  "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-D7-5577         TCGA-D7-5578         TCGA-D7-5579 
  "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-D7-6518         TCGA-D7-6519         TCGA-D7-6520 
  "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-D7-6521         TCGA-D7-6522         TCGA-D7-6524 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-D7-6525         TCGA-D7-6526         TCGA-D7-6527 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" 
        TCGA-D7-6528         TCGA-D7-6815         TCGA-D7-6817 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-D7-6818         TCGA-D7-6820         TCGA-D7-6822 
"13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" 
        TCGA-EQ-5647         TCGA-EQ-8122         TCGA-F1-6177 
  "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-F1-6874         TCGA-F1-6875         TCGA-FP-7735 
"13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" 
        TCGA-FP-7829         TCGA-FP-7916         TCGA-FP-7998 
  "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-HJ-7597         TCGA-IN-7806         TCGA-IN-7808 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-IP-7968 
"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 MUTATED" "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-BR-7958 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-BR-7959         TCGA-BR-8059         TCGA-BR-8060 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-BR-8077         TCGA-BR-8078         TCGA-BR-8080 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-BR-8081         TCGA-BR-8284         TCGA-BR-8285 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-BR-8286         TCGA-BR-8289         TCGA-BR-8291 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-BR-8295         TCGA-BR-8296         TCGA-BR-8297 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-CD-5798         TCGA-CD-5799         TCGA-CD-5800 
"13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED"   "13Q GAIN MUTATED" 
        TCGA-CD-5801         TCGA-CD-5802         TCGA-CD-5803 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-CG-4300         TCGA-CG-4301         TCGA-CG-4304 
  "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-CG-4305         TCGA-CG-4306         TCGA-CG-4436 
  "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" 
        TCGA-CG-4437         TCGA-CG-4438         TCGA-CG-4440 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-CG-4441         TCGA-CG-4443         TCGA-CG-4444 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-CG-4449         TCGA-CG-4455         TCGA-CG-4460 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-CG-4462         TCGA-CG-4465         TCGA-CG-4466 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-CG-4469         TCGA-CG-4472         TCGA-CG-4474 
  "13Q GAIN MUTATED"   "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" 
        TCGA-CG-4477         TCGA-CG-5716         TCGA-CG-5717 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-CG-5718         TCGA-CG-5719         TCGA-CG-5720 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-CG-5721         TCGA-CG-5722         TCGA-CG-5723 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-CG-5724         TCGA-CG-5725         TCGA-CG-5726 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-CG-5727         TCGA-CG-5728         TCGA-CG-5730 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" 
        TCGA-CG-5732         TCGA-CG-5733         TCGA-CG-5734 
  "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-D7-5577         TCGA-D7-5578         TCGA-D7-5579 
  "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-D7-6518         TCGA-D7-6519         TCGA-D7-6520 
  "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-D7-6521         TCGA-D7-6522         TCGA-D7-6524 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-D7-6525         TCGA-D7-6526         TCGA-D7-6527 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" 
        TCGA-D7-6528         TCGA-D7-6815         TCGA-D7-6817 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-D7-6818         TCGA-D7-6820         TCGA-D7-6822 
"13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" 
        TCGA-EQ-5647         TCGA-EQ-8122         TCGA-F1-6177 
  "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-F1-6874         TCGA-F1-6875         TCGA-FP-7735 
"13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" 
        TCGA-FP-7829         TCGA-FP-7916         TCGA-FP-7998 
  "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-HJ-7597         TCGA-IN-7806         TCGA-IN-7808 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-IP-7968 
"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 MUTATED" "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-BR-7958 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-BR-7959         TCGA-BR-8059         TCGA-BR-8060 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-BR-8077         TCGA-BR-8078         TCGA-BR-8080 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-BR-8081         TCGA-BR-8284         TCGA-BR-8285 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-BR-8286         TCGA-BR-8289         TCGA-BR-8291 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-BR-8295         TCGA-BR-8296         TCGA-BR-8297 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-CD-5798         TCGA-CD-5799         TCGA-CD-5800 
"13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED"   "13Q GAIN MUTATED" 
        TCGA-CD-5801         TCGA-CD-5802         TCGA-CD-5803 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-CG-4300         TCGA-CG-4301         TCGA-CG-4304 
  "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-CG-4305         TCGA-CG-4306         TCGA-CG-4436 
  "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" 
        TCGA-CG-4437         TCGA-CG-4438         TCGA-CG-4440 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-CG-4441         TCGA-CG-4443         TCGA-CG-4444 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-CG-4449         TCGA-CG-4455         TCGA-CG-4460 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-CG-4462         TCGA-CG-4465         TCGA-CG-4466 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-CG-4469         TCGA-CG-4472         TCGA-CG-4474 
  "13Q GAIN MUTATED"   "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" 
        TCGA-CG-4477         TCGA-CG-5716         TCGA-CG-5717 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-CG-5718         TCGA-CG-5719         TCGA-CG-5720 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-CG-5721         TCGA-CG-5722         TCGA-CG-5723 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-CG-5724         TCGA-CG-5725         TCGA-CG-5726 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-CG-5727         TCGA-CG-5728         TCGA-CG-5730 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" 
        TCGA-CG-5732         TCGA-CG-5733         TCGA-CG-5734 
  "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-D7-5577         TCGA-D7-5578         TCGA-D7-5579 
  "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-D7-6518         TCGA-D7-6519         TCGA-D7-6520 
  "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-D7-6521         TCGA-D7-6522         TCGA-D7-6524 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-D7-6525         TCGA-D7-6526         TCGA-D7-6527 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" 
        TCGA-D7-6528         TCGA-D7-6815         TCGA-D7-6817 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-D7-6818         TCGA-D7-6820         TCGA-D7-6822 
"13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" 
        TCGA-EQ-5647         TCGA-EQ-8122         TCGA-F1-6177 
  "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-F1-6874         TCGA-F1-6875         TCGA-FP-7735 
"13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" 
        TCGA-FP-7829         TCGA-FP-7916         TCGA-FP-7998 
  "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-HJ-7597         TCGA-IN-7806         TCGA-IN-7808 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-IP-7968 
"13Q GAIN WILD-TYPE" 
[1] "hr=" "2.1"
D24V2, continuous
D24V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED      9   21
  13Q GAIN WILD-TYPE   56   75
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  FEMALE                9                 56
  MALE                 21                 75
                    vv
clus                 STOMACH ADENOCARCINOMA - DIFFUSE TYPE
  13Q GAIN MUTATED                                       3
  13Q GAIN WILD-TYPE                                    16
                    vv
clus                 STOMACH ADENOCARCINOMA - NOT OTHERWISE SPECIFIED (NOS)
  13Q GAIN MUTATED                                                       14
  13Q GAIN WILD-TYPE                                                     65
                    vv
clus                 STOMACH ADENOCARCINOMA - SIGNET RING TYPE
  13Q GAIN MUTATED                                           0
  13Q GAIN WILD-TYPE                                         1
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - MUCINOUS TYPE
  13Q GAIN MUTATED                                                   1
  13Q GAIN WILD-TYPE                                                 8
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - PAPILLARY TYPE
  13Q GAIN MUTATED                                                    2
  13Q GAIN WILD-TYPE                                                  1
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - TUBULAR TYPE
  13Q GAIN MUTATED                                                  2
  13Q GAIN WILD-TYPE                                                8
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - TYPE NOT OTHERWISE SPECIFIED (NOS)
  13Q GAIN MUTATED                                                                        7
  13Q GAIN WILD-TYPE                                                                     28
D24V4, multiclass
                    vv
clus                 T1 T2 T3 T4
  13Q GAIN MUTATED    1 13 10  5
  13Q GAIN WILD-TYPE  5 40 49 28
D24V5, multiclass
                    vv
clus                 N0 N1 N2 N3
  13Q GAIN MUTATED    9 10  3  6
  13Q GAIN WILD-TYPE 41 47 21 13
D24V6, multiclass
                    vv
clus                  M0  M1  MX
  13Q GAIN MUTATED    27   2   1
  13Q GAIN WILD-TYPE 105  16  10
D24V7, multiclass
                    vv
clus                  I II III IV
  13Q GAIN MUTATED    4  9   7  7
  13Q GAIN WILD-TYPE 21 34  41 22
D24V8, multiclass
D24V9, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED      1   29
  13Q GAIN WILD-TYPE    4  127
     clus
vv    13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  NO                 1                  4
  YES               29                127

Clustering(25) Variable = 15q gain mutation analysis
D25V1, survival
                    sevent
clus2                  0   1
  15Q GAIN MUTATED     5   1
  15Q GAIN WILD-TYPE 103  15
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                 6                118 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                 1                 15 
$`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-BR-7958 TCGA-BR-7959 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
        0.69         0.16         1.08         0.82         1.32         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
        0.95         0.49         0.46         0.72         0.26         0.43 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-CD-5798 
        0.26         1.18         1.55         1.48         0.76         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-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-D7-6521 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-EQ-8122 TCGA-F1-6177 TCGA-F1-6874 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
        7.79         6.54         2.01         0.39         0.20         3.02 
TCGA-FP-7998 TCGA-HJ-7597 TCGA-IN-7806 TCGA-IP-7968 
        3.58        26.43         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               1.38 
[1] "1.5 - 72.2 (6.6)" "0.1 - 70.1 (1.4)"
        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-BR-7958 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BR-7959         TCGA-BR-8059         TCGA-BR-8060 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BR-8077         TCGA-BR-8078         TCGA-BR-8080 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BR-8081         TCGA-BR-8284         TCGA-BR-8285 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BR-8286         TCGA-BR-8289         TCGA-BR-8291 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BR-8295         TCGA-BR-8296         TCGA-BR-8297 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-CD-5798         TCGA-CD-5799         TCGA-CD-5800 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-CD-5801         TCGA-CD-5802         TCGA-CD-5803 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-CG-4300         TCGA-CG-4301         TCGA-CG-4304 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-CG-4305         TCGA-CG-4306         TCGA-CG-4436 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-CG-4437         TCGA-CG-4438         TCGA-CG-4440 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-CG-4441         TCGA-CG-4443         TCGA-CG-4444 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-CG-4449         TCGA-CG-4455         TCGA-CG-4460 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-CG-4462         TCGA-CG-4465         TCGA-CG-4466 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-CG-4469         TCGA-CG-4472         TCGA-CG-4474 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-CG-4477         TCGA-CG-5716         TCGA-CG-5717 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-CG-5718         TCGA-CG-5719         TCGA-CG-5720 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-CG-5721         TCGA-CG-5722         TCGA-CG-5723 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-CG-5724         TCGA-CG-5725         TCGA-CG-5726 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-CG-5727         TCGA-CG-5728         TCGA-CG-5730 
  "15Q GAIN MUTATED" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-CG-5732         TCGA-CG-5733         TCGA-CG-5734 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-D7-5577         TCGA-D7-5578         TCGA-D7-5579 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-D7-6518         TCGA-D7-6519         TCGA-D7-6520 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" 
        TCGA-D7-6521         TCGA-D7-6522         TCGA-D7-6524 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-D7-6525         TCGA-D7-6526         TCGA-D7-6527 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-D7-6528         TCGA-D7-6815         TCGA-D7-6817 
  "15Q GAIN MUTATED" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-D7-6818         TCGA-D7-6820         TCGA-D7-6822 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EQ-5647         TCGA-EQ-8122         TCGA-F1-6177 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-F1-6874         TCGA-F1-6875         TCGA-FP-7735 
"15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" "15Q GAIN WILD-TYPE" 
        TCGA-FP-7829         TCGA-FP-7916         TCGA-FP-7998 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-HJ-7597         TCGA-IN-7806         TCGA-IN-7808 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" 
        TCGA-IP-7968 
"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-BR-7958 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BR-7959         TCGA-BR-8059         TCGA-BR-8060 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BR-8077         TCGA-BR-8078         TCGA-BR-8080 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BR-8081         TCGA-BR-8284         TCGA-BR-8285 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BR-8286         TCGA-BR-8289         TCGA-BR-8291 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BR-8295         TCGA-BR-8296         TCGA-BR-8297 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-CD-5798         TCGA-CD-5799         TCGA-CD-5800 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-CD-5801         TCGA-CD-5802         TCGA-CD-5803 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-CG-4300         TCGA-CG-4301         TCGA-CG-4304 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-CG-4305         TCGA-CG-4306         TCGA-CG-4436 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-CG-4437         TCGA-CG-4438         TCGA-CG-4440 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-CG-4441         TCGA-CG-4443         TCGA-CG-4444 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-CG-4449         TCGA-CG-4455         TCGA-CG-4460 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-CG-4462         TCGA-CG-4465         TCGA-CG-4466 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-CG-4469         TCGA-CG-4472         TCGA-CG-4474 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-CG-4477         TCGA-CG-5716         TCGA-CG-5717 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-CG-5718         TCGA-CG-5719         TCGA-CG-5720 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-CG-5721         TCGA-CG-5722         TCGA-CG-5723 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-CG-5724         TCGA-CG-5725         TCGA-CG-5726 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-CG-5727         TCGA-CG-5728         TCGA-CG-5730 
  "15Q GAIN MUTATED" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-CG-5732         TCGA-CG-5733         TCGA-CG-5734 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-D7-5577         TCGA-D7-5578         TCGA-D7-5579 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-D7-6518         TCGA-D7-6519         TCGA-D7-6520 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" 
        TCGA-D7-6521         TCGA-D7-6522         TCGA-D7-6524 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-D7-6525         TCGA-D7-6526         TCGA-D7-6527 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-D7-6528         TCGA-D7-6815         TCGA-D7-6817 
  "15Q GAIN MUTATED" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-D7-6818         TCGA-D7-6820         TCGA-D7-6822 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EQ-5647         TCGA-EQ-8122         TCGA-F1-6177 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-F1-6874         TCGA-F1-6875         TCGA-FP-7735 
"15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" "15Q GAIN WILD-TYPE" 
        TCGA-FP-7829         TCGA-FP-7916         TCGA-FP-7998 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-HJ-7597         TCGA-IN-7806         TCGA-IN-7808 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" 
        TCGA-IP-7968 
"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-BR-7958 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BR-7959         TCGA-BR-8059         TCGA-BR-8060 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BR-8077         TCGA-BR-8078         TCGA-BR-8080 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BR-8081         TCGA-BR-8284         TCGA-BR-8285 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BR-8286         TCGA-BR-8289         TCGA-BR-8291 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BR-8295         TCGA-BR-8296         TCGA-BR-8297 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-CD-5798         TCGA-CD-5799         TCGA-CD-5800 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-CD-5801         TCGA-CD-5802         TCGA-CD-5803 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-CG-4300         TCGA-CG-4301         TCGA-CG-4304 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-CG-4305         TCGA-CG-4306         TCGA-CG-4436 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-CG-4437         TCGA-CG-4438         TCGA-CG-4440 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-CG-4441         TCGA-CG-4443         TCGA-CG-4444 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-CG-4449         TCGA-CG-4455         TCGA-CG-4460 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-CG-4462         TCGA-CG-4465         TCGA-CG-4466 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-CG-4469         TCGA-CG-4472         TCGA-CG-4474 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-CG-4477         TCGA-CG-5716         TCGA-CG-5717 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-CG-5718         TCGA-CG-5719         TCGA-CG-5720 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-CG-5721         TCGA-CG-5722         TCGA-CG-5723 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-CG-5724         TCGA-CG-5725         TCGA-CG-5726 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-CG-5727         TCGA-CG-5728         TCGA-CG-5730 
  "15Q GAIN MUTATED" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-CG-5732         TCGA-CG-5733         TCGA-CG-5734 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-D7-5577         TCGA-D7-5578         TCGA-D7-5579 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-D7-6518         TCGA-D7-6519         TCGA-D7-6520 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" 
        TCGA-D7-6521         TCGA-D7-6522         TCGA-D7-6524 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-D7-6525         TCGA-D7-6526         TCGA-D7-6527 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-D7-6528         TCGA-D7-6815         TCGA-D7-6817 
  "15Q GAIN MUTATED" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-D7-6818         TCGA-D7-6820         TCGA-D7-6822 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EQ-5647         TCGA-EQ-8122         TCGA-F1-6177 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-F1-6874         TCGA-F1-6875         TCGA-FP-7735 
"15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" "15Q GAIN WILD-TYPE" 
        TCGA-FP-7829         TCGA-FP-7916         TCGA-FP-7998 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-HJ-7597         TCGA-IN-7806         TCGA-IN-7808 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" 
        TCGA-IP-7968 
"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   64   90
        clus
vv       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  FEMALE                1                 64
  MALE                  6                 90
                    vv
clus                 STOMACH ADENOCARCINOMA - DIFFUSE TYPE
  15Q GAIN MUTATED                                       1
  15Q GAIN WILD-TYPE                                    18
                    vv
clus                 STOMACH ADENOCARCINOMA - NOT OTHERWISE SPECIFIED (NOS)
  15Q GAIN MUTATED                                                        3
  15Q GAIN WILD-TYPE                                                     76
                    vv
clus                 STOMACH ADENOCARCINOMA - SIGNET RING TYPE
  15Q GAIN MUTATED                                           0
  15Q GAIN WILD-TYPE                                         1
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - MUCINOUS TYPE
  15Q GAIN MUTATED                                                   0
  15Q GAIN WILD-TYPE                                                 9
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - PAPILLARY TYPE
  15Q GAIN MUTATED                                                    0
  15Q GAIN WILD-TYPE                                                  3
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - TUBULAR TYPE
  15Q GAIN MUTATED                                                  2
  15Q GAIN WILD-TYPE                                                8
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - TYPE NOT OTHERWISE SPECIFIED (NOS)
  15Q GAIN MUTATED                                                                        1
  15Q GAIN WILD-TYPE                                                                     34
D25V4, multiclass
                    vv
clus                 T1 T2 T3 T4
  15Q GAIN MUTATED    0  3  4  0
  15Q GAIN WILD-TYPE  6 50 55 33
D25V5, multiclass
                    vv
clus                 N0 N1 N2 N3
  15Q GAIN MUTATED    5  0  1  1
  15Q GAIN WILD-TYPE 45 57 23 18
D25V6, multiclass
                    vv
clus                  M0  M1  MX
  15Q GAIN MUTATED     6   1   0
  15Q GAIN WILD-TYPE 126  17  11
D25V7, multiclass
                    vv
clus                  I II III IV
  15Q GAIN MUTATED    2  3   2  0
  15Q GAIN WILD-TYPE 23 40  46 29
D25V8, multiclass
D25V9, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED      0    7
  15Q GAIN WILD-TYPE    5  149
     clus
vv    15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  NO                 0                  5
  YES                7                149

Clustering(26) Variable = 16p gain mutation analysis
D26V1, survival
                    sevent
clus2                 0  1
  16P GAIN MUTATED    9  1
  16P GAIN WILD-TYPE 99 15
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                10                114 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                 1                 15 
$`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-BR-7958 TCGA-BR-7959 TCGA-BR-8059 TCGA-BR-8060 
        0.95         0.69         0.16         1.08         0.82         1.32 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
        0.69         0.95         0.49         0.46         0.72         0.26 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
        0.43         0.26         1.18         1.55         1.48         0.76 
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-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-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-D7-6519 TCGA-D7-6520 TCGA-D7-6522 
        3.58         4.54         9.80        15.65         9.63         6.90 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6820 
        0.69         5.95         4.14         1.68         3.65         2.93 
TCGA-D7-6822 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6177 TCGA-F1-6874 TCGA-F1-6875 
        4.27         0.62         7.79         6.54         2.01        72.23 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-HJ-7597 TCGA-IN-7806 TCGA-IN-7808 
        0.20         3.02         3.58        26.43         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              1.380 
[1] "0.4 - 54.0 (5.7)" "0.1 - 72.2 (1.4)"
        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-BR-7958 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BR-7959         TCGA-BR-8059         TCGA-BR-8060 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BR-8077         TCGA-BR-8078         TCGA-BR-8080 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BR-8081         TCGA-BR-8284         TCGA-BR-8285 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BR-8286         TCGA-BR-8289         TCGA-BR-8291 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BR-8295         TCGA-BR-8296         TCGA-BR-8297 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-CD-5798         TCGA-CD-5799         TCGA-CD-5800 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-CD-5801         TCGA-CD-5802         TCGA-CD-5803 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-CG-4300         TCGA-CG-4301         TCGA-CG-4304 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-CG-4305         TCGA-CG-4306         TCGA-CG-4436 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-CG-4437         TCGA-CG-4438         TCGA-CG-4440 
"16P GAIN WILD-TYPE"   "16P GAIN MUTATED" "16P GAIN WILD-TYPE" 
        TCGA-CG-4441         TCGA-CG-4443         TCGA-CG-4444 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-CG-4449         TCGA-CG-4455         TCGA-CG-4460 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE"   "16P GAIN MUTATED" 
        TCGA-CG-4462         TCGA-CG-4465         TCGA-CG-4466 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-CG-4469         TCGA-CG-4472         TCGA-CG-4474 
"16P GAIN WILD-TYPE"   "16P GAIN MUTATED" "16P GAIN WILD-TYPE" 
        TCGA-CG-4477         TCGA-CG-5716         TCGA-CG-5717 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-CG-5718         TCGA-CG-5719         TCGA-CG-5720 
"16P GAIN WILD-TYPE"   "16P GAIN MUTATED" "16P GAIN WILD-TYPE" 
        TCGA-CG-5721         TCGA-CG-5722         TCGA-CG-5723 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-CG-5724         TCGA-CG-5725         TCGA-CG-5726 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-CG-5727         TCGA-CG-5728         TCGA-CG-5730 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-CG-5732         TCGA-CG-5733         TCGA-CG-5734 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-D7-5577         TCGA-D7-5578         TCGA-D7-5579 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-D7-6518         TCGA-D7-6519         TCGA-D7-6520 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-D7-6521         TCGA-D7-6522         TCGA-D7-6524 
  "16P GAIN MUTATED" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-D7-6525         TCGA-D7-6526         TCGA-D7-6527 
"16P GAIN WILD-TYPE"   "16P GAIN MUTATED" "16P GAIN WILD-TYPE" 
        TCGA-D7-6528         TCGA-D7-6815         TCGA-D7-6817 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE"   "16P GAIN MUTATED" 
        TCGA-D7-6818         TCGA-D7-6820         TCGA-D7-6822 
  "16P GAIN MUTATED" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-EQ-5647         TCGA-EQ-8122         TCGA-F1-6177 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-F1-6874         TCGA-F1-6875         TCGA-FP-7735 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE"   "16P GAIN MUTATED" 
        TCGA-FP-7829         TCGA-FP-7916         TCGA-FP-7998 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-HJ-7597         TCGA-IN-7806         TCGA-IN-7808 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-IP-7968 
  "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-BR-7958 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BR-7959         TCGA-BR-8059         TCGA-BR-8060 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BR-8077         TCGA-BR-8078         TCGA-BR-8080 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BR-8081         TCGA-BR-8284         TCGA-BR-8285 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BR-8286         TCGA-BR-8289         TCGA-BR-8291 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BR-8295         TCGA-BR-8296         TCGA-BR-8297 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-CD-5798         TCGA-CD-5799         TCGA-CD-5800 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-CD-5801         TCGA-CD-5802         TCGA-CD-5803 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-CG-4300         TCGA-CG-4301         TCGA-CG-4304 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-CG-4305         TCGA-CG-4306         TCGA-CG-4436 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-CG-4437         TCGA-CG-4438         TCGA-CG-4440 
"16P GAIN WILD-TYPE"   "16P GAIN MUTATED" "16P GAIN WILD-TYPE" 
        TCGA-CG-4441         TCGA-CG-4443         TCGA-CG-4444 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-CG-4449         TCGA-CG-4455         TCGA-CG-4460 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE"   "16P GAIN MUTATED" 
        TCGA-CG-4462         TCGA-CG-4465         TCGA-CG-4466 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-CG-4469         TCGA-CG-4472         TCGA-CG-4474 
"16P GAIN WILD-TYPE"   "16P GAIN MUTATED" "16P GAIN WILD-TYPE" 
        TCGA-CG-4477         TCGA-CG-5716         TCGA-CG-5717 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-CG-5718         TCGA-CG-5719         TCGA-CG-5720 
"16P GAIN WILD-TYPE"   "16P GAIN MUTATED" "16P GAIN WILD-TYPE" 
        TCGA-CG-5721         TCGA-CG-5722         TCGA-CG-5723 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-CG-5724         TCGA-CG-5725         TCGA-CG-5726 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-CG-5727         TCGA-CG-5728         TCGA-CG-5730 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-CG-5732         TCGA-CG-5733         TCGA-CG-5734 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-D7-5577         TCGA-D7-5578         TCGA-D7-5579 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-D7-6518         TCGA-D7-6519         TCGA-D7-6520 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-D7-6521         TCGA-D7-6522         TCGA-D7-6524 
  "16P GAIN MUTATED" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-D7-6525         TCGA-D7-6526         TCGA-D7-6527 
"16P GAIN WILD-TYPE"   "16P GAIN MUTATED" "16P GAIN WILD-TYPE" 
        TCGA-D7-6528         TCGA-D7-6815         TCGA-D7-6817 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE"   "16P GAIN MUTATED" 
        TCGA-D7-6818         TCGA-D7-6820         TCGA-D7-6822 
  "16P GAIN MUTATED" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-EQ-5647         TCGA-EQ-8122         TCGA-F1-6177 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-F1-6874         TCGA-F1-6875         TCGA-FP-7735 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE"   "16P GAIN MUTATED" 
        TCGA-FP-7829         TCGA-FP-7916         TCGA-FP-7998 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-HJ-7597         TCGA-IN-7806         TCGA-IN-7808 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-IP-7968 
  "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-BR-7958 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BR-7959         TCGA-BR-8059         TCGA-BR-8060 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BR-8077         TCGA-BR-8078         TCGA-BR-8080 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BR-8081         TCGA-BR-8284         TCGA-BR-8285 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BR-8286         TCGA-BR-8289         TCGA-BR-8291 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BR-8295         TCGA-BR-8296         TCGA-BR-8297 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-CD-5798         TCGA-CD-5799         TCGA-CD-5800 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-CD-5801         TCGA-CD-5802         TCGA-CD-5803 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-CG-4300         TCGA-CG-4301         TCGA-CG-4304 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-CG-4305         TCGA-CG-4306         TCGA-CG-4436 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-CG-4437         TCGA-CG-4438         TCGA-CG-4440 
"16P GAIN WILD-TYPE"   "16P GAIN MUTATED" "16P GAIN WILD-TYPE" 
        TCGA-CG-4441         TCGA-CG-4443         TCGA-CG-4444 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-CG-4449         TCGA-CG-4455         TCGA-CG-4460 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE"   "16P GAIN MUTATED" 
        TCGA-CG-4462         TCGA-CG-4465         TCGA-CG-4466 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-CG-4469         TCGA-CG-4472         TCGA-CG-4474 
"16P GAIN WILD-TYPE"   "16P GAIN MUTATED" "16P GAIN WILD-TYPE" 
        TCGA-CG-4477         TCGA-CG-5716         TCGA-CG-5717 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-CG-5718         TCGA-CG-5719         TCGA-CG-5720 
"16P GAIN WILD-TYPE"   "16P GAIN MUTATED" "16P GAIN WILD-TYPE" 
        TCGA-CG-5721         TCGA-CG-5722         TCGA-CG-5723 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-CG-5724         TCGA-CG-5725         TCGA-CG-5726 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-CG-5727         TCGA-CG-5728         TCGA-CG-5730 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-CG-5732         TCGA-CG-5733         TCGA-CG-5734 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-D7-5577         TCGA-D7-5578         TCGA-D7-5579 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-D7-6518         TCGA-D7-6519         TCGA-D7-6520 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-D7-6521         TCGA-D7-6522         TCGA-D7-6524 
  "16P GAIN MUTATED" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-D7-6525         TCGA-D7-6526         TCGA-D7-6527 
"16P GAIN WILD-TYPE"   "16P GAIN MUTATED" "16P GAIN WILD-TYPE" 
        TCGA-D7-6528         TCGA-D7-6815         TCGA-D7-6817 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE"   "16P GAIN MUTATED" 
        TCGA-D7-6818         TCGA-D7-6820         TCGA-D7-6822 
  "16P GAIN MUTATED" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-EQ-5647         TCGA-EQ-8122         TCGA-F1-6177 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-F1-6874         TCGA-F1-6875         TCGA-FP-7735 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE"   "16P GAIN MUTATED" 
        TCGA-FP-7829         TCGA-FP-7916         TCGA-FP-7998 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-HJ-7597         TCGA-IN-7806         TCGA-IN-7808 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-IP-7968 
  "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   61   88
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  FEMALE                4                 61
  MALE                  8                 88
                    vv
clus                 STOMACH ADENOCARCINOMA - DIFFUSE TYPE
  16P GAIN MUTATED                                       2
  16P GAIN WILD-TYPE                                    17
                    vv
clus                 STOMACH ADENOCARCINOMA - NOT OTHERWISE SPECIFIED (NOS)
  16P GAIN MUTATED                                                        4
  16P GAIN WILD-TYPE                                                     75
                    vv
clus                 STOMACH ADENOCARCINOMA - SIGNET RING TYPE
  16P GAIN MUTATED                                           0
  16P GAIN WILD-TYPE                                         1
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - MUCINOUS TYPE
  16P GAIN MUTATED                                                   0
  16P GAIN WILD-TYPE                                                 9
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - PAPILLARY TYPE
  16P GAIN MUTATED                                                    0
  16P GAIN WILD-TYPE                                                  3
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - TUBULAR TYPE
  16P GAIN MUTATED                                                  2
  16P GAIN WILD-TYPE                                                8
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - TYPE NOT OTHERWISE SPECIFIED (NOS)
  16P GAIN MUTATED                                                                        3
  16P GAIN WILD-TYPE                                                                     32
D26V4, multiclass
                    vv
clus                 T1 T2 T3 T4
  16P GAIN MUTATED    0  4  3  5
  16P GAIN WILD-TYPE  6 49 56 28
D26V5, multiclass
                    vv
clus                 N0 N1 N2 N3
  16P GAIN MUTATED    2  3  5  2
  16P GAIN WILD-TYPE 48 54 19 17
D26V6, multiclass
                    vv
clus                  M0  M1  MX
  16P GAIN MUTATED     8   2   2
  16P GAIN WILD-TYPE 124  16   9
D26V7, multiclass
                    vv
clus                  I II III IV
  16P GAIN MUTATED    1  0   5  6
  16P GAIN WILD-TYPE 24 43  43 23
D26V8, multiclass
D26V9, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED      1   11
  16P GAIN WILD-TYPE    4  145
     clus
vv    16P GAIN MUTATED 16P GAIN WILD-TYPE
  NO                 1                  4
  YES               11                145

Clustering(27) Variable = 16q gain mutation analysis
D27V1, survival
                    sevent
clus2                  0   1
  16Q GAIN MUTATED     5   1
  16Q GAIN WILD-TYPE 103  15
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                 6                118 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                 1                 15 
$`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-BR-7958 TCGA-BR-7959 TCGA-BR-8059 TCGA-BR-8060 
        0.95         0.69         0.16         1.08         0.82         1.32 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
        0.69         0.95         0.49         0.46         0.72         0.26 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
        0.43         0.26         1.18         1.55         1.48         0.76 
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-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-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-D7-6519 TCGA-D7-6520 TCGA-D7-6522 
        3.58         4.54         9.80        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-EQ-8122 
        4.70         4.04         2.93         4.27         0.62         7.79 
TCGA-F1-6177 TCGA-F1-6874 TCGA-F1-6875 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
        6.54         2.01        72.23         0.20         3.02         3.58 
TCGA-HJ-7597 TCGA-IN-7806 TCGA-IN-7808 TCGA-IP-7968 
       26.43         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              1.480 
[1] "0.4 - 54.0 (10.1)" "0.1 - 72.2 (1.5)" 
        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-BR-7958 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BR-7959         TCGA-BR-8059         TCGA-BR-8060 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BR-8077         TCGA-BR-8078         TCGA-BR-8080 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BR-8081         TCGA-BR-8284         TCGA-BR-8285 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BR-8286         TCGA-BR-8289         TCGA-BR-8291 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BR-8295         TCGA-BR-8296         TCGA-BR-8297 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-CD-5798         TCGA-CD-5799         TCGA-CD-5800 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-CD-5801         TCGA-CD-5802         TCGA-CD-5803 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-CG-4300         TCGA-CG-4301         TCGA-CG-4304 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-CG-4305         TCGA-CG-4306         TCGA-CG-4436 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-CG-4437         TCGA-CG-4438         TCGA-CG-4440 
"16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" 
        TCGA-CG-4441         TCGA-CG-4443         TCGA-CG-4444 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-CG-4449         TCGA-CG-4455         TCGA-CG-4460 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" 
        TCGA-CG-4462         TCGA-CG-4465         TCGA-CG-4466 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-CG-4469         TCGA-CG-4472         TCGA-CG-4474 
"16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" 
        TCGA-CG-4477         TCGA-CG-5716         TCGA-CG-5717 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-CG-5718         TCGA-CG-5719         TCGA-CG-5720 
"16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" 
        TCGA-CG-5721         TCGA-CG-5722         TCGA-CG-5723 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-CG-5724         TCGA-CG-5725         TCGA-CG-5726 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-CG-5727         TCGA-CG-5728         TCGA-CG-5730 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-CG-5732         TCGA-CG-5733         TCGA-CG-5734 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-D7-5577         TCGA-D7-5578         TCGA-D7-5579 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-D7-6518         TCGA-D7-6519         TCGA-D7-6520 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-D7-6521         TCGA-D7-6522         TCGA-D7-6524 
  "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-D7-6525         TCGA-D7-6526         TCGA-D7-6527 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-D7-6528         TCGA-D7-6815         TCGA-D7-6817 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-D7-6818         TCGA-D7-6820         TCGA-D7-6822 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EQ-5647         TCGA-EQ-8122         TCGA-F1-6177 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-F1-6874         TCGA-F1-6875         TCGA-FP-7735 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" 
        TCGA-FP-7829         TCGA-FP-7916         TCGA-FP-7998 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-HJ-7597         TCGA-IN-7806         TCGA-IN-7808 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-IP-7968 
"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-BR-7958 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BR-7959         TCGA-BR-8059         TCGA-BR-8060 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BR-8077         TCGA-BR-8078         TCGA-BR-8080 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BR-8081         TCGA-BR-8284         TCGA-BR-8285 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BR-8286         TCGA-BR-8289         TCGA-BR-8291 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BR-8295         TCGA-BR-8296         TCGA-BR-8297 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-CD-5798         TCGA-CD-5799         TCGA-CD-5800 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-CD-5801         TCGA-CD-5802         TCGA-CD-5803 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-CG-4300         TCGA-CG-4301         TCGA-CG-4304 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-CG-4305         TCGA-CG-4306         TCGA-CG-4436 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-CG-4437         TCGA-CG-4438         TCGA-CG-4440 
"16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" 
        TCGA-CG-4441         TCGA-CG-4443         TCGA-CG-4444 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-CG-4449         TCGA-CG-4455         TCGA-CG-4460 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" 
        TCGA-CG-4462         TCGA-CG-4465         TCGA-CG-4466 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-CG-4469         TCGA-CG-4472         TCGA-CG-4474 
"16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" 
        TCGA-CG-4477         TCGA-CG-5716         TCGA-CG-5717 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-CG-5718         TCGA-CG-5719         TCGA-CG-5720 
"16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" 
        TCGA-CG-5721         TCGA-CG-5722         TCGA-CG-5723 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-CG-5724         TCGA-CG-5725         TCGA-CG-5726 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-CG-5727         TCGA-CG-5728         TCGA-CG-5730 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-CG-5732         TCGA-CG-5733         TCGA-CG-5734 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-D7-5577         TCGA-D7-5578         TCGA-D7-5579 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-D7-6518         TCGA-D7-6519         TCGA-D7-6520 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-D7-6521         TCGA-D7-6522         TCGA-D7-6524 
  "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-D7-6525         TCGA-D7-6526         TCGA-D7-6527 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-D7-6528         TCGA-D7-6815         TCGA-D7-6817 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-D7-6818         TCGA-D7-6820         TCGA-D7-6822 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EQ-5647         TCGA-EQ-8122         TCGA-F1-6177 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-F1-6874         TCGA-F1-6875         TCGA-FP-7735 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" 
        TCGA-FP-7829         TCGA-FP-7916         TCGA-FP-7998 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-HJ-7597         TCGA-IN-7806         TCGA-IN-7808 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-IP-7968 
"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-BR-7958 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BR-7959         TCGA-BR-8059         TCGA-BR-8060 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BR-8077         TCGA-BR-8078         TCGA-BR-8080 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BR-8081         TCGA-BR-8284         TCGA-BR-8285 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BR-8286         TCGA-BR-8289         TCGA-BR-8291 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BR-8295         TCGA-BR-8296         TCGA-BR-8297 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-CD-5798         TCGA-CD-5799         TCGA-CD-5800 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-CD-5801         TCGA-CD-5802         TCGA-CD-5803 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-CG-4300         TCGA-CG-4301         TCGA-CG-4304 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-CG-4305         TCGA-CG-4306         TCGA-CG-4436 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-CG-4437         TCGA-CG-4438         TCGA-CG-4440 
"16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" 
        TCGA-CG-4441         TCGA-CG-4443         TCGA-CG-4444 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-CG-4449         TCGA-CG-4455         TCGA-CG-4460 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" 
        TCGA-CG-4462         TCGA-CG-4465         TCGA-CG-4466 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-CG-4469         TCGA-CG-4472         TCGA-CG-4474 
"16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" 
        TCGA-CG-4477         TCGA-CG-5716         TCGA-CG-5717 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-CG-5718         TCGA-CG-5719         TCGA-CG-5720 
"16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" 
        TCGA-CG-5721         TCGA-CG-5722         TCGA-CG-5723 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-CG-5724         TCGA-CG-5725         TCGA-CG-5726 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-CG-5727         TCGA-CG-5728         TCGA-CG-5730 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-CG-5732         TCGA-CG-5733         TCGA-CG-5734 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-D7-5577         TCGA-D7-5578         TCGA-D7-5579 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-D7-6518         TCGA-D7-6519         TCGA-D7-6520 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-D7-6521         TCGA-D7-6522         TCGA-D7-6524 
  "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-D7-6525         TCGA-D7-6526         TCGA-D7-6527 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-D7-6528         TCGA-D7-6815         TCGA-D7-6817 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-D7-6818         TCGA-D7-6820         TCGA-D7-6822 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EQ-5647         TCGA-EQ-8122         TCGA-F1-6177 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-F1-6874         TCGA-F1-6875         TCGA-FP-7735 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" 
        TCGA-FP-7829         TCGA-FP-7916         TCGA-FP-7998 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-HJ-7597         TCGA-IN-7806         TCGA-IN-7808 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-IP-7968 
"16Q GAIN WILD-TYPE" 
[1] "hr=" "1.5"
D27V2, continuous
D27V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED      3    5
  16Q GAIN WILD-TYPE   62   91
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  FEMALE                3                 62
  MALE                  5                 91
                    vv
clus                 STOMACH ADENOCARCINOMA - DIFFUSE TYPE
  16Q GAIN MUTATED                                       1
  16Q GAIN WILD-TYPE                                    18
                    vv
clus                 STOMACH ADENOCARCINOMA - NOT OTHERWISE SPECIFIED (NOS)
  16Q GAIN MUTATED                                                        3
  16Q GAIN WILD-TYPE                                                     76
                    vv
clus                 STOMACH ADENOCARCINOMA - SIGNET RING TYPE
  16Q GAIN MUTATED                                           0
  16Q GAIN WILD-TYPE                                         1
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - MUCINOUS TYPE
  16Q GAIN MUTATED                                                   0
  16Q GAIN WILD-TYPE                                                 9
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - PAPILLARY TYPE
  16Q GAIN MUTATED                                                    0
  16Q GAIN WILD-TYPE                                                  3
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - TUBULAR TYPE
  16Q GAIN MUTATED                                                  0
  16Q GAIN WILD-TYPE                                               10
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - TYPE NOT OTHERWISE SPECIFIED (NOS)
  16Q GAIN MUTATED                                                                        3
  16Q GAIN WILD-TYPE                                                                     32
D27V4, multiclass
                    vv
clus                 T1 T2 T3 T4
  16Q GAIN MUTATED    0  2  1  5
  16Q GAIN WILD-TYPE  6 51 58 28
D27V5, multiclass
                    vv
clus                 N0 N1 N2 N3
  16Q GAIN MUTATED    2  3  3  0
  16Q GAIN WILD-TYPE 48 54 21 19
D27V6, multiclass
                    vv
clus                  M0  M1  MX
  16Q GAIN MUTATED     5   2   1
  16Q GAIN WILD-TYPE 127  16  10
D27V7, multiclass
                    vv
clus                  I II III IV
  16Q GAIN MUTATED    1  0   2  5
  16Q GAIN WILD-TYPE 24 43  46 24
D27V8, multiclass
D27V9, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED      0    8
  16Q GAIN WILD-TYPE    5  148
     clus
vv    16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  NO                 0                  5
  YES                8                148

Clustering(28) Variable = 17p gain mutation analysis
D28V1, survival
                    sevent
clus2                  0   1
  17P GAIN MUTATED     2   4
  17P GAIN WILD-TYPE 106  12
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                 6                118 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                 4                 12 
$`17P GAIN MUTATED`
TCGA-CG-4460 TCGA-CG-5724 TCGA-D7-6817 TCGA-EQ-5647 TCGA-F1-6875 TCGA-FP-7829 
       21.99        12.03         4.70         0.62        72.23         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-BR-7958 TCGA-BR-7959 TCGA-BR-8059 TCGA-BR-8060 
        0.95         0.69         0.16         1.08         0.82         1.32 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
        0.69         0.95         0.49         0.46         0.72         0.26 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
        0.43         0.26         1.18         1.55         1.48         0.76 
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-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-EQ-8122 TCGA-F1-6177 TCGA-F1-6874 TCGA-FP-7735 TCGA-FP-7916 TCGA-FP-7998 
        7.79         6.54         2.01         0.39         3.02         3.58 
TCGA-HJ-7597 TCGA-IN-7806 TCGA-IN-7808 TCGA-IP-7968 
       26.43         6.87         3.55         2.53 

  17P GAIN MUTATED 17P GAIN WILD-TYPE 
              0.20               0.07 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
             72.23              70.06 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
             8.365              1.480 
[1] "0.2 - 72.2 (8.4)" "0.1 - 70.1 (1.5)"
        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-BR-7958 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BR-7959         TCGA-BR-8059         TCGA-BR-8060 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BR-8077         TCGA-BR-8078         TCGA-BR-8080 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BR-8081         TCGA-BR-8284         TCGA-BR-8285 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BR-8286         TCGA-BR-8289         TCGA-BR-8291 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BR-8295         TCGA-BR-8296         TCGA-BR-8297 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-CD-5798         TCGA-CD-5799         TCGA-CD-5800 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-CD-5801         TCGA-CD-5802         TCGA-CD-5803 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-CG-4300         TCGA-CG-4301         TCGA-CG-4304 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-CG-4305         TCGA-CG-4306         TCGA-CG-4436 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-CG-4437         TCGA-CG-4438         TCGA-CG-4440 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-CG-4441         TCGA-CG-4443         TCGA-CG-4444 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-CG-4449         TCGA-CG-4455         TCGA-CG-4460 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE"   "17P GAIN MUTATED" 
        TCGA-CG-4462         TCGA-CG-4465         TCGA-CG-4466 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-CG-4469         TCGA-CG-4472         TCGA-CG-4474 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-CG-4477         TCGA-CG-5716         TCGA-CG-5717 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-CG-5718         TCGA-CG-5719         TCGA-CG-5720 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-CG-5721         TCGA-CG-5722         TCGA-CG-5723 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-CG-5724         TCGA-CG-5725         TCGA-CG-5726 
  "17P GAIN MUTATED" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-CG-5727         TCGA-CG-5728         TCGA-CG-5730 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-CG-5732         TCGA-CG-5733         TCGA-CG-5734 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-D7-5577         TCGA-D7-5578         TCGA-D7-5579 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-D7-6518         TCGA-D7-6519         TCGA-D7-6520 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-D7-6521         TCGA-D7-6522         TCGA-D7-6524 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-D7-6525         TCGA-D7-6526         TCGA-D7-6527 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-D7-6528         TCGA-D7-6815         TCGA-D7-6817 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE"   "17P GAIN MUTATED" 
        TCGA-D7-6818         TCGA-D7-6820         TCGA-D7-6822 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EQ-5647         TCGA-EQ-8122         TCGA-F1-6177 
  "17P GAIN MUTATED" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-F1-6874         TCGA-F1-6875         TCGA-FP-7735 
"17P GAIN WILD-TYPE"   "17P GAIN MUTATED" "17P GAIN WILD-TYPE" 
        TCGA-FP-7829         TCGA-FP-7916         TCGA-FP-7998 
  "17P GAIN MUTATED" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-HJ-7597         TCGA-IN-7806         TCGA-IN-7808 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-IP-7968 
"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-BR-7958 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BR-7959         TCGA-BR-8059         TCGA-BR-8060 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BR-8077         TCGA-BR-8078         TCGA-BR-8080 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BR-8081         TCGA-BR-8284         TCGA-BR-8285 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BR-8286         TCGA-BR-8289         TCGA-BR-8291 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BR-8295         TCGA-BR-8296         TCGA-BR-8297 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-CD-5798         TCGA-CD-5799         TCGA-CD-5800 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-CD-5801         TCGA-CD-5802         TCGA-CD-5803 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-CG-4300         TCGA-CG-4301         TCGA-CG-4304 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-CG-4305         TCGA-CG-4306         TCGA-CG-4436 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-CG-4437         TCGA-CG-4438         TCGA-CG-4440 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-CG-4441         TCGA-CG-4443         TCGA-CG-4444 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-CG-4449         TCGA-CG-4455         TCGA-CG-4460 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE"   "17P GAIN MUTATED" 
        TCGA-CG-4462         TCGA-CG-4465         TCGA-CG-4466 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-CG-4469         TCGA-CG-4472         TCGA-CG-4474 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-CG-4477         TCGA-CG-5716         TCGA-CG-5717 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-CG-5718         TCGA-CG-5719         TCGA-CG-5720 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-CG-5721         TCGA-CG-5722         TCGA-CG-5723 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-CG-5724         TCGA-CG-5725         TCGA-CG-5726 
  "17P GAIN MUTATED" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-CG-5727         TCGA-CG-5728         TCGA-CG-5730 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-CG-5732         TCGA-CG-5733         TCGA-CG-5734 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-D7-5577         TCGA-D7-5578         TCGA-D7-5579 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-D7-6518         TCGA-D7-6519         TCGA-D7-6520 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-D7-6521         TCGA-D7-6522         TCGA-D7-6524 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-D7-6525         TCGA-D7-6526         TCGA-D7-6527 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-D7-6528         TCGA-D7-6815         TCGA-D7-6817 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE"   "17P GAIN MUTATED" 
        TCGA-D7-6818         TCGA-D7-6820         TCGA-D7-6822 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EQ-5647         TCGA-EQ-8122         TCGA-F1-6177 
  "17P GAIN MUTATED" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-F1-6874         TCGA-F1-6875         TCGA-FP-7735 
"17P GAIN WILD-TYPE"   "17P GAIN MUTATED" "17P GAIN WILD-TYPE" 
        TCGA-FP-7829         TCGA-FP-7916         TCGA-FP-7998 
  "17P GAIN MUTATED" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-HJ-7597         TCGA-IN-7806         TCGA-IN-7808 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-IP-7968 
"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-BR-7958 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BR-7959         TCGA-BR-8059         TCGA-BR-8060 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BR-8077         TCGA-BR-8078         TCGA-BR-8080 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BR-8081         TCGA-BR-8284         TCGA-BR-8285 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BR-8286         TCGA-BR-8289         TCGA-BR-8291 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BR-8295         TCGA-BR-8296         TCGA-BR-8297 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-CD-5798         TCGA-CD-5799         TCGA-CD-5800 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-CD-5801         TCGA-CD-5802         TCGA-CD-5803 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-CG-4300         TCGA-CG-4301         TCGA-CG-4304 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-CG-4305         TCGA-CG-4306         TCGA-CG-4436 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-CG-4437         TCGA-CG-4438         TCGA-CG-4440 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-CG-4441         TCGA-CG-4443         TCGA-CG-4444 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-CG-4449         TCGA-CG-4455         TCGA-CG-4460 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE"   "17P GAIN MUTATED" 
        TCGA-CG-4462         TCGA-CG-4465         TCGA-CG-4466 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-CG-4469         TCGA-CG-4472         TCGA-CG-4474 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-CG-4477         TCGA-CG-5716         TCGA-CG-5717 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-CG-5718         TCGA-CG-5719         TCGA-CG-5720 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-CG-5721         TCGA-CG-5722         TCGA-CG-5723 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-CG-5724         TCGA-CG-5725         TCGA-CG-5726 
  "17P GAIN MUTATED" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-CG-5727         TCGA-CG-5728         TCGA-CG-5730 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-CG-5732         TCGA-CG-5733         TCGA-CG-5734 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-D7-5577         TCGA-D7-5578         TCGA-D7-5579 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-D7-6518         TCGA-D7-6519         TCGA-D7-6520 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-D7-6521         TCGA-D7-6522         TCGA-D7-6524 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-D7-6525         TCGA-D7-6526         TCGA-D7-6527 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-D7-6528         TCGA-D7-6815         TCGA-D7-6817 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE"   "17P GAIN MUTATED" 
        TCGA-D7-6818         TCGA-D7-6820         TCGA-D7-6822 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EQ-5647         TCGA-EQ-8122         TCGA-F1-6177 
  "17P GAIN MUTATED" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-F1-6874         TCGA-F1-6875         TCGA-FP-7735 
"17P GAIN WILD-TYPE"   "17P GAIN MUTATED" "17P GAIN WILD-TYPE" 
        TCGA-FP-7829         TCGA-FP-7916         TCGA-FP-7998 
  "17P GAIN MUTATED" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-HJ-7597         TCGA-IN-7806         TCGA-IN-7808 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-IP-7968 
"17P GAIN WILD-TYPE" 
[1] "hr=" "2.4"
D28V2, continuous
D28V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED      2    4
  17P GAIN WILD-TYPE   63   92
        clus
vv       17P GAIN MUTATED 17P GAIN WILD-TYPE
  FEMALE                2                 63
  MALE                  4                 92
                    vv
clus                 STOMACH ADENOCARCINOMA - DIFFUSE TYPE
  17P GAIN MUTATED                                       1
  17P GAIN WILD-TYPE                                    18
                    vv
clus                 STOMACH ADENOCARCINOMA - NOT OTHERWISE SPECIFIED (NOS)
  17P GAIN MUTATED                                                        2
  17P GAIN WILD-TYPE                                                     77
                    vv
clus                 STOMACH ADENOCARCINOMA - SIGNET RING TYPE
  17P GAIN MUTATED                                           0
  17P GAIN WILD-TYPE                                         1
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - MUCINOUS TYPE
  17P GAIN MUTATED                                                   1
  17P GAIN WILD-TYPE                                                 8
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - PAPILLARY TYPE
  17P GAIN MUTATED                                                    0
  17P GAIN WILD-TYPE                                                  3
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - TUBULAR TYPE
  17P GAIN MUTATED                                                  1
  17P GAIN WILD-TYPE                                                9
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - TYPE NOT OTHERWISE SPECIFIED (NOS)
  17P GAIN MUTATED                                                                        1
  17P GAIN WILD-TYPE                                                                     34
D28V4, multiclass
                    vv
clus                 T1 T2 T3 T4
  17P GAIN MUTATED    0  2  2  2
  17P GAIN WILD-TYPE  6 51 57 31
D28V5, multiclass
                    vv
clus                 N0 N1 N2 N3
  17P GAIN MUTATED    1  2  0  3
  17P GAIN WILD-TYPE 49 55 24 16
D28V6, multiclass
                    vv
clus                  M0  M1  MX
  17P GAIN MUTATED     3   3   0
  17P GAIN WILD-TYPE 129  15  11
D28V7, multiclass
                    vv
clus                  I II III IV
  17P GAIN MUTATED    1  0   2  3
  17P GAIN WILD-TYPE 24 43  46 26
D28V8, multiclass
D28V9, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED      0    6
  17P GAIN WILD-TYPE    5  150
     clus
vv    17P GAIN MUTATED 17P GAIN WILD-TYPE
  NO                 0                  5
  YES                6                150

Clustering(29) Variable = 17q gain mutation analysis
D29V1, survival
                    sevent
clus2                  0   1
  17Q GAIN MUTATED     4   4
  17Q GAIN WILD-TYPE 104  12
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                 8                116 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                 4                 12 
$`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-BR-7958 TCGA-BR-7959 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
        0.69         0.16         1.08         0.82         1.32         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
        0.95         0.49         0.46         0.72         0.26         0.43 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-CD-5798 
        0.26         1.18         1.55         1.48         0.76         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-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-4477 TCGA-CG-5716 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5720 
        1.02         1.02         1.02         6.94         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-D7-6519 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-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-EQ-8122 TCGA-F1-6177 
        3.65         4.04         2.93         4.27         7.79         6.54 
TCGA-F1-6874 TCGA-FP-7735 TCGA-FP-7916 TCGA-FP-7998 TCGA-HJ-7597 TCGA-IN-7806 
        2.01         0.39         3.02         3.58        26.43         6.87 
TCGA-IN-7808 TCGA-IP-7968 
        3.55         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 
             2.860              1.515 
[1] "0.1 - 72.2 (2.9)" "0.1 - 70.1 (1.5)"
        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-BR-7958 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-BR-7959         TCGA-BR-8059         TCGA-BR-8060 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-BR-8077         TCGA-BR-8078         TCGA-BR-8080 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-BR-8081         TCGA-BR-8284         TCGA-BR-8285 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-BR-8286         TCGA-BR-8289         TCGA-BR-8291 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-BR-8295         TCGA-BR-8296         TCGA-BR-8297 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-CD-5798         TCGA-CD-5799         TCGA-CD-5800 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-CD-5801         TCGA-CD-5802         TCGA-CD-5803 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-CG-4300         TCGA-CG-4301         TCGA-CG-4304 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-CG-4305         TCGA-CG-4306         TCGA-CG-4436 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-CG-4437         TCGA-CG-4438         TCGA-CG-4440 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-CG-4441         TCGA-CG-4443         TCGA-CG-4444 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-CG-4449         TCGA-CG-4455         TCGA-CG-4460 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
        TCGA-CG-4462         TCGA-CG-4465         TCGA-CG-4466 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-CG-4469         TCGA-CG-4472         TCGA-CG-4474 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-CG-4477         TCGA-CG-5716         TCGA-CG-5717 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-CG-5718         TCGA-CG-5719         TCGA-CG-5720 
"17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" 
        TCGA-CG-5721         TCGA-CG-5722         TCGA-CG-5723 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-CG-5724         TCGA-CG-5725         TCGA-CG-5726 
  "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-CG-5727         TCGA-CG-5728         TCGA-CG-5730 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-CG-5732         TCGA-CG-5733         TCGA-CG-5734 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-D7-5577         TCGA-D7-5578         TCGA-D7-5579 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-D7-6518         TCGA-D7-6519         TCGA-D7-6520 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-D7-6521         TCGA-D7-6522         TCGA-D7-6524 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-D7-6525         TCGA-D7-6526         TCGA-D7-6527 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-D7-6528         TCGA-D7-6815         TCGA-D7-6817 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
        TCGA-D7-6818         TCGA-D7-6820         TCGA-D7-6822 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-EQ-5647         TCGA-EQ-8122         TCGA-F1-6177 
  "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-F1-6874         TCGA-F1-6875         TCGA-FP-7735 
"17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" 
        TCGA-FP-7829         TCGA-FP-7916         TCGA-FP-7998 
  "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-HJ-7597         TCGA-IN-7806         TCGA-IN-7808 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-IP-7968 
"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-BR-7958 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-BR-7959         TCGA-BR-8059         TCGA-BR-8060 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-BR-8077         TCGA-BR-8078         TCGA-BR-8080 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-BR-8081         TCGA-BR-8284         TCGA-BR-8285 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-BR-8286         TCGA-BR-8289         TCGA-BR-8291 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-BR-8295         TCGA-BR-8296         TCGA-BR-8297 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-CD-5798         TCGA-CD-5799         TCGA-CD-5800 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-CD-5801         TCGA-CD-5802         TCGA-CD-5803 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-CG-4300         TCGA-CG-4301         TCGA-CG-4304 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-CG-4305         TCGA-CG-4306         TCGA-CG-4436 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-CG-4437         TCGA-CG-4438         TCGA-CG-4440 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-CG-4441         TCGA-CG-4443         TCGA-CG-4444 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-CG-4449         TCGA-CG-4455         TCGA-CG-4460 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
        TCGA-CG-4462         TCGA-CG-4465         TCGA-CG-4466 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-CG-4469         TCGA-CG-4472         TCGA-CG-4474 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-CG-4477         TCGA-CG-5716         TCGA-CG-5717 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-CG-5718         TCGA-CG-5719         TCGA-CG-5720 
"17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" 
        TCGA-CG-5721         TCGA-CG-5722         TCGA-CG-5723 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-CG-5724         TCGA-CG-5725         TCGA-CG-5726 
  "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-CG-5727         TCGA-CG-5728         TCGA-CG-5730 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-CG-5732         TCGA-CG-5733         TCGA-CG-5734 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-D7-5577         TCGA-D7-5578         TCGA-D7-5579 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-D7-6518         TCGA-D7-6519         TCGA-D7-6520 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-D7-6521         TCGA-D7-6522         TCGA-D7-6524 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-D7-6525         TCGA-D7-6526         TCGA-D7-6527 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-D7-6528         TCGA-D7-6815         TCGA-D7-6817 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
        TCGA-D7-6818         TCGA-D7-6820         TCGA-D7-6822 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-EQ-5647         TCGA-EQ-8122         TCGA-F1-6177 
  "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-F1-6874         TCGA-F1-6875         TCGA-FP-7735 
"17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" 
        TCGA-FP-7829         TCGA-FP-7916         TCGA-FP-7998 
  "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-HJ-7597         TCGA-IN-7806         TCGA-IN-7808 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-IP-7968 
"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-BR-7958 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-BR-7959         TCGA-BR-8059         TCGA-BR-8060 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-BR-8077         TCGA-BR-8078         TCGA-BR-8080 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-BR-8081         TCGA-BR-8284         TCGA-BR-8285 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-BR-8286         TCGA-BR-8289         TCGA-BR-8291 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-BR-8295         TCGA-BR-8296         TCGA-BR-8297 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-CD-5798         TCGA-CD-5799         TCGA-CD-5800 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-CD-5801         TCGA-CD-5802         TCGA-CD-5803 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-CG-4300         TCGA-CG-4301         TCGA-CG-4304 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-CG-4305         TCGA-CG-4306         TCGA-CG-4436 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-CG-4437         TCGA-CG-4438         TCGA-CG-4440 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-CG-4441         TCGA-CG-4443         TCGA-CG-4444 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-CG-4449         TCGA-CG-4455         TCGA-CG-4460 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
        TCGA-CG-4462         TCGA-CG-4465         TCGA-CG-4466 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-CG-4469         TCGA-CG-4472         TCGA-CG-4474 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-CG-4477         TCGA-CG-5716         TCGA-CG-5717 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-CG-5718         TCGA-CG-5719         TCGA-CG-5720 
"17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" 
        TCGA-CG-5721         TCGA-CG-5722         TCGA-CG-5723 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-CG-5724         TCGA-CG-5725         TCGA-CG-5726 
  "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-CG-5727         TCGA-CG-5728         TCGA-CG-5730 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-CG-5732         TCGA-CG-5733         TCGA-CG-5734 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-D7-5577         TCGA-D7-5578         TCGA-D7-5579 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-D7-6518         TCGA-D7-6519         TCGA-D7-6520 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-D7-6521         TCGA-D7-6522         TCGA-D7-6524 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-D7-6525         TCGA-D7-6526         TCGA-D7-6527 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-D7-6528         TCGA-D7-6815         TCGA-D7-6817 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
        TCGA-D7-6818         TCGA-D7-6820         TCGA-D7-6822 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-EQ-5647         TCGA-EQ-8122         TCGA-F1-6177 
  "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-F1-6874         TCGA-F1-6875         TCGA-FP-7735 
"17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" 
        TCGA-FP-7829         TCGA-FP-7916         TCGA-FP-7998 
  "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-HJ-7597         TCGA-IN-7806         TCGA-IN-7808 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-IP-7968 
"17Q GAIN WILD-TYPE" 
[1] "hr=" "2.4"
D29V2, continuous
D29V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED      3    6
  17Q GAIN WILD-TYPE   62   90
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  FEMALE                3                 62
  MALE                  6                 90
                    vv
clus                 STOMACH ADENOCARCINOMA - DIFFUSE TYPE
  17Q GAIN MUTATED                                       2
  17Q GAIN WILD-TYPE                                    17
                    vv
clus                 STOMACH ADENOCARCINOMA - NOT OTHERWISE SPECIFIED (NOS)
  17Q GAIN MUTATED                                                        3
  17Q GAIN WILD-TYPE                                                     76
                    vv
clus                 STOMACH ADENOCARCINOMA - SIGNET RING TYPE
  17Q GAIN MUTATED                                           0
  17Q GAIN WILD-TYPE                                         1
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - MUCINOUS TYPE
  17Q GAIN MUTATED                                                   1
  17Q GAIN WILD-TYPE                                                 8
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - PAPILLARY TYPE
  17Q GAIN MUTATED                                                    0
  17Q GAIN WILD-TYPE                                                  3
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - TUBULAR TYPE
  17Q GAIN MUTATED                                                  1
  17Q GAIN WILD-TYPE                                                9
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - TYPE NOT OTHERWISE SPECIFIED (NOS)
  17Q GAIN MUTATED                                                                        2
  17Q GAIN WILD-TYPE                                                                     33
D29V4, multiclass
                    vv
clus                 T1 T2 T3 T4
  17Q GAIN MUTATED    0  3  3  3
  17Q GAIN WILD-TYPE  6 50 56 30
D29V5, multiclass
                    vv
clus                 N0 N1 N2 N3
  17Q GAIN MUTATED    4  2  0  3
  17Q GAIN WILD-TYPE 46 55 24 16
D29V6, multiclass
                    vv
clus                  M0  M1  MX
  17Q GAIN MUTATED     5   4   0
  17Q GAIN WILD-TYPE 127  14  11
D29V7, multiclass
                    vv
clus                  I II III IV
  17Q GAIN MUTATED    2  1   2  4
  17Q GAIN WILD-TYPE 23 42  46 25
D29V8, multiclass
D29V9, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED      0    9
  17Q GAIN WILD-TYPE    5  147
     clus
vv    17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  NO                 0                  5
  YES                9                147

Clustering(30) Variable = 18p gain mutation analysis
D30V1, survival
                    sevent
clus2                  0   1
  18P GAIN MUTATED     6   1
  18P GAIN WILD-TYPE 102  15
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                 7                117 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                 1                 15 
$`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-BR-7958 TCGA-BR-7959 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 
        0.16         1.08         0.82         1.32         0.69         0.95 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
        0.49         0.46         0.72         0.26         0.43         0.26 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-CD-5798 TCGA-CD-5800 
        1.18         1.55         1.48         0.76         0.82         0.36 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
        0.49         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-4472 TCGA-CG-4477 TCGA-CG-5716 
        8.98        18.94         7.07        12.00         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-D7-6815 TCGA-D7-6818 
        0.69         5.95         6.61         4.14         3.65         4.04 
TCGA-D7-6820 TCGA-D7-6822 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6177 TCGA-F1-6874 
        2.93         4.27         0.62         7.79         6.54         2.01 
TCGA-F1-6875 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-HJ-7597 
       72.23         0.39         0.20         3.02         3.58        26.43 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IP-7968 
        6.87         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 
              1.02               1.55 
[1] "0.2 - 22.0 (1.0)" "0.1 - 72.2 (1.6)"
        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-BR-7958 
  "18P GAIN MUTATED" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BR-7959         TCGA-BR-8059         TCGA-BR-8060 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BR-8077         TCGA-BR-8078         TCGA-BR-8080 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BR-8081         TCGA-BR-8284         TCGA-BR-8285 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BR-8286         TCGA-BR-8289         TCGA-BR-8291 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BR-8295         TCGA-BR-8296         TCGA-BR-8297 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-CD-5798         TCGA-CD-5799         TCGA-CD-5800 
"18P GAIN WILD-TYPE"   "18P GAIN MUTATED" "18P GAIN WILD-TYPE" 
        TCGA-CD-5801         TCGA-CD-5802         TCGA-CD-5803 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-CG-4300         TCGA-CG-4301         TCGA-CG-4304 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-CG-4305         TCGA-CG-4306         TCGA-CG-4436 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-CG-4437         TCGA-CG-4438         TCGA-CG-4440 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-CG-4441         TCGA-CG-4443         TCGA-CG-4444 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-CG-4449         TCGA-CG-4455         TCGA-CG-4460 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE"   "18P GAIN MUTATED" 
        TCGA-CG-4462         TCGA-CG-4465         TCGA-CG-4466 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-CG-4469         TCGA-CG-4472         TCGA-CG-4474 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE"   "18P GAIN MUTATED" 
        TCGA-CG-4477         TCGA-CG-5716         TCGA-CG-5717 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-CG-5718         TCGA-CG-5719         TCGA-CG-5720 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-CG-5721         TCGA-CG-5722         TCGA-CG-5723 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-CG-5724         TCGA-CG-5725         TCGA-CG-5726 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-CG-5727         TCGA-CG-5728         TCGA-CG-5730 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-CG-5732         TCGA-CG-5733         TCGA-CG-5734 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-D7-5577         TCGA-D7-5578         TCGA-D7-5579 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-D7-6518         TCGA-D7-6519         TCGA-D7-6520 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-D7-6521         TCGA-D7-6522         TCGA-D7-6524 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-D7-6525         TCGA-D7-6526         TCGA-D7-6527 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-D7-6528         TCGA-D7-6815         TCGA-D7-6817 
  "18P GAIN MUTATED" "18P GAIN WILD-TYPE"   "18P GAIN MUTATED" 
        TCGA-D7-6818         TCGA-D7-6820         TCGA-D7-6822 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EQ-5647         TCGA-EQ-8122         TCGA-F1-6177 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-F1-6874         TCGA-F1-6875         TCGA-FP-7735 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-FP-7829         TCGA-FP-7916         TCGA-FP-7998 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-HJ-7597         TCGA-IN-7806         TCGA-IN-7808 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-IP-7968 
"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-BR-7958 
  "18P GAIN MUTATED" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BR-7959         TCGA-BR-8059         TCGA-BR-8060 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BR-8077         TCGA-BR-8078         TCGA-BR-8080 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BR-8081         TCGA-BR-8284         TCGA-BR-8285 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BR-8286         TCGA-BR-8289         TCGA-BR-8291 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BR-8295         TCGA-BR-8296         TCGA-BR-8297 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-CD-5798         TCGA-CD-5799         TCGA-CD-5800 
"18P GAIN WILD-TYPE"   "18P GAIN MUTATED" "18P GAIN WILD-TYPE" 
        TCGA-CD-5801         TCGA-CD-5802         TCGA-CD-5803 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-CG-4300         TCGA-CG-4301         TCGA-CG-4304 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-CG-4305         TCGA-CG-4306         TCGA-CG-4436 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-CG-4437         TCGA-CG-4438         TCGA-CG-4440 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-CG-4441         TCGA-CG-4443         TCGA-CG-4444 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-CG-4449         TCGA-CG-4455         TCGA-CG-4460 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE"   "18P GAIN MUTATED" 
        TCGA-CG-4462         TCGA-CG-4465         TCGA-CG-4466 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-CG-4469         TCGA-CG-4472         TCGA-CG-4474 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE"   "18P GAIN MUTATED" 
        TCGA-CG-4477         TCGA-CG-5716         TCGA-CG-5717 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-CG-5718         TCGA-CG-5719         TCGA-CG-5720 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-CG-5721         TCGA-CG-5722         TCGA-CG-5723 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-CG-5724         TCGA-CG-5725         TCGA-CG-5726 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-CG-5727         TCGA-CG-5728         TCGA-CG-5730 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-CG-5732         TCGA-CG-5733         TCGA-CG-5734 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-D7-5577         TCGA-D7-5578         TCGA-D7-5579 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-D7-6518         TCGA-D7-6519         TCGA-D7-6520 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-D7-6521         TCGA-D7-6522         TCGA-D7-6524 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-D7-6525         TCGA-D7-6526         TCGA-D7-6527 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-D7-6528         TCGA-D7-6815         TCGA-D7-6817 
  "18P GAIN MUTATED" "18P GAIN WILD-TYPE"   "18P GAIN MUTATED" 
        TCGA-D7-6818         TCGA-D7-6820         TCGA-D7-6822 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EQ-5647         TCGA-EQ-8122         TCGA-F1-6177 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-F1-6874         TCGA-F1-6875         TCGA-FP-7735 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-FP-7829         TCGA-FP-7916         TCGA-FP-7998 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-HJ-7597         TCGA-IN-7806         TCGA-IN-7808 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-IP-7968 
"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-BR-7958 
  "18P GAIN MUTATED" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BR-7959         TCGA-BR-8059         TCGA-BR-8060 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BR-8077         TCGA-BR-8078         TCGA-BR-8080 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BR-8081         TCGA-BR-8284         TCGA-BR-8285 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BR-8286         TCGA-BR-8289         TCGA-BR-8291 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BR-8295         TCGA-BR-8296         TCGA-BR-8297 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-CD-5798         TCGA-CD-5799         TCGA-CD-5800 
"18P GAIN WILD-TYPE"   "18P GAIN MUTATED" "18P GAIN WILD-TYPE" 
        TCGA-CD-5801         TCGA-CD-5802         TCGA-CD-5803 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-CG-4300         TCGA-CG-4301         TCGA-CG-4304 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-CG-4305         TCGA-CG-4306         TCGA-CG-4436 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-CG-4437         TCGA-CG-4438         TCGA-CG-4440 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-CG-4441         TCGA-CG-4443         TCGA-CG-4444 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-CG-4449         TCGA-CG-4455         TCGA-CG-4460 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE"   "18P GAIN MUTATED" 
        TCGA-CG-4462         TCGA-CG-4465         TCGA-CG-4466 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-CG-4469         TCGA-CG-4472         TCGA-CG-4474 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE"   "18P GAIN MUTATED" 
        TCGA-CG-4477         TCGA-CG-5716         TCGA-CG-5717 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-CG-5718         TCGA-CG-5719         TCGA-CG-5720 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-CG-5721         TCGA-CG-5722         TCGA-CG-5723 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-CG-5724         TCGA-CG-5725         TCGA-CG-5726 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-CG-5727         TCGA-CG-5728         TCGA-CG-5730 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-CG-5732         TCGA-CG-5733         TCGA-CG-5734 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-D7-5577         TCGA-D7-5578         TCGA-D7-5579 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-D7-6518         TCGA-D7-6519         TCGA-D7-6520 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-D7-6521         TCGA-D7-6522         TCGA-D7-6524 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-D7-6525         TCGA-D7-6526         TCGA-D7-6527 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-D7-6528         TCGA-D7-6815         TCGA-D7-6817 
  "18P GAIN MUTATED" "18P GAIN WILD-TYPE"   "18P GAIN MUTATED" 
        TCGA-D7-6818         TCGA-D7-6820         TCGA-D7-6822 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EQ-5647         TCGA-EQ-8122         TCGA-F1-6177 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-F1-6874         TCGA-F1-6875         TCGA-FP-7735 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-FP-7829         TCGA-FP-7916         TCGA-FP-7998 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-HJ-7597         TCGA-IN-7806         TCGA-IN-7808 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-IP-7968 
"18P GAIN WILD-TYPE" 
[1] "hr=" "1.7"
D30V2, continuous
D30V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED      5    8
  18P GAIN WILD-TYPE   60   88
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  FEMALE                5                 60
  MALE                  8                 88
                    vv
clus                 STOMACH ADENOCARCINOMA - DIFFUSE TYPE
  18P GAIN MUTATED                                       1
  18P GAIN WILD-TYPE                                    18
                    vv
clus                 STOMACH ADENOCARCINOMA - NOT OTHERWISE SPECIFIED (NOS)
  18P GAIN MUTATED                                                        6
  18P GAIN WILD-TYPE                                                     73
                    vv
clus                 STOMACH ADENOCARCINOMA - SIGNET RING TYPE
  18P GAIN MUTATED                                           0
  18P GAIN WILD-TYPE                                         1
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - MUCINOUS TYPE
  18P GAIN MUTATED                                                   1
  18P GAIN WILD-TYPE                                                 8
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - PAPILLARY TYPE
  18P GAIN MUTATED                                                    0
  18P GAIN WILD-TYPE                                                  3
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - TUBULAR TYPE
  18P GAIN MUTATED                                                  2
  18P GAIN WILD-TYPE                                                8
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - TYPE NOT OTHERWISE SPECIFIED (NOS)
  18P GAIN MUTATED                                                                        2
  18P GAIN WILD-TYPE                                                                     33
D30V4, multiclass
                    vv
clus                 T1 T2 T3 T4
  18P GAIN MUTATED    0  4  5  2
  18P GAIN WILD-TYPE  6 49 54 31
D30V5, multiclass
                    vv
clus                 N0 N1 N2 N3
  18P GAIN MUTATED    1  8  1  2
  18P GAIN WILD-TYPE 49 49 23 17
D30V6, multiclass
                    vv
clus                  M0  M1  MX
  18P GAIN MUTATED    10   2   1
  18P GAIN WILD-TYPE 122  16  10
D30V7, multiclass
                    vv
clus                  I II III IV
  18P GAIN MUTATED    1  2   5  3
  18P GAIN WILD-TYPE 24 41  43 26
D30V8, multiclass
D30V9, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED      1   12
  18P GAIN WILD-TYPE    4  144
     clus
vv    18P GAIN MUTATED 18P GAIN WILD-TYPE
  NO                 1                  4
  YES               12                144

Clustering(31) Variable = 18q gain mutation analysis
D31V1, survival
                    sevent
clus2                  0   1
  18Q GAIN MUTATED     4   1
  18Q GAIN WILD-TYPE 104  15
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 5                119 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 1                 15 
$`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-BR-7958 TCGA-BR-7959 TCGA-BR-8059 TCGA-BR-8060 
        0.95         0.69         0.16         1.08         0.82         1.32 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
        0.69         0.95         0.49         0.46         0.72         0.26 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
        0.43         0.26         1.18         1.55         1.48         0.76 
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-EQ-8122 
        3.65         4.04         2.93         4.27         0.62         7.79 
TCGA-F1-6177 TCGA-F1-6874 TCGA-F1-6875 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
        6.54         2.01        72.23         0.39         0.20         3.02 
TCGA-FP-7998 TCGA-HJ-7597 TCGA-IN-7806 TCGA-IN-7808 TCGA-IP-7968 
        3.58        26.43         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 
              1.68               1.48 
[1] "0.7 - 22.0 (1.7)" "0.1 - 72.2 (1.5)"
        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-BR-7958 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BR-7959         TCGA-BR-8059         TCGA-BR-8060 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BR-8077         TCGA-BR-8078         TCGA-BR-8080 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BR-8081         TCGA-BR-8284         TCGA-BR-8285 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BR-8286         TCGA-BR-8289         TCGA-BR-8291 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BR-8295         TCGA-BR-8296         TCGA-BR-8297 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-CD-5798         TCGA-CD-5799         TCGA-CD-5800 
"18Q GAIN WILD-TYPE"   "18Q GAIN MUTATED" "18Q GAIN WILD-TYPE" 
        TCGA-CD-5801         TCGA-CD-5802         TCGA-CD-5803 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-CG-4300         TCGA-CG-4301         TCGA-CG-4304 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-CG-4305         TCGA-CG-4306         TCGA-CG-4436 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-CG-4437         TCGA-CG-4438         TCGA-CG-4440 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-CG-4441         TCGA-CG-4443         TCGA-CG-4444 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-CG-4449         TCGA-CG-4455         TCGA-CG-4460 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE"   "18Q GAIN MUTATED" 
        TCGA-CG-4462         TCGA-CG-4465         TCGA-CG-4466 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-CG-4469         TCGA-CG-4472         TCGA-CG-4474 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE"   "18Q GAIN MUTATED" 
        TCGA-CG-4477         TCGA-CG-5716         TCGA-CG-5717 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-CG-5718         TCGA-CG-5719         TCGA-CG-5720 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-CG-5721         TCGA-CG-5722         TCGA-CG-5723 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-CG-5724         TCGA-CG-5725         TCGA-CG-5726 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-CG-5727         TCGA-CG-5728         TCGA-CG-5730 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-CG-5732         TCGA-CG-5733         TCGA-CG-5734 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-D7-5577         TCGA-D7-5578         TCGA-D7-5579 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-D7-6518         TCGA-D7-6519         TCGA-D7-6520 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-D7-6521         TCGA-D7-6522         TCGA-D7-6524 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-D7-6525         TCGA-D7-6526         TCGA-D7-6527 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-D7-6528         TCGA-D7-6815         TCGA-D7-6817 
  "18Q GAIN MUTATED" "18Q GAIN WILD-TYPE"   "18Q GAIN MUTATED" 
        TCGA-D7-6818         TCGA-D7-6820         TCGA-D7-6822 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EQ-5647         TCGA-EQ-8122         TCGA-F1-6177 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-F1-6874         TCGA-F1-6875         TCGA-FP-7735 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-FP-7829         TCGA-FP-7916         TCGA-FP-7998 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-HJ-7597         TCGA-IN-7806         TCGA-IN-7808 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-IP-7968 
"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-BR-7958 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BR-7959         TCGA-BR-8059         TCGA-BR-8060 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BR-8077         TCGA-BR-8078         TCGA-BR-8080 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BR-8081         TCGA-BR-8284         TCGA-BR-8285 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BR-8286         TCGA-BR-8289         TCGA-BR-8291 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BR-8295         TCGA-BR-8296         TCGA-BR-8297 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-CD-5798         TCGA-CD-5799         TCGA-CD-5800 
"18Q GAIN WILD-TYPE"   "18Q GAIN MUTATED" "18Q GAIN WILD-TYPE" 
        TCGA-CD-5801         TCGA-CD-5802         TCGA-CD-5803 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-CG-4300         TCGA-CG-4301         TCGA-CG-4304 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-CG-4305         TCGA-CG-4306         TCGA-CG-4436 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-CG-4437         TCGA-CG-4438         TCGA-CG-4440 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-CG-4441         TCGA-CG-4443         TCGA-CG-4444 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-CG-4449         TCGA-CG-4455         TCGA-CG-4460 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE"   "18Q GAIN MUTATED" 
        TCGA-CG-4462         TCGA-CG-4465         TCGA-CG-4466 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-CG-4469         TCGA-CG-4472         TCGA-CG-4474 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE"   "18Q GAIN MUTATED" 
        TCGA-CG-4477         TCGA-CG-5716         TCGA-CG-5717 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-CG-5718         TCGA-CG-5719         TCGA-CG-5720 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-CG-5721         TCGA-CG-5722         TCGA-CG-5723 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-CG-5724         TCGA-CG-5725         TCGA-CG-5726 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-CG-5727         TCGA-CG-5728         TCGA-CG-5730 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-CG-5732         TCGA-CG-5733         TCGA-CG-5734 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-D7-5577         TCGA-D7-5578         TCGA-D7-5579 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-D7-6518         TCGA-D7-6519         TCGA-D7-6520 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-D7-6521         TCGA-D7-6522         TCGA-D7-6524 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-D7-6525         TCGA-D7-6526         TCGA-D7-6527 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-D7-6528         TCGA-D7-6815         TCGA-D7-6817 
  "18Q GAIN MUTATED" "18Q GAIN WILD-TYPE"   "18Q GAIN MUTATED" 
        TCGA-D7-6818         TCGA-D7-6820         TCGA-D7-6822 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EQ-5647         TCGA-EQ-8122         TCGA-F1-6177 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-F1-6874         TCGA-F1-6875         TCGA-FP-7735 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-FP-7829         TCGA-FP-7916         TCGA-FP-7998 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-HJ-7597         TCGA-IN-7806         TCGA-IN-7808 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-IP-7968 
"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-BR-7958 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BR-7959         TCGA-BR-8059         TCGA-BR-8060 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BR-8077         TCGA-BR-8078         TCGA-BR-8080 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BR-8081         TCGA-BR-8284         TCGA-BR-8285 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BR-8286         TCGA-BR-8289         TCGA-BR-8291 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BR-8295         TCGA-BR-8296         TCGA-BR-8297 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-CD-5798         TCGA-CD-5799         TCGA-CD-5800 
"18Q GAIN WILD-TYPE"   "18Q GAIN MUTATED" "18Q GAIN WILD-TYPE" 
        TCGA-CD-5801         TCGA-CD-5802         TCGA-CD-5803 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-CG-4300         TCGA-CG-4301         TCGA-CG-4304 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-CG-4305         TCGA-CG-4306         TCGA-CG-4436 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-CG-4437         TCGA-CG-4438         TCGA-CG-4440 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-CG-4441         TCGA-CG-4443         TCGA-CG-4444 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-CG-4449         TCGA-CG-4455         TCGA-CG-4460 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE"   "18Q GAIN MUTATED" 
        TCGA-CG-4462         TCGA-CG-4465         TCGA-CG-4466 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-CG-4469         TCGA-CG-4472         TCGA-CG-4474 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE"   "18Q GAIN MUTATED" 
        TCGA-CG-4477         TCGA-CG-5716         TCGA-CG-5717 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-CG-5718         TCGA-CG-5719         TCGA-CG-5720 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-CG-5721         TCGA-CG-5722         TCGA-CG-5723 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-CG-5724         TCGA-CG-5725         TCGA-CG-5726 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-CG-5727         TCGA-CG-5728         TCGA-CG-5730 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-CG-5732         TCGA-CG-5733         TCGA-CG-5734 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-D7-5577         TCGA-D7-5578         TCGA-D7-5579 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-D7-6518         TCGA-D7-6519         TCGA-D7-6520 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-D7-6521         TCGA-D7-6522         TCGA-D7-6524 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-D7-6525         TCGA-D7-6526         TCGA-D7-6527 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-D7-6528         TCGA-D7-6815         TCGA-D7-6817 
  "18Q GAIN MUTATED" "18Q GAIN WILD-TYPE"   "18Q GAIN MUTATED" 
        TCGA-D7-6818         TCGA-D7-6820         TCGA-D7-6822 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EQ-5647         TCGA-EQ-8122         TCGA-F1-6177 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-F1-6874         TCGA-F1-6875         TCGA-FP-7735 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-FP-7829         TCGA-FP-7916         TCGA-FP-7998 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-HJ-7597         TCGA-IN-7806         TCGA-IN-7808 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-IP-7968 
"18Q GAIN WILD-TYPE" 
[1] "hr=" "1.7"
D31V2, continuous
D31V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      4    3
  18Q GAIN WILD-TYPE   61   93
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  FEMALE                4                 61
  MALE                  3                 93
                    vv
clus                 STOMACH ADENOCARCINOMA - DIFFUSE TYPE
  18Q GAIN MUTATED                                       1
  18Q GAIN WILD-TYPE                                    18
                    vv
clus                 STOMACH ADENOCARCINOMA - NOT OTHERWISE SPECIFIED (NOS)
  18Q GAIN MUTATED                                                        2
  18Q GAIN WILD-TYPE                                                     77
                    vv
clus                 STOMACH ADENOCARCINOMA - SIGNET RING TYPE
  18Q GAIN MUTATED                                           0
  18Q GAIN WILD-TYPE                                         1
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - MUCINOUS TYPE
  18Q GAIN MUTATED                                                   0
  18Q GAIN WILD-TYPE                                                 9
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - PAPILLARY TYPE
  18Q GAIN MUTATED                                                    0
  18Q GAIN WILD-TYPE                                                  3
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - TUBULAR TYPE
  18Q GAIN MUTATED                                                  2
  18Q GAIN WILD-TYPE                                                8
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - TYPE NOT OTHERWISE SPECIFIED (NOS)
  18Q GAIN MUTATED                                                                        2
  18Q GAIN WILD-TYPE                                                                     33
D31V4, multiclass
                    vv
clus                 T1 T2 T3 T4
  18Q GAIN MUTATED    0  3  1  2
  18Q GAIN WILD-TYPE  6 50 58 31
D31V5, multiclass
                    vv
clus                 N0 N1 N2 N3
  18Q GAIN MUTATED    1  3  1  1
  18Q GAIN WILD-TYPE 49 54 23 18
D31V6, multiclass
                    vv
clus                  M0  M1  MX
  18Q GAIN MUTATED     4   2   1
  18Q GAIN WILD-TYPE 128  16  10
D31V7, multiclass
                    vv
clus                  I II III IV
  18Q GAIN MUTATED    1  1   2  2
  18Q GAIN WILD-TYPE 24 42  46 27
D31V8, multiclass
D31V9, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      0    7
  18Q GAIN WILD-TYPE    5  149
     clus
vv    18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  NO                 0                  5
  YES                7                149

Clustering(32) Variable = 19p gain mutation analysis
D32V1, survival
                    sevent
clus2                  0   1
  19P GAIN MUTATED     6   1
  19P GAIN WILD-TYPE 102  15
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                 7                117 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                 1                 15 
$`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-BR-7958 TCGA-BR-7959 TCGA-BR-8059 TCGA-BR-8060 
        0.95         0.69         0.16         1.08         0.82         1.32 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
        0.69         0.95         0.49         0.46         0.72         0.26 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
        0.43         0.26         1.18         1.55         1.48         0.76 
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-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-D7-6822 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6177 TCGA-F1-6874 
        2.93         4.27         0.62         7.79         6.54         2.01 
TCGA-F1-6875 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-HJ-7597 
       72.23         0.39         0.20         3.02         3.58        26.43 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IP-7968 
        6.87         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               1.48 
[1] "0.9 - 22.0 (8.2)" "0.1 - 72.2 (1.5)"
        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-BR-7958 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-BR-7959         TCGA-BR-8059         TCGA-BR-8060 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-BR-8077         TCGA-BR-8078         TCGA-BR-8080 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-BR-8081         TCGA-BR-8284         TCGA-BR-8285 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-BR-8286         TCGA-BR-8289         TCGA-BR-8291 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-BR-8295         TCGA-BR-8296         TCGA-BR-8297 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-CD-5798         TCGA-CD-5799         TCGA-CD-5800 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-CD-5801         TCGA-CD-5802         TCGA-CD-5803 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-CG-4300         TCGA-CG-4301         TCGA-CG-4304 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-CG-4305         TCGA-CG-4306         TCGA-CG-4436 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-CG-4437         TCGA-CG-4438         TCGA-CG-4440 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-CG-4441         TCGA-CG-4443         TCGA-CG-4444 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-CG-4449         TCGA-CG-4455         TCGA-CG-4460 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE"   "19P GAIN MUTATED" 
        TCGA-CG-4462         TCGA-CG-4465         TCGA-CG-4466 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-CG-4469         TCGA-CG-4472         TCGA-CG-4474 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE"   "19P GAIN MUTATED" 
        TCGA-CG-4477         TCGA-CG-5716         TCGA-CG-5717 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-CG-5718         TCGA-CG-5719         TCGA-CG-5720 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-CG-5721         TCGA-CG-5722         TCGA-CG-5723 
"19P GAIN WILD-TYPE"   "19P GAIN MUTATED" "19P GAIN WILD-TYPE" 
        TCGA-CG-5724         TCGA-CG-5725         TCGA-CG-5726 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-CG-5727         TCGA-CG-5728         TCGA-CG-5730 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE"   "19P GAIN MUTATED" 
        TCGA-CG-5732         TCGA-CG-5733         TCGA-CG-5734 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-D7-5577         TCGA-D7-5578         TCGA-D7-5579 
  "19P GAIN MUTATED" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-D7-6518         TCGA-D7-6519         TCGA-D7-6520 
  "19P GAIN MUTATED" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-D7-6521         TCGA-D7-6522         TCGA-D7-6524 
  "19P GAIN MUTATED" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-D7-6525         TCGA-D7-6526         TCGA-D7-6527 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-D7-6528         TCGA-D7-6815         TCGA-D7-6817 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-D7-6818         TCGA-D7-6820         TCGA-D7-6822 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EQ-5647         TCGA-EQ-8122         TCGA-F1-6177 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-F1-6874         TCGA-F1-6875         TCGA-FP-7735 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-FP-7829         TCGA-FP-7916         TCGA-FP-7998 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-HJ-7597         TCGA-IN-7806         TCGA-IN-7808 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-IP-7968 
"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-BR-7958 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-BR-7959         TCGA-BR-8059         TCGA-BR-8060 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-BR-8077         TCGA-BR-8078         TCGA-BR-8080 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-BR-8081         TCGA-BR-8284         TCGA-BR-8285 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-BR-8286         TCGA-BR-8289         TCGA-BR-8291 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-BR-8295         TCGA-BR-8296         TCGA-BR-8297 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-CD-5798         TCGA-CD-5799         TCGA-CD-5800 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-CD-5801         TCGA-CD-5802         TCGA-CD-5803 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-CG-4300         TCGA-CG-4301         TCGA-CG-4304 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-CG-4305         TCGA-CG-4306         TCGA-CG-4436 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-CG-4437         TCGA-CG-4438         TCGA-CG-4440 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-CG-4441         TCGA-CG-4443         TCGA-CG-4444 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-CG-4449         TCGA-CG-4455         TCGA-CG-4460 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE"   "19P GAIN MUTATED" 
        TCGA-CG-4462         TCGA-CG-4465         TCGA-CG-4466 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-CG-4469         TCGA-CG-4472         TCGA-CG-4474 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE"   "19P GAIN MUTATED" 
        TCGA-CG-4477         TCGA-CG-5716         TCGA-CG-5717 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-CG-5718         TCGA-CG-5719         TCGA-CG-5720 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-CG-5721         TCGA-CG-5722         TCGA-CG-5723 
"19P GAIN WILD-TYPE"   "19P GAIN MUTATED" "19P GAIN WILD-TYPE" 
        TCGA-CG-5724         TCGA-CG-5725         TCGA-CG-5726 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-CG-5727         TCGA-CG-5728         TCGA-CG-5730 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE"   "19P GAIN MUTATED" 
        TCGA-CG-5732         TCGA-CG-5733         TCGA-CG-5734 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-D7-5577         TCGA-D7-5578         TCGA-D7-5579 
  "19P GAIN MUTATED" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-D7-6518         TCGA-D7-6519         TCGA-D7-6520 
  "19P GAIN MUTATED" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-D7-6521         TCGA-D7-6522         TCGA-D7-6524 
  "19P GAIN MUTATED" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-D7-6525         TCGA-D7-6526         TCGA-D7-6527 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-D7-6528         TCGA-D7-6815         TCGA-D7-6817 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-D7-6818         TCGA-D7-6820         TCGA-D7-6822 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EQ-5647         TCGA-EQ-8122         TCGA-F1-6177 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-F1-6874         TCGA-F1-6875         TCGA-FP-7735 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-FP-7829         TCGA-FP-7916         TCGA-FP-7998 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-HJ-7597         TCGA-IN-7806         TCGA-IN-7808 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-IP-7968 
"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-BR-7958 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-BR-7959         TCGA-BR-8059         TCGA-BR-8060 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-BR-8077         TCGA-BR-8078         TCGA-BR-8080 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-BR-8081         TCGA-BR-8284         TCGA-BR-8285 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-BR-8286         TCGA-BR-8289         TCGA-BR-8291 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-BR-8295         TCGA-BR-8296         TCGA-BR-8297 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-CD-5798         TCGA-CD-5799         TCGA-CD-5800 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-CD-5801         TCGA-CD-5802         TCGA-CD-5803 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-CG-4300         TCGA-CG-4301         TCGA-CG-4304 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-CG-4305         TCGA-CG-4306         TCGA-CG-4436 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-CG-4437         TCGA-CG-4438         TCGA-CG-4440 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-CG-4441         TCGA-CG-4443         TCGA-CG-4444 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-CG-4449         TCGA-CG-4455         TCGA-CG-4460 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE"   "19P GAIN MUTATED" 
        TCGA-CG-4462         TCGA-CG-4465         TCGA-CG-4466 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-CG-4469         TCGA-CG-4472         TCGA-CG-4474 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE"   "19P GAIN MUTATED" 
        TCGA-CG-4477         TCGA-CG-5716         TCGA-CG-5717 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-CG-5718         TCGA-CG-5719         TCGA-CG-5720 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-CG-5721         TCGA-CG-5722         TCGA-CG-5723 
"19P GAIN WILD-TYPE"   "19P GAIN MUTATED" "19P GAIN WILD-TYPE" 
        TCGA-CG-5724         TCGA-CG-5725         TCGA-CG-5726 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-CG-5727         TCGA-CG-5728         TCGA-CG-5730 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE"   "19P GAIN MUTATED" 
        TCGA-CG-5732         TCGA-CG-5733         TCGA-CG-5734 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-D7-5577         TCGA-D7-5578         TCGA-D7-5579 
  "19P GAIN MUTATED" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-D7-6518         TCGA-D7-6519         TCGA-D7-6520 
  "19P GAIN MUTATED" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-D7-6521         TCGA-D7-6522         TCGA-D7-6524 
  "19P GAIN MUTATED" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-D7-6525         TCGA-D7-6526         TCGA-D7-6527 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-D7-6528         TCGA-D7-6815         TCGA-D7-6817 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-D7-6818         TCGA-D7-6820         TCGA-D7-6822 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EQ-5647         TCGA-EQ-8122         TCGA-F1-6177 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-F1-6874         TCGA-F1-6875         TCGA-FP-7735 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-FP-7829         TCGA-FP-7916         TCGA-FP-7998 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-HJ-7597         TCGA-IN-7806         TCGA-IN-7808 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-IP-7968 
"19P GAIN WILD-TYPE" 
[1] "hr=" "1"  
D32V2, continuous
D32V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED      8    2
  19P GAIN WILD-TYPE   57   94
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  FEMALE                8                 57
  MALE                  2                 94
                    vv
clus                 STOMACH ADENOCARCINOMA - DIFFUSE TYPE
  19P GAIN MUTATED                                       3
  19P GAIN WILD-TYPE                                    16
                    vv
clus                 STOMACH ADENOCARCINOMA - NOT OTHERWISE SPECIFIED (NOS)
  19P GAIN MUTATED                                                        3
  19P GAIN WILD-TYPE                                                     76
                    vv
clus                 STOMACH ADENOCARCINOMA - SIGNET RING TYPE
  19P GAIN MUTATED                                           0
  19P GAIN WILD-TYPE                                         1
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - MUCINOUS TYPE
  19P GAIN MUTATED                                                   0
  19P GAIN WILD-TYPE                                                 9
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - PAPILLARY TYPE
  19P GAIN MUTATED                                                    0
  19P GAIN WILD-TYPE                                                  3
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - TUBULAR TYPE
  19P GAIN MUTATED                                                  1
  19P GAIN WILD-TYPE                                                9
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - TYPE NOT OTHERWISE SPECIFIED (NOS)
  19P GAIN MUTATED                                                                        3
  19P GAIN WILD-TYPE                                                                     32
D32V4, multiclass
                    vv
clus                 T1 T2 T3 T4
  19P GAIN MUTATED    0  5  3  2
  19P GAIN WILD-TYPE  6 48 56 31
D32V5, multiclass
                    vv
clus                 N0 N1 N2 N3
  19P GAIN MUTATED    0  4  3  2
  19P GAIN WILD-TYPE 50 53 21 17
D32V6, multiclass
                    vv
clus                  M0  M1  MX
  19P GAIN MUTATED     6   4   0
  19P GAIN WILD-TYPE 126  14  11
D32V7, multiclass
                    vv
clus                  I II III IV
  19P GAIN MUTATED    0  1   3  5
  19P GAIN WILD-TYPE 25 42  45 24
D32V8, multiclass
D32V9, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED      0   10
  19P GAIN WILD-TYPE    5  146
     clus
vv    19P GAIN MUTATED 19P GAIN WILD-TYPE
  NO                 0                  5
  YES               10                146

Clustering(33) Variable = 19q gain mutation analysis
D33V1, survival
                    sevent
clus2                 0  1
  19Q GAIN MUTATED   10  2
  19Q GAIN WILD-TYPE 98 14
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                12                112 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                 2                 14 
$`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 TCGA-FP-7916 
        8.65         9.80         8.19         4.27        72.23         3.02 

$`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-BR-7958 TCGA-BR-7959 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
        0.69         0.16         1.08         0.82         1.32         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
        0.95         0.49         0.46         0.72         0.26         0.43 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-CD-5798 
        0.26         1.18         1.55         1.48         0.76         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-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-4477 
        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-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-D7-5578 TCGA-D7-5579 TCGA-D7-6519 
       55.04        21.07         7.99         3.58         4.54        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-EQ-5647 
        1.68         3.65         4.70         4.04         2.93         0.62 
TCGA-EQ-8122 TCGA-F1-6177 TCGA-F1-6874 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7998 
        7.79         6.54         2.01         0.39         0.20         3.58 
TCGA-HJ-7597 TCGA-IN-7806 TCGA-IN-7808 TCGA-IP-7968 
       26.43         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 
              6.23               1.38 
[1] "0.8 - 72.2 (6.2)" "0.1 - 70.1 (1.4)"
        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-BR-7958 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-BR-7959         TCGA-BR-8059         TCGA-BR-8060 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-BR-8077         TCGA-BR-8078         TCGA-BR-8080 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-BR-8081         TCGA-BR-8284         TCGA-BR-8285 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-BR-8286         TCGA-BR-8289         TCGA-BR-8291 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-BR-8295         TCGA-BR-8296         TCGA-BR-8297 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-CD-5798         TCGA-CD-5799         TCGA-CD-5800 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-CD-5801         TCGA-CD-5802         TCGA-CD-5803 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-CG-4300         TCGA-CG-4301         TCGA-CG-4304 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-CG-4305         TCGA-CG-4306         TCGA-CG-4436 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-CG-4437         TCGA-CG-4438         TCGA-CG-4440 
"19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" 
        TCGA-CG-4441         TCGA-CG-4443         TCGA-CG-4444 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-CG-4449         TCGA-CG-4455         TCGA-CG-4460 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" 
        TCGA-CG-4462         TCGA-CG-4465         TCGA-CG-4466 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-CG-4469         TCGA-CG-4472         TCGA-CG-4474 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" 
        TCGA-CG-4477         TCGA-CG-5716         TCGA-CG-5717 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-CG-5718         TCGA-CG-5719         TCGA-CG-5720 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-CG-5721         TCGA-CG-5722         TCGA-CG-5723 
"19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" 
        TCGA-CG-5724         TCGA-CG-5725         TCGA-CG-5726 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-CG-5727         TCGA-CG-5728         TCGA-CG-5730 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" 
        TCGA-CG-5732         TCGA-CG-5733         TCGA-CG-5734 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-D7-5577         TCGA-D7-5578         TCGA-D7-5579 
  "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-D7-6518         TCGA-D7-6519         TCGA-D7-6520 
  "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-D7-6521         TCGA-D7-6522         TCGA-D7-6524 
  "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-D7-6525         TCGA-D7-6526         TCGA-D7-6527 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-D7-6528         TCGA-D7-6815         TCGA-D7-6817 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-D7-6818         TCGA-D7-6820         TCGA-D7-6822 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" 
        TCGA-EQ-5647         TCGA-EQ-8122         TCGA-F1-6177 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-F1-6874         TCGA-F1-6875         TCGA-FP-7735 
"19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" 
        TCGA-FP-7829         TCGA-FP-7916         TCGA-FP-7998 
"19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" 
        TCGA-HJ-7597         TCGA-IN-7806         TCGA-IN-7808 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-IP-7968 
"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-BR-7958 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-BR-7959         TCGA-BR-8059         TCGA-BR-8060 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-BR-8077         TCGA-BR-8078         TCGA-BR-8080 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-BR-8081         TCGA-BR-8284         TCGA-BR-8285 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-BR-8286         TCGA-BR-8289         TCGA-BR-8291 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-BR-8295         TCGA-BR-8296         TCGA-BR-8297 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-CD-5798         TCGA-CD-5799         TCGA-CD-5800 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-CD-5801         TCGA-CD-5802         TCGA-CD-5803 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-CG-4300         TCGA-CG-4301         TCGA-CG-4304 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-CG-4305         TCGA-CG-4306         TCGA-CG-4436 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-CG-4437         TCGA-CG-4438         TCGA-CG-4440 
"19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" 
        TCGA-CG-4441         TCGA-CG-4443         TCGA-CG-4444 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-CG-4449         TCGA-CG-4455         TCGA-CG-4460 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" 
        TCGA-CG-4462         TCGA-CG-4465         TCGA-CG-4466 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-CG-4469         TCGA-CG-4472         TCGA-CG-4474 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" 
        TCGA-CG-4477         TCGA-CG-5716         TCGA-CG-5717 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-CG-5718         TCGA-CG-5719         TCGA-CG-5720 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-CG-5721         TCGA-CG-5722         TCGA-CG-5723 
"19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" 
        TCGA-CG-5724         TCGA-CG-5725         TCGA-CG-5726 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-CG-5727         TCGA-CG-5728         TCGA-CG-5730 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" 
        TCGA-CG-5732         TCGA-CG-5733         TCGA-CG-5734 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-D7-5577         TCGA-D7-5578         TCGA-D7-5579 
  "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-D7-6518         TCGA-D7-6519         TCGA-D7-6520 
  "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-D7-6521         TCGA-D7-6522         TCGA-D7-6524 
  "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-D7-6525         TCGA-D7-6526         TCGA-D7-6527 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-D7-6528         TCGA-D7-6815         TCGA-D7-6817 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-D7-6818         TCGA-D7-6820         TCGA-D7-6822 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" 
        TCGA-EQ-5647         TCGA-EQ-8122         TCGA-F1-6177 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-F1-6874         TCGA-F1-6875         TCGA-FP-7735 
"19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" 
        TCGA-FP-7829         TCGA-FP-7916         TCGA-FP-7998 
"19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" 
        TCGA-HJ-7597         TCGA-IN-7806         TCGA-IN-7808 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-IP-7968 
"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-BR-7958 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-BR-7959         TCGA-BR-8059         TCGA-BR-8060 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-BR-8077         TCGA-BR-8078         TCGA-BR-8080 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-BR-8081         TCGA-BR-8284         TCGA-BR-8285 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-BR-8286         TCGA-BR-8289         TCGA-BR-8291 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-BR-8295         TCGA-BR-8296         TCGA-BR-8297 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-CD-5798         TCGA-CD-5799         TCGA-CD-5800 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-CD-5801         TCGA-CD-5802         TCGA-CD-5803 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-CG-4300         TCGA-CG-4301         TCGA-CG-4304 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-CG-4305         TCGA-CG-4306         TCGA-CG-4436 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-CG-4437         TCGA-CG-4438         TCGA-CG-4440 
"19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" 
        TCGA-CG-4441         TCGA-CG-4443         TCGA-CG-4444 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-CG-4449         TCGA-CG-4455         TCGA-CG-4460 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" 
        TCGA-CG-4462         TCGA-CG-4465         TCGA-CG-4466 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-CG-4469         TCGA-CG-4472         TCGA-CG-4474 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" 
        TCGA-CG-4477         TCGA-CG-5716         TCGA-CG-5717 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-CG-5718         TCGA-CG-5719         TCGA-CG-5720 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-CG-5721         TCGA-CG-5722         TCGA-CG-5723 
"19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" 
        TCGA-CG-5724         TCGA-CG-5725         TCGA-CG-5726 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-CG-5727         TCGA-CG-5728         TCGA-CG-5730 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" 
        TCGA-CG-5732         TCGA-CG-5733         TCGA-CG-5734 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-D7-5577         TCGA-D7-5578         TCGA-D7-5579 
  "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-D7-6518         TCGA-D7-6519         TCGA-D7-6520 
  "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-D7-6521         TCGA-D7-6522         TCGA-D7-6524 
  "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-D7-6525         TCGA-D7-6526         TCGA-D7-6527 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-D7-6528         TCGA-D7-6815         TCGA-D7-6817 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-D7-6818         TCGA-D7-6820         TCGA-D7-6822 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" 
        TCGA-EQ-5647         TCGA-EQ-8122         TCGA-F1-6177 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-F1-6874         TCGA-F1-6875         TCGA-FP-7735 
"19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" 
        TCGA-FP-7829         TCGA-FP-7916         TCGA-FP-7998 
"19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" 
        TCGA-HJ-7597         TCGA-IN-7806         TCGA-IN-7808 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-IP-7968 
"19Q GAIN WILD-TYPE" 
[1] "hr=" "2.8"
D33V2, continuous
D33V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED     10    7
  19Q GAIN WILD-TYPE   55   89
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  FEMALE               10                 55
  MALE                  7                 89
                    vv
clus                 STOMACH ADENOCARCINOMA - DIFFUSE TYPE
  19Q GAIN MUTATED                                       4
  19Q GAIN WILD-TYPE                                    15
                    vv
clus                 STOMACH ADENOCARCINOMA - NOT OTHERWISE SPECIFIED (NOS)
  19Q GAIN MUTATED                                                        5
  19Q GAIN WILD-TYPE                                                     74
                    vv
clus                 STOMACH ADENOCARCINOMA - SIGNET RING TYPE
  19Q GAIN MUTATED                                           0
  19Q GAIN WILD-TYPE                                         1
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - MUCINOUS TYPE
  19Q GAIN MUTATED                                                   1
  19Q GAIN WILD-TYPE                                                 8
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - PAPILLARY TYPE
  19Q GAIN MUTATED                                                    0
  19Q GAIN WILD-TYPE                                                  3
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - TUBULAR TYPE
  19Q GAIN MUTATED                                                  2
  19Q GAIN WILD-TYPE                                                8
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - TYPE NOT OTHERWISE SPECIFIED (NOS)
  19Q GAIN MUTATED                                                                        4
  19Q GAIN WILD-TYPE                                                                     31
D33V4, multiclass
                    vv
clus                 T1 T2 T3 T4
  19Q GAIN MUTATED    0  8  4  5
  19Q GAIN WILD-TYPE  6 45 55 28
D33V5, multiclass
                    vv
clus                 N0 N1 N2 N3
  19Q GAIN MUTATED    2  6  4  4
  19Q GAIN WILD-TYPE 48 51 20 15
D33V6, multiclass
                    vv
clus                  M0  M1  MX
  19Q GAIN MUTATED    12   4   1
  19Q GAIN WILD-TYPE 120  14  10
D33V7, multiclass
                    vv
clus                  I II III IV
  19Q GAIN MUTATED    2  2   4  8
  19Q GAIN WILD-TYPE 23 41  44 21
D33V8, multiclass
D33V9, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED      1   16
  19Q GAIN WILD-TYPE    4  140
     clus
vv    19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  NO                 1                  4
  YES               16                140

Clustering(34) Variable = 20p gain mutation analysis
D34V1, survival
                    sevent
clus2                 0  1
  20P GAIN MUTATED   41  5
  20P GAIN WILD-TYPE 67 11
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                46                 78 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                 5                 11 
$`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-7916 TCGA-FP-7998 TCGA-IN-7806 TCGA-IN-7808 
        3.02         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-BR-7958 TCGA-BR-7959 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
        0.69         0.16         1.08         0.82         1.32         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
        0.95         0.49         0.46         0.72         0.26         0.43 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-CD-5798 
        0.26         1.18         1.55         1.48         0.76         0.82 
TCGA-CD-5800 TCGA-CD-5802 TCGA-CD-5803 TCGA-CG-4301 TCGA-CG-4306 TCGA-CG-4437 
        0.36         0.30         0.07         3.02         1.02         8.05 
TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4460 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4472 
       29.98        19.07        21.99         1.02         8.98        12.00 
TCGA-CG-4474 TCGA-CG-4477 TCGA-CG-5716 TCGA-CG-5717 TCGA-CG-5719 TCGA-CG-5720 
        1.02         1.02         1.02         6.94         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5728 
        5.98         0.95        70.06        12.03        15.02        65.10 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6522 
       55.04        21.07         7.99        15.65         9.63         6.90 
TCGA-D7-6524 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6820 
        0.69         6.61         4.14         3.65         4.70         2.93 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6177 TCGA-FP-7735 TCGA-HJ-7597 TCGA-IP-7968 
        0.62         7.79         6.54         0.39        26.43         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               1.02 
[1] "0.2 - 72.2 (4.0)" "0.1 - 70.1 (1.0)"
        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-BR-7958 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-BR-7959         TCGA-BR-8059         TCGA-BR-8060 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-BR-8077         TCGA-BR-8078         TCGA-BR-8080 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-BR-8081         TCGA-BR-8284         TCGA-BR-8285 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-BR-8286         TCGA-BR-8289         TCGA-BR-8291 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-BR-8295         TCGA-BR-8296         TCGA-BR-8297 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-CD-5798         TCGA-CD-5799         TCGA-CD-5800 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-CD-5801         TCGA-CD-5802         TCGA-CD-5803 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-CG-4300         TCGA-CG-4301         TCGA-CG-4304 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-CG-4305         TCGA-CG-4306         TCGA-CG-4436 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-CG-4437         TCGA-CG-4438         TCGA-CG-4440 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED"   "20P GAIN MUTATED" 
        TCGA-CG-4441         TCGA-CG-4443         TCGA-CG-4444 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-CG-4449         TCGA-CG-4455         TCGA-CG-4460 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-CG-4462         TCGA-CG-4465         TCGA-CG-4466 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-CG-4469         TCGA-CG-4472         TCGA-CG-4474 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-CG-4477         TCGA-CG-5716         TCGA-CG-5717 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-CG-5718         TCGA-CG-5719         TCGA-CG-5720 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-CG-5721         TCGA-CG-5722         TCGA-CG-5723 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-CG-5724         TCGA-CG-5725         TCGA-CG-5726 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-CG-5727         TCGA-CG-5728         TCGA-CG-5730 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-CG-5732         TCGA-CG-5733         TCGA-CG-5734 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-D7-5577         TCGA-D7-5578         TCGA-D7-5579 
  "20P GAIN MUTATED"   "20P GAIN MUTATED"   "20P GAIN MUTATED" 
        TCGA-D7-6518         TCGA-D7-6519         TCGA-D7-6520 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-D7-6521         TCGA-D7-6522         TCGA-D7-6524 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-D7-6525         TCGA-D7-6526         TCGA-D7-6527 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-D7-6528         TCGA-D7-6815         TCGA-D7-6817 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-D7-6818         TCGA-D7-6820         TCGA-D7-6822 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-EQ-5647         TCGA-EQ-8122         TCGA-F1-6177 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-F1-6874         TCGA-F1-6875         TCGA-FP-7735 
  "20P GAIN MUTATED"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-FP-7829         TCGA-FP-7916         TCGA-FP-7998 
  "20P GAIN MUTATED"   "20P GAIN MUTATED"   "20P GAIN MUTATED" 
        TCGA-HJ-7597         TCGA-IN-7806         TCGA-IN-7808 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED"   "20P GAIN MUTATED" 
        TCGA-IP-7968 
"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-BR-7958 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-BR-7959         TCGA-BR-8059         TCGA-BR-8060 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-BR-8077         TCGA-BR-8078         TCGA-BR-8080 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-BR-8081         TCGA-BR-8284         TCGA-BR-8285 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-BR-8286         TCGA-BR-8289         TCGA-BR-8291 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-BR-8295         TCGA-BR-8296         TCGA-BR-8297 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-CD-5798         TCGA-CD-5799         TCGA-CD-5800 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-CD-5801         TCGA-CD-5802         TCGA-CD-5803 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-CG-4300         TCGA-CG-4301         TCGA-CG-4304 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-CG-4305         TCGA-CG-4306         TCGA-CG-4436 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-CG-4437         TCGA-CG-4438         TCGA-CG-4440 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED"   "20P GAIN MUTATED" 
        TCGA-CG-4441         TCGA-CG-4443         TCGA-CG-4444 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-CG-4449         TCGA-CG-4455         TCGA-CG-4460 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-CG-4462         TCGA-CG-4465         TCGA-CG-4466 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-CG-4469         TCGA-CG-4472         TCGA-CG-4474 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-CG-4477         TCGA-CG-5716         TCGA-CG-5717 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-CG-5718         TCGA-CG-5719         TCGA-CG-5720 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-CG-5721         TCGA-CG-5722         TCGA-CG-5723 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-CG-5724         TCGA-CG-5725         TCGA-CG-5726 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-CG-5727         TCGA-CG-5728         TCGA-CG-5730 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-CG-5732         TCGA-CG-5733         TCGA-CG-5734 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-D7-5577         TCGA-D7-5578         TCGA-D7-5579 
  "20P GAIN MUTATED"   "20P GAIN MUTATED"   "20P GAIN MUTATED" 
        TCGA-D7-6518         TCGA-D7-6519         TCGA-D7-6520 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-D7-6521         TCGA-D7-6522         TCGA-D7-6524 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-D7-6525         TCGA-D7-6526         TCGA-D7-6527 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-D7-6528         TCGA-D7-6815         TCGA-D7-6817 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-D7-6818         TCGA-D7-6820         TCGA-D7-6822 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-EQ-5647         TCGA-EQ-8122         TCGA-F1-6177 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-F1-6874         TCGA-F1-6875         TCGA-FP-7735 
  "20P GAIN MUTATED"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-FP-7829         TCGA-FP-7916         TCGA-FP-7998 
  "20P GAIN MUTATED"   "20P GAIN MUTATED"   "20P GAIN MUTATED" 
        TCGA-HJ-7597         TCGA-IN-7806         TCGA-IN-7808 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED"   "20P GAIN MUTATED" 
        TCGA-IP-7968 
"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-BR-7958 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-BR-7959         TCGA-BR-8059         TCGA-BR-8060 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-BR-8077         TCGA-BR-8078         TCGA-BR-8080 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-BR-8081         TCGA-BR-8284         TCGA-BR-8285 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-BR-8286         TCGA-BR-8289         TCGA-BR-8291 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-BR-8295         TCGA-BR-8296         TCGA-BR-8297 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-CD-5798         TCGA-CD-5799         TCGA-CD-5800 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-CD-5801         TCGA-CD-5802         TCGA-CD-5803 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-CG-4300         TCGA-CG-4301         TCGA-CG-4304 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-CG-4305         TCGA-CG-4306         TCGA-CG-4436 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-CG-4437         TCGA-CG-4438         TCGA-CG-4440 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED"   "20P GAIN MUTATED" 
        TCGA-CG-4441         TCGA-CG-4443         TCGA-CG-4444 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-CG-4449         TCGA-CG-4455         TCGA-CG-4460 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-CG-4462         TCGA-CG-4465         TCGA-CG-4466 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-CG-4469         TCGA-CG-4472         TCGA-CG-4474 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-CG-4477         TCGA-CG-5716         TCGA-CG-5717 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-CG-5718         TCGA-CG-5719         TCGA-CG-5720 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-CG-5721         TCGA-CG-5722         TCGA-CG-5723 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-CG-5724         TCGA-CG-5725         TCGA-CG-5726 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-CG-5727         TCGA-CG-5728         TCGA-CG-5730 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-CG-5732         TCGA-CG-5733         TCGA-CG-5734 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-D7-5577         TCGA-D7-5578         TCGA-D7-5579 
  "20P GAIN MUTATED"   "20P GAIN MUTATED"   "20P GAIN MUTATED" 
        TCGA-D7-6518         TCGA-D7-6519         TCGA-D7-6520 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-D7-6521         TCGA-D7-6522         TCGA-D7-6524 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-D7-6525         TCGA-D7-6526         TCGA-D7-6527 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-D7-6528         TCGA-D7-6815         TCGA-D7-6817 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-D7-6818         TCGA-D7-6820         TCGA-D7-6822 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-EQ-5647         TCGA-EQ-8122         TCGA-F1-6177 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-F1-6874         TCGA-F1-6875         TCGA-FP-7735 
  "20P GAIN MUTATED"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-FP-7829         TCGA-FP-7916         TCGA-FP-7998 
  "20P GAIN MUTATED"   "20P GAIN MUTATED"   "20P GAIN MUTATED" 
        TCGA-HJ-7597         TCGA-IN-7806         TCGA-IN-7808 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED"   "20P GAIN MUTATED" 
        TCGA-IP-7968 
"20P GAIN WILD-TYPE" 
[1] "hr=" "2.8"
D34V2, continuous
D34V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED     13   48
  20P GAIN WILD-TYPE   52   48
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  FEMALE               13                 52
  MALE                 48                 48
                    vv
clus                 STOMACH ADENOCARCINOMA - DIFFUSE TYPE
  20P GAIN MUTATED                                       9
  20P GAIN WILD-TYPE                                    10
                    vv
clus                 STOMACH ADENOCARCINOMA - NOT OTHERWISE SPECIFIED (NOS)
  20P GAIN MUTATED                                                       29
  20P GAIN WILD-TYPE                                                     50
                    vv
clus                 STOMACH ADENOCARCINOMA - SIGNET RING TYPE
  20P GAIN MUTATED                                           0
  20P GAIN WILD-TYPE                                         1
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - MUCINOUS TYPE
  20P GAIN MUTATED                                                   3
  20P GAIN WILD-TYPE                                                 6
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - PAPILLARY TYPE
  20P GAIN MUTATED                                                    0
  20P GAIN WILD-TYPE                                                  3
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - TUBULAR TYPE
  20P GAIN MUTATED                                                  5
  20P GAIN WILD-TYPE                                                5
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - TYPE NOT OTHERWISE SPECIFIED (NOS)
  20P GAIN MUTATED                                                                       14
  20P GAIN WILD-TYPE                                                                     21
D34V4, multiclass
                    vv
clus                 T1 T2 T3 T4
  20P GAIN MUTATED    2 23 26  6
  20P GAIN WILD-TYPE  4 30 33 27
D34V5, multiclass
                    vv
clus                 N0 N1 N2 N3
  20P GAIN MUTATED   16 21  9  9
  20P GAIN WILD-TYPE 34 36 15 10
D34V6, multiclass
                    vv
clus                 M0 M1 MX
  20P GAIN MUTATED   54  3  4
  20P GAIN WILD-TYPE 78 15  7
D34V7, multiclass
                    vv
clus                  I II III IV
  20P GAIN MUTATED    9 14  23  7
  20P GAIN WILD-TYPE 16 29  25 22
D34V8, multiclass
D34V9, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED      1   60
  20P GAIN WILD-TYPE    4   96
     clus
vv    20P GAIN MUTATED 20P GAIN WILD-TYPE
  NO                 1                  4
  YES               60                 96

Clustering(35) Variable = 20q gain mutation analysis
D35V1, survival
                    sevent
clus2                 0  1
  20Q GAIN MUTATED   48  6
  20Q GAIN WILD-TYPE 60 10
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                54                 70 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                 6                 10 
$`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-7916 TCGA-FP-7998 TCGA-IN-7806 TCGA-IN-7808 TCGA-IP-7968 
        0.20         3.02         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-BR-7958 TCGA-BR-7959 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
        0.69         0.16         1.08         0.82         1.32         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
        0.95         0.49         0.46         0.72         0.26         0.43 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-CD-5798 
        0.26         1.18         1.55         1.48         0.76         0.82 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CG-4301 TCGA-CG-4306 TCGA-CG-4437 TCGA-CG-4443 
        0.30         0.07         3.02         1.02         8.05        29.98 
TCGA-CG-4449 TCGA-CG-4460 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4472 TCGA-CG-4474 
       19.07        21.99         1.02         8.98        12.00         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-5725 TCGA-CG-5728 TCGA-CG-5733 TCGA-CG-5734 
        0.95        70.06        15.02        65.10        21.07         7.99 
TCGA-D7-6519 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6527 TCGA-D7-6817 TCGA-D7-6820 
       15.65         6.90         0.69         4.14         4.70         2.93 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6177 TCGA-HJ-7597 
        0.62         7.79         6.54        26.43 

  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-BR-7958 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-BR-7959         TCGA-BR-8059         TCGA-BR-8060 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-BR-8077         TCGA-BR-8078         TCGA-BR-8080 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-BR-8081         TCGA-BR-8284         TCGA-BR-8285 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-BR-8286         TCGA-BR-8289         TCGA-BR-8291 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-BR-8295         TCGA-BR-8296         TCGA-BR-8297 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-CD-5798         TCGA-CD-5799         TCGA-CD-5800 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-CD-5801         TCGA-CD-5802         TCGA-CD-5803 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-CG-4300         TCGA-CG-4301         TCGA-CG-4304 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-CG-4305         TCGA-CG-4306         TCGA-CG-4436 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-CG-4437         TCGA-CG-4438         TCGA-CG-4440 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-CG-4441         TCGA-CG-4443         TCGA-CG-4444 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-CG-4449         TCGA-CG-4455         TCGA-CG-4460 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-CG-4462         TCGA-CG-4465         TCGA-CG-4466 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-CG-4469         TCGA-CG-4472         TCGA-CG-4474 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-CG-4477         TCGA-CG-5716         TCGA-CG-5717 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-CG-5718         TCGA-CG-5719         TCGA-CG-5720 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-CG-5721         TCGA-CG-5722         TCGA-CG-5723 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-CG-5724         TCGA-CG-5725         TCGA-CG-5726 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-CG-5727         TCGA-CG-5728         TCGA-CG-5730 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-CG-5732         TCGA-CG-5733         TCGA-CG-5734 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-D7-5577         TCGA-D7-5578         TCGA-D7-5579 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-D7-6518         TCGA-D7-6519         TCGA-D7-6520 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-D7-6521         TCGA-D7-6522         TCGA-D7-6524 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-D7-6525         TCGA-D7-6526         TCGA-D7-6527 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-D7-6528         TCGA-D7-6815         TCGA-D7-6817 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-D7-6818         TCGA-D7-6820         TCGA-D7-6822 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-EQ-5647         TCGA-EQ-8122         TCGA-F1-6177 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-F1-6874         TCGA-F1-6875         TCGA-FP-7735 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-FP-7829         TCGA-FP-7916         TCGA-FP-7998 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-HJ-7597         TCGA-IN-7806         TCGA-IN-7808 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-IP-7968 
  "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-BR-7958 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-BR-7959         TCGA-BR-8059         TCGA-BR-8060 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-BR-8077         TCGA-BR-8078         TCGA-BR-8080 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-BR-8081         TCGA-BR-8284         TCGA-BR-8285 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-BR-8286         TCGA-BR-8289         TCGA-BR-8291 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-BR-8295         TCGA-BR-8296         TCGA-BR-8297 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-CD-5798         TCGA-CD-5799         TCGA-CD-5800 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-CD-5801         TCGA-CD-5802         TCGA-CD-5803 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-CG-4300         TCGA-CG-4301         TCGA-CG-4304 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-CG-4305         TCGA-CG-4306         TCGA-CG-4436 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-CG-4437         TCGA-CG-4438         TCGA-CG-4440 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-CG-4441         TCGA-CG-4443         TCGA-CG-4444 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-CG-4449         TCGA-CG-4455         TCGA-CG-4460 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-CG-4462         TCGA-CG-4465         TCGA-CG-4466 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-CG-4469         TCGA-CG-4472         TCGA-CG-4474 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-CG-4477         TCGA-CG-5716         TCGA-CG-5717 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-CG-5718         TCGA-CG-5719         TCGA-CG-5720 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-CG-5721         TCGA-CG-5722         TCGA-CG-5723 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-CG-5724         TCGA-CG-5725         TCGA-CG-5726 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-CG-5727         TCGA-CG-5728         TCGA-CG-5730 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-CG-5732         TCGA-CG-5733         TCGA-CG-5734 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-D7-5577         TCGA-D7-5578         TCGA-D7-5579 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-D7-6518         TCGA-D7-6519         TCGA-D7-6520 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-D7-6521         TCGA-D7-6522         TCGA-D7-6524 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-D7-6525         TCGA-D7-6526         TCGA-D7-6527 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-D7-6528         TCGA-D7-6815         TCGA-D7-6817 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-D7-6818         TCGA-D7-6820         TCGA-D7-6822 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-EQ-5647         TCGA-EQ-8122         TCGA-F1-6177 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-F1-6874         TCGA-F1-6875         TCGA-FP-7735 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-FP-7829         TCGA-FP-7916         TCGA-FP-7998 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-HJ-7597         TCGA-IN-7806         TCGA-IN-7808 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-IP-7968 
  "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-BR-7958 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-BR-7959         TCGA-BR-8059         TCGA-BR-8060 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-BR-8077         TCGA-BR-8078         TCGA-BR-8080 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-BR-8081         TCGA-BR-8284         TCGA-BR-8285 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-BR-8286         TCGA-BR-8289         TCGA-BR-8291 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-BR-8295         TCGA-BR-8296         TCGA-BR-8297 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-CD-5798         TCGA-CD-5799         TCGA-CD-5800 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-CD-5801         TCGA-CD-5802         TCGA-CD-5803 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-CG-4300         TCGA-CG-4301         TCGA-CG-4304 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-CG-4305         TCGA-CG-4306         TCGA-CG-4436 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-CG-4437         TCGA-CG-4438         TCGA-CG-4440 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-CG-4441         TCGA-CG-4443         TCGA-CG-4444 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-CG-4449         TCGA-CG-4455         TCGA-CG-4460 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-CG-4462         TCGA-CG-4465         TCGA-CG-4466 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-CG-4469         TCGA-CG-4472         TCGA-CG-4474 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-CG-4477         TCGA-CG-5716         TCGA-CG-5717 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-CG-5718         TCGA-CG-5719         TCGA-CG-5720 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-CG-5721         TCGA-CG-5722         TCGA-CG-5723 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-CG-5724         TCGA-CG-5725         TCGA-CG-5726 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-CG-5727         TCGA-CG-5728         TCGA-CG-5730 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-CG-5732         TCGA-CG-5733         TCGA-CG-5734 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-D7-5577         TCGA-D7-5578         TCGA-D7-5579 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-D7-6518         TCGA-D7-6519         TCGA-D7-6520 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-D7-6521         TCGA-D7-6522         TCGA-D7-6524 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-D7-6525         TCGA-D7-6526         TCGA-D7-6527 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-D7-6528         TCGA-D7-6815         TCGA-D7-6817 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-D7-6818         TCGA-D7-6820         TCGA-D7-6822 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-EQ-5647         TCGA-EQ-8122         TCGA-F1-6177 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-F1-6874         TCGA-F1-6875         TCGA-FP-7735 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-FP-7829         TCGA-FP-7916         TCGA-FP-7998 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-HJ-7597         TCGA-IN-7806         TCGA-IN-7808 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-IP-7968 
  "20Q GAIN MUTATED" 
[1] "hr=" "2.8"
D35V2, continuous
D35V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED     19   56
  20Q GAIN WILD-TYPE   46   40
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  FEMALE               19                 46
  MALE                 56                 40
                    vv
clus                 STOMACH ADENOCARCINOMA - DIFFUSE TYPE
  20Q GAIN MUTATED                                      10
  20Q GAIN WILD-TYPE                                     9
                    vv
clus                 STOMACH ADENOCARCINOMA - NOT OTHERWISE SPECIFIED (NOS)
  20Q GAIN MUTATED                                                       35
  20Q GAIN WILD-TYPE                                                     44
                    vv
clus                 STOMACH ADENOCARCINOMA - SIGNET RING TYPE
  20Q GAIN MUTATED                                           0
  20Q GAIN WILD-TYPE                                         1
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - MUCINOUS TYPE
  20Q GAIN MUTATED                                                   4
  20Q GAIN WILD-TYPE                                                 5
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - PAPILLARY TYPE
  20Q GAIN MUTATED                                                    1
  20Q GAIN WILD-TYPE                                                  2
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - TUBULAR TYPE
  20Q GAIN MUTATED                                                  8
  20Q GAIN WILD-TYPE                                                2
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - TYPE NOT OTHERWISE SPECIFIED (NOS)
  20Q GAIN MUTATED                                                                       15
  20Q GAIN WILD-TYPE                                                                     20
D35V4, multiclass
                    vv
clus                 T1 T2 T3 T4
  20Q GAIN MUTATED    2 29 34  6
  20Q GAIN WILD-TYPE  4 24 25 27
D35V5, multiclass
                    vv
clus                 N0 N1 N2 N3
  20Q GAIN MUTATED   20 24 13 12
  20Q GAIN WILD-TYPE 30 33 11  7
D35V6, multiclass
                    vv
clus                 M0 M1 MX
  20Q GAIN MUTATED   64  4  7
  20Q GAIN WILD-TYPE 68 14  4
D35V7, multiclass
                    vv
clus                  I II III IV
  20Q GAIN MUTATED   11 18  28 10
  20Q GAIN WILD-TYPE 14 25  20 19
D35V8, multiclass
D35V9, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED      3   72
  20Q GAIN WILD-TYPE    2   84
     clus
vv    20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  NO                 3                  2
  YES               72                 84

Clustering(36) Variable = 22q gain mutation analysis
D36V1, survival
                    sevent
clus2                  0   1
  22Q GAIN MUTATED     3   0
  22Q GAIN WILD-TYPE 105  16
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                 3                121 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                 0                 16 
$`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-BR-7958 
        0.69         0.16         0.99         0.95         0.69         0.16 
TCGA-BR-7959 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
        1.08         0.82         1.32         0.69         0.95         0.49 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
        0.46         0.72         0.26         0.43         0.26         1.18 
TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
        1.55         1.48         0.76         0.82         0.69         0.36 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
        0.49         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-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-D7-6822 
        1.68         3.65         4.70         4.04         2.93         4.27 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6177 TCGA-F1-6874 TCGA-F1-6875 TCGA-FP-7735 
        0.62         7.79         6.54         2.01        72.23         0.39 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-HJ-7597 TCGA-IN-7806 TCGA-IN-7808 
        0.20         3.02         3.58        26.43         6.87         3.55 
TCGA-IP-7968 
        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 
              1.25               1.55 
[1] "0.1 - 4.5 (1.2)"  "0.1 - 72.2 (1.6)"
        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-BR-7958 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BR-7959         TCGA-BR-8059         TCGA-BR-8060 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BR-8077         TCGA-BR-8078         TCGA-BR-8080 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BR-8081         TCGA-BR-8284         TCGA-BR-8285 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BR-8286         TCGA-BR-8289         TCGA-BR-8291 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BR-8295         TCGA-BR-8296         TCGA-BR-8297 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-CD-5798         TCGA-CD-5799         TCGA-CD-5800 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-CD-5801         TCGA-CD-5802         TCGA-CD-5803 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-CG-4300         TCGA-CG-4301         TCGA-CG-4304 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-CG-4305         TCGA-CG-4306         TCGA-CG-4436 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-CG-4437         TCGA-CG-4438         TCGA-CG-4440 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-CG-4441         TCGA-CG-4443         TCGA-CG-4444 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-CG-4449         TCGA-CG-4455         TCGA-CG-4460 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-CG-4462         TCGA-CG-4465         TCGA-CG-4466 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-CG-4469         TCGA-CG-4472         TCGA-CG-4474 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-CG-4477         TCGA-CG-5716         TCGA-CG-5717 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-CG-5718         TCGA-CG-5719         TCGA-CG-5720 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-CG-5721         TCGA-CG-5722         TCGA-CG-5723 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-CG-5724         TCGA-CG-5725         TCGA-CG-5726 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-CG-5727         TCGA-CG-5728         TCGA-CG-5730 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-CG-5732         TCGA-CG-5733         TCGA-CG-5734 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-D7-5577         TCGA-D7-5578         TCGA-D7-5579 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-D7-6518         TCGA-D7-6519         TCGA-D7-6520 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-D7-6521         TCGA-D7-6522         TCGA-D7-6524 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-D7-6525         TCGA-D7-6526         TCGA-D7-6527 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-D7-6528         TCGA-D7-6815         TCGA-D7-6817 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-D7-6818         TCGA-D7-6820         TCGA-D7-6822 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EQ-5647         TCGA-EQ-8122         TCGA-F1-6177 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-F1-6874         TCGA-F1-6875         TCGA-FP-7735 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-FP-7829         TCGA-FP-7916         TCGA-FP-7998 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-HJ-7597         TCGA-IN-7806         TCGA-IN-7808 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-IP-7968 
"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-BR-7958 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BR-7959         TCGA-BR-8059         TCGA-BR-8060 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BR-8077         TCGA-BR-8078         TCGA-BR-8080 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BR-8081         TCGA-BR-8284         TCGA-BR-8285 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BR-8286         TCGA-BR-8289         TCGA-BR-8291 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BR-8295         TCGA-BR-8296         TCGA-BR-8297 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-CD-5798         TCGA-CD-5799         TCGA-CD-5800 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-CD-5801         TCGA-CD-5802         TCGA-CD-5803 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-CG-4300         TCGA-CG-4301         TCGA-CG-4304 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-CG-4305         TCGA-CG-4306         TCGA-CG-4436 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-CG-4437         TCGA-CG-4438         TCGA-CG-4440 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-CG-4441         TCGA-CG-4443         TCGA-CG-4444 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-CG-4449         TCGA-CG-4455         TCGA-CG-4460 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-CG-4462         TCGA-CG-4465         TCGA-CG-4466 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-CG-4469         TCGA-CG-4472         TCGA-CG-4474 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-CG-4477         TCGA-CG-5716         TCGA-CG-5717 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-CG-5718         TCGA-CG-5719         TCGA-CG-5720 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-CG-5721         TCGA-CG-5722         TCGA-CG-5723 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-CG-5724         TCGA-CG-5725         TCGA-CG-5726 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-CG-5727         TCGA-CG-5728         TCGA-CG-5730 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-CG-5732         TCGA-CG-5733         TCGA-CG-5734 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-D7-5577         TCGA-D7-5578         TCGA-D7-5579 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-D7-6518         TCGA-D7-6519         TCGA-D7-6520 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-D7-6521         TCGA-D7-6522         TCGA-D7-6524 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-D7-6525         TCGA-D7-6526         TCGA-D7-6527 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-D7-6528         TCGA-D7-6815         TCGA-D7-6817 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-D7-6818         TCGA-D7-6820         TCGA-D7-6822 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EQ-5647         TCGA-EQ-8122         TCGA-F1-6177 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-F1-6874         TCGA-F1-6875         TCGA-FP-7735 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-FP-7829         TCGA-FP-7916         TCGA-FP-7998 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-HJ-7597         TCGA-IN-7806         TCGA-IN-7808 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-IP-7968 
"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-BR-7958 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BR-7959         TCGA-BR-8059         TCGA-BR-8060 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BR-8077         TCGA-BR-8078         TCGA-BR-8080 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BR-8081         TCGA-BR-8284         TCGA-BR-8285 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BR-8286         TCGA-BR-8289         TCGA-BR-8291 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BR-8295         TCGA-BR-8296         TCGA-BR-8297 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-CD-5798         TCGA-CD-5799         TCGA-CD-5800 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-CD-5801         TCGA-CD-5802         TCGA-CD-5803 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-CG-4300         TCGA-CG-4301         TCGA-CG-4304 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-CG-4305         TCGA-CG-4306         TCGA-CG-4436 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-CG-4437         TCGA-CG-4438         TCGA-CG-4440 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-CG-4441         TCGA-CG-4443         TCGA-CG-4444 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-CG-4449         TCGA-CG-4455         TCGA-CG-4460 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-CG-4462         TCGA-CG-4465         TCGA-CG-4466 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-CG-4469         TCGA-CG-4472         TCGA-CG-4474 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-CG-4477         TCGA-CG-5716         TCGA-CG-5717 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-CG-5718         TCGA-CG-5719         TCGA-CG-5720 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-CG-5721         TCGA-CG-5722         TCGA-CG-5723 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-CG-5724         TCGA-CG-5725         TCGA-CG-5726 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-CG-5727         TCGA-CG-5728         TCGA-CG-5730 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-CG-5732         TCGA-CG-5733         TCGA-CG-5734 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-D7-5577         TCGA-D7-5578         TCGA-D7-5579 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-D7-6518         TCGA-D7-6519         TCGA-D7-6520 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-D7-6521         TCGA-D7-6522         TCGA-D7-6524 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-D7-6525         TCGA-D7-6526         TCGA-D7-6527 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-D7-6528         TCGA-D7-6815         TCGA-D7-6817 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-D7-6818         TCGA-D7-6820         TCGA-D7-6822 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EQ-5647         TCGA-EQ-8122         TCGA-F1-6177 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-F1-6874         TCGA-F1-6875         TCGA-FP-7735 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-FP-7829         TCGA-FP-7916         TCGA-FP-7998 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-HJ-7597         TCGA-IN-7806         TCGA-IN-7808 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-IP-7968 
"22Q GAIN WILD-TYPE" 
[1] "hr="     "3400000"
D36V2, continuous
D36V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED      1    2
  22Q GAIN WILD-TYPE   64   94
        clus
vv       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  FEMALE                1                 64
  MALE                  2                 94
                    vv
clus                 STOMACH ADENOCARCINOMA - DIFFUSE TYPE
  22Q GAIN MUTATED                                       1
  22Q GAIN WILD-TYPE                                    18
                    vv
clus                 STOMACH ADENOCARCINOMA - NOT OTHERWISE SPECIFIED (NOS)
  22Q GAIN MUTATED                                                        1
  22Q GAIN WILD-TYPE                                                     78
                    vv
clus                 STOMACH ADENOCARCINOMA - SIGNET RING TYPE
  22Q GAIN MUTATED                                           0
  22Q GAIN WILD-TYPE                                         1
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - MUCINOUS TYPE
  22Q GAIN MUTATED                                                   0
  22Q GAIN WILD-TYPE                                                 9
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - PAPILLARY TYPE
  22Q GAIN MUTATED                                                    0
  22Q GAIN WILD-TYPE                                                  3
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - TUBULAR TYPE
  22Q GAIN MUTATED                                                  0
  22Q GAIN WILD-TYPE                                               10
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - TYPE NOT OTHERWISE SPECIFIED (NOS)
  22Q GAIN MUTATED                                                                        1
  22Q GAIN WILD-TYPE                                                                     34
D36V4, multiclass
                    vv
clus                 T1 T2 T3 T4
  22Q GAIN MUTATED    0  1  2  0
  22Q GAIN WILD-TYPE  6 52 57 33
D36V5, multiclass
                    vv
clus                 N0 N1 N2 N3
  22Q GAIN MUTATED    2  0  1  0
  22Q GAIN WILD-TYPE 48 57 23 19
D36V6, multiclass
                    vv
clus                  M0  M1  MX
  22Q GAIN MUTATED     3   0   0
  22Q GAIN WILD-TYPE 129  18  11
D36V7, multiclass
                    vv
clus                  I II III IV
  22Q GAIN MUTATED    1  2   0  0
  22Q GAIN WILD-TYPE 24 41  48 29
D36V8, multiclass
D36V9, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED      0    3
  22Q GAIN WILD-TYPE    5  153
     clus
vv    22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  NO                 0                  5
  YES                3                153

Clustering(37) Variable = 1p loss mutation analysis
D37V1, survival
                   sevent
clus2                 0   1
  1P LOSS MUTATED     3   2
  1P LOSS WILD-TYPE 105  14
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
                5               119 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
                2                14 
$`1P LOSS MUTATED`
TCGA-CG-4301 TCGA-CG-5719 TCGA-CG-5724 TCGA-CG-5730 TCGA-EQ-5647 
        3.02         1.02        12.03         4.01         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-BR-7958 TCGA-BR-7959 TCGA-BR-8059 TCGA-BR-8060 
        0.95         0.69         0.16         1.08         0.82         1.32 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
        0.69         0.95         0.49         0.46         0.72         0.26 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
        0.43         0.26         1.18         1.55         1.48         0.76 
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-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-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-D7-5577 
       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-D7-6525 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-8122 
        3.65         4.70         4.04         2.93         4.27         7.79 
TCGA-F1-6177 TCGA-F1-6874 TCGA-F1-6875 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
        6.54         2.01        72.23         0.39         0.20         3.02 
TCGA-FP-7998 TCGA-HJ-7597 TCGA-IN-7806 TCGA-IN-7808 TCGA-IP-7968 
        3.58        26.43         6.87         3.55         2.53 

  1P LOSS MUTATED 1P LOSS WILD-TYPE 
             0.62              0.07 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
            12.03             72.23 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
             3.02              1.48 
[1] "0.6 - 12.0 (3.0)" "0.1 - 72.2 (1.5)"
       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-BR-7958        TCGA-BR-7959        TCGA-BR-8059        TCGA-BR-8060 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BR-8077        TCGA-BR-8078        TCGA-BR-8080        TCGA-BR-8081 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BR-8284        TCGA-BR-8285        TCGA-BR-8286        TCGA-BR-8289 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BR-8291        TCGA-BR-8295        TCGA-BR-8296        TCGA-BR-8297 
"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 WILD-TYPE" "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-EQ-8122        TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-FP-7735        TCGA-FP-7829        TCGA-FP-7916        TCGA-FP-7998 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-HJ-7597        TCGA-IN-7806        TCGA-IN-7808        TCGA-IP-7968 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "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-BR-7958        TCGA-BR-7959        TCGA-BR-8059        TCGA-BR-8060 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BR-8077        TCGA-BR-8078        TCGA-BR-8080        TCGA-BR-8081 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BR-8284        TCGA-BR-8285        TCGA-BR-8286        TCGA-BR-8289 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BR-8291        TCGA-BR-8295        TCGA-BR-8296        TCGA-BR-8297 
"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 WILD-TYPE" "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-EQ-8122        TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-FP-7735        TCGA-FP-7829        TCGA-FP-7916        TCGA-FP-7998 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-HJ-7597        TCGA-IN-7806        TCGA-IN-7808        TCGA-IP-7968 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "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-BR-7958        TCGA-BR-7959        TCGA-BR-8059        TCGA-BR-8060 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BR-8077        TCGA-BR-8078        TCGA-BR-8080        TCGA-BR-8081 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BR-8284        TCGA-BR-8285        TCGA-BR-8286        TCGA-BR-8289 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BR-8291        TCGA-BR-8295        TCGA-BR-8296        TCGA-BR-8297 
"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 WILD-TYPE" "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-EQ-8122        TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-FP-7735        TCGA-FP-7829        TCGA-FP-7916        TCGA-FP-7998 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-HJ-7597        TCGA-IN-7806        TCGA-IN-7808        TCGA-IP-7968 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
[1] "hr=" "7"  
D37V2, continuous
D37V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED      4    2
  1P LOSS WILD-TYPE   61   94
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  FEMALE               4                61
  MALE                 2                94
                   vv
clus                STOMACH ADENOCARCINOMA - DIFFUSE TYPE
  1P LOSS MUTATED                                       1
  1P LOSS WILD-TYPE                                    18
                   vv
clus                STOMACH ADENOCARCINOMA - NOT OTHERWISE SPECIFIED (NOS)
  1P LOSS MUTATED                                                        2
  1P LOSS WILD-TYPE                                                     77
                   vv
clus                STOMACH ADENOCARCINOMA - SIGNET RING TYPE
  1P LOSS MUTATED                                           0
  1P LOSS WILD-TYPE                                         1
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - MUCINOUS TYPE
  1P LOSS MUTATED                                                   0
  1P LOSS WILD-TYPE                                                 9
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - PAPILLARY TYPE
  1P LOSS MUTATED                                                    0
  1P LOSS WILD-TYPE                                                  3
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - TUBULAR TYPE
  1P LOSS MUTATED                                                  1
  1P LOSS WILD-TYPE                                                9
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - TYPE NOT OTHERWISE SPECIFIED (NOS)
  1P LOSS MUTATED                                                                        2
  1P LOSS WILD-TYPE                                                                     33
D37V4, multiclass
                   vv
clus                T1 T2 T3 T4
  1P LOSS MUTATED    0  2  1  3
  1P LOSS WILD-TYPE  6 51 58 30
D37V5, multiclass
                   vv
clus                N0 N1 N2 N3
  1P LOSS MUTATED    1  2  0  2
  1P LOSS WILD-TYPE 49 55 24 17
D37V6, multiclass
                   vv
clus                 M0  M1  MX
  1P LOSS MUTATED     1   5   0
  1P LOSS WILD-TYPE 131  13  11
D37V7, multiclass
                   vv
clus                 I II III IV
  1P LOSS MUTATED    0  0   0  5
  1P LOSS WILD-TYPE 25 43  48 24
D37V8, multiclass
D37V9, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED      0    6
  1P LOSS WILD-TYPE    5  150
     clus
vv    1P LOSS MUTATED 1P LOSS WILD-TYPE
  NO                0                 5
  YES               6               150

Clustering(38) Variable = 2p loss mutation analysis
D38V1, survival
                   sevent
clus2                 0   1
  2P LOSS MUTATED     1   0
  2P LOSS WILD-TYPE 107  16
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
                1               123 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
                0                16 
$`2P LOSS MUTATED`
TCGA-EQ-8122 
        7.79 

$`2P 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-BR-7958 TCGA-BR-7959 TCGA-BR-8059 TCGA-BR-8060 
        0.95         0.69         0.16         1.08         0.82         1.32 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
        0.69         0.95         0.49         0.46         0.72         0.26 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
        0.43         0.26         1.18         1.55         1.48         0.76 
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-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-7916 TCGA-FP-7998 TCGA-HJ-7597 
       72.23         0.39         0.20         3.02         3.58        26.43 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IP-7968 
        6.87         3.55         2.53 

  2P LOSS MUTATED 2P LOSS WILD-TYPE 
             7.79              0.07 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
             7.79             72.23 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
             7.79              1.48 
[1] "7.8 - 7.8 (7.8)"  "0.1 - 72.2 (1.5)"
       TCGA-B7-5816        TCGA-B7-5818        TCGA-BR-6452        TCGA-BR-6455 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BR-6457        TCGA-BR-6458        TCGA-BR-6563        TCGA-BR-6564 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BR-6565        TCGA-BR-6566        TCGA-BR-6705        TCGA-BR-6706 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BR-6707        TCGA-BR-6709        TCGA-BR-6710        TCGA-BR-6801 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BR-6802        TCGA-BR-6803        TCGA-BR-6852        TCGA-BR-7196 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BR-7197        TCGA-BR-7703        TCGA-BR-7704        TCGA-BR-7707 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BR-7715        TCGA-BR-7716        TCGA-BR-7717        TCGA-BR-7722 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BR-7723        TCGA-BR-7851        TCGA-BR-7901        TCGA-BR-7957 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BR-7958        TCGA-BR-7959        TCGA-BR-8059        TCGA-BR-8060 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BR-8077        TCGA-BR-8078        TCGA-BR-8080        TCGA-BR-8081 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BR-8284        TCGA-BR-8285        TCGA-BR-8286        TCGA-BR-8289 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BR-8291        TCGA-BR-8295        TCGA-BR-8296        TCGA-BR-8297 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CD-5798        TCGA-CD-5799        TCGA-CD-5800        TCGA-CD-5801 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CD-5802        TCGA-CD-5803        TCGA-CG-4300        TCGA-CG-4301 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CG-4304        TCGA-CG-4305        TCGA-CG-4306        TCGA-CG-4436 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CG-4437        TCGA-CG-4438        TCGA-CG-4440        TCGA-CG-4441 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CG-4443        TCGA-CG-4444        TCGA-CG-4449        TCGA-CG-4455 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CG-4460        TCGA-CG-4462        TCGA-CG-4465        TCGA-CG-4466 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CG-4469        TCGA-CG-4472        TCGA-CG-4474        TCGA-CG-4477 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CG-5716        TCGA-CG-5717        TCGA-CG-5718        TCGA-CG-5719 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CG-5720        TCGA-CG-5721        TCGA-CG-5722        TCGA-CG-5723 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CG-5724        TCGA-CG-5725        TCGA-CG-5726        TCGA-CG-5727 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CG-5728        TCGA-CG-5730        TCGA-CG-5732        TCGA-CG-5733 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CG-5734        TCGA-D7-5577        TCGA-D7-5578        TCGA-D7-5579 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-D7-6518        TCGA-D7-6519        TCGA-D7-6520        TCGA-D7-6521 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-D7-6522        TCGA-D7-6524        TCGA-D7-6525        TCGA-D7-6526 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-D7-6527        TCGA-D7-6528        TCGA-D7-6815        TCGA-D7-6817 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-D7-6818        TCGA-D7-6820        TCGA-D7-6822        TCGA-EQ-5647 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-EQ-8122        TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875 
  "2P LOSS MUTATED" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-FP-7735        TCGA-FP-7829        TCGA-FP-7916        TCGA-FP-7998 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-HJ-7597        TCGA-IN-7806        TCGA-IN-7808        TCGA-IP-7968 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-B7-5816        TCGA-B7-5818        TCGA-BR-6452        TCGA-BR-6455 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BR-6457        TCGA-BR-6458        TCGA-BR-6563        TCGA-BR-6564 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BR-6565        TCGA-BR-6566        TCGA-BR-6705        TCGA-BR-6706 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BR-6707        TCGA-BR-6709        TCGA-BR-6710        TCGA-BR-6801 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BR-6802        TCGA-BR-6803        TCGA-BR-6852        TCGA-BR-7196 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BR-7197        TCGA-BR-7703        TCGA-BR-7704        TCGA-BR-7707 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BR-7715        TCGA-BR-7716        TCGA-BR-7717        TCGA-BR-7722 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BR-7723        TCGA-BR-7851        TCGA-BR-7901        TCGA-BR-7957 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BR-7958        TCGA-BR-7959        TCGA-BR-8059        TCGA-BR-8060 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BR-8077        TCGA-BR-8078        TCGA-BR-8080        TCGA-BR-8081 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BR-8284        TCGA-BR-8285        TCGA-BR-8286        TCGA-BR-8289 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BR-8291        TCGA-BR-8295        TCGA-BR-8296        TCGA-BR-8297 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CD-5798        TCGA-CD-5799        TCGA-CD-5800        TCGA-CD-5801 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CD-5802        TCGA-CD-5803        TCGA-CG-4300        TCGA-CG-4301 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CG-4304        TCGA-CG-4305        TCGA-CG-4306        TCGA-CG-4436 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CG-4437        TCGA-CG-4438        TCGA-CG-4440        TCGA-CG-4441 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CG-4443        TCGA-CG-4444        TCGA-CG-4449        TCGA-CG-4455 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CG-4460        TCGA-CG-4462        TCGA-CG-4465        TCGA-CG-4466 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CG-4469        TCGA-CG-4472        TCGA-CG-4474        TCGA-CG-4477 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CG-5716        TCGA-CG-5717        TCGA-CG-5718        TCGA-CG-5719 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CG-5720        TCGA-CG-5721        TCGA-CG-5722        TCGA-CG-5723 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CG-5724        TCGA-CG-5725        TCGA-CG-5726        TCGA-CG-5727 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CG-5728        TCGA-CG-5730        TCGA-CG-5732        TCGA-CG-5733 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CG-5734        TCGA-D7-5577        TCGA-D7-5578        TCGA-D7-5579 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-D7-6518        TCGA-D7-6519        TCGA-D7-6520        TCGA-D7-6521 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-D7-6522        TCGA-D7-6524        TCGA-D7-6525        TCGA-D7-6526 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-D7-6527        TCGA-D7-6528        TCGA-D7-6815        TCGA-D7-6817 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-D7-6818        TCGA-D7-6820        TCGA-D7-6822        TCGA-EQ-5647 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-EQ-8122        TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875 
  "2P LOSS MUTATED" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-FP-7735        TCGA-FP-7829        TCGA-FP-7916        TCGA-FP-7998 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-HJ-7597        TCGA-IN-7806        TCGA-IN-7808        TCGA-IP-7968 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-B7-5816        TCGA-B7-5818        TCGA-BR-6452        TCGA-BR-6455 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BR-6457        TCGA-BR-6458        TCGA-BR-6563        TCGA-BR-6564 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BR-6565        TCGA-BR-6566        TCGA-BR-6705        TCGA-BR-6706 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BR-6707        TCGA-BR-6709        TCGA-BR-6710        TCGA-BR-6801 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BR-6802        TCGA-BR-6803        TCGA-BR-6852        TCGA-BR-7196 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BR-7197        TCGA-BR-7703        TCGA-BR-7704        TCGA-BR-7707 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BR-7715        TCGA-BR-7716        TCGA-BR-7717        TCGA-BR-7722 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BR-7723        TCGA-BR-7851        TCGA-BR-7901        TCGA-BR-7957 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BR-7958        TCGA-BR-7959        TCGA-BR-8059        TCGA-BR-8060 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BR-8077        TCGA-BR-8078        TCGA-BR-8080        TCGA-BR-8081 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BR-8284        TCGA-BR-8285        TCGA-BR-8286        TCGA-BR-8289 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BR-8291        TCGA-BR-8295        TCGA-BR-8296        TCGA-BR-8297 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CD-5798        TCGA-CD-5799        TCGA-CD-5800        TCGA-CD-5801 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CD-5802        TCGA-CD-5803        TCGA-CG-4300        TCGA-CG-4301 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CG-4304        TCGA-CG-4305        TCGA-CG-4306        TCGA-CG-4436 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CG-4437        TCGA-CG-4438        TCGA-CG-4440        TCGA-CG-4441 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CG-4443        TCGA-CG-4444        TCGA-CG-4449        TCGA-CG-4455 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CG-4460        TCGA-CG-4462        TCGA-CG-4465        TCGA-CG-4466 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CG-4469        TCGA-CG-4472        TCGA-CG-4474        TCGA-CG-4477 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CG-5716        TCGA-CG-5717        TCGA-CG-5718        TCGA-CG-5719 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CG-5720        TCGA-CG-5721        TCGA-CG-5722        TCGA-CG-5723 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CG-5724        TCGA-CG-5725        TCGA-CG-5726        TCGA-CG-5727 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CG-5728        TCGA-CG-5730        TCGA-CG-5732        TCGA-CG-5733 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CG-5734        TCGA-D7-5577        TCGA-D7-5578        TCGA-D7-5579 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-D7-6518        TCGA-D7-6519        TCGA-D7-6520        TCGA-D7-6521 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-D7-6522        TCGA-D7-6524        TCGA-D7-6525        TCGA-D7-6526 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-D7-6527        TCGA-D7-6528        TCGA-D7-6815        TCGA-D7-6817 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-D7-6818        TCGA-D7-6820        TCGA-D7-6822        TCGA-EQ-5647 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-EQ-8122        TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875 
  "2P LOSS MUTATED" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-FP-7735        TCGA-FP-7829        TCGA-FP-7916        TCGA-FP-7998 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-HJ-7597        TCGA-IN-7806        TCGA-IN-7808        TCGA-IP-7968 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
[1] "Remove cluster labels:" "2P LOSS MUTATED"       
clus
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
                1               123 
       TCGA-B7-5816        TCGA-B7-5818        TCGA-BR-6452        TCGA-BR-6455 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BR-6457        TCGA-BR-6458        TCGA-BR-6563        TCGA-BR-6564 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BR-6565        TCGA-BR-6566        TCGA-BR-6705        TCGA-BR-6706 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BR-6707        TCGA-BR-6709        TCGA-BR-6710        TCGA-BR-6801 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BR-6802        TCGA-BR-6803        TCGA-BR-6852        TCGA-BR-7196 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BR-7197        TCGA-BR-7703        TCGA-BR-7704        TCGA-BR-7707 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BR-7715        TCGA-BR-7716        TCGA-BR-7717        TCGA-BR-7722 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BR-7723        TCGA-BR-7851        TCGA-BR-7901        TCGA-BR-7957 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BR-7958        TCGA-BR-7959        TCGA-BR-8059        TCGA-BR-8060 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BR-8077        TCGA-BR-8078        TCGA-BR-8080        TCGA-BR-8081 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BR-8284        TCGA-BR-8285        TCGA-BR-8286        TCGA-BR-8289 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BR-8291        TCGA-BR-8295        TCGA-BR-8296        TCGA-BR-8297 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CD-5798        TCGA-CD-5799        TCGA-CD-5800        TCGA-CD-5801 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CD-5802        TCGA-CD-5803        TCGA-CG-4300        TCGA-CG-4301 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CG-4304        TCGA-CG-4305        TCGA-CG-4306        TCGA-CG-4436 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CG-4437        TCGA-CG-4438        TCGA-CG-4440        TCGA-CG-4441 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CG-4443        TCGA-CG-4444        TCGA-CG-4449        TCGA-CG-4455 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CG-4460        TCGA-CG-4462        TCGA-CG-4465        TCGA-CG-4466 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CG-4469        TCGA-CG-4472        TCGA-CG-4474        TCGA-CG-4477 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CG-5716        TCGA-CG-5717        TCGA-CG-5718        TCGA-CG-5719 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CG-5720        TCGA-CG-5721        TCGA-CG-5722        TCGA-CG-5723 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CG-5724        TCGA-CG-5725        TCGA-CG-5726        TCGA-CG-5727 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CG-5728        TCGA-CG-5730        TCGA-CG-5732        TCGA-CG-5733 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CG-5734        TCGA-D7-5577        TCGA-D7-5578        TCGA-D7-5579 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-D7-6518        TCGA-D7-6519        TCGA-D7-6520        TCGA-D7-6521 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-D7-6522        TCGA-D7-6524        TCGA-D7-6525        TCGA-D7-6526 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-D7-6527        TCGA-D7-6528        TCGA-D7-6815        TCGA-D7-6817 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-D7-6818        TCGA-D7-6820        TCGA-D7-6822        TCGA-EQ-5647 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875        TCGA-FP-7735 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-FP-7829        TCGA-FP-7916        TCGA-FP-7998        TCGA-HJ-7597 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-IN-7806        TCGA-IN-7808        TCGA-IP-7968 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
D38V2, continuous
[1] "Remove cluster labels:" "2P LOSS MUTATED"       
clus
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
                2               152 
       TCGA-B7-5816        TCGA-B7-5818        TCGA-BR-4183        TCGA-BR-4184 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BR-4187        TCGA-BR-4188        TCGA-BR-4191        TCGA-BR-4201 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BR-4253        TCGA-BR-4255        TCGA-BR-4256        TCGA-BR-4257 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BR-4267        TCGA-BR-4279        TCGA-BR-4280        TCGA-BR-4292 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BR-4294        TCGA-BR-4357        TCGA-BR-4361        TCGA-BR-4362 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BR-4363        TCGA-BR-4366        TCGA-BR-4367        TCGA-BR-4368 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BR-4369        TCGA-BR-4370        TCGA-BR-4371        TCGA-BR-6452 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BR-6453        TCGA-BR-6454        TCGA-BR-6455        TCGA-BR-6456 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BR-6457        TCGA-BR-6458        TCGA-BR-6563        TCGA-BR-6564 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BR-6565        TCGA-BR-6566        TCGA-BR-6705        TCGA-BR-6706 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BR-6707        TCGA-BR-6709        TCGA-BR-6710        TCGA-BR-6801 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BR-6802        TCGA-BR-6803        TCGA-BR-6852        TCGA-BR-7196 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BR-7197        TCGA-BR-7703        TCGA-BR-7704        TCGA-BR-7707 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BR-7715        TCGA-BR-7716        TCGA-BR-7717        TCGA-BR-7722 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BR-7723        TCGA-BR-7851        TCGA-BR-7901        TCGA-BR-7957 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BR-7958        TCGA-BR-7959        TCGA-BR-8059        TCGA-BR-8060 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BR-8077        TCGA-BR-8078        TCGA-BR-8080        TCGA-BR-8081 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BR-8284        TCGA-BR-8285        TCGA-BR-8286        TCGA-BR-8289 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BR-8291        TCGA-BR-8295        TCGA-BR-8296        TCGA-BR-8297 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CD-5798        TCGA-CD-5799        TCGA-CD-5802        TCGA-CD-5803 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CD-5804        TCGA-CG-4300        TCGA-CG-4301        TCGA-CG-4304 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CG-4305        TCGA-CG-4306        TCGA-CG-4436        TCGA-CG-4437 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CG-4438        TCGA-CG-4440        TCGA-CG-4441        TCGA-CG-4442 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CG-4443        TCGA-CG-4444        TCGA-CG-4449        TCGA-CG-4455 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CG-4460        TCGA-CG-4462        TCGA-CG-4465        TCGA-CG-4466 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CG-4469        TCGA-CG-4472        TCGA-CG-4474        TCGA-CG-4476 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CG-4477        TCGA-CG-5716        TCGA-CG-5717        TCGA-CG-5718 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CG-5719        TCGA-CG-5720        TCGA-CG-5721        TCGA-CG-5722 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CG-5723        TCGA-CG-5724        TCGA-CG-5725        TCGA-CG-5726 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CG-5727        TCGA-CG-5728        TCGA-CG-5730        TCGA-CG-5732 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CG-5733        TCGA-CG-5734        TCGA-D7-5577        TCGA-D7-5578 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-D7-5579        TCGA-D7-6518        TCGA-D7-6519        TCGA-D7-6520 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-D7-6521        TCGA-D7-6522        TCGA-D7-6524        TCGA-D7-6525 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-D7-6526        TCGA-D7-6527        TCGA-D7-6528        TCGA-D7-6815 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-D7-6817        TCGA-D7-6818        TCGA-D7-6820        TCGA-D7-6822 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-EQ-5647        TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-FP-7735        TCGA-FP-7829        TCGA-FP-7916        TCGA-FP-7998 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-HJ-7597        TCGA-IN-7806        TCGA-IN-7808        TCGA-IP-7968 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
D38V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED      2    1
  2P LOSS WILD-TYPE   63   95
        clus
vv       2P LOSS MUTATED 2P LOSS WILD-TYPE
  FEMALE               2                63
  MALE                 1                95
                   vv
clus                STOMACH ADENOCARCINOMA - DIFFUSE TYPE
  2P LOSS MUTATED                                       0
  2P LOSS WILD-TYPE                                    19
                   vv
clus                STOMACH ADENOCARCINOMA - NOT OTHERWISE SPECIFIED (NOS)
  2P LOSS MUTATED                                                        0
  2P LOSS WILD-TYPE                                                     79
                   vv
clus                STOMACH ADENOCARCINOMA - SIGNET RING TYPE
  2P LOSS MUTATED                                           0
  2P LOSS WILD-TYPE                                         1
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - MUCINOUS TYPE
  2P LOSS MUTATED                                                   1
  2P LOSS WILD-TYPE                                                 8
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - PAPILLARY TYPE
  2P LOSS MUTATED                                                    0
  2P LOSS WILD-TYPE                                                  3
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - TUBULAR TYPE
  2P LOSS MUTATED                                                  0
  2P LOSS WILD-TYPE                                               10
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - TYPE NOT OTHERWISE SPECIFIED (NOS)
  2P LOSS MUTATED                                                                        1
  2P LOSS WILD-TYPE                                                                     34
D38V4, multiclass
[1] "Remove cluster labels:" "2P LOSS MUTATED"       
clus
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
                2               154 
       TCGA-B7-5816        TCGA-B7-5818        TCGA-BR-4183        TCGA-BR-4184 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BR-4187        TCGA-BR-4188        TCGA-BR-4191        TCGA-BR-4201 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BR-4253        TCGA-BR-4255        TCGA-BR-4256        TCGA-BR-4257 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BR-4267        TCGA-BR-4279        TCGA-BR-4280        TCGA-BR-4292 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BR-4294        TCGA-BR-4357        TCGA-BR-4361        TCGA-BR-4362 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BR-4363        TCGA-BR-4366        TCGA-BR-4367        TCGA-BR-4368 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BR-4369        TCGA-BR-4370        TCGA-BR-4371        TCGA-BR-6452 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BR-6453        TCGA-BR-6454        TCGA-BR-6455        TCGA-BR-6456 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BR-6457        TCGA-BR-6458        TCGA-BR-6563        TCGA-BR-6564 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BR-6565        TCGA-BR-6566        TCGA-BR-6705        TCGA-BR-6706 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BR-6707        TCGA-BR-6709        TCGA-BR-6710        TCGA-BR-6801 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BR-6802        TCGA-BR-6803        TCGA-BR-6852        TCGA-BR-7196 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BR-7197        TCGA-BR-7703        TCGA-BR-7704        TCGA-BR-7707 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BR-7715        TCGA-BR-7716        TCGA-BR-7717        TCGA-BR-7722 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BR-7723        TCGA-BR-7851        TCGA-BR-7901        TCGA-BR-7957 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BR-7958        TCGA-BR-7959        TCGA-BR-8059        TCGA-BR-8060 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BR-8077        TCGA-BR-8078        TCGA-BR-8080        TCGA-BR-8081 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BR-8284        TCGA-BR-8285        TCGA-BR-8286        TCGA-BR-8289 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BR-8291        TCGA-BR-8295        TCGA-BR-8296        TCGA-BR-8297 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CD-5798        TCGA-CD-5799        TCGA-CD-5800        TCGA-CD-5801 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CD-5802        TCGA-CD-5803        TCGA-CD-5804        TCGA-CG-4300 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CG-4301        TCGA-CG-4304        TCGA-CG-4305        TCGA-CG-4306 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CG-4436        TCGA-CG-4437        TCGA-CG-4438        TCGA-CG-4440 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CG-4441        TCGA-CG-4442        TCGA-CG-4443        TCGA-CG-4449 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CG-4455        TCGA-CG-4460        TCGA-CG-4466        TCGA-CG-4469 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CG-4474        TCGA-CG-4476        TCGA-CG-4477        TCGA-CG-5716 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CG-5717        TCGA-CG-5718        TCGA-CG-5719        TCGA-CG-5720 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CG-5721        TCGA-CG-5722        TCGA-CG-5723        TCGA-CG-5724 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CG-5725        TCGA-CG-5726        TCGA-CG-5727        TCGA-CG-5728 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CG-5730        TCGA-CG-5732        TCGA-CG-5733        TCGA-CG-5734 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-D7-5577        TCGA-D7-5578        TCGA-D7-5579        TCGA-D7-6518 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-D7-6519        TCGA-D7-6520        TCGA-D7-6521        TCGA-D7-6522 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-D7-6524        TCGA-D7-6525        TCGA-D7-6526        TCGA-D7-6527 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-D7-6528        TCGA-D7-6815        TCGA-D7-6817        TCGA-D7-6818 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-D7-6820        TCGA-D7-6822        TCGA-EQ-5647        TCGA-F1-6177 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-F1-6874        TCGA-F1-6875        TCGA-FP-7735        TCGA-FP-7829 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-FP-7916        TCGA-FP-7998        TCGA-HF-7131        TCGA-HF-7132 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-HF-7134        TCGA-HF-7136        TCGA-HJ-7597        TCGA-IN-7806 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-IN-7808        TCGA-IP-7968 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
                   vv
clus                T1 T2 T3 T4
  2P LOSS MUTATED    0  1  2  0
  2P LOSS WILD-TYPE  6 52 57 33
D38V5, multiclass
                   vv
clus                N0 N1 N2 N3
  2P LOSS MUTATED    0  2  0  1
  2P LOSS WILD-TYPE 50 55 24 18
D38V6, multiclass
                   vv
clus                 M0  M1  MX
  2P LOSS MUTATED     2   0   1
  2P LOSS WILD-TYPE 130  18  10
D38V7, multiclass
                   vv
clus                 I II III IV
  2P LOSS MUTATED    0  2   0  1
  2P LOSS WILD-TYPE 25 41  48 28
D38V8, multiclass
D38V9, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED      1    2
  2P LOSS WILD-TYPE    4  154
     clus
vv    2P LOSS MUTATED 2P LOSS WILD-TYPE
  NO                1                 4
  YES               2               154

Clustering(39) Variable = 2q loss mutation analysis
D39V1, survival
                   sevent
clus2                 0   1
  2Q LOSS MUTATED     1   1
  2Q LOSS WILD-TYPE 107  15
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
                2               122 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
                1                15 
$`2Q LOSS MUTATED`
TCGA-CG-5724 TCGA-EQ-8122 
       12.03         7.79 

$`2Q 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-BR-7958 TCGA-BR-7959 TCGA-BR-8059 TCGA-BR-8060 
        0.95         0.69         0.16         1.08         0.82         1.32 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
        0.69         0.95         0.49         0.46         0.72         0.26 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
        0.43         0.26         1.18         1.55         1.48         0.76 
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-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-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-7916 TCGA-FP-7998 TCGA-HJ-7597 TCGA-IN-7806 
        0.39         0.20         3.02         3.58        26.43         6.87 
TCGA-IN-7808 TCGA-IP-7968 
        3.55         2.53 

  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
             7.79              0.07 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
            12.03             72.23 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
             9.91              1.48 
[1] "7.8 - 12.0 (9.9)" "0.1 - 72.2 (1.5)"
       TCGA-B7-5816        TCGA-B7-5818        TCGA-BR-6452        TCGA-BR-6455 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-BR-6457        TCGA-BR-6458        TCGA-BR-6563        TCGA-BR-6564 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-BR-6565        TCGA-BR-6566        TCGA-BR-6705        TCGA-BR-6706 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-BR-6707        TCGA-BR-6709        TCGA-BR-6710        TCGA-BR-6801 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-BR-6802        TCGA-BR-6803        TCGA-BR-6852        TCGA-BR-7196 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-BR-7197        TCGA-BR-7703        TCGA-BR-7704        TCGA-BR-7707 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-BR-7715        TCGA-BR-7716        TCGA-BR-7717        TCGA-BR-7722 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-BR-7723        TCGA-BR-7851        TCGA-BR-7901        TCGA-BR-7957 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-BR-7958        TCGA-BR-7959        TCGA-BR-8059        TCGA-BR-8060 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-BR-8077        TCGA-BR-8078        TCGA-BR-8080        TCGA-BR-8081 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-BR-8284        TCGA-BR-8285        TCGA-BR-8286        TCGA-BR-8289 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-BR-8291        TCGA-BR-8295        TCGA-BR-8296        TCGA-BR-8297 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-CD-5798        TCGA-CD-5799        TCGA-CD-5800        TCGA-CD-5801 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-CD-5802        TCGA-CD-5803        TCGA-CG-4300        TCGA-CG-4301 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-CG-4304        TCGA-CG-4305        TCGA-CG-4306        TCGA-CG-4436 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-CG-4437        TCGA-CG-4438        TCGA-CG-4440        TCGA-CG-4441 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-CG-4443        TCGA-CG-4444        TCGA-CG-4449        TCGA-CG-4455 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-CG-4460        TCGA-CG-4462        TCGA-CG-4465        TCGA-CG-4466 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-CG-4469        TCGA-CG-4472        TCGA-CG-4474        TCGA-CG-4477 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-CG-5716        TCGA-CG-5717        TCGA-CG-5718        TCGA-CG-5719 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-CG-5720        TCGA-CG-5721        TCGA-CG-5722        TCGA-CG-5723 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-CG-5724        TCGA-CG-5725        TCGA-CG-5726        TCGA-CG-5727 
  "2Q LOSS MUTATED" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-CG-5728        TCGA-CG-5730        TCGA-CG-5732        TCGA-CG-5733 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-CG-5734        TCGA-D7-5577        TCGA-D7-5578        TCGA-D7-5579 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-D7-6518        TCGA-D7-6519        TCGA-D7-6520        TCGA-D7-6521 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-D7-6522        TCGA-D7-6524        TCGA-D7-6525        TCGA-D7-6526 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-D7-6527        TCGA-D7-6528        TCGA-D7-6815        TCGA-D7-6817 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-D7-6818        TCGA-D7-6820        TCGA-D7-6822        TCGA-EQ-5647 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-EQ-8122        TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875 
  "2Q LOSS MUTATED" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-FP-7735        TCGA-FP-7829        TCGA-FP-7916        TCGA-FP-7998 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-HJ-7597        TCGA-IN-7806        TCGA-IN-7808        TCGA-IP-7968 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-B7-5816        TCGA-B7-5818        TCGA-BR-6452        TCGA-BR-6455 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-BR-6457        TCGA-BR-6458        TCGA-BR-6563        TCGA-BR-6564 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-BR-6565        TCGA-BR-6566        TCGA-BR-6705        TCGA-BR-6706 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-BR-6707        TCGA-BR-6709        TCGA-BR-6710        TCGA-BR-6801 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-BR-6802        TCGA-BR-6803        TCGA-BR-6852        TCGA-BR-7196 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-BR-7197        TCGA-BR-7703        TCGA-BR-7704        TCGA-BR-7707 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-BR-7715        TCGA-BR-7716        TCGA-BR-7717        TCGA-BR-7722 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-BR-7723        TCGA-BR-7851        TCGA-BR-7901        TCGA-BR-7957 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-BR-7958        TCGA-BR-7959        TCGA-BR-8059        TCGA-BR-8060 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-BR-8077        TCGA-BR-8078        TCGA-BR-8080        TCGA-BR-8081 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-BR-8284        TCGA-BR-8285        TCGA-BR-8286        TCGA-BR-8289 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-BR-8291        TCGA-BR-8295        TCGA-BR-8296        TCGA-BR-8297 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-CD-5798        TCGA-CD-5799        TCGA-CD-5800        TCGA-CD-5801 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-CD-5802        TCGA-CD-5803        TCGA-CG-4300        TCGA-CG-4301 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-CG-4304        TCGA-CG-4305        TCGA-CG-4306        TCGA-CG-4436 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-CG-4437        TCGA-CG-4438        TCGA-CG-4440        TCGA-CG-4441 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-CG-4443        TCGA-CG-4444        TCGA-CG-4449        TCGA-CG-4455 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-CG-4460        TCGA-CG-4462        TCGA-CG-4465        TCGA-CG-4466 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-CG-4469        TCGA-CG-4472        TCGA-CG-4474        TCGA-CG-4477 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-CG-5716        TCGA-CG-5717        TCGA-CG-5718        TCGA-CG-5719 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-CG-5720        TCGA-CG-5721        TCGA-CG-5722        TCGA-CG-5723 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-CG-5724        TCGA-CG-5725        TCGA-CG-5726        TCGA-CG-5727 
  "2Q LOSS MUTATED" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-CG-5728        TCGA-CG-5730        TCGA-CG-5732        TCGA-CG-5733 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-CG-5734        TCGA-D7-5577        TCGA-D7-5578        TCGA-D7-5579 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-D7-6518        TCGA-D7-6519        TCGA-D7-6520        TCGA-D7-6521 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-D7-6522        TCGA-D7-6524        TCGA-D7-6525        TCGA-D7-6526 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-D7-6527        TCGA-D7-6528        TCGA-D7-6815        TCGA-D7-6817 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-D7-6818        TCGA-D7-6820        TCGA-D7-6822        TCGA-EQ-5647 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-EQ-8122        TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875 
  "2Q LOSS MUTATED" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-FP-7735        TCGA-FP-7829        TCGA-FP-7916        TCGA-FP-7998 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-HJ-7597        TCGA-IN-7806        TCGA-IN-7808        TCGA-IP-7968 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-B7-5816        TCGA-B7-5818        TCGA-BR-6452        TCGA-BR-6455 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-BR-6457        TCGA-BR-6458        TCGA-BR-6563        TCGA-BR-6564 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-BR-6565        TCGA-BR-6566        TCGA-BR-6705        TCGA-BR-6706 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-BR-6707        TCGA-BR-6709        TCGA-BR-6710        TCGA-BR-6801 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-BR-6802        TCGA-BR-6803        TCGA-BR-6852        TCGA-BR-7196 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-BR-7197        TCGA-BR-7703        TCGA-BR-7704        TCGA-BR-7707 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-BR-7715        TCGA-BR-7716        TCGA-BR-7717        TCGA-BR-7722 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-BR-7723        TCGA-BR-7851        TCGA-BR-7901        TCGA-BR-7957 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-BR-7958        TCGA-BR-7959        TCGA-BR-8059        TCGA-BR-8060 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-BR-8077        TCGA-BR-8078        TCGA-BR-8080        TCGA-BR-8081 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-BR-8284        TCGA-BR-8285        TCGA-BR-8286        TCGA-BR-8289 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-BR-8291        TCGA-BR-8295        TCGA-BR-8296        TCGA-BR-8297 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-CD-5798        TCGA-CD-5799        TCGA-CD-5800        TCGA-CD-5801 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-CD-5802        TCGA-CD-5803        TCGA-CG-4300        TCGA-CG-4301 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-CG-4304        TCGA-CG-4305        TCGA-CG-4306        TCGA-CG-4436 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-CG-4437        TCGA-CG-4438        TCGA-CG-4440        TCGA-CG-4441 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-CG-4443        TCGA-CG-4444        TCGA-CG-4449        TCGA-CG-4455 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-CG-4460        TCGA-CG-4462        TCGA-CG-4465        TCGA-CG-4466 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-CG-4469        TCGA-CG-4472        TCGA-CG-4474        TCGA-CG-4477 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-CG-5716        TCGA-CG-5717        TCGA-CG-5718        TCGA-CG-5719 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-CG-5720        TCGA-CG-5721        TCGA-CG-5722        TCGA-CG-5723 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-CG-5724        TCGA-CG-5725        TCGA-CG-5726        TCGA-CG-5727 
  "2Q LOSS MUTATED" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-CG-5728        TCGA-CG-5730        TCGA-CG-5732        TCGA-CG-5733 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-CG-5734        TCGA-D7-5577        TCGA-D7-5578        TCGA-D7-5579 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-D7-6518        TCGA-D7-6519        TCGA-D7-6520        TCGA-D7-6521 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-D7-6522        TCGA-D7-6524        TCGA-D7-6525        TCGA-D7-6526 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-D7-6527        TCGA-D7-6528        TCGA-D7-6815        TCGA-D7-6817 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-D7-6818        TCGA-D7-6820        TCGA-D7-6822        TCGA-EQ-5647 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-EQ-8122        TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875 
  "2Q LOSS MUTATED" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-FP-7735        TCGA-FP-7829        TCGA-FP-7916        TCGA-FP-7998 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-HJ-7597        TCGA-IN-7806        TCGA-IN-7808        TCGA-IP-7968 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
[1] "Remove cluster labels:" "2Q LOSS MUTATED"       
clus
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
                2               122 
       TCGA-B7-5816        TCGA-B7-5818        TCGA-BR-6452        TCGA-BR-6455 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-BR-6457        TCGA-BR-6458        TCGA-BR-6563        TCGA-BR-6564 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-BR-6565        TCGA-BR-6566        TCGA-BR-6705        TCGA-BR-6706 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-BR-6707        TCGA-BR-6709        TCGA-BR-6710        TCGA-BR-6801 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-BR-6802        TCGA-BR-6803        TCGA-BR-6852        TCGA-BR-7196 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-BR-7197        TCGA-BR-7703        TCGA-BR-7704        TCGA-BR-7707 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-BR-7715        TCGA-BR-7716        TCGA-BR-7717        TCGA-BR-7722 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-BR-7723        TCGA-BR-7851        TCGA-BR-7901        TCGA-BR-7957 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-BR-7958        TCGA-BR-7959        TCGA-BR-8059        TCGA-BR-8060 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-BR-8077        TCGA-BR-8078        TCGA-BR-8080        TCGA-BR-8081 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-BR-8284        TCGA-BR-8285        TCGA-BR-8286        TCGA-BR-8289 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-BR-8291        TCGA-BR-8295        TCGA-BR-8296        TCGA-BR-8297 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-CD-5798        TCGA-CD-5799        TCGA-CD-5800        TCGA-CD-5801 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-CD-5802        TCGA-CD-5803        TCGA-CG-4300        TCGA-CG-4301 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-CG-4304        TCGA-CG-4305        TCGA-CG-4306        TCGA-CG-4436 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-CG-4437        TCGA-CG-4438        TCGA-CG-4440        TCGA-CG-4441 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-CG-4443        TCGA-CG-4444        TCGA-CG-4449        TCGA-CG-4455 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-CG-4460        TCGA-CG-4462        TCGA-CG-4465        TCGA-CG-4466 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-CG-4469        TCGA-CG-4472        TCGA-CG-4474        TCGA-CG-4477 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-CG-5716        TCGA-CG-5717        TCGA-CG-5718        TCGA-CG-5719 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-CG-5720        TCGA-CG-5721        TCGA-CG-5722        TCGA-CG-5723 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-CG-5725        TCGA-CG-5726        TCGA-CG-5727        TCGA-CG-5728 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-CG-5730        TCGA-CG-5732        TCGA-CG-5733        TCGA-CG-5734 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-D7-5577        TCGA-D7-5578        TCGA-D7-5579        TCGA-D7-6518 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-D7-6519        TCGA-D7-6520        TCGA-D7-6521        TCGA-D7-6522 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-D7-6524        TCGA-D7-6525        TCGA-D7-6526        TCGA-D7-6527 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-D7-6528        TCGA-D7-6815        TCGA-D7-6817        TCGA-D7-6818 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-D7-6820        TCGA-D7-6822        TCGA-EQ-5647        TCGA-F1-6177 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-F1-6874        TCGA-F1-6875        TCGA-FP-7735        TCGA-FP-7829 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-FP-7916        TCGA-FP-7998        TCGA-HJ-7597        TCGA-IN-7806 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-IN-7808        TCGA-IP-7968 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
D39V2, continuous
D39V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED      2    2
  2Q LOSS WILD-TYPE   63   94
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  FEMALE               2                63
  MALE                 2                94
                   vv
clus                STOMACH ADENOCARCINOMA - DIFFUSE TYPE
  2Q LOSS MUTATED                                       1
  2Q LOSS WILD-TYPE                                    18
                   vv
clus                STOMACH ADENOCARCINOMA - NOT OTHERWISE SPECIFIED (NOS)
  2Q LOSS MUTATED                                                        0
  2Q LOSS WILD-TYPE                                                     79
                   vv
clus                STOMACH ADENOCARCINOMA - SIGNET RING TYPE
  2Q LOSS MUTATED                                           0
  2Q LOSS WILD-TYPE                                         1
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - MUCINOUS TYPE
  2Q LOSS MUTATED                                                   1
  2Q LOSS WILD-TYPE                                                 8
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - PAPILLARY TYPE
  2Q LOSS MUTATED                                                    0
  2Q LOSS WILD-TYPE                                                  3
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - TUBULAR TYPE
  2Q LOSS MUTATED                                                  0
  2Q LOSS WILD-TYPE                                               10
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - TYPE NOT OTHERWISE SPECIFIED (NOS)
  2Q LOSS MUTATED                                                                        1
  2Q LOSS WILD-TYPE                                                                     34
D39V4, multiclass
                   vv
clus                T1 T2 T3 T4
  2Q LOSS MUTATED    0  1  3  0
  2Q LOSS WILD-TYPE  6 52 56 33
D39V5, multiclass
                   vv
clus                N0 N1 N2 N3
  2Q LOSS MUTATED    0  2  0  2
  2Q LOSS WILD-TYPE 50 55 24 17
D39V6, multiclass
                   vv
clus                 M0  M1  MX
  2Q LOSS MUTATED     2   1   1
  2Q LOSS WILD-TYPE 130  17  10
D39V7, multiclass
                   vv
clus                 I II III IV
  2Q LOSS MUTATED    0  2   0  2
  2Q LOSS WILD-TYPE 25 41  48 27
D39V8, multiclass
D39V9, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED      1    3
  2Q LOSS WILD-TYPE    4  153
     clus
vv    2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  NO                1                 4
  YES               3               153

Clustering(40) Variable = 3p loss mutation analysis
D40V1, survival
                   sevent
clus2                0  1
  3P LOSS MUTATED    9  1
  3P LOSS WILD-TYPE 99 15
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               10               114 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
                1                15 
$`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-BR-7958 TCGA-BR-7959 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 
        0.16         1.08         0.82         1.32         0.69         0.95 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
        0.49         0.46         0.72         0.26         0.43         0.26 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-CD-5798 TCGA-CD-5799 
        1.18         1.55         1.48         0.76         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-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-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-D7-6526 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-EQ-8122 TCGA-F1-6177 TCGA-F1-6874 TCGA-F1-6875 
        4.27         0.62         7.79         6.54         2.01        72.23 
TCGA-FP-7735 TCGA-FP-7916 TCGA-FP-7998 TCGA-HJ-7597 TCGA-IN-7808 TCGA-IP-7968 
        0.39         3.02         3.58        26.43         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 
            4.980             1.445 
[1] "0.2 - 54.0 (5.0)" "0.1 - 72.2 (1.4)"
       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-BR-7958        TCGA-BR-7959        TCGA-BR-8059        TCGA-BR-8060 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-BR-8077        TCGA-BR-8078        TCGA-BR-8080        TCGA-BR-8081 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-BR-8284        TCGA-BR-8285        TCGA-BR-8286        TCGA-BR-8289 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-BR-8291        TCGA-BR-8295        TCGA-BR-8296        TCGA-BR-8297 
"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-EQ-8122        TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-FP-7735        TCGA-FP-7829        TCGA-FP-7916        TCGA-FP-7998 
"3P LOSS WILD-TYPE"   "3P LOSS MUTATED" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-HJ-7597        TCGA-IN-7806        TCGA-IN-7808        TCGA-IP-7968 
"3P LOSS WILD-TYPE"   "3P LOSS MUTATED" "3P LOSS WILD-TYPE" "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-BR-7958        TCGA-BR-7959        TCGA-BR-8059        TCGA-BR-8060 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-BR-8077        TCGA-BR-8078        TCGA-BR-8080        TCGA-BR-8081 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-BR-8284        TCGA-BR-8285        TCGA-BR-8286        TCGA-BR-8289 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-BR-8291        TCGA-BR-8295        TCGA-BR-8296        TCGA-BR-8297 
"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-EQ-8122        TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-FP-7735        TCGA-FP-7829        TCGA-FP-7916        TCGA-FP-7998 
"3P LOSS WILD-TYPE"   "3P LOSS MUTATED" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-HJ-7597        TCGA-IN-7806        TCGA-IN-7808        TCGA-IP-7968 
"3P LOSS WILD-TYPE"   "3P LOSS MUTATED" "3P LOSS WILD-TYPE" "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-BR-7958        TCGA-BR-7959        TCGA-BR-8059        TCGA-BR-8060 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-BR-8077        TCGA-BR-8078        TCGA-BR-8080        TCGA-BR-8081 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-BR-8284        TCGA-BR-8285        TCGA-BR-8286        TCGA-BR-8289 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-BR-8291        TCGA-BR-8295        TCGA-BR-8296        TCGA-BR-8297 
"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-EQ-8122        TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-FP-7735        TCGA-FP-7829        TCGA-FP-7916        TCGA-FP-7998 
"3P LOSS WILD-TYPE"   "3P LOSS MUTATED" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-HJ-7597        TCGA-IN-7806        TCGA-IN-7808        TCGA-IP-7968 
"3P LOSS WILD-TYPE"   "3P LOSS MUTATED" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
[1] "hr=" "1.6"
D40V2, continuous
D40V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED      4    6
  3P LOSS WILD-TYPE   61   90
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  FEMALE               4                61
  MALE                 6                90
                   vv
clus                STOMACH ADENOCARCINOMA - DIFFUSE TYPE
  3P LOSS MUTATED                                       2
  3P LOSS WILD-TYPE                                    17
                   vv
clus                STOMACH ADENOCARCINOMA - NOT OTHERWISE SPECIFIED (NOS)
  3P LOSS MUTATED                                                        3
  3P LOSS WILD-TYPE                                                     76
                   vv
clus                STOMACH ADENOCARCINOMA - SIGNET RING TYPE
  3P LOSS MUTATED                                           0
  3P LOSS WILD-TYPE                                         1
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - MUCINOUS TYPE
  3P LOSS MUTATED                                                   1
  3P LOSS WILD-TYPE                                                 8
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - PAPILLARY TYPE
  3P LOSS MUTATED                                                    0
  3P LOSS WILD-TYPE                                                  3
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - TUBULAR TYPE
  3P LOSS MUTATED                                                  1
  3P LOSS WILD-TYPE                                                9
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - TYPE NOT OTHERWISE SPECIFIED (NOS)
  3P LOSS MUTATED                                                                        3
  3P LOSS WILD-TYPE                                                                     32
D40V4, multiclass
                   vv
clus                T1 T2 T3 T4
  3P LOSS MUTATED    0  5  4  1
  3P LOSS WILD-TYPE  6 48 55 32
D40V5, multiclass
                   vv
clus                N0 N1 N2 N3
  3P LOSS MUTATED    4  4  2  0
  3P LOSS WILD-TYPE 46 53 22 19
D40V6, multiclass
                   vv
clus                 M0  M1  MX
  3P LOSS MUTATED     9   1   0
  3P LOSS WILD-TYPE 123  17  11
D40V7, multiclass
                   vv
clus                 I II III IV
  3P LOSS MUTATED    3  2   3  2
  3P LOSS WILD-TYPE 22 41  45 27
D40V8, multiclass
D40V9, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED      0   10
  3P LOSS WILD-TYPE    5  146
     clus
vv    3P LOSS MUTATED 3P LOSS WILD-TYPE
  NO                0                 5
  YES              10               146

Clustering(41) Variable = 3q loss mutation analysis
D41V1, survival
                   sevent
clus2                 0   1
  3Q LOSS MUTATED     5   1
  3Q LOSS WILD-TYPE 103  15
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
                6               118 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
                1                15 
$`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-BR-7958 TCGA-BR-7959 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
        0.69         0.16         1.08         0.82         1.32         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
        0.95         0.49         0.46         0.72         0.26         0.43 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-CD-5798 
        0.26         1.18         1.55         1.48         0.76         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-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-4469 TCGA-CG-4472 TCGA-CG-4474 
       21.99         1.02         8.98         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-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-D7-6519 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-EQ-8122 TCGA-F1-6177 TCGA-F1-6874 TCGA-F1-6875 TCGA-FP-7735 TCGA-FP-7916 
        7.79         6.54         2.01        72.23         0.39         3.02 
TCGA-FP-7998 TCGA-HJ-7597 TCGA-IN-7808 TCGA-IP-7968 
        3.58        26.43         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             1.480 
[1] "0.2 - 54.0 (10.9)" "0.1 - 72.2 (1.5)" 
       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-BR-7958        TCGA-BR-7959        TCGA-BR-8059        TCGA-BR-8060 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-BR-8077        TCGA-BR-8078        TCGA-BR-8080        TCGA-BR-8081 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-BR-8284        TCGA-BR-8285        TCGA-BR-8286        TCGA-BR-8289 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-BR-8291        TCGA-BR-8295        TCGA-BR-8296        TCGA-BR-8297 
"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-EQ-8122        TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-FP-7735        TCGA-FP-7829        TCGA-FP-7916        TCGA-FP-7998 
"3Q LOSS WILD-TYPE"   "3Q LOSS MUTATED" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-HJ-7597        TCGA-IN-7806        TCGA-IN-7808        TCGA-IP-7968 
"3Q LOSS WILD-TYPE"   "3Q LOSS MUTATED" "3Q LOSS WILD-TYPE" "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-BR-7958        TCGA-BR-7959        TCGA-BR-8059        TCGA-BR-8060 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-BR-8077        TCGA-BR-8078        TCGA-BR-8080        TCGA-BR-8081 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-BR-8284        TCGA-BR-8285        TCGA-BR-8286        TCGA-BR-8289 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-BR-8291        TCGA-BR-8295        TCGA-BR-8296        TCGA-BR-8297 
"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-EQ-8122        TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-FP-7735        TCGA-FP-7829        TCGA-FP-7916        TCGA-FP-7998 
"3Q LOSS WILD-TYPE"   "3Q LOSS MUTATED" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-HJ-7597        TCGA-IN-7806        TCGA-IN-7808        TCGA-IP-7968 
"3Q LOSS WILD-TYPE"   "3Q LOSS MUTATED" "3Q LOSS WILD-TYPE" "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-BR-7958        TCGA-BR-7959        TCGA-BR-8059        TCGA-BR-8060 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-BR-8077        TCGA-BR-8078        TCGA-BR-8080        TCGA-BR-8081 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-BR-8284        TCGA-BR-8285        TCGA-BR-8286        TCGA-BR-8289 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-BR-8291        TCGA-BR-8295        TCGA-BR-8296        TCGA-BR-8297 
"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-EQ-8122        TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-FP-7735        TCGA-FP-7829        TCGA-FP-7916        TCGA-FP-7998 
"3Q LOSS WILD-TYPE"   "3Q LOSS MUTATED" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-HJ-7597        TCGA-IN-7806        TCGA-IN-7808        TCGA-IP-7968 
"3Q LOSS WILD-TYPE"   "3Q LOSS MUTATED" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
[1] "hr=" "1.4"
D41V2, continuous
D41V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED      1    5
  3Q LOSS WILD-TYPE   64   91
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  FEMALE               1                64
  MALE                 5                91
                   vv
clus                STOMACH ADENOCARCINOMA - DIFFUSE TYPE
  3Q LOSS MUTATED                                       1
  3Q LOSS WILD-TYPE                                    18
                   vv
clus                STOMACH ADENOCARCINOMA - NOT OTHERWISE SPECIFIED (NOS)
  3Q LOSS MUTATED                                                        2
  3Q LOSS WILD-TYPE                                                     77
                   vv
clus                STOMACH ADENOCARCINOMA - SIGNET RING TYPE
  3Q LOSS MUTATED                                           0
  3Q LOSS WILD-TYPE                                         1
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - MUCINOUS TYPE
  3Q LOSS MUTATED                                                   1
  3Q LOSS WILD-TYPE                                                 8
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - PAPILLARY TYPE
  3Q LOSS MUTATED                                                    0
  3Q LOSS WILD-TYPE                                                  3
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - TUBULAR TYPE
  3Q LOSS MUTATED                                                  0
  3Q LOSS WILD-TYPE                                               10
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - TYPE NOT OTHERWISE SPECIFIED (NOS)
  3Q LOSS MUTATED                                                                        2
  3Q LOSS WILD-TYPE                                                                     33
D41V4, multiclass
                   vv
clus                T1 T2 T3 T4
  3Q LOSS MUTATED    0  2  3  1
  3Q LOSS WILD-TYPE  6 51 56 32
D41V5, multiclass
                   vv
clus                N0 N1 N2 N3
  3Q LOSS MUTATED    3  2  1  0
  3Q LOSS WILD-TYPE 47 55 23 19
D41V6, multiclass
                   vv
clus                 M0  M1  MX
  3Q LOSS MUTATED     6   0   0
  3Q LOSS WILD-TYPE 126  18  11
D41V7, multiclass
                   vv
clus                 I II III IV
  3Q LOSS MUTATED    2  1   2  1
  3Q LOSS WILD-TYPE 23 42  46 28
D41V8, multiclass
D41V9, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED      0    6
  3Q LOSS WILD-TYPE    5  150
     clus
vv    3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  NO                0                 5
  YES               6               150

Clustering(42) Variable = 4p loss mutation analysis
D42V1, survival
                   sevent
clus2                0  1
  4P LOSS MUTATED   15  4
  4P LOSS WILD-TYPE 93 12
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               19               105 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
                4                12 
$`4P LOSS MUTATED`
TCGA-BR-6458 TCGA-BR-7197 TCGA-BR-7723 TCGA-CD-5799 TCGA-CD-5802 TCGA-CG-4300 
        1.35         1.48         4.54         0.69         0.30        20.02 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4449 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 
       54.05         4.01        19.07        18.94         7.07         1.02 
TCGA-CG-5725 TCGA-D7-6519 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6820 TCGA-EQ-8122 
       15.02        15.65         4.14         1.68         2.93         7.79 
TCGA-HJ-7597 
       26.43 

$`4P 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-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
        0.69         0.16         0.99         0.95         0.69         0.16 
TCGA-BR-7959 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
        1.08         0.82         1.32         0.69         0.95         0.49 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
        0.46         0.72         0.26         0.43         0.26         1.18 
TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-CD-5798 TCGA-CD-5800 TCGA-CD-5801 
        1.55         1.48         0.76         0.82         0.36         0.49 
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-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4455 TCGA-CG-4460 
        8.05        14.01        29.98        47.05        12.03        21.99 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4472 TCGA-CG-4474 TCGA-CG-5716 TCGA-CG-5717 
        1.02         8.98        12.00         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-5732 
       12.03        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-D7-6520 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-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6822 TCGA-EQ-5647 TCGA-F1-6177 
        3.65         4.70         4.04         4.27         0.62         6.54 
TCGA-F1-6874 TCGA-F1-6875 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
        2.01        72.23         0.39         0.20         3.02         3.58 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IP-7968 
        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 
             4.54              1.25 
[1] "0.3 - 54.0 (4.5)" "0.1 - 72.2 (1.2)"
       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 MUTATED" "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-BR-7958        TCGA-BR-7959        TCGA-BR-8059        TCGA-BR-8060 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-BR-8077        TCGA-BR-8078        TCGA-BR-8080        TCGA-BR-8081 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-BR-8284        TCGA-BR-8285        TCGA-BR-8286        TCGA-BR-8289 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-BR-8291        TCGA-BR-8295        TCGA-BR-8296        TCGA-BR-8297 
"4P LOSS WILD-TYPE" "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-EQ-8122        TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875 
  "4P LOSS MUTATED" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-FP-7735        TCGA-FP-7829        TCGA-FP-7916        TCGA-FP-7998 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-HJ-7597        TCGA-IN-7806        TCGA-IN-7808        TCGA-IP-7968 
  "4P LOSS MUTATED" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "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 MUTATED" "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-BR-7958        TCGA-BR-7959        TCGA-BR-8059        TCGA-BR-8060 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-BR-8077        TCGA-BR-8078        TCGA-BR-8080        TCGA-BR-8081 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-BR-8284        TCGA-BR-8285        TCGA-BR-8286        TCGA-BR-8289 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-BR-8291        TCGA-BR-8295        TCGA-BR-8296        TCGA-BR-8297 
"4P LOSS WILD-TYPE" "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-EQ-8122        TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875 
  "4P LOSS MUTATED" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-FP-7735        TCGA-FP-7829        TCGA-FP-7916        TCGA-FP-7998 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-HJ-7597        TCGA-IN-7806        TCGA-IN-7808        TCGA-IP-7968 
  "4P LOSS MUTATED" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "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 MUTATED" "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-BR-7958        TCGA-BR-7959        TCGA-BR-8059        TCGA-BR-8060 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-BR-8077        TCGA-BR-8078        TCGA-BR-8080        TCGA-BR-8081 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-BR-8284        TCGA-BR-8285        TCGA-BR-8286        TCGA-BR-8289 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-BR-8291        TCGA-BR-8295        TCGA-BR-8296        TCGA-BR-8297 
"4P LOSS WILD-TYPE" "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-EQ-8122        TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875 
  "4P LOSS MUTATED" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-FP-7735        TCGA-FP-7829        TCGA-FP-7916        TCGA-FP-7998 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-HJ-7597        TCGA-IN-7806        TCGA-IN-7808        TCGA-IP-7968 
  "4P LOSS MUTATED" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
[1] "hr=" "1.3"
D42V2, continuous
D42V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED      9   15
  4P LOSS WILD-TYPE   56   81
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  FEMALE               9                56
  MALE                15                81
                   vv
clus                STOMACH ADENOCARCINOMA - DIFFUSE TYPE
  4P LOSS MUTATED                                       1
  4P LOSS WILD-TYPE                                    18
                   vv
clus                STOMACH ADENOCARCINOMA - NOT OTHERWISE SPECIFIED (NOS)
  4P LOSS MUTATED                                                        9
  4P LOSS WILD-TYPE                                                     70
                   vv
clus                STOMACH ADENOCARCINOMA - SIGNET RING TYPE
  4P LOSS MUTATED                                           1
  4P LOSS WILD-TYPE                                         0
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - MUCINOUS TYPE
  4P LOSS MUTATED                                                   2
  4P LOSS WILD-TYPE                                                 7
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - PAPILLARY TYPE
  4P LOSS MUTATED                                                    1
  4P LOSS WILD-TYPE                                                  2
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - TUBULAR TYPE
  4P LOSS MUTATED                                                  3
  4P LOSS WILD-TYPE                                                7
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - TYPE NOT OTHERWISE SPECIFIED (NOS)
  4P LOSS MUTATED                                                                        7
  4P LOSS WILD-TYPE                                                                     28
D42V4, multiclass
                   vv
clus                T1 T2 T3 T4
  4P LOSS MUTATED    0 13 10  1
  4P LOSS WILD-TYPE  6 40 49 32
D42V5, multiclass
                   vv
clus                N0 N1 N2 N3
  4P LOSS MUTATED    8  9  3  3
  4P LOSS WILD-TYPE 42 48 21 16
D42V6, multiclass
                   vv
clus                 M0  M1  MX
  4P LOSS MUTATED    21   1   2
  4P LOSS WILD-TYPE 111  17   9
D42V7, multiclass
                   vv
clus                 I II III IV
  4P LOSS MUTATED    5 11   3  4
  4P LOSS WILD-TYPE 20 32  45 25
D42V8, multiclass
D42V9, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED      2   22
  4P LOSS WILD-TYPE    3  134
     clus
vv    4P LOSS MUTATED 4P LOSS WILD-TYPE
  NO                2                 3
  YES              22               134

Clustering(43) Variable = 4q loss mutation analysis
D43V1, survival
                   sevent
clus2                0  1
  4Q LOSS MUTATED   15  2
  4Q LOSS WILD-TYPE 93 14
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               17               107 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
                2                14 
$`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 TCGA-EQ-8122 
        4.14         1.68         3.65         2.93         7.79 

$`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-BR-7958 TCGA-BR-7959 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 
        0.16         1.08         0.82         1.32         0.69         0.95 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
        0.49         0.46         0.72         0.26         0.43         0.26 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-CD-5798 TCGA-CD-5800 
        1.18         1.55         1.48         0.76         0.82         0.36 
TCGA-CD-5801 TCGA-CD-5803 TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
        0.49         0.07        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 
        1.02        52.96         8.05        14.01        29.98        47.05 
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-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-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-D7-6817 TCGA-D7-6818 TCGA-D7-6822 TCGA-EQ-5647 
        5.95         6.61         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-7916 
        6.54         2.01        72.23         0.39         0.20         3.02 
TCGA-FP-7998 TCGA-HJ-7597 TCGA-IN-7806 TCGA-IN-7808 TCGA-IP-7968 
        3.58        26.43         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              1.32 
[1] "0.3 - 54.0 (4.0)" "0.1 - 72.2 (1.3)"
       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-BR-7958        TCGA-BR-7959        TCGA-BR-8059        TCGA-BR-8060 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-BR-8077        TCGA-BR-8078        TCGA-BR-8080        TCGA-BR-8081 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-BR-8284        TCGA-BR-8285        TCGA-BR-8286        TCGA-BR-8289 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-BR-8291        TCGA-BR-8295        TCGA-BR-8296        TCGA-BR-8297 
"4Q LOSS WILD-TYPE" "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-EQ-8122        TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875 
  "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-FP-7735        TCGA-FP-7829        TCGA-FP-7916        TCGA-FP-7998 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-HJ-7597        TCGA-IN-7806        TCGA-IN-7808        TCGA-IP-7968 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "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-BR-7958        TCGA-BR-7959        TCGA-BR-8059        TCGA-BR-8060 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-BR-8077        TCGA-BR-8078        TCGA-BR-8080        TCGA-BR-8081 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-BR-8284        TCGA-BR-8285        TCGA-BR-8286        TCGA-BR-8289 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-BR-8291        TCGA-BR-8295        TCGA-BR-8296        TCGA-BR-8297 
"4Q LOSS WILD-TYPE" "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-EQ-8122        TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875 
  "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-FP-7735        TCGA-FP-7829        TCGA-FP-7916        TCGA-FP-7998 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-HJ-7597        TCGA-IN-7806        TCGA-IN-7808        TCGA-IP-7968 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "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-BR-7958        TCGA-BR-7959        TCGA-BR-8059        TCGA-BR-8060 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-BR-8077        TCGA-BR-8078        TCGA-BR-8080        TCGA-BR-8081 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-BR-8284        TCGA-BR-8285        TCGA-BR-8286        TCGA-BR-8289 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-BR-8291        TCGA-BR-8295        TCGA-BR-8296        TCGA-BR-8297 
"4Q LOSS WILD-TYPE" "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-EQ-8122        TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875 
  "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-FP-7735        TCGA-FP-7829        TCGA-FP-7916        TCGA-FP-7998 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-HJ-7597        TCGA-IN-7806        TCGA-IN-7808        TCGA-IP-7968 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
[1] "hr=" "1.3"
D43V2, continuous
D43V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED     10   10
  4Q LOSS WILD-TYPE   55   86
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  FEMALE              10                55
  MALE                10                86
                   vv
clus                STOMACH ADENOCARCINOMA - DIFFUSE TYPE
  4Q LOSS MUTATED                                       1
  4Q LOSS WILD-TYPE                                    18
                   vv
clus                STOMACH ADENOCARCINOMA - NOT OTHERWISE SPECIFIED (NOS)
  4Q LOSS MUTATED                                                        5
  4Q LOSS WILD-TYPE                                                     74
                   vv
clus                STOMACH ADENOCARCINOMA - SIGNET RING TYPE
  4Q LOSS MUTATED                                           0
  4Q LOSS WILD-TYPE                                         1
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - MUCINOUS TYPE
  4Q LOSS MUTATED                                                   2
  4Q LOSS WILD-TYPE                                                 7
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - PAPILLARY TYPE
  4Q LOSS MUTATED                                                    1
  4Q LOSS WILD-TYPE                                                  2
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - TUBULAR TYPE
  4Q LOSS MUTATED                                                  4
  4Q LOSS WILD-TYPE                                                6
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - TYPE NOT OTHERWISE SPECIFIED (NOS)
  4Q LOSS MUTATED                                                                        7
  4Q LOSS WILD-TYPE                                                                     28
D43V4, multiclass
                   vv
clus                T1 T2 T3 T4
  4Q LOSS MUTATED    0 13  6  1
  4Q LOSS WILD-TYPE  6 40 53 32
D43V5, multiclass
                   vv
clus                N0 N1 N2 N3
  4Q LOSS MUTATED    5  9  3  2
  4Q LOSS WILD-TYPE 45 48 21 17
D43V6, multiclass
                   vv
clus                 M0  M1  MX
  4Q LOSS MUTATED    17   2   1
  4Q LOSS WILD-TYPE 115  16  10
D43V7, multiclass
                   vv
clus                 I II III IV
  4Q LOSS MUTATED    4  8   3  4
  4Q LOSS WILD-TYPE 21 35  45 25
D43V8, multiclass
D43V9, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED      2   18
  4Q LOSS WILD-TYPE    3  138
     clus
vv    4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  NO                2                 3
  YES              18               138

Clustering(44) Variable = 5p loss mutation analysis
D44V1, survival
                   sevent
clus2                 0   1
  5P LOSS MUTATED     6   0
  5P LOSS WILD-TYPE 102  16
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
                6               118 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
                0                16 
$`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-BR-7958 TCGA-BR-7959 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
        0.69         0.16         1.08         0.82         1.32         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
        0.95         0.49         0.46         0.72         0.26         0.43 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-CD-5798 
        0.26         1.18         1.55         1.48         0.76         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-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-4455 TCGA-CG-4460 
        4.01        14.01        29.98        47.05        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-D7-6521 
        8.65         3.58         4.54         9.80        15.65         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-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-EQ-5647 TCGA-EQ-8122 
        4.70         4.04         2.93         4.27         0.62         7.79 
TCGA-F1-6177 TCGA-F1-6874 TCGA-F1-6875 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
        6.54         2.01        72.23         0.39         0.20         3.02 
TCGA-FP-7998 TCGA-HJ-7597 TCGA-IN-7808 TCGA-IP-7968 
        3.58        26.43         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              1.48 
[1] "0.4 - 19.1 (5.3)" "0.1 - 72.2 (1.5)"
       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-BR-7958        TCGA-BR-7959        TCGA-BR-8059        TCGA-BR-8060 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-BR-8077        TCGA-BR-8078        TCGA-BR-8080        TCGA-BR-8081 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-BR-8284        TCGA-BR-8285        TCGA-BR-8286        TCGA-BR-8289 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-BR-8291        TCGA-BR-8295        TCGA-BR-8296        TCGA-BR-8297 
"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-EQ-8122        TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-FP-7735        TCGA-FP-7829        TCGA-FP-7916        TCGA-FP-7998 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-HJ-7597        TCGA-IN-7806        TCGA-IN-7808        TCGA-IP-7968 
"5P LOSS WILD-TYPE"   "5P LOSS MUTATED" "5P LOSS WILD-TYPE" "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-BR-7958        TCGA-BR-7959        TCGA-BR-8059        TCGA-BR-8060 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-BR-8077        TCGA-BR-8078        TCGA-BR-8080        TCGA-BR-8081 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-BR-8284        TCGA-BR-8285        TCGA-BR-8286        TCGA-BR-8289 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-BR-8291        TCGA-BR-8295        TCGA-BR-8296        TCGA-BR-8297 
"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-EQ-8122        TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-FP-7735        TCGA-FP-7829        TCGA-FP-7916        TCGA-FP-7998 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-HJ-7597        TCGA-IN-7806        TCGA-IN-7808        TCGA-IP-7968 
"5P LOSS WILD-TYPE"   "5P LOSS MUTATED" "5P LOSS WILD-TYPE" "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-BR-7958        TCGA-BR-7959        TCGA-BR-8059        TCGA-BR-8060 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-BR-8077        TCGA-BR-8078        TCGA-BR-8080        TCGA-BR-8081 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-BR-8284        TCGA-BR-8285        TCGA-BR-8286        TCGA-BR-8289 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-BR-8291        TCGA-BR-8295        TCGA-BR-8296        TCGA-BR-8297 
"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-EQ-8122        TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-FP-7735        TCGA-FP-7829        TCGA-FP-7916        TCGA-FP-7998 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-HJ-7597        TCGA-IN-7806        TCGA-IN-7808        TCGA-IP-7968 
"5P LOSS WILD-TYPE"   "5P LOSS MUTATED" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
[1] "hr="     "2.7e+07"
D44V2, continuous
D44V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED      3    4
  5P LOSS WILD-TYPE   62   92
        clus
vv       5P LOSS MUTATED 5P LOSS WILD-TYPE
  FEMALE               3                62
  MALE                 4                92
                   vv
clus                STOMACH ADENOCARCINOMA - DIFFUSE TYPE
  5P LOSS MUTATED                                       1
  5P LOSS WILD-TYPE                                    18
                   vv
clus                STOMACH ADENOCARCINOMA - NOT OTHERWISE SPECIFIED (NOS)
  5P LOSS MUTATED                                                        2
  5P LOSS WILD-TYPE                                                     77
                   vv
clus                STOMACH ADENOCARCINOMA - SIGNET RING TYPE
  5P LOSS MUTATED                                           0
  5P LOSS WILD-TYPE                                         1
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - MUCINOUS TYPE
  5P LOSS MUTATED                                                   1
  5P LOSS WILD-TYPE                                                 8
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - PAPILLARY TYPE
  5P LOSS MUTATED                                                    1
  5P LOSS WILD-TYPE                                                  2
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - TUBULAR TYPE
  5P LOSS MUTATED                                                  2
  5P LOSS WILD-TYPE                                                8
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - TYPE NOT OTHERWISE SPECIFIED (NOS)
  5P LOSS MUTATED                                                                        0
  5P LOSS WILD-TYPE                                                                     35
D44V4, multiclass
                   vv
clus                T1 T2 T3 T4
  5P LOSS MUTATED    0  3  3  0
  5P LOSS WILD-TYPE  6 50 56 33
D44V5, multiclass
                   vv
clus                N0 N1 N2 N3
  5P LOSS MUTATED    1  4  2  0
  5P LOSS WILD-TYPE 49 53 22 19
D44V6, multiclass
                   vv
clus                 M0  M1  MX
  5P LOSS MUTATED     7   0   0
  5P LOSS WILD-TYPE 125  18  11
D44V7, multiclass
                   vv
clus                 I II III IV
  5P LOSS MUTATED    0  3   3  0
  5P LOSS WILD-TYPE 25 40  45 29
D44V8, multiclass
D44V9, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED      0    7
  5P LOSS WILD-TYPE    5  149
     clus
vv    5P LOSS MUTATED 5P LOSS WILD-TYPE
  NO                0                 5
  YES               7               149

Clustering(45) Variable = 5q loss mutation analysis
D45V1, survival
                   sevent
clus2                0  1
  5Q LOSS MUTATED   13  1
  5Q LOSS WILD-TYPE 95 15
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               14               110 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
                1                15 
$`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-BR-7958 
        0.69         0.16         4.54         0.99         0.69         0.16 
TCGA-BR-7959 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
        1.08         0.82         1.32         0.69         0.95         0.49 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
        0.46         0.72         0.26         0.43         0.26         1.18 
TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5801 
        1.55         1.48         0.76         0.82         0.69         0.49 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4305 TCGA-CG-4306 
        0.30         0.07        20.02         3.02        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-4455 TCGA-CG-4460 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       47.05        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-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-D7-6528 TCGA-D7-6818 TCGA-D7-6820 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6177 
        1.68         4.04         2.93         0.62         7.79         6.54 
TCGA-F1-6874 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-HJ-7597 
        2.01         0.39         0.20         3.02         3.58        26.43 
TCGA-IN-7808 TCGA-IP-7968 
        3.55         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             1.380 
[1] "0.4 - 72.2 (4.2)" "0.1 - 70.1 (1.4)"
       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-BR-7958        TCGA-BR-7959        TCGA-BR-8059        TCGA-BR-8060 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-BR-8077        TCGA-BR-8078        TCGA-BR-8080        TCGA-BR-8081 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-BR-8284        TCGA-BR-8285        TCGA-BR-8286        TCGA-BR-8289 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-BR-8291        TCGA-BR-8295        TCGA-BR-8296        TCGA-BR-8297 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "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-EQ-8122        TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" 
       TCGA-FP-7735        TCGA-FP-7829        TCGA-FP-7916        TCGA-FP-7998 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-HJ-7597        TCGA-IN-7806        TCGA-IN-7808        TCGA-IP-7968 
"5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" "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-BR-7958        TCGA-BR-7959        TCGA-BR-8059        TCGA-BR-8060 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-BR-8077        TCGA-BR-8078        TCGA-BR-8080        TCGA-BR-8081 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-BR-8284        TCGA-BR-8285        TCGA-BR-8286        TCGA-BR-8289 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-BR-8291        TCGA-BR-8295        TCGA-BR-8296        TCGA-BR-8297 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "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-EQ-8122        TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" 
       TCGA-FP-7735        TCGA-FP-7829        TCGA-FP-7916        TCGA-FP-7998 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-HJ-7597        TCGA-IN-7806        TCGA-IN-7808        TCGA-IP-7968 
"5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" "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-BR-7958        TCGA-BR-7959        TCGA-BR-8059        TCGA-BR-8060 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-BR-8077        TCGA-BR-8078        TCGA-BR-8080        TCGA-BR-8081 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-BR-8284        TCGA-BR-8285        TCGA-BR-8286        TCGA-BR-8289 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-BR-8291        TCGA-BR-8295        TCGA-BR-8296        TCGA-BR-8297 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "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-EQ-8122        TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" 
       TCGA-FP-7735        TCGA-FP-7829        TCGA-FP-7916        TCGA-FP-7998 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-HJ-7597        TCGA-IN-7806        TCGA-IN-7808        TCGA-IP-7968 
"5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
[1] "hr="     "2.3e+08"
D45V2, continuous
D45V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED      4   11
  5Q LOSS WILD-TYPE   61   85
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  FEMALE               4                61
  MALE                11                85
                   vv
clus                STOMACH ADENOCARCINOMA - DIFFUSE TYPE
  5Q LOSS MUTATED                                       1
  5Q LOSS WILD-TYPE                                    18
                   vv
clus                STOMACH ADENOCARCINOMA - NOT OTHERWISE SPECIFIED (NOS)
  5Q LOSS MUTATED                                                        6
  5Q LOSS WILD-TYPE                                                     73
                   vv
clus                STOMACH ADENOCARCINOMA - SIGNET RING TYPE
  5Q LOSS MUTATED                                           0
  5Q LOSS WILD-TYPE                                         1
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - MUCINOUS TYPE
  5Q LOSS MUTATED                                                   1
  5Q LOSS WILD-TYPE                                                 8
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - PAPILLARY TYPE
  5Q LOSS MUTATED                                                    2
  5Q LOSS WILD-TYPE                                                  1
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - TUBULAR TYPE
  5Q LOSS MUTATED                                                  4
  5Q LOSS WILD-TYPE                                                6
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - TYPE NOT OTHERWISE SPECIFIED (NOS)
  5Q LOSS MUTATED                                                                        1
  5Q LOSS WILD-TYPE                                                                     34
D45V4, multiclass
                   vv
clus                T1 T2 T3 T4
  5Q LOSS MUTATED    0  9  5  0
  5Q LOSS WILD-TYPE  6 44 54 33
D45V5, multiclass
                   vv
clus                N0 N1 N2 N3
  5Q LOSS MUTATED    5  7  2  1
  5Q LOSS WILD-TYPE 45 50 22 18
D45V6, multiclass
                   vv
clus                 M0  M1  MX
  5Q LOSS MUTATED    15   0   0
  5Q LOSS WILD-TYPE 117  18  11
D45V7, multiclass
                   vv
clus                 I II III IV
  5Q LOSS MUTATED    3  6   5  0
  5Q LOSS WILD-TYPE 22 37  43 29
D45V8, multiclass
D45V9, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED      1   14
  5Q LOSS WILD-TYPE    4  142
     clus
vv    5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  NO                1                 4
  YES              14               142

Clustering(46) Variable = 6p loss mutation analysis
D46V1, survival
                   sevent
clus2                 0   1
  6P LOSS MUTATED     5   1
  6P LOSS WILD-TYPE 103  15
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
                6               118 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
                1                15 
$`6P LOSS MUTATED`
TCGA-CG-5719 TCGA-CG-5725 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6525 TCGA-D7-6815 
        1.02        15.02        15.65         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-BR-7958 TCGA-BR-7959 TCGA-BR-8059 TCGA-BR-8060 
        0.95         0.69         0.16         1.08         0.82         1.32 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
        0.69         0.95         0.49         0.46         0.72         0.26 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
        0.43         0.26         1.18         1.55         1.48         0.76 
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-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-D7-6521 
        7.99         8.65         3.58         4.54         9.80         8.19 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6817 
        6.90         0.69         6.61         4.14         1.68         4.70 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6177 
        4.04         2.93         4.27         0.62         7.79         6.54 
TCGA-F1-6874 TCGA-F1-6875 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
        2.01        72.23         0.39         0.20         3.02         3.58 
TCGA-HJ-7597 TCGA-IN-7806 TCGA-IN-7808 TCGA-IP-7968 
       26.43         6.87         3.55         2.53 

  6P LOSS MUTATED 6P LOSS WILD-TYPE 
             1.02              0.07 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
            15.65             72.23 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
            7.790             1.445 
[1] "1.0 - 15.7 (7.8)" "0.1 - 72.2 (1.4)"
       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-BR-7958        TCGA-BR-7959        TCGA-BR-8059        TCGA-BR-8060 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-BR-8077        TCGA-BR-8078        TCGA-BR-8080        TCGA-BR-8081 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-BR-8284        TCGA-BR-8285        TCGA-BR-8286        TCGA-BR-8289 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-BR-8291        TCGA-BR-8295        TCGA-BR-8296        TCGA-BR-8297 
"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 MUTATED"   "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-EQ-8122        TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-FP-7735        TCGA-FP-7829        TCGA-FP-7916        TCGA-FP-7998 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-HJ-7597        TCGA-IN-7806        TCGA-IN-7808        TCGA-IP-7968 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "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-BR-7958        TCGA-BR-7959        TCGA-BR-8059        TCGA-BR-8060 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-BR-8077        TCGA-BR-8078        TCGA-BR-8080        TCGA-BR-8081 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-BR-8284        TCGA-BR-8285        TCGA-BR-8286        TCGA-BR-8289 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-BR-8291        TCGA-BR-8295        TCGA-BR-8296        TCGA-BR-8297 
"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 MUTATED"   "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-EQ-8122        TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-FP-7735        TCGA-FP-7829        TCGA-FP-7916        TCGA-FP-7998 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-HJ-7597        TCGA-IN-7806        TCGA-IN-7808        TCGA-IP-7968 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "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-BR-7958        TCGA-BR-7959        TCGA-BR-8059        TCGA-BR-8060 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-BR-8077        TCGA-BR-8078        TCGA-BR-8080        TCGA-BR-8081 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-BR-8284        TCGA-BR-8285        TCGA-BR-8286        TCGA-BR-8289 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-BR-8291        TCGA-BR-8295        TCGA-BR-8296        TCGA-BR-8297 
"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 MUTATED"   "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-EQ-8122        TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-FP-7735        TCGA-FP-7829        TCGA-FP-7916        TCGA-FP-7998 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-HJ-7597        TCGA-IN-7806        TCGA-IN-7808        TCGA-IP-7968 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
[1] "hr=" "1.1"
D46V2, continuous
D46V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED      4    4
  6P LOSS WILD-TYPE   61   92
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  FEMALE               4                61
  MALE                 4                92
                   vv
clus                STOMACH ADENOCARCINOMA - DIFFUSE TYPE
  6P LOSS MUTATED                                       2
  6P LOSS WILD-TYPE                                    17
                   vv
clus                STOMACH ADENOCARCINOMA - NOT OTHERWISE SPECIFIED (NOS)
  6P LOSS MUTATED                                                        2
  6P LOSS WILD-TYPE                                                     77
                   vv
clus                STOMACH ADENOCARCINOMA - SIGNET RING TYPE
  6P LOSS MUTATED                                           0
  6P LOSS WILD-TYPE                                         1
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - MUCINOUS TYPE
  6P LOSS MUTATED                                                   0
  6P LOSS WILD-TYPE                                                 9
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - PAPILLARY TYPE
  6P LOSS MUTATED                                                    0
  6P LOSS WILD-TYPE                                                  3
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - TUBULAR TYPE
  6P LOSS MUTATED                                                  3
  6P LOSS WILD-TYPE                                                7
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - TYPE NOT OTHERWISE SPECIFIED (NOS)
  6P LOSS MUTATED                                                                        1
  6P LOSS WILD-TYPE                                                                     34
D46V4, multiclass
                   vv
clus                T1 T2 T3 T4
  6P LOSS MUTATED    0  6  1  1
  6P LOSS WILD-TYPE  6 47 58 32
D46V5, multiclass
                   vv
clus                N0 N1 N2 N3
  6P LOSS MUTATED    2  1  3  0
  6P LOSS WILD-TYPE 48 56 21 19
D46V6, multiclass
                   vv
clus                 M0  M1  MX
  6P LOSS MUTATED     6   1   1
  6P LOSS WILD-TYPE 126  17  10
D46V7, multiclass
                   vv
clus                 I II III IV
  6P LOSS MUTATED    1  0   4  1
  6P LOSS WILD-TYPE 24 43  44 28
D46V8, multiclass
D46V9, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED      0    8
  6P LOSS WILD-TYPE    5  148
     clus
vv    6P LOSS MUTATED 6P LOSS WILD-TYPE
  NO                0                 5
  YES               8               148

Clustering(47) Variable = 6q loss mutation analysis
D47V1, survival
                   sevent
clus2                 0   1
  6Q LOSS MUTATED     7   1
  6Q LOSS WILD-TYPE 101  15
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
                8               116 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
                1                15 
$`6Q LOSS MUTATED`
TCGA-BR-7722 TCGA-CG-4443 TCGA-CG-5719 TCGA-CG-5725 TCGA-D7-6519 TCGA-D7-6520 
        0.16        29.98         1.02        15.02        15.65         9.63 
TCGA-D7-6525 TCGA-D7-6815 
        5.95         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-BR-7958 TCGA-BR-7959 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
        0.69         0.16         1.08         0.82         1.32         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
        0.95         0.49         0.46         0.72         0.26         0.43 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-CD-5798 
        0.26         1.18         1.55         1.48         0.76         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-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-5720 
        1.02         1.02         1.02         6.94         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-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
        3.58         4.54         9.80         8.19         6.90         0.69 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
        6.61         4.14         1.68         4.70         4.04         2.93 
TCGA-D7-6822 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6177 TCGA-F1-6874 TCGA-F1-6875 
        4.27         0.62         7.79         6.54         2.01        72.23 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-HJ-7597 TCGA-IN-7806 
        0.39         0.20         3.02         3.58        26.43         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 
            7.790             1.445 
[1] "0.2 - 30.0 (7.8)" "0.1 - 72.2 (1.4)"
       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-BR-7958        TCGA-BR-7959        TCGA-BR-8059        TCGA-BR-8060 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-BR-8077        TCGA-BR-8078        TCGA-BR-8080        TCGA-BR-8081 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-BR-8284        TCGA-BR-8285        TCGA-BR-8286        TCGA-BR-8289 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-BR-8291        TCGA-BR-8295        TCGA-BR-8296        TCGA-BR-8297 
"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 MUTATED"   "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-EQ-8122        TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-FP-7735        TCGA-FP-7829        TCGA-FP-7916        TCGA-FP-7998 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-HJ-7597        TCGA-IN-7806        TCGA-IN-7808        TCGA-IP-7968 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "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-BR-7958        TCGA-BR-7959        TCGA-BR-8059        TCGA-BR-8060 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-BR-8077        TCGA-BR-8078        TCGA-BR-8080        TCGA-BR-8081 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-BR-8284        TCGA-BR-8285        TCGA-BR-8286        TCGA-BR-8289 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-BR-8291        TCGA-BR-8295        TCGA-BR-8296        TCGA-BR-8297 
"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 MUTATED"   "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-EQ-8122        TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-FP-7735        TCGA-FP-7829        TCGA-FP-7916        TCGA-FP-7998 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-HJ-7597        TCGA-IN-7806        TCGA-IN-7808        TCGA-IP-7968 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "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-BR-7958        TCGA-BR-7959        TCGA-BR-8059        TCGA-BR-8060 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-BR-8077        TCGA-BR-8078        TCGA-BR-8080        TCGA-BR-8081 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-BR-8284        TCGA-BR-8285        TCGA-BR-8286        TCGA-BR-8289 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-BR-8291        TCGA-BR-8295        TCGA-BR-8296        TCGA-BR-8297 
"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 MUTATED"   "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-EQ-8122        TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-FP-7735        TCGA-FP-7829        TCGA-FP-7916        TCGA-FP-7998 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-HJ-7597        TCGA-IN-7806        TCGA-IN-7808        TCGA-IP-7968 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
[1] "hr=" "1.7"
D47V2, continuous
D47V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED      4    8
  6Q LOSS WILD-TYPE   61   88
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  FEMALE               4                61
  MALE                 8                88
                   vv
clus                STOMACH ADENOCARCINOMA - DIFFUSE TYPE
  6Q LOSS MUTATED                                       2
  6Q LOSS WILD-TYPE                                    17
                   vv
clus                STOMACH ADENOCARCINOMA - NOT OTHERWISE SPECIFIED (NOS)
  6Q LOSS MUTATED                                                        5
  6Q LOSS WILD-TYPE                                                     74
                   vv
clus                STOMACH ADENOCARCINOMA - SIGNET RING TYPE
  6Q LOSS MUTATED                                           0
  6Q LOSS WILD-TYPE                                         1
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - MUCINOUS TYPE
  6Q LOSS MUTATED                                                   0
  6Q LOSS WILD-TYPE                                                 9
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - PAPILLARY TYPE
  6Q LOSS MUTATED                                                    0
  6Q LOSS WILD-TYPE                                                  3
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - TUBULAR TYPE
  6Q LOSS MUTATED                                                  3
  6Q LOSS WILD-TYPE                                                7
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - TYPE NOT OTHERWISE SPECIFIED (NOS)
  6Q LOSS MUTATED                                                                        2
  6Q LOSS WILD-TYPE                                                                     33
D47V4, multiclass
                   vv
clus                T1 T2 T3 T4
  6Q LOSS MUTATED    1  7  3  1
  6Q LOSS WILD-TYPE  5 46 56 32
D47V5, multiclass
                   vv
clus                N0 N1 N2 N3
  6Q LOSS MUTATED    4  3  3  0
  6Q LOSS WILD-TYPE 46 54 21 19
D47V6, multiclass
                   vv
clus                 M0  M1  MX
  6Q LOSS MUTATED    10   1   1
  6Q LOSS WILD-TYPE 122  17  10
D47V7, multiclass
                   vv
clus                 I II III IV
  6Q LOSS MUTATED    3  0   6  1
  6Q LOSS WILD-TYPE 22 43  42 28
D47V8, multiclass
D47V9, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED      0   12
  6Q LOSS WILD-TYPE    5  144
     clus
vv    6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  NO                0                 5
  YES              12               144

Clustering(48) Variable = 7p loss mutation analysis
D48V1, survival
                   sevent
clus2                 0   1
  7P LOSS MUTATED     3   0
  7P LOSS WILD-TYPE 105  16
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
                3               121 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
                0                16 
$`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-BR-7958 TCGA-BR-7959 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
        0.69         0.16         1.08         0.82         1.32         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
        0.95         0.49         0.46         0.72         0.26         0.43 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-CD-5798 
        0.26         1.18         1.55         1.48         0.76         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-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-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-D7-6822 
        1.68         3.65         4.70         4.04         2.93         4.27 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6177 TCGA-F1-6874 TCGA-F1-6875 TCGA-FP-7735 
        0.62         7.79         6.54         2.01        72.23         0.39 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-HJ-7597 TCGA-IN-7806 TCGA-IN-7808 
        0.20         3.02         3.58        26.43         6.87         3.55 
TCGA-IP-7968 
        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              1.48 
[1] "4.5 - 54.0 (30.0)" "0.1 - 72.2 (1.5)" 
       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-BR-7958        TCGA-BR-7959        TCGA-BR-8059        TCGA-BR-8060 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-BR-8077        TCGA-BR-8078        TCGA-BR-8080        TCGA-BR-8081 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-BR-8284        TCGA-BR-8285        TCGA-BR-8286        TCGA-BR-8289 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-BR-8291        TCGA-BR-8295        TCGA-BR-8296        TCGA-BR-8297 
"7P LOSS WILD-TYPE" "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-EQ-8122        TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-FP-7735        TCGA-FP-7829        TCGA-FP-7916        TCGA-FP-7998 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-HJ-7597        TCGA-IN-7806        TCGA-IN-7808        TCGA-IP-7968 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "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-BR-7958        TCGA-BR-7959        TCGA-BR-8059        TCGA-BR-8060 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-BR-8077        TCGA-BR-8078        TCGA-BR-8080        TCGA-BR-8081 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-BR-8284        TCGA-BR-8285        TCGA-BR-8286        TCGA-BR-8289 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-BR-8291        TCGA-BR-8295        TCGA-BR-8296        TCGA-BR-8297 
"7P LOSS WILD-TYPE" "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-EQ-8122        TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-FP-7735        TCGA-FP-7829        TCGA-FP-7916        TCGA-FP-7998 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-HJ-7597        TCGA-IN-7806        TCGA-IN-7808        TCGA-IP-7968 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "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-BR-7958        TCGA-BR-7959        TCGA-BR-8059        TCGA-BR-8060 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-BR-8077        TCGA-BR-8078        TCGA-BR-8080        TCGA-BR-8081 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-BR-8284        TCGA-BR-8285        TCGA-BR-8286        TCGA-BR-8289 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-BR-8291        TCGA-BR-8295        TCGA-BR-8296        TCGA-BR-8297 
"7P LOSS WILD-TYPE" "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-EQ-8122        TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-FP-7735        TCGA-FP-7829        TCGA-FP-7916        TCGA-FP-7998 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-HJ-7597        TCGA-IN-7806        TCGA-IN-7808        TCGA-IP-7968 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
[1] "hr="     "8.1e+07"
D48V2, continuous
D48V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED      0    3
  7P LOSS WILD-TYPE   65   93
        clus
vv       7P LOSS MUTATED 7P LOSS WILD-TYPE
  FEMALE               0                65
  MALE                 3                93
                   vv
clus                STOMACH ADENOCARCINOMA - DIFFUSE TYPE
  7P LOSS MUTATED                                       0
  7P LOSS WILD-TYPE                                    19
                   vv
clus                STOMACH ADENOCARCINOMA - NOT OTHERWISE SPECIFIED (NOS)
  7P LOSS MUTATED                                                        1
  7P LOSS WILD-TYPE                                                     78
                   vv
clus                STOMACH ADENOCARCINOMA - SIGNET RING TYPE
  7P LOSS MUTATED                                           0
  7P LOSS WILD-TYPE                                         1
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - MUCINOUS TYPE
  7P LOSS MUTATED                                                   0
  7P LOSS WILD-TYPE                                                 9
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - PAPILLARY TYPE
  7P LOSS MUTATED                                                    0
  7P LOSS WILD-TYPE                                                  3
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - TUBULAR TYPE
  7P LOSS MUTATED                                                  0
  7P LOSS WILD-TYPE                                               10
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - TYPE NOT OTHERWISE SPECIFIED (NOS)
  7P LOSS MUTATED                                                                        2
  7P LOSS WILD-TYPE                                                                     33
D48V4, multiclass
                   vv
clus                T1 T2 T3 T4
  7P LOSS MUTATED    1  0  1  1
  7P LOSS WILD-TYPE  5 53 58 32
D48V5, multiclass
                   vv
clus                N0 N1 N2 N3
  7P LOSS MUTATED    1  0  2  0
  7P LOSS WILD-TYPE 49 57 22 19
D48V6, multiclass
                   vv
clus                 M0  M1  MX
  7P LOSS MUTATED     3   0   0
  7P LOSS WILD-TYPE 129  18  11
D48V7, multiclass
                   vv
clus                 I II III IV
  7P LOSS MUTATED    1  1   0  1
  7P LOSS WILD-TYPE 24 42  48 28
D48V8, multiclass
D48V9, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED      0    3
  7P LOSS WILD-TYPE    5  153
     clus
vv    7P LOSS MUTATED 7P LOSS WILD-TYPE
  NO                0                 5
  YES               3               153

Clustering(49) Variable = 7q loss mutation analysis
D49V1, survival
                   sevent
clus2                 0   1
  7Q LOSS MUTATED     5   0
  7Q LOSS WILD-TYPE 103  16
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
                5               119 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
                0                16 
$`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-BR-7958 TCGA-BR-7959 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
        0.69         0.16         1.08         0.82         1.32         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
        0.95         0.49         0.46         0.72         0.26         0.43 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-CD-5798 
        0.26         1.18         1.55         1.48         0.76         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-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-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-D7-6822 TCGA-EQ-5647 
        1.68         3.65         4.70         4.04         4.27         0.62 
TCGA-EQ-8122 TCGA-F1-6177 TCGA-F1-6874 TCGA-F1-6875 TCGA-FP-7735 TCGA-FP-7916 
        7.79         6.54         2.01        72.23         0.39         3.02 
TCGA-FP-7998 TCGA-HJ-7597 TCGA-IN-7806 TCGA-IN-7808 TCGA-IP-7968 
        3.58        26.43         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              1.48 
[1] "0.2 - 54.0 (4.5)" "0.1 - 72.2 (1.5)"
       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-BR-7958        TCGA-BR-7959        TCGA-BR-8059        TCGA-BR-8060 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-BR-8077        TCGA-BR-8078        TCGA-BR-8080        TCGA-BR-8081 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-BR-8284        TCGA-BR-8285        TCGA-BR-8286        TCGA-BR-8289 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-BR-8291        TCGA-BR-8295        TCGA-BR-8296        TCGA-BR-8297 
"7Q LOSS WILD-TYPE" "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-EQ-8122        TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-FP-7735        TCGA-FP-7829        TCGA-FP-7916        TCGA-FP-7998 
"7Q LOSS WILD-TYPE"   "7Q LOSS MUTATED" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-HJ-7597        TCGA-IN-7806        TCGA-IN-7808        TCGA-IP-7968 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "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-BR-7958        TCGA-BR-7959        TCGA-BR-8059        TCGA-BR-8060 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-BR-8077        TCGA-BR-8078        TCGA-BR-8080        TCGA-BR-8081 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-BR-8284        TCGA-BR-8285        TCGA-BR-8286        TCGA-BR-8289 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-BR-8291        TCGA-BR-8295        TCGA-BR-8296        TCGA-BR-8297 
"7Q LOSS WILD-TYPE" "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-EQ-8122        TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-FP-7735        TCGA-FP-7829        TCGA-FP-7916        TCGA-FP-7998 
"7Q LOSS WILD-TYPE"   "7Q LOSS MUTATED" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-HJ-7597        TCGA-IN-7806        TCGA-IN-7808        TCGA-IP-7968 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "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-BR-7958        TCGA-BR-7959        TCGA-BR-8059        TCGA-BR-8060 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-BR-8077        TCGA-BR-8078        TCGA-BR-8080        TCGA-BR-8081 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-BR-8284        TCGA-BR-8285        TCGA-BR-8286        TCGA-BR-8289 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-BR-8291        TCGA-BR-8295        TCGA-BR-8296        TCGA-BR-8297 
"7Q LOSS WILD-TYPE" "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-EQ-8122        TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-FP-7735        TCGA-FP-7829        TCGA-FP-7916        TCGA-FP-7998 
"7Q LOSS WILD-TYPE"   "7Q LOSS MUTATED" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-HJ-7597        TCGA-IN-7806        TCGA-IN-7808        TCGA-IP-7968 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
[1] "hr="   "8e+07"
D49V2, continuous
D49V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED      0    5
  7Q LOSS WILD-TYPE   65   91
        clus
vv       7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  FEMALE               0                65
  MALE                 5                91
                   vv
clus                STOMACH ADENOCARCINOMA - DIFFUSE TYPE
  7Q LOSS MUTATED                                       0
  7Q LOSS WILD-TYPE                                    19
                   vv
clus                STOMACH ADENOCARCINOMA - NOT OTHERWISE SPECIFIED (NOS)
  7Q LOSS MUTATED                                                        1
  7Q LOSS WILD-TYPE                                                     78
                   vv
clus                STOMACH ADENOCARCINOMA - SIGNET RING TYPE
  7Q LOSS MUTATED                                           0
  7Q LOSS WILD-TYPE                                         1
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - MUCINOUS TYPE
  7Q LOSS MUTATED                                                   1
  7Q LOSS WILD-TYPE                                                 8
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - PAPILLARY TYPE
  7Q LOSS MUTATED                                                    0
  7Q LOSS WILD-TYPE                                                  3
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - TUBULAR TYPE
  7Q LOSS MUTATED                                                  1
  7Q LOSS WILD-TYPE                                                9
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - TYPE NOT OTHERWISE SPECIFIED (NOS)
  7Q LOSS MUTATED                                                                        2
  7Q LOSS WILD-TYPE                                                                     33
D49V4, multiclass
                   vv
clus                T1 T2 T3 T4
  7Q LOSS MUTATED    1  1  2  1
  7Q LOSS WILD-TYPE  5 52 57 32
D49V5, multiclass
                   vv
clus                N0 N1 N2 N3
  7Q LOSS MUTATED    1  2  2  0
  7Q LOSS WILD-TYPE 49 55 22 19
D49V6, multiclass
                   vv
clus                 M0  M1  MX
  7Q LOSS MUTATED     5   0   0
  7Q LOSS WILD-TYPE 127  18  11
D49V7, multiclass
                   vv
clus                 I II III IV
  7Q LOSS MUTATED    1  2   1  1
  7Q LOSS WILD-TYPE 24 41  47 28
D49V8, multiclass
D49V9, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED      0    5
  7Q LOSS WILD-TYPE    5  151
     clus
vv    7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  NO                0                 5
  YES               5               151

Clustering(50) Variable = 8p loss mutation analysis
D50V1, survival
                   sevent
clus2                 0   1
  8P LOSS MUTATED     7   0
  8P LOSS WILD-TYPE 101  16
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
                7               117 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
                0                16 
$`8P LOSS MUTATED`
TCGA-BR-7716 TCGA-CG-4301 TCGA-CG-4436 TCGA-CG-4449 TCGA-D7-6528 TCGA-D7-6820 
        0.82         3.02        52.96        19.07         1.68         2.93 
TCGA-IP-7968 
        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-BR-7958 TCGA-BR-7959 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
        0.69         0.16         1.08         0.82         1.32         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
        0.95         0.49         0.46         0.72         0.26         0.43 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-CD-5798 
        0.26         1.18         1.55         1.48         0.76         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-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       27.02        15.95         1.02         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-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-D7-6822 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6177 
        4.70         4.04         4.27         0.62         7.79         6.54 
TCGA-F1-6874 TCGA-F1-6875 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
        2.01        72.23         0.39         0.20         3.02         3.58 
TCGA-HJ-7597 TCGA-IN-7806 TCGA-IN-7808 
       26.43         6.87         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 
             2.93              1.41 
[1] "0.8 - 53.0 (2.9)" "0.1 - 72.2 (1.4)"
       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-BR-7958        TCGA-BR-7959        TCGA-BR-8059        TCGA-BR-8060 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-BR-8077        TCGA-BR-8078        TCGA-BR-8080        TCGA-BR-8081 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-BR-8284        TCGA-BR-8285        TCGA-BR-8286        TCGA-BR-8289 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-BR-8291        TCGA-BR-8295        TCGA-BR-8296        TCGA-BR-8297 
"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 WILD-TYPE"   "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 MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EQ-8122        TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-FP-7735        TCGA-FP-7829        TCGA-FP-7916        TCGA-FP-7998 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-HJ-7597        TCGA-IN-7806        TCGA-IN-7808        TCGA-IP-7968 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"   "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-BR-7958        TCGA-BR-7959        TCGA-BR-8059        TCGA-BR-8060 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-BR-8077        TCGA-BR-8078        TCGA-BR-8080        TCGA-BR-8081 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-BR-8284        TCGA-BR-8285        TCGA-BR-8286        TCGA-BR-8289 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-BR-8291        TCGA-BR-8295        TCGA-BR-8296        TCGA-BR-8297 
"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 WILD-TYPE"   "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 MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EQ-8122        TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-FP-7735        TCGA-FP-7829        TCGA-FP-7916        TCGA-FP-7998 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-HJ-7597        TCGA-IN-7806        TCGA-IN-7808        TCGA-IP-7968 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"   "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-BR-7958        TCGA-BR-7959        TCGA-BR-8059        TCGA-BR-8060 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-BR-8077        TCGA-BR-8078        TCGA-BR-8080        TCGA-BR-8081 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-BR-8284        TCGA-BR-8285        TCGA-BR-8286        TCGA-BR-8289 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-BR-8291        TCGA-BR-8295        TCGA-BR-8296        TCGA-BR-8297 
"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 WILD-TYPE"   "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 MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EQ-8122        TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-FP-7735        TCGA-FP-7829        TCGA-FP-7916        TCGA-FP-7998 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-HJ-7597        TCGA-IN-7806        TCGA-IN-7808        TCGA-IP-7968 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" 
[1] "hr="     "7.5e+07"
D50V2, continuous
D50V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED      3    7
  8P LOSS WILD-TYPE   62   89
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  FEMALE               3                62
  MALE                 7                89
                   vv
clus                STOMACH ADENOCARCINOMA - DIFFUSE TYPE
  8P LOSS MUTATED                                       0
  8P LOSS WILD-TYPE                                    19
                   vv
clus                STOMACH ADENOCARCINOMA - NOT OTHERWISE SPECIFIED (NOS)
  8P LOSS MUTATED                                                        4
  8P LOSS WILD-TYPE                                                     75
                   vv
clus                STOMACH ADENOCARCINOMA - SIGNET RING TYPE
  8P LOSS MUTATED                                           0
  8P LOSS WILD-TYPE                                         1
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - MUCINOUS TYPE
  8P LOSS MUTATED                                                   1
  8P LOSS WILD-TYPE                                                 8
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - PAPILLARY TYPE
  8P LOSS MUTATED                                                    0
  8P LOSS WILD-TYPE                                                  3
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - TUBULAR TYPE
  8P LOSS MUTATED                                                  3
  8P LOSS WILD-TYPE                                                7
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - TYPE NOT OTHERWISE SPECIFIED (NOS)
  8P LOSS MUTATED                                                                        1
  8P LOSS WILD-TYPE                                                                     34
D50V4, multiclass
                   vv
clus                T1 T2 T3 T4
  8P LOSS MUTATED    0  5  2  2
  8P LOSS WILD-TYPE  6 48 57 31
D50V5, multiclass
                   vv
clus                N0 N1 N2 N3
  8P LOSS MUTATED    2  6  1  0
  8P LOSS WILD-TYPE 48 51 23 19
D50V6, multiclass
                   vv
clus                 M0  M1  MX
  8P LOSS MUTATED     8   1   1
  8P LOSS WILD-TYPE 124  17  10
D50V7, multiclass
                   vv
clus                 I II III IV
  8P LOSS MUTATED    2  3   1  2
  8P LOSS WILD-TYPE 23 40  47 27
D50V8, multiclass
D50V9, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED      0   10
  8P LOSS WILD-TYPE    5  146
     clus
vv    8P LOSS MUTATED 8P LOSS WILD-TYPE
  NO                0                 5
  YES              10               146

Clustering(51) Variable = 8q loss mutation analysis
D51V1, survival
                   sevent
clus2                 0   1
  8Q LOSS MUTATED     1   0
  8Q LOSS WILD-TYPE 107  16
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                1               123 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                0                16 
$`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-BR-7958 TCGA-BR-7959 TCGA-BR-8059 TCGA-BR-8060 
        0.95         0.69         0.16         1.08         0.82         1.32 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
        0.69         0.95         0.49         0.46         0.72         0.26 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
        0.43         0.26         1.18         1.55         1.48         0.76 
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-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-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
        5.95         6.61         4.14         3.65         4.70         4.04 
TCGA-D7-6820 TCGA-D7-6822 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6177 TCGA-F1-6874 
        2.93         4.27         0.62         7.79         6.54         2.01 
TCGA-F1-6875 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-HJ-7597 
       72.23         0.39         0.20         3.02         3.58        26.43 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IP-7968 
        6.87         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 
             1.68              1.48 
[1] "1.7 - 1.7 (1.7)"  "0.1 - 72.2 (1.5)"
       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-BR-7958        TCGA-BR-7959        TCGA-BR-8059        TCGA-BR-8060 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BR-8077        TCGA-BR-8078        TCGA-BR-8080        TCGA-BR-8081 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BR-8284        TCGA-BR-8285        TCGA-BR-8286        TCGA-BR-8289 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BR-8291        TCGA-BR-8295        TCGA-BR-8296        TCGA-BR-8297 
"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-EQ-8122        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-7916        TCGA-FP-7998 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-HJ-7597        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" 
       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-BR-7958        TCGA-BR-7959        TCGA-BR-8059        TCGA-BR-8060 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BR-8077        TCGA-BR-8078        TCGA-BR-8080        TCGA-BR-8081 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BR-8284        TCGA-BR-8285        TCGA-BR-8286        TCGA-BR-8289 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BR-8291        TCGA-BR-8295        TCGA-BR-8296        TCGA-BR-8297 
"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-EQ-8122        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-7916        TCGA-FP-7998 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-HJ-7597        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" 
       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-BR-7958        TCGA-BR-7959        TCGA-BR-8059        TCGA-BR-8060 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BR-8077        TCGA-BR-8078        TCGA-BR-8080        TCGA-BR-8081 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BR-8284        TCGA-BR-8285        TCGA-BR-8286        TCGA-BR-8289 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BR-8291        TCGA-BR-8295        TCGA-BR-8296        TCGA-BR-8297 
"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-EQ-8122        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-7916        TCGA-FP-7998 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-HJ-7597        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" 
[1] "Remove cluster labels:" "8Q LOSS MUTATED"       
clus
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                1               123 
       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-BR-7958        TCGA-BR-7959        TCGA-BR-8059        TCGA-BR-8060 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BR-8077        TCGA-BR-8078        TCGA-BR-8080        TCGA-BR-8081 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BR-8284        TCGA-BR-8285        TCGA-BR-8286        TCGA-BR-8289 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BR-8291        TCGA-BR-8295        TCGA-BR-8296        TCGA-BR-8297 
"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-EQ-8122 
"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-7916        TCGA-FP-7998        TCGA-HJ-7597 
"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" 
D51V2, continuous
D51V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED      1    2
  8Q LOSS WILD-TYPE   64   94
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  FEMALE               1                64
  MALE                 2                94
                   vv
clus                STOMACH ADENOCARCINOMA - DIFFUSE TYPE
  8Q LOSS MUTATED                                       0
  8Q LOSS WILD-TYPE                                    19
                   vv
clus                STOMACH ADENOCARCINOMA - NOT OTHERWISE SPECIFIED (NOS)
  8Q LOSS MUTATED                                                        1
  8Q LOSS WILD-TYPE                                                     78
                   vv
clus                STOMACH ADENOCARCINOMA - SIGNET RING TYPE
  8Q LOSS MUTATED                                           0
  8Q LOSS WILD-TYPE                                         1
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - MUCINOUS TYPE
  8Q LOSS MUTATED                                                   0
  8Q LOSS WILD-TYPE                                                 9
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - PAPILLARY TYPE
  8Q LOSS MUTATED                                                    0
  8Q LOSS WILD-TYPE                                                  3
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - TUBULAR TYPE
  8Q LOSS MUTATED                                                  2
  8Q LOSS WILD-TYPE                                                8
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - TYPE NOT OTHERWISE SPECIFIED (NOS)
  8Q LOSS MUTATED                                                                        0
  8Q LOSS WILD-TYPE                                                                     35
D51V4, multiclass
                   vv
clus                T1 T2 T3 T4
  8Q LOSS MUTATED    0  2  0  0
  8Q LOSS WILD-TYPE  6 51 59 33
D51V5, multiclass
[1] "Remove cluster labels:" "8Q LOSS MUTATED"       
clus
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                2               149 
       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-4201        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-4279        TCGA-BR-4280        TCGA-BR-4292        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-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-BR-7958        TCGA-BR-7959        TCGA-BR-8059 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BR-8060        TCGA-BR-8077        TCGA-BR-8078        TCGA-BR-8080 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BR-8081        TCGA-BR-8284        TCGA-BR-8285        TCGA-BR-8286 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BR-8289        TCGA-BR-8291        TCGA-BR-8295        TCGA-BR-8296 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BR-8297        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-EQ-8122        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-7916        TCGA-FP-7998 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-HF-7131        TCGA-HF-7132        TCGA-HF-7133        TCGA-HF-7134 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-HF-7136        TCGA-HJ-7597        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" 
                   vv
clus                N0 N1 N2 N3
  8Q LOSS MUTATED    1  1  0  0
  8Q LOSS WILD-TYPE 49 56 24 19
D51V6, multiclass
[1] "Remove cluster labels:" "8Q LOSS MUTATED"       
clus
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                2               148 
       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-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-4267        TCGA-BR-4279        TCGA-BR-4280        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-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-BR-7958        TCGA-BR-7959        TCGA-BR-8059        TCGA-BR-8060 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BR-8077        TCGA-BR-8078        TCGA-BR-8080        TCGA-BR-8081 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BR-8284        TCGA-BR-8285        TCGA-BR-8286        TCGA-BR-8289 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BR-8291        TCGA-BR-8295        TCGA-BR-8296        TCGA-BR-8297 
"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-EQ-8122 
"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-7916        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-HJ-7597        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" 
                   vv
clus                 M0  M1  MX
  8Q LOSS MUTATED     3   0   0
  8Q LOSS WILD-TYPE 129  18  11
D51V7, multiclass
                   vv
clus                 I II III IV
  8Q LOSS MUTATED    1  0   0  0
  8Q LOSS WILD-TYPE 24 43  48 29
D51V8, multiclass
[1] "Remove cluster labels:" "8Q LOSS MUTATED"       
clus
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                1               144 
       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-4253        TCGA-BR-4255        TCGA-BR-4267        TCGA-BR-4279 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BR-4280        TCGA-BR-4361        TCGA-BR-4368        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-BR-7958        TCGA-BR-7959        TCGA-BR-8059        TCGA-BR-8060 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BR-8077        TCGA-BR-8078        TCGA-BR-8080        TCGA-BR-8081 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BR-8284        TCGA-BR-8285        TCGA-BR-8286        TCGA-BR-8289 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BR-8291        TCGA-BR-8295        TCGA-BR-8296        TCGA-BR-8297 
"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-EQ-8122 
"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-7916        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-HJ-7597        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" 
D51V9, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED      0    3
  8Q LOSS WILD-TYPE    5  153
     clus
vv    8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  NO                0                 5
  YES               3               153

Clustering(52) Variable = 9p loss mutation analysis
D52V1, survival
                   sevent
clus2                0  1
  9P LOSS MUTATED   20  2
  9P LOSS WILD-TYPE 88 14
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               22               102 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
                2                14 
$`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-EQ-8122 TCGA-F1-6875 TCGA-IN-7806 
        4.70         7.79        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-BR-7958 TCGA-BR-7959 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 
        0.16         1.08         0.82         1.32         0.69         0.95 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
        0.49         0.46         0.72         0.26         0.43         0.26 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-CD-5798 TCGA-CD-5800 
        1.18         1.55         1.48         0.76         0.82         0.36 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CG-4300 TCGA-CG-4304 TCGA-CG-4305 
        0.49         0.30         0.07        20.02        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-4455 TCGA-CG-4460 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4469 
       47.05        12.03        21.99         1.02         8.98         7.07 
TCGA-CG-4474 TCGA-CG-4477 TCGA-CG-5716 TCGA-CG-5717 TCGA-CG-5720 TCGA-CG-5721 
        1.02         1.02         1.02         6.94         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-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-D7-6522 TCGA-D7-6524 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6818 
        6.90         0.69         4.14         1.68         3.65         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-7916 TCGA-FP-7998 TCGA-HJ-7597 TCGA-IN-7808 TCGA-IP-7968 
        0.20         3.02         3.58        26.43         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 
             7.33              1.22 
[1] "0.7 - 72.2 (7.3)" "0.1 - 70.1 (1.2)"
       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-BR-7958        TCGA-BR-7959        TCGA-BR-8059        TCGA-BR-8060 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-BR-8077        TCGA-BR-8078        TCGA-BR-8080        TCGA-BR-8081 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-BR-8284        TCGA-BR-8285        TCGA-BR-8286        TCGA-BR-8289 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-BR-8291        TCGA-BR-8295        TCGA-BR-8296        TCGA-BR-8297 
"9P LOSS WILD-TYPE" "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-EQ-8122        TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875 
  "9P LOSS MUTATED" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" 
       TCGA-FP-7735        TCGA-FP-7829        TCGA-FP-7916        TCGA-FP-7998 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-HJ-7597        TCGA-IN-7806        TCGA-IN-7808        TCGA-IP-7968 
"9P LOSS WILD-TYPE"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" "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-BR-7958        TCGA-BR-7959        TCGA-BR-8059        TCGA-BR-8060 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-BR-8077        TCGA-BR-8078        TCGA-BR-8080        TCGA-BR-8081 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-BR-8284        TCGA-BR-8285        TCGA-BR-8286        TCGA-BR-8289 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-BR-8291        TCGA-BR-8295        TCGA-BR-8296        TCGA-BR-8297 
"9P LOSS WILD-TYPE" "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-EQ-8122        TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875 
  "9P LOSS MUTATED" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" 
       TCGA-FP-7735        TCGA-FP-7829        TCGA-FP-7916        TCGA-FP-7998 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-HJ-7597        TCGA-IN-7806        TCGA-IN-7808        TCGA-IP-7968 
"9P LOSS WILD-TYPE"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" "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-BR-7958        TCGA-BR-7959        TCGA-BR-8059        TCGA-BR-8060 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-BR-8077        TCGA-BR-8078        TCGA-BR-8080        TCGA-BR-8081 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-BR-8284        TCGA-BR-8285        TCGA-BR-8286        TCGA-BR-8289 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-BR-8291        TCGA-BR-8295        TCGA-BR-8296        TCGA-BR-8297 
"9P LOSS WILD-TYPE" "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-EQ-8122        TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875 
  "9P LOSS MUTATED" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" 
       TCGA-FP-7735        TCGA-FP-7829        TCGA-FP-7916        TCGA-FP-7998 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-HJ-7597        TCGA-IN-7806        TCGA-IN-7808        TCGA-IP-7968 
"9P LOSS WILD-TYPE"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
[1] "hr=" "5.8"
D52V2, continuous
D52V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED      9   17
  9P LOSS WILD-TYPE   56   79
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  FEMALE               9                56
  MALE                17                79
                   vv
clus                STOMACH ADENOCARCINOMA - DIFFUSE TYPE
  9P LOSS MUTATED                                       4
  9P LOSS WILD-TYPE                                    15
                   vv
clus                STOMACH ADENOCARCINOMA - NOT OTHERWISE SPECIFIED (NOS)
  9P LOSS MUTATED                                                        8
  9P LOSS WILD-TYPE                                                     71
                   vv
clus                STOMACH ADENOCARCINOMA - SIGNET RING TYPE
  9P LOSS MUTATED                                           0
  9P LOSS WILD-TYPE                                         1
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - MUCINOUS TYPE
  9P LOSS MUTATED                                                   2
  9P LOSS WILD-TYPE                                                 7
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - PAPILLARY TYPE
  9P LOSS MUTATED                                                    0
  9P LOSS WILD-TYPE                                                  3
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - TUBULAR TYPE
  9P LOSS MUTATED                                                  3
  9P LOSS WILD-TYPE                                                7
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - TYPE NOT OTHERWISE SPECIFIED (NOS)
  9P LOSS MUTATED                                                                        8
  9P LOSS WILD-TYPE                                                                     27
D52V4, multiclass
                   vv
clus                T1 T2 T3 T4
  9P LOSS MUTATED    0 14  5  4
  9P LOSS WILD-TYPE  6 39 54 29
D52V5, multiclass
                   vv
clus                N0 N1 N2 N3
  9P LOSS MUTATED    5 11  6  3
  9P LOSS WILD-TYPE 45 46 18 16
D52V6, multiclass
                   vv
clus                 M0  M1  MX
  9P LOSS MUTATED    22   3   1
  9P LOSS WILD-TYPE 110  15  10
D52V7, multiclass
                   vv
clus                 I II III IV
  9P LOSS MUTATED    3  6   7  7
  9P LOSS WILD-TYPE 22 37  41 22
D52V8, multiclass
D52V9, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED      1   25
  9P LOSS WILD-TYPE    4  131
     clus
vv    9P LOSS MUTATED 9P LOSS WILD-TYPE
  NO                1                 4
  YES              25               131

Clustering(53) Variable = 9q loss mutation analysis
D53V1, survival
                   sevent
clus2                 0   1
  9Q LOSS MUTATED     8   1
  9Q LOSS WILD-TYPE 100  15
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
                9               115 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
                1                15 
$`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-EQ-8122 TCGA-F1-6875 
        4.70         7.79        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-BR-7958 TCGA-BR-7959 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
        0.69         0.16         1.08         0.82         1.32         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
        0.95         0.49         0.46         0.72         0.26         0.43 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-CD-5798 
        0.26         1.18         1.55         1.48         0.76         0.82 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CG-4300 TCGA-CG-4304 
        0.36         0.49         0.30         0.07        20.02        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-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-D7-6521 TCGA-D7-6522 
        8.65         3.58         4.54         9.80         8.19         6.90 
TCGA-D7-6524 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6818 
        0.69         6.61         4.14         1.68         3.65         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-7916 TCGA-FP-7998 TCGA-HJ-7597 TCGA-IN-7806 TCGA-IN-7808 
        0.20         3.02         3.58        26.43         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 
             5.95              1.35 
[1] "0.7 - 72.2 (6.0)" "0.1 - 70.1 (1.4)"
       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-BR-7958        TCGA-BR-7959        TCGA-BR-8059        TCGA-BR-8060 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-BR-8077        TCGA-BR-8078        TCGA-BR-8080        TCGA-BR-8081 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-BR-8284        TCGA-BR-8285        TCGA-BR-8286        TCGA-BR-8289 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-BR-8291        TCGA-BR-8295        TCGA-BR-8296        TCGA-BR-8297 
"9Q LOSS WILD-TYPE" "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-EQ-8122        TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875 
  "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" 
       TCGA-FP-7735        TCGA-FP-7829        TCGA-FP-7916        TCGA-FP-7998 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-HJ-7597        TCGA-IN-7806        TCGA-IN-7808        TCGA-IP-7968 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "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-BR-7958        TCGA-BR-7959        TCGA-BR-8059        TCGA-BR-8060 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-BR-8077        TCGA-BR-8078        TCGA-BR-8080        TCGA-BR-8081 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-BR-8284        TCGA-BR-8285        TCGA-BR-8286        TCGA-BR-8289 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-BR-8291        TCGA-BR-8295        TCGA-BR-8296        TCGA-BR-8297 
"9Q LOSS WILD-TYPE" "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-EQ-8122        TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875 
  "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" 
       TCGA-FP-7735        TCGA-FP-7829        TCGA-FP-7916        TCGA-FP-7998 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-HJ-7597        TCGA-IN-7806        TCGA-IN-7808        TCGA-IP-7968 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "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-BR-7958        TCGA-BR-7959        TCGA-BR-8059        TCGA-BR-8060 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-BR-8077        TCGA-BR-8078        TCGA-BR-8080        TCGA-BR-8081 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-BR-8284        TCGA-BR-8285        TCGA-BR-8286        TCGA-BR-8289 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-BR-8291        TCGA-BR-8295        TCGA-BR-8296        TCGA-BR-8297 
"9Q LOSS WILD-TYPE" "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-EQ-8122        TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875 
  "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" 
       TCGA-FP-7735        TCGA-FP-7829        TCGA-FP-7916        TCGA-FP-7998 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-HJ-7597        TCGA-IN-7806        TCGA-IN-7808        TCGA-IP-7968 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
[1] "hr="     "7.8e+07"
D53V2, continuous
D53V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED      4    7
  9Q LOSS WILD-TYPE   61   89
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  FEMALE               4                61
  MALE                 7                89
                   vv
clus                STOMACH ADENOCARCINOMA - DIFFUSE TYPE
  9Q LOSS MUTATED                                       2
  9Q LOSS WILD-TYPE                                    17
                   vv
clus                STOMACH ADENOCARCINOMA - NOT OTHERWISE SPECIFIED (NOS)
  9Q LOSS MUTATED                                                        4
  9Q LOSS WILD-TYPE                                                     75
                   vv
clus                STOMACH ADENOCARCINOMA - SIGNET RING TYPE
  9Q LOSS MUTATED                                           0
  9Q LOSS WILD-TYPE                                         1
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - MUCINOUS TYPE
  9Q LOSS MUTATED                                                   1
  9Q LOSS WILD-TYPE                                                 8
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - PAPILLARY TYPE
  9Q LOSS MUTATED                                                    0
  9Q LOSS WILD-TYPE                                                  3
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - TUBULAR TYPE
  9Q LOSS MUTATED                                                  2
  9Q LOSS WILD-TYPE                                                8
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - TYPE NOT OTHERWISE SPECIFIED (NOS)
  9Q LOSS MUTATED                                                                        2
  9Q LOSS WILD-TYPE                                                                     33
D53V4, multiclass
                   vv
clus                T1 T2 T3 T4
  9Q LOSS MUTATED    0  7  2  1
  9Q LOSS WILD-TYPE  6 46 57 32
D53V5, multiclass
                   vv
clus                N0 N1 N2 N3
  9Q LOSS MUTATED    1  5  3  2
  9Q LOSS WILD-TYPE 49 52 21 17
D53V6, multiclass
                   vv
clus                 M0  M1  MX
  9Q LOSS MUTATED     9   1   1
  9Q LOSS WILD-TYPE 123  17  10
D53V7, multiclass
                   vv
clus                 I II III IV
  9Q LOSS MUTATED    1  3   4  2
  9Q LOSS WILD-TYPE 24 40  44 27
D53V8, multiclass
D53V9, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED      1   10
  9Q LOSS WILD-TYPE    4  146
     clus
vv    9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  NO                1                 4
  YES              10               146

Clustering(54) Variable = 10p loss mutation analysis
D54V1, survival
                    sevent
clus2                  0   1
  10P LOSS MUTATED     6   0
  10P LOSS WILD-TYPE 102  16
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                 6                118 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                 0                 16 
$`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-BR-7958 TCGA-BR-7959 TCGA-BR-8059 TCGA-BR-8060 
        0.95         0.69         0.16         1.08         0.82         1.32 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
        0.69         0.95         0.49         0.46         0.72         0.26 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
        0.43         0.26         1.18         1.55         1.48         0.76 
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-5733 
       15.02        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-D7-6520 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-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6822 TCGA-EQ-5647 TCGA-EQ-8122 
        3.65         4.70         4.04         4.27         0.62         7.79 
TCGA-F1-6177 TCGA-F1-6874 TCGA-F1-6875 TCGA-FP-7735 TCGA-FP-7916 TCGA-FP-7998 
        6.54         2.01        72.23         0.39         3.02         3.58 
TCGA-HJ-7597 TCGA-IN-7806 TCGA-IN-7808 TCGA-IP-7968 
       26.43         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              1.445 
[1] "0.2 - 55.0 (3.5)" "0.1 - 72.2 (1.4)"
        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-BR-7958 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-BR-7959         TCGA-BR-8059         TCGA-BR-8060 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-BR-8077         TCGA-BR-8078         TCGA-BR-8080 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-BR-8081         TCGA-BR-8284         TCGA-BR-8285 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-BR-8286         TCGA-BR-8289         TCGA-BR-8291 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-BR-8295         TCGA-BR-8296         TCGA-BR-8297 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-CD-5798         TCGA-CD-5799         TCGA-CD-5800 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-CD-5801         TCGA-CD-5802         TCGA-CD-5803 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-CG-4300         TCGA-CG-4301         TCGA-CG-4304 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-CG-4305         TCGA-CG-4306         TCGA-CG-4436 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE"   "10P LOSS MUTATED" 
        TCGA-CG-4437         TCGA-CG-4438         TCGA-CG-4440 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-CG-4441         TCGA-CG-4443         TCGA-CG-4444 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-CG-4449         TCGA-CG-4455         TCGA-CG-4460 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-CG-4462         TCGA-CG-4465         TCGA-CG-4466 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-CG-4469         TCGA-CG-4472         TCGA-CG-4474 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-CG-4477         TCGA-CG-5716         TCGA-CG-5717 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-CG-5718         TCGA-CG-5719         TCGA-CG-5720 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-CG-5721         TCGA-CG-5722         TCGA-CG-5723 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-CG-5724         TCGA-CG-5725         TCGA-CG-5726 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-CG-5727         TCGA-CG-5728         TCGA-CG-5730 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-CG-5732         TCGA-CG-5733         TCGA-CG-5734 
  "10P LOSS MUTATED" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-D7-5577         TCGA-D7-5578         TCGA-D7-5579 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-D7-6518         TCGA-D7-6519         TCGA-D7-6520 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-D7-6521         TCGA-D7-6522         TCGA-D7-6524 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-D7-6525         TCGA-D7-6526         TCGA-D7-6527 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE"   "10P LOSS MUTATED" 
        TCGA-D7-6528         TCGA-D7-6815         TCGA-D7-6817 
  "10P LOSS MUTATED" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-D7-6818         TCGA-D7-6820         TCGA-D7-6822 
"10P LOSS WILD-TYPE"   "10P LOSS MUTATED" "10P LOSS WILD-TYPE" 
        TCGA-EQ-5647         TCGA-EQ-8122         TCGA-F1-6177 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-F1-6874         TCGA-F1-6875         TCGA-FP-7735 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-FP-7829         TCGA-FP-7916         TCGA-FP-7998 
  "10P LOSS MUTATED" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-HJ-7597         TCGA-IN-7806         TCGA-IN-7808 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-IP-7968 
"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-BR-7958 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-BR-7959         TCGA-BR-8059         TCGA-BR-8060 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-BR-8077         TCGA-BR-8078         TCGA-BR-8080 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-BR-8081         TCGA-BR-8284         TCGA-BR-8285 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-BR-8286         TCGA-BR-8289         TCGA-BR-8291 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-BR-8295         TCGA-BR-8296         TCGA-BR-8297 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-CD-5798         TCGA-CD-5799         TCGA-CD-5800 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-CD-5801         TCGA-CD-5802         TCGA-CD-5803 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-CG-4300         TCGA-CG-4301         TCGA-CG-4304 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-CG-4305         TCGA-CG-4306         TCGA-CG-4436 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE"   "10P LOSS MUTATED" 
        TCGA-CG-4437         TCGA-CG-4438         TCGA-CG-4440 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-CG-4441         TCGA-CG-4443         TCGA-CG-4444 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-CG-4449         TCGA-CG-4455         TCGA-CG-4460 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-CG-4462         TCGA-CG-4465         TCGA-CG-4466 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-CG-4469         TCGA-CG-4472         TCGA-CG-4474 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-CG-4477         TCGA-CG-5716         TCGA-CG-5717 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-CG-5718         TCGA-CG-5719         TCGA-CG-5720 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-CG-5721         TCGA-CG-5722         TCGA-CG-5723 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-CG-5724         TCGA-CG-5725         TCGA-CG-5726 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-CG-5727         TCGA-CG-5728         TCGA-CG-5730 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-CG-5732         TCGA-CG-5733         TCGA-CG-5734 
  "10P LOSS MUTATED" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-D7-5577         TCGA-D7-5578         TCGA-D7-5579 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-D7-6518         TCGA-D7-6519         TCGA-D7-6520 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-D7-6521         TCGA-D7-6522         TCGA-D7-6524 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-D7-6525         TCGA-D7-6526         TCGA-D7-6527 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE"   "10P LOSS MUTATED" 
        TCGA-D7-6528         TCGA-D7-6815         TCGA-D7-6817 
  "10P LOSS MUTATED" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-D7-6818         TCGA-D7-6820         TCGA-D7-6822 
"10P LOSS WILD-TYPE"   "10P LOSS MUTATED" "10P LOSS WILD-TYPE" 
        TCGA-EQ-5647         TCGA-EQ-8122         TCGA-F1-6177 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-F1-6874         TCGA-F1-6875         TCGA-FP-7735 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-FP-7829         TCGA-FP-7916         TCGA-FP-7998 
  "10P LOSS MUTATED" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-HJ-7597         TCGA-IN-7806         TCGA-IN-7808 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-IP-7968 
"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-BR-7958 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-BR-7959         TCGA-BR-8059         TCGA-BR-8060 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-BR-8077         TCGA-BR-8078         TCGA-BR-8080 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-BR-8081         TCGA-BR-8284         TCGA-BR-8285 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-BR-8286         TCGA-BR-8289         TCGA-BR-8291 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-BR-8295         TCGA-BR-8296         TCGA-BR-8297 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-CD-5798         TCGA-CD-5799         TCGA-CD-5800 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-CD-5801         TCGA-CD-5802         TCGA-CD-5803 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-CG-4300         TCGA-CG-4301         TCGA-CG-4304 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-CG-4305         TCGA-CG-4306         TCGA-CG-4436 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE"   "10P LOSS MUTATED" 
        TCGA-CG-4437         TCGA-CG-4438         TCGA-CG-4440 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-CG-4441         TCGA-CG-4443         TCGA-CG-4444 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-CG-4449         TCGA-CG-4455         TCGA-CG-4460 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-CG-4462         TCGA-CG-4465         TCGA-CG-4466 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-CG-4469         TCGA-CG-4472         TCGA-CG-4474 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-CG-4477         TCGA-CG-5716         TCGA-CG-5717 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-CG-5718         TCGA-CG-5719         TCGA-CG-5720 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-CG-5721         TCGA-CG-5722         TCGA-CG-5723 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-CG-5724         TCGA-CG-5725         TCGA-CG-5726 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-CG-5727         TCGA-CG-5728         TCGA-CG-5730 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-CG-5732         TCGA-CG-5733         TCGA-CG-5734 
  "10P LOSS MUTATED" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-D7-5577         TCGA-D7-5578         TCGA-D7-5579 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-D7-6518         TCGA-D7-6519         TCGA-D7-6520 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-D7-6521         TCGA-D7-6522         TCGA-D7-6524 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-D7-6525         TCGA-D7-6526         TCGA-D7-6527 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE"   "10P LOSS MUTATED" 
        TCGA-D7-6528         TCGA-D7-6815         TCGA-D7-6817 
  "10P LOSS MUTATED" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-D7-6818         TCGA-D7-6820         TCGA-D7-6822 
"10P LOSS WILD-TYPE"   "10P LOSS MUTATED" "10P LOSS WILD-TYPE" 
        TCGA-EQ-5647         TCGA-EQ-8122         TCGA-F1-6177 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-F1-6874         TCGA-F1-6875         TCGA-FP-7735 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-FP-7829         TCGA-FP-7916         TCGA-FP-7998 
  "10P LOSS MUTATED" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-HJ-7597         TCGA-IN-7806         TCGA-IN-7808 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-IP-7968 
"10P LOSS WILD-TYPE" 
[1] "hr="   "8e+07"
D54V2, continuous
D54V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED      2    8
  10P LOSS WILD-TYPE   63   88
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  FEMALE                2                 63
  MALE                  8                 88
                    vv
clus                 STOMACH ADENOCARCINOMA - DIFFUSE TYPE
  10P LOSS MUTATED                                       0
  10P LOSS WILD-TYPE                                    19
                    vv
clus                 STOMACH ADENOCARCINOMA - NOT OTHERWISE SPECIFIED (NOS)
  10P LOSS MUTATED                                                        2
  10P LOSS WILD-TYPE                                                     77
                    vv
clus                 STOMACH ADENOCARCINOMA - SIGNET RING TYPE
  10P LOSS MUTATED                                           0
  10P LOSS WILD-TYPE                                         1
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - MUCINOUS TYPE
  10P LOSS MUTATED                                                   2
  10P LOSS WILD-TYPE                                                 7
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - PAPILLARY TYPE
  10P LOSS MUTATED                                                    1
  10P LOSS WILD-TYPE                                                  2
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - TUBULAR TYPE
  10P LOSS MUTATED                                                  2
  10P LOSS WILD-TYPE                                                8
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - TYPE NOT OTHERWISE SPECIFIED (NOS)
  10P LOSS MUTATED                                                                        2
  10P LOSS WILD-TYPE                                                                     33
D54V4, multiclass
                    vv
clus                 T1 T2 T3 T4
  10P LOSS MUTATED    0  7  2  0
  10P LOSS WILD-TYPE  6 46 57 33
D54V5, multiclass
                    vv
clus                 N0 N1 N2 N3
  10P LOSS MUTATED    3  5  0  2
  10P LOSS WILD-TYPE 47 52 24 17
D54V6, multiclass
                    vv
clus                  M0  M1  MX
  10P LOSS MUTATED    10   0   0
  10P LOSS WILD-TYPE 122  18  11
D54V7, multiclass
                    vv
clus                  I II III IV
  10P LOSS MUTATED    3  3   1  2
  10P LOSS WILD-TYPE 22 40  47 27
D54V8, multiclass
D54V9, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED      2    8
  10P LOSS WILD-TYPE    3  148
     clus
vv    10P LOSS MUTATED 10P LOSS WILD-TYPE
  NO                 2                  3
  YES                8                148

Clustering(55) Variable = 10q loss mutation analysis
D55V1, survival
                    sevent
clus2                  0   1
  10Q LOSS MUTATED     7   0
  10Q LOSS WILD-TYPE 101  16
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                 7                117 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                 0                 16 
$`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-BR-7958 TCGA-BR-7959 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
        0.69         0.16         1.08         0.82         1.32         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
        0.95         0.49         0.46         0.72         0.26         0.43 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-CD-5798 
        0.26         1.18         1.55         1.48         0.76         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-4469 TCGA-CG-4472 TCGA-CG-4474 
       21.99         1.02         8.98         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-D7-6815 
        8.19         6.90         0.69         5.95         6.61         3.65 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6177 
        4.04         2.93         4.27         0.62         7.79         6.54 
TCGA-F1-6874 TCGA-F1-6875 TCGA-FP-7735 TCGA-FP-7916 TCGA-FP-7998 TCGA-HJ-7597 
        2.01        72.23         0.39         3.02         3.58        26.43 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IP-7968 
        6.87         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               1.48 
[1] "0.2 - 53.0 (4.1)" "0.1 - 72.2 (1.5)"
        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-BR-7958 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BR-7959         TCGA-BR-8059         TCGA-BR-8060 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BR-8077         TCGA-BR-8078         TCGA-BR-8080 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BR-8081         TCGA-BR-8284         TCGA-BR-8285 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BR-8286         TCGA-BR-8289         TCGA-BR-8291 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BR-8295         TCGA-BR-8296         TCGA-BR-8297 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-CD-5798         TCGA-CD-5799         TCGA-CD-5800 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-CD-5801         TCGA-CD-5802         TCGA-CD-5803 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-CG-4300         TCGA-CG-4301         TCGA-CG-4304 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-CG-4305         TCGA-CG-4306         TCGA-CG-4436 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" 
        TCGA-CG-4437         TCGA-CG-4438         TCGA-CG-4440 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-CG-4441         TCGA-CG-4443         TCGA-CG-4444 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-CG-4449         TCGA-CG-4455         TCGA-CG-4460 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-CG-4462         TCGA-CG-4465         TCGA-CG-4466 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" 
        TCGA-CG-4469         TCGA-CG-4472         TCGA-CG-4474 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-CG-4477         TCGA-CG-5716         TCGA-CG-5717 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-CG-5718         TCGA-CG-5719         TCGA-CG-5720 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-CG-5721         TCGA-CG-5722         TCGA-CG-5723 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-CG-5724         TCGA-CG-5725         TCGA-CG-5726 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-CG-5727         TCGA-CG-5728         TCGA-CG-5730 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-CG-5732         TCGA-CG-5733         TCGA-CG-5734 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-D7-5577         TCGA-D7-5578         TCGA-D7-5579 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-D7-6518         TCGA-D7-6519         TCGA-D7-6520 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-D7-6521         TCGA-D7-6522         TCGA-D7-6524 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-D7-6525         TCGA-D7-6526         TCGA-D7-6527 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" 
        TCGA-D7-6528         TCGA-D7-6815         TCGA-D7-6817 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" 
        TCGA-D7-6818         TCGA-D7-6820         TCGA-D7-6822 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EQ-5647         TCGA-EQ-8122         TCGA-F1-6177 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-F1-6874         TCGA-F1-6875         TCGA-FP-7735 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-FP-7829         TCGA-FP-7916         TCGA-FP-7998 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-HJ-7597         TCGA-IN-7806         TCGA-IN-7808 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-IP-7968 
"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-BR-7958 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BR-7959         TCGA-BR-8059         TCGA-BR-8060 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BR-8077         TCGA-BR-8078         TCGA-BR-8080 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BR-8081         TCGA-BR-8284         TCGA-BR-8285 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BR-8286         TCGA-BR-8289         TCGA-BR-8291 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BR-8295         TCGA-BR-8296         TCGA-BR-8297 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-CD-5798         TCGA-CD-5799         TCGA-CD-5800 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-CD-5801         TCGA-CD-5802         TCGA-CD-5803 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-CG-4300         TCGA-CG-4301         TCGA-CG-4304 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-CG-4305         TCGA-CG-4306         TCGA-CG-4436 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" 
        TCGA-CG-4437         TCGA-CG-4438         TCGA-CG-4440 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-CG-4441         TCGA-CG-4443         TCGA-CG-4444 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-CG-4449         TCGA-CG-4455         TCGA-CG-4460 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-CG-4462         TCGA-CG-4465         TCGA-CG-4466 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" 
        TCGA-CG-4469         TCGA-CG-4472         TCGA-CG-4474 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-CG-4477         TCGA-CG-5716         TCGA-CG-5717 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-CG-5718         TCGA-CG-5719         TCGA-CG-5720 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-CG-5721         TCGA-CG-5722         TCGA-CG-5723 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-CG-5724         TCGA-CG-5725         TCGA-CG-5726 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-CG-5727         TCGA-CG-5728         TCGA-CG-5730 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-CG-5732         TCGA-CG-5733         TCGA-CG-5734 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-D7-5577         TCGA-D7-5578         TCGA-D7-5579 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-D7-6518         TCGA-D7-6519         TCGA-D7-6520 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-D7-6521         TCGA-D7-6522         TCGA-D7-6524 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-D7-6525         TCGA-D7-6526         TCGA-D7-6527 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" 
        TCGA-D7-6528         TCGA-D7-6815         TCGA-D7-6817 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" 
        TCGA-D7-6818         TCGA-D7-6820         TCGA-D7-6822 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EQ-5647         TCGA-EQ-8122         TCGA-F1-6177 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-F1-6874         TCGA-F1-6875         TCGA-FP-7735 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-FP-7829         TCGA-FP-7916         TCGA-FP-7998 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-HJ-7597         TCGA-IN-7806         TCGA-IN-7808 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-IP-7968 
"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-BR-7958 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BR-7959         TCGA-BR-8059         TCGA-BR-8060 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BR-8077         TCGA-BR-8078         TCGA-BR-8080 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BR-8081         TCGA-BR-8284         TCGA-BR-8285 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BR-8286         TCGA-BR-8289         TCGA-BR-8291 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BR-8295         TCGA-BR-8296         TCGA-BR-8297 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-CD-5798         TCGA-CD-5799         TCGA-CD-5800 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-CD-5801         TCGA-CD-5802         TCGA-CD-5803 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-CG-4300         TCGA-CG-4301         TCGA-CG-4304 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-CG-4305         TCGA-CG-4306         TCGA-CG-4436 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" 
        TCGA-CG-4437         TCGA-CG-4438         TCGA-CG-4440 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-CG-4441         TCGA-CG-4443         TCGA-CG-4444 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-CG-4449         TCGA-CG-4455         TCGA-CG-4460 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-CG-4462         TCGA-CG-4465         TCGA-CG-4466 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" 
        TCGA-CG-4469         TCGA-CG-4472         TCGA-CG-4474 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-CG-4477         TCGA-CG-5716         TCGA-CG-5717 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-CG-5718         TCGA-CG-5719         TCGA-CG-5720 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-CG-5721         TCGA-CG-5722         TCGA-CG-5723 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-CG-5724         TCGA-CG-5725         TCGA-CG-5726 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-CG-5727         TCGA-CG-5728         TCGA-CG-5730 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-CG-5732         TCGA-CG-5733         TCGA-CG-5734 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-D7-5577         TCGA-D7-5578         TCGA-D7-5579 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-D7-6518         TCGA-D7-6519         TCGA-D7-6520 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-D7-6521         TCGA-D7-6522         TCGA-D7-6524 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-D7-6525         TCGA-D7-6526         TCGA-D7-6527 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" 
        TCGA-D7-6528         TCGA-D7-6815         TCGA-D7-6817 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" 
        TCGA-D7-6818         TCGA-D7-6820         TCGA-D7-6822 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EQ-5647         TCGA-EQ-8122         TCGA-F1-6177 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-F1-6874         TCGA-F1-6875         TCGA-FP-7735 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-FP-7829         TCGA-FP-7916         TCGA-FP-7998 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-HJ-7597         TCGA-IN-7806         TCGA-IN-7808 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-IP-7968 
"10Q LOSS WILD-TYPE" 
[1] "hr="     "7.5e+07"
D55V2, continuous
D55V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED      3    6
  10Q LOSS WILD-TYPE   62   90
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  FEMALE                3                 62
  MALE                  6                 90
                    vv
clus                 STOMACH ADENOCARCINOMA - DIFFUSE TYPE
  10Q LOSS MUTATED                                       0
  10Q LOSS WILD-TYPE                                    19
                    vv
clus                 STOMACH ADENOCARCINOMA - NOT OTHERWISE SPECIFIED (NOS)
  10Q LOSS MUTATED                                                        1
  10Q LOSS WILD-TYPE                                                     78
                    vv
clus                 STOMACH ADENOCARCINOMA - SIGNET RING TYPE
  10Q LOSS MUTATED                                           0
  10Q LOSS WILD-TYPE                                         1
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - MUCINOUS TYPE
  10Q LOSS MUTATED                                                   1
  10Q LOSS WILD-TYPE                                                 8
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - PAPILLARY TYPE
  10Q LOSS MUTATED                                                    1
  10Q LOSS WILD-TYPE                                                  2
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - TUBULAR TYPE
  10Q LOSS MUTATED                                                  2
  10Q LOSS WILD-TYPE                                                8
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - TYPE NOT OTHERWISE SPECIFIED (NOS)
  10Q LOSS MUTATED                                                                        3
  10Q LOSS WILD-TYPE                                                                     32
D55V4, multiclass
                    vv
clus                 T1 T2 T3 T4
  10Q LOSS MUTATED    0  5  3  0
  10Q LOSS WILD-TYPE  6 48 56 33
D55V5, multiclass
                    vv
clus                 N0 N1 N2 N3
  10Q LOSS MUTATED    4  4  0  1
  10Q LOSS WILD-TYPE 46 53 24 18
D55V6, multiclass
                    vv
clus                  M0  M1  MX
  10Q LOSS MUTATED     9   0   0
  10Q LOSS WILD-TYPE 123  18  11
D55V7, multiclass
                    vv
clus                  I II III IV
  10Q LOSS MUTATED    3  3   2  0
  10Q LOSS WILD-TYPE 22 40  46 29
D55V8, multiclass
D55V9, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED      1    8
  10Q LOSS WILD-TYPE    4  148
     clus
vv    10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  NO                 1                  4
  YES                8                148

Clustering(56) Variable = 11p loss mutation analysis
D56V1, survival
                    sevent
clus2                  0   1
  11P LOSS MUTATED     7   3
  11P LOSS WILD-TYPE 101  13
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                10                114 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                 3                 13 
$`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-BR-7958 TCGA-BR-7959 TCGA-BR-8059 TCGA-BR-8060 
        0.95         0.69         0.16         1.08         0.82         1.32 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
        0.69         0.95         0.49         0.46         0.72         0.26 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
        0.43         0.26         1.18         1.55         1.48         0.76 
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-4438 
       27.02        15.95         1.02        52.96         8.05        54.05 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
        4.01        14.01        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-5716 
        8.98        18.94         7.07        12.00         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-5732 
       70.06        15.02        28.96        31.04        65.10        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-D7-6520 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-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
        4.14         1.68         4.70         4.04         2.93         4.27 
TCGA-EQ-8122 TCGA-F1-6177 TCGA-F1-6874 TCGA-F1-6875 TCGA-FP-7735 TCGA-FP-7829 
        7.79         6.54         2.01        72.23         0.39         0.20 
TCGA-FP-7916 TCGA-FP-7998 TCGA-HJ-7597 TCGA-IN-7806 TCGA-IN-7808 TCGA-IP-7968 
        3.02         3.58        26.43         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               1.48 
[1] "0.3 - 30.0 (3.8)" "0.1 - 72.2 (1.5)"
        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-BR-7958 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BR-7959         TCGA-BR-8059         TCGA-BR-8060 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BR-8077         TCGA-BR-8078         TCGA-BR-8080 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BR-8081         TCGA-BR-8284         TCGA-BR-8285 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BR-8286         TCGA-BR-8289         TCGA-BR-8291 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BR-8295         TCGA-BR-8296         TCGA-BR-8297 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-CD-5798         TCGA-CD-5799         TCGA-CD-5800 
"11P LOSS WILD-TYPE"   "11P LOSS MUTATED" "11P LOSS WILD-TYPE" 
        TCGA-CD-5801         TCGA-CD-5802         TCGA-CD-5803 
"11P LOSS WILD-TYPE"   "11P LOSS MUTATED" "11P LOSS WILD-TYPE" 
        TCGA-CG-4300         TCGA-CG-4301         TCGA-CG-4304 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-CG-4305         TCGA-CG-4306         TCGA-CG-4436 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-CG-4437         TCGA-CG-4438         TCGA-CG-4440 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-CG-4441         TCGA-CG-4443         TCGA-CG-4444 
"11P LOSS WILD-TYPE"   "11P LOSS MUTATED" "11P LOSS WILD-TYPE" 
        TCGA-CG-4449         TCGA-CG-4455         TCGA-CG-4460 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE"   "11P LOSS MUTATED" 
        TCGA-CG-4462         TCGA-CG-4465         TCGA-CG-4466 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-CG-4469         TCGA-CG-4472         TCGA-CG-4474 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-CG-4477         TCGA-CG-5716         TCGA-CG-5717 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-CG-5718         TCGA-CG-5719         TCGA-CG-5720 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-CG-5721         TCGA-CG-5722         TCGA-CG-5723 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-CG-5724         TCGA-CG-5725         TCGA-CG-5726 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-CG-5727         TCGA-CG-5728         TCGA-CG-5730 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE"   "11P LOSS MUTATED" 
        TCGA-CG-5732         TCGA-CG-5733         TCGA-CG-5734 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-D7-5577         TCGA-D7-5578         TCGA-D7-5579 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-D7-6518         TCGA-D7-6519         TCGA-D7-6520 
"11P LOSS WILD-TYPE"   "11P LOSS MUTATED" "11P LOSS WILD-TYPE" 
        TCGA-D7-6521         TCGA-D7-6522         TCGA-D7-6524 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-D7-6525         TCGA-D7-6526         TCGA-D7-6527 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-D7-6528         TCGA-D7-6815         TCGA-D7-6817 
"11P LOSS WILD-TYPE"   "11P LOSS MUTATED" "11P LOSS WILD-TYPE" 
        TCGA-D7-6818         TCGA-D7-6820         TCGA-D7-6822 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-EQ-5647         TCGA-EQ-8122         TCGA-F1-6177 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-F1-6874         TCGA-F1-6875         TCGA-FP-7735 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-FP-7829         TCGA-FP-7916         TCGA-FP-7998 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-HJ-7597         TCGA-IN-7806         TCGA-IN-7808 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-IP-7968 
"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-BR-7958 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BR-7959         TCGA-BR-8059         TCGA-BR-8060 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BR-8077         TCGA-BR-8078         TCGA-BR-8080 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BR-8081         TCGA-BR-8284         TCGA-BR-8285 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BR-8286         TCGA-BR-8289         TCGA-BR-8291 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BR-8295         TCGA-BR-8296         TCGA-BR-8297 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-CD-5798         TCGA-CD-5799         TCGA-CD-5800 
"11P LOSS WILD-TYPE"   "11P LOSS MUTATED" "11P LOSS WILD-TYPE" 
        TCGA-CD-5801         TCGA-CD-5802         TCGA-CD-5803 
"11P LOSS WILD-TYPE"   "11P LOSS MUTATED" "11P LOSS WILD-TYPE" 
        TCGA-CG-4300         TCGA-CG-4301         TCGA-CG-4304 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-CG-4305         TCGA-CG-4306         TCGA-CG-4436 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-CG-4437         TCGA-CG-4438         TCGA-CG-4440 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-CG-4441         TCGA-CG-4443         TCGA-CG-4444 
"11P LOSS WILD-TYPE"   "11P LOSS MUTATED" "11P LOSS WILD-TYPE" 
        TCGA-CG-4449         TCGA-CG-4455         TCGA-CG-4460 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE"   "11P LOSS MUTATED" 
        TCGA-CG-4462         TCGA-CG-4465         TCGA-CG-4466 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-CG-4469         TCGA-CG-4472         TCGA-CG-4474 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-CG-4477         TCGA-CG-5716         TCGA-CG-5717 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-CG-5718         TCGA-CG-5719         TCGA-CG-5720 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-CG-5721         TCGA-CG-5722         TCGA-CG-5723 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-CG-5724         TCGA-CG-5725         TCGA-CG-5726 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-CG-5727         TCGA-CG-5728         TCGA-CG-5730 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE"   "11P LOSS MUTATED" 
        TCGA-CG-5732         TCGA-CG-5733         TCGA-CG-5734 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-D7-5577         TCGA-D7-5578         TCGA-D7-5579 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-D7-6518         TCGA-D7-6519         TCGA-D7-6520 
"11P LOSS WILD-TYPE"   "11P LOSS MUTATED" "11P LOSS WILD-TYPE" 
        TCGA-D7-6521         TCGA-D7-6522         TCGA-D7-6524 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-D7-6525         TCGA-D7-6526         TCGA-D7-6527 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-D7-6528         TCGA-D7-6815         TCGA-D7-6817 
"11P LOSS WILD-TYPE"   "11P LOSS MUTATED" "11P LOSS WILD-TYPE" 
        TCGA-D7-6818         TCGA-D7-6820         TCGA-D7-6822 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-EQ-5647         TCGA-EQ-8122         TCGA-F1-6177 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-F1-6874         TCGA-F1-6875         TCGA-FP-7735 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-FP-7829         TCGA-FP-7916         TCGA-FP-7998 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-HJ-7597         TCGA-IN-7806         TCGA-IN-7808 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-IP-7968 
"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-BR-7958 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BR-7959         TCGA-BR-8059         TCGA-BR-8060 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BR-8077         TCGA-BR-8078         TCGA-BR-8080 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BR-8081         TCGA-BR-8284         TCGA-BR-8285 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BR-8286         TCGA-BR-8289         TCGA-BR-8291 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BR-8295         TCGA-BR-8296         TCGA-BR-8297 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-CD-5798         TCGA-CD-5799         TCGA-CD-5800 
"11P LOSS WILD-TYPE"   "11P LOSS MUTATED" "11P LOSS WILD-TYPE" 
        TCGA-CD-5801         TCGA-CD-5802         TCGA-CD-5803 
"11P LOSS WILD-TYPE"   "11P LOSS MUTATED" "11P LOSS WILD-TYPE" 
        TCGA-CG-4300         TCGA-CG-4301         TCGA-CG-4304 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-CG-4305         TCGA-CG-4306         TCGA-CG-4436 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-CG-4437         TCGA-CG-4438         TCGA-CG-4440 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-CG-4441         TCGA-CG-4443         TCGA-CG-4444 
"11P LOSS WILD-TYPE"   "11P LOSS MUTATED" "11P LOSS WILD-TYPE" 
        TCGA-CG-4449         TCGA-CG-4455         TCGA-CG-4460 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE"   "11P LOSS MUTATED" 
        TCGA-CG-4462         TCGA-CG-4465         TCGA-CG-4466 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-CG-4469         TCGA-CG-4472         TCGA-CG-4474 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-CG-4477         TCGA-CG-5716         TCGA-CG-5717 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-CG-5718         TCGA-CG-5719         TCGA-CG-5720 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-CG-5721         TCGA-CG-5722         TCGA-CG-5723 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-CG-5724         TCGA-CG-5725         TCGA-CG-5726 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-CG-5727         TCGA-CG-5728         TCGA-CG-5730 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE"   "11P LOSS MUTATED" 
        TCGA-CG-5732         TCGA-CG-5733         TCGA-CG-5734 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-D7-5577         TCGA-D7-5578         TCGA-D7-5579 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-D7-6518         TCGA-D7-6519         TCGA-D7-6520 
"11P LOSS WILD-TYPE"   "11P LOSS MUTATED" "11P LOSS WILD-TYPE" 
        TCGA-D7-6521         TCGA-D7-6522         TCGA-D7-6524 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-D7-6525         TCGA-D7-6526         TCGA-D7-6527 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-D7-6528         TCGA-D7-6815         TCGA-D7-6817 
"11P LOSS WILD-TYPE"   "11P LOSS MUTATED" "11P LOSS WILD-TYPE" 
        TCGA-D7-6818         TCGA-D7-6820         TCGA-D7-6822 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-EQ-5647         TCGA-EQ-8122         TCGA-F1-6177 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-F1-6874         TCGA-F1-6875         TCGA-FP-7735 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-FP-7829         TCGA-FP-7916         TCGA-FP-7998 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-HJ-7597         TCGA-IN-7806         TCGA-IN-7808 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-IP-7968 
"11P LOSS WILD-TYPE" 
[1] "hr=" "1.8"
D56V2, continuous
D56V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED      6    6
  11P LOSS WILD-TYPE   59   90
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  FEMALE                6                 59
  MALE                  6                 90
                    vv
clus                 STOMACH ADENOCARCINOMA - DIFFUSE TYPE
  11P LOSS MUTATED                                       2
  11P LOSS WILD-TYPE                                    17
                    vv
clus                 STOMACH ADENOCARCINOMA - NOT OTHERWISE SPECIFIED (NOS)
  11P LOSS MUTATED                                                        3
  11P LOSS WILD-TYPE                                                     76
                    vv
clus                 STOMACH ADENOCARCINOMA - SIGNET RING TYPE
  11P LOSS MUTATED                                           0
  11P LOSS WILD-TYPE                                         1
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - MUCINOUS TYPE
  11P LOSS MUTATED                                                   0
  11P LOSS WILD-TYPE                                                 9
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - PAPILLARY TYPE
  11P LOSS MUTATED                                                    0
  11P LOSS WILD-TYPE                                                  3
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - TUBULAR TYPE
  11P LOSS MUTATED                                                  2
  11P LOSS WILD-TYPE                                                8
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - TYPE NOT OTHERWISE SPECIFIED (NOS)
  11P LOSS MUTATED                                                                        5
  11P LOSS WILD-TYPE                                                                     30
D56V4, multiclass
                    vv
clus                 T1 T2 T3 T4
  11P LOSS MUTATED    1  7  2  2
  11P LOSS WILD-TYPE  5 46 57 31
D56V5, multiclass
                    vv
clus                 N0 N1 N2 N3
  11P LOSS MUTATED    3  5  1  2
  11P LOSS WILD-TYPE 47 52 23 17
D56V6, multiclass
                    vv
clus                  M0  M1  MX
  11P LOSS MUTATED     8   4   0
  11P LOSS WILD-TYPE 124  14  11
D56V7, multiclass
                    vv
clus                  I II III IV
  11P LOSS MUTATED    2  3   2  4
  11P LOSS WILD-TYPE 23 40  46 25
D56V8, multiclass
D56V9, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED      0   12
  11P LOSS WILD-TYPE    5  144
     clus
vv    11P LOSS MUTATED 11P LOSS WILD-TYPE
  NO                 0                  5
  YES               12                144

Clustering(57) Variable = 11q loss mutation analysis
D57V1, survival
                    sevent
clus2                  0   1
  11Q LOSS MUTATED     5   2
  11Q LOSS WILD-TYPE 103  14
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                 7                117 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                 2                 14 
$`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-BR-7958 TCGA-BR-7959 TCGA-BR-8059 TCGA-BR-8060 
        0.95         0.69         0.16         1.08         0.82         1.32 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
        0.69         0.95         0.49         0.46         0.72         0.26 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
        0.43         0.26         1.18         1.55         1.48         0.76 
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-4438 TCGA-CG-4440 
       27.02        15.95         1.02        52.96        54.05         4.01 
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-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-5725 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 
        0.95        70.06        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-D7-6817 
        0.69         5.95         6.61         4.14         1.68         4.70 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-EQ-8122 TCGA-F1-6177 TCGA-F1-6874 
        4.04         2.93         4.27         7.79         6.54         2.01 
TCGA-F1-6875 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-HJ-7597 
       72.23         0.39         0.20         3.02         3.58        26.43 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IP-7968 
        6.87         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               1.48 
[1] "0.3 - 30.0 (3.6)" "0.1 - 72.2 (1.5)"
        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-BR-7958 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-BR-7959         TCGA-BR-8059         TCGA-BR-8060 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-BR-8077         TCGA-BR-8078         TCGA-BR-8080 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-BR-8081         TCGA-BR-8284         TCGA-BR-8285 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-BR-8286         TCGA-BR-8289         TCGA-BR-8291 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-BR-8295         TCGA-BR-8296         TCGA-BR-8297 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-CD-5798         TCGA-CD-5799         TCGA-CD-5800 
"11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" 
        TCGA-CD-5801         TCGA-CD-5802         TCGA-CD-5803 
"11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" 
        TCGA-CG-4300         TCGA-CG-4301         TCGA-CG-4304 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-CG-4305         TCGA-CG-4306         TCGA-CG-4436 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-CG-4437         TCGA-CG-4438         TCGA-CG-4440 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-CG-4441         TCGA-CG-4443         TCGA-CG-4444 
"11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" 
        TCGA-CG-4449         TCGA-CG-4455         TCGA-CG-4460 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-CG-4462         TCGA-CG-4465         TCGA-CG-4466 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-CG-4469         TCGA-CG-4472         TCGA-CG-4474 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-CG-4477         TCGA-CG-5716         TCGA-CG-5717 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-CG-5718         TCGA-CG-5719         TCGA-CG-5720 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-CG-5721         TCGA-CG-5722         TCGA-CG-5723 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-CG-5724         TCGA-CG-5725         TCGA-CG-5726 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-CG-5727         TCGA-CG-5728         TCGA-CG-5730 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-CG-5732         TCGA-CG-5733         TCGA-CG-5734 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-D7-5577         TCGA-D7-5578         TCGA-D7-5579 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-D7-6518         TCGA-D7-6519         TCGA-D7-6520 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-D7-6521         TCGA-D7-6522         TCGA-D7-6524 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-D7-6525         TCGA-D7-6526         TCGA-D7-6527 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-D7-6528         TCGA-D7-6815         TCGA-D7-6817 
"11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" 
        TCGA-D7-6818         TCGA-D7-6820         TCGA-D7-6822 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-EQ-5647         TCGA-EQ-8122         TCGA-F1-6177 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-F1-6874         TCGA-F1-6875         TCGA-FP-7735 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-FP-7829         TCGA-FP-7916         TCGA-FP-7998 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-HJ-7597         TCGA-IN-7806         TCGA-IN-7808 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-IP-7968 
"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-BR-7958 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-BR-7959         TCGA-BR-8059         TCGA-BR-8060 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-BR-8077         TCGA-BR-8078         TCGA-BR-8080 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-BR-8081         TCGA-BR-8284         TCGA-BR-8285 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-BR-8286         TCGA-BR-8289         TCGA-BR-8291 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-BR-8295         TCGA-BR-8296         TCGA-BR-8297 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-CD-5798         TCGA-CD-5799         TCGA-CD-5800 
"11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" 
        TCGA-CD-5801         TCGA-CD-5802         TCGA-CD-5803 
"11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" 
        TCGA-CG-4300         TCGA-CG-4301         TCGA-CG-4304 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-CG-4305         TCGA-CG-4306         TCGA-CG-4436 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-CG-4437         TCGA-CG-4438         TCGA-CG-4440 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-CG-4441         TCGA-CG-4443         TCGA-CG-4444 
"11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" 
        TCGA-CG-4449         TCGA-CG-4455         TCGA-CG-4460 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-CG-4462         TCGA-CG-4465         TCGA-CG-4466 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-CG-4469         TCGA-CG-4472         TCGA-CG-4474 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-CG-4477         TCGA-CG-5716         TCGA-CG-5717 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-CG-5718         TCGA-CG-5719         TCGA-CG-5720 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-CG-5721         TCGA-CG-5722         TCGA-CG-5723 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-CG-5724         TCGA-CG-5725         TCGA-CG-5726 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-CG-5727         TCGA-CG-5728         TCGA-CG-5730 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-CG-5732         TCGA-CG-5733         TCGA-CG-5734 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-D7-5577         TCGA-D7-5578         TCGA-D7-5579 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-D7-6518         TCGA-D7-6519         TCGA-D7-6520 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-D7-6521         TCGA-D7-6522         TCGA-D7-6524 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-D7-6525         TCGA-D7-6526         TCGA-D7-6527 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-D7-6528         TCGA-D7-6815         TCGA-D7-6817 
"11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" 
        TCGA-D7-6818         TCGA-D7-6820         TCGA-D7-6822 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-EQ-5647         TCGA-EQ-8122         TCGA-F1-6177 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-F1-6874         TCGA-F1-6875         TCGA-FP-7735 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-FP-7829         TCGA-FP-7916         TCGA-FP-7998 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-HJ-7597         TCGA-IN-7806         TCGA-IN-7808 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-IP-7968 
"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-BR-7958 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-BR-7959         TCGA-BR-8059         TCGA-BR-8060 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-BR-8077         TCGA-BR-8078         TCGA-BR-8080 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-BR-8081         TCGA-BR-8284         TCGA-BR-8285 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-BR-8286         TCGA-BR-8289         TCGA-BR-8291 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-BR-8295         TCGA-BR-8296         TCGA-BR-8297 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-CD-5798         TCGA-CD-5799         TCGA-CD-5800 
"11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" 
        TCGA-CD-5801         TCGA-CD-5802         TCGA-CD-5803 
"11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" 
        TCGA-CG-4300         TCGA-CG-4301         TCGA-CG-4304 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-CG-4305         TCGA-CG-4306         TCGA-CG-4436 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-CG-4437         TCGA-CG-4438         TCGA-CG-4440 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-CG-4441         TCGA-CG-4443         TCGA-CG-4444 
"11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" 
        TCGA-CG-4449         TCGA-CG-4455         TCGA-CG-4460 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-CG-4462         TCGA-CG-4465         TCGA-CG-4466 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-CG-4469         TCGA-CG-4472         TCGA-CG-4474 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-CG-4477         TCGA-CG-5716         TCGA-CG-5717 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-CG-5718         TCGA-CG-5719         TCGA-CG-5720 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-CG-5721         TCGA-CG-5722         TCGA-CG-5723 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-CG-5724         TCGA-CG-5725         TCGA-CG-5726 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-CG-5727         TCGA-CG-5728         TCGA-CG-5730 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-CG-5732         TCGA-CG-5733         TCGA-CG-5734 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-D7-5577         TCGA-D7-5578         TCGA-D7-5579 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-D7-6518         TCGA-D7-6519         TCGA-D7-6520 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-D7-6521         TCGA-D7-6522         TCGA-D7-6524 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-D7-6525         TCGA-D7-6526         TCGA-D7-6527 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-D7-6528         TCGA-D7-6815         TCGA-D7-6817 
"11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" 
        TCGA-D7-6818         TCGA-D7-6820         TCGA-D7-6822 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-EQ-5647         TCGA-EQ-8122         TCGA-F1-6177 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-F1-6874         TCGA-F1-6875         TCGA-FP-7735 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-FP-7829         TCGA-FP-7916         TCGA-FP-7998 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-HJ-7597         TCGA-IN-7806         TCGA-IN-7808 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-IP-7968 
"11Q LOSS WILD-TYPE" 
[1] "hr=" "2"  
D57V2, continuous
D57V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED      2    7
  11Q LOSS WILD-TYPE   63   89
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  FEMALE                2                 63
  MALE                  7                 89
                    vv
clus                 STOMACH ADENOCARCINOMA - DIFFUSE TYPE
  11Q LOSS MUTATED                                       1
  11Q LOSS WILD-TYPE                                    18
                    vv
clus                 STOMACH ADENOCARCINOMA - NOT OTHERWISE SPECIFIED (NOS)
  11Q LOSS MUTATED                                                        3
  11Q LOSS WILD-TYPE                                                     76
                    vv
clus                 STOMACH ADENOCARCINOMA - SIGNET RING TYPE
  11Q LOSS MUTATED                                           0
  11Q LOSS WILD-TYPE                                         1
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - MUCINOUS TYPE
  11Q LOSS MUTATED                                                   0
  11Q LOSS WILD-TYPE                                                 9
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - PAPILLARY TYPE
  11Q LOSS MUTATED                                                    0
  11Q LOSS WILD-TYPE                                                  3
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - TUBULAR TYPE
  11Q LOSS MUTATED                                                  2
  11Q LOSS WILD-TYPE                                                8
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - TYPE NOT OTHERWISE SPECIFIED (NOS)
  11Q LOSS MUTATED                                                                        3
  11Q LOSS WILD-TYPE                                                                     32
D57V4, multiclass
                    vv
clus                 T1 T2 T3 T4
  11Q LOSS MUTATED    1  5  2  1
  11Q LOSS WILD-TYPE  5 48 57 32
D57V5, multiclass
                    vv
clus                 N0 N1 N2 N3
  11Q LOSS MUTATED    2  3  1  2
  11Q LOSS WILD-TYPE 48 54 23 17
D57V6, multiclass
                    vv
clus                  M0  M1  MX
  11Q LOSS MUTATED     7   2   0
  11Q LOSS WILD-TYPE 125  16  11
D57V7, multiclass
                    vv
clus                  I II III IV
  11Q LOSS MUTATED    1  4   1  2
  11Q LOSS WILD-TYPE 24 39  47 27
D57V8, multiclass
D57V9, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED      0    9
  11Q LOSS WILD-TYPE    5  147
     clus
vv    11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  NO                 0                  5
  YES                9                147

Clustering(58) Variable = 12p loss mutation analysis
D58V1, survival
                    sevent
clus2                  0   1
  12P LOSS MUTATED     8   2
  12P LOSS WILD-TYPE 100  14
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                10                114 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                 2                 14 
$`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-BR-7958 TCGA-BR-7959 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
        0.69         0.16         1.08         0.82         1.32         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
        0.95         0.49         0.46         0.72         0.26         0.43 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-CD-5798 
        0.26         1.18         1.55         1.48         0.76         0.82 
TCGA-CD-5799 TCGA-CD-5801 TCGA-CD-5803 TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
        0.69         0.49         0.07        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
       15.95         1.02         8.05        54.05         4.01        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-4466 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4474 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-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-D7-6520 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-EQ-5647 TCGA-EQ-8122 TCGA-F1-6177 TCGA-F1-6874 TCGA-FP-7735 TCGA-FP-7829 
        0.62         7.79         6.54         2.01         0.39         0.20 
TCGA-FP-7916 TCGA-FP-7998 TCGA-HJ-7597 TCGA-IN-7806 TCGA-IN-7808 TCGA-IP-7968 
        3.02         3.58        26.43         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              1.480 
[1] "0.3 - 72.2 (9.6)" "0.1 - 70.1 (1.5)"
        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-BR-7958 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-BR-7959         TCGA-BR-8059         TCGA-BR-8060 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-BR-8077         TCGA-BR-8078         TCGA-BR-8080 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-BR-8081         TCGA-BR-8284         TCGA-BR-8285 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-BR-8286         TCGA-BR-8289         TCGA-BR-8291 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-BR-8295         TCGA-BR-8296         TCGA-BR-8297 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-CD-5798         TCGA-CD-5799         TCGA-CD-5800 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE"   "12P LOSS MUTATED" 
        TCGA-CD-5801         TCGA-CD-5802         TCGA-CD-5803 
"12P LOSS WILD-TYPE"   "12P LOSS MUTATED" "12P LOSS WILD-TYPE" 
        TCGA-CG-4300         TCGA-CG-4301         TCGA-CG-4304 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-CG-4305         TCGA-CG-4306         TCGA-CG-4436 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE"   "12P LOSS MUTATED" 
        TCGA-CG-4437         TCGA-CG-4438         TCGA-CG-4440 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-CG-4441         TCGA-CG-4443         TCGA-CG-4444 
"12P LOSS WILD-TYPE"   "12P LOSS MUTATED" "12P LOSS WILD-TYPE" 
        TCGA-CG-4449         TCGA-CG-4455         TCGA-CG-4460 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-CG-4462         TCGA-CG-4465         TCGA-CG-4466 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-CG-4469         TCGA-CG-4472         TCGA-CG-4474 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-CG-4477         TCGA-CG-5716         TCGA-CG-5717 
  "12P LOSS MUTATED" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-CG-5718         TCGA-CG-5719         TCGA-CG-5720 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-CG-5721         TCGA-CG-5722         TCGA-CG-5723 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-CG-5724         TCGA-CG-5725         TCGA-CG-5726 
"12P LOSS WILD-TYPE"   "12P LOSS MUTATED" "12P LOSS WILD-TYPE" 
        TCGA-CG-5727         TCGA-CG-5728         TCGA-CG-5730 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-CG-5732         TCGA-CG-5733         TCGA-CG-5734 
  "12P LOSS MUTATED" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-D7-5577         TCGA-D7-5578         TCGA-D7-5579 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-D7-6518         TCGA-D7-6519         TCGA-D7-6520 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-D7-6521         TCGA-D7-6522         TCGA-D7-6524 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-D7-6525         TCGA-D7-6526         TCGA-D7-6527 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-D7-6528         TCGA-D7-6815         TCGA-D7-6817 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-D7-6818         TCGA-D7-6820         TCGA-D7-6822 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE"   "12P LOSS MUTATED" 
        TCGA-EQ-5647         TCGA-EQ-8122         TCGA-F1-6177 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-F1-6874         TCGA-F1-6875         TCGA-FP-7735 
"12P LOSS WILD-TYPE"   "12P LOSS MUTATED" "12P LOSS WILD-TYPE" 
        TCGA-FP-7829         TCGA-FP-7916         TCGA-FP-7998 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-HJ-7597         TCGA-IN-7806         TCGA-IN-7808 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-IP-7968 
"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-BR-7958 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-BR-7959         TCGA-BR-8059         TCGA-BR-8060 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-BR-8077         TCGA-BR-8078         TCGA-BR-8080 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-BR-8081         TCGA-BR-8284         TCGA-BR-8285 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-BR-8286         TCGA-BR-8289         TCGA-BR-8291 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-BR-8295         TCGA-BR-8296         TCGA-BR-8297 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-CD-5798         TCGA-CD-5799         TCGA-CD-5800 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE"   "12P LOSS MUTATED" 
        TCGA-CD-5801         TCGA-CD-5802         TCGA-CD-5803 
"12P LOSS WILD-TYPE"   "12P LOSS MUTATED" "12P LOSS WILD-TYPE" 
        TCGA-CG-4300         TCGA-CG-4301         TCGA-CG-4304 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-CG-4305         TCGA-CG-4306         TCGA-CG-4436 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE"   "12P LOSS MUTATED" 
        TCGA-CG-4437         TCGA-CG-4438         TCGA-CG-4440 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-CG-4441         TCGA-CG-4443         TCGA-CG-4444 
"12P LOSS WILD-TYPE"   "12P LOSS MUTATED" "12P LOSS WILD-TYPE" 
        TCGA-CG-4449         TCGA-CG-4455         TCGA-CG-4460 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-CG-4462         TCGA-CG-4465         TCGA-CG-4466 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-CG-4469         TCGA-CG-4472         TCGA-CG-4474 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-CG-4477         TCGA-CG-5716         TCGA-CG-5717 
  "12P LOSS MUTATED" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-CG-5718         TCGA-CG-5719         TCGA-CG-5720 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-CG-5721         TCGA-CG-5722         TCGA-CG-5723 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-CG-5724         TCGA-CG-5725         TCGA-CG-5726 
"12P LOSS WILD-TYPE"   "12P LOSS MUTATED" "12P LOSS WILD-TYPE" 
        TCGA-CG-5727         TCGA-CG-5728         TCGA-CG-5730 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-CG-5732         TCGA-CG-5733         TCGA-CG-5734 
  "12P LOSS MUTATED" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-D7-5577         TCGA-D7-5578         TCGA-D7-5579 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-D7-6518         TCGA-D7-6519         TCGA-D7-6520 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-D7-6521         TCGA-D7-6522         TCGA-D7-6524 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-D7-6525         TCGA-D7-6526         TCGA-D7-6527 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-D7-6528         TCGA-D7-6815         TCGA-D7-6817 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-D7-6818         TCGA-D7-6820         TCGA-D7-6822 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE"   "12P LOSS MUTATED" 
        TCGA-EQ-5647         TCGA-EQ-8122         TCGA-F1-6177 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-F1-6874         TCGA-F1-6875         TCGA-FP-7735 
"12P LOSS WILD-TYPE"   "12P LOSS MUTATED" "12P LOSS WILD-TYPE" 
        TCGA-FP-7829         TCGA-FP-7916         TCGA-FP-7998 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-HJ-7597         TCGA-IN-7806         TCGA-IN-7808 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-IP-7968 
"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-BR-7958 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-BR-7959         TCGA-BR-8059         TCGA-BR-8060 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-BR-8077         TCGA-BR-8078         TCGA-BR-8080 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-BR-8081         TCGA-BR-8284         TCGA-BR-8285 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-BR-8286         TCGA-BR-8289         TCGA-BR-8291 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-BR-8295         TCGA-BR-8296         TCGA-BR-8297 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-CD-5798         TCGA-CD-5799         TCGA-CD-5800 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE"   "12P LOSS MUTATED" 
        TCGA-CD-5801         TCGA-CD-5802         TCGA-CD-5803 
"12P LOSS WILD-TYPE"   "12P LOSS MUTATED" "12P LOSS WILD-TYPE" 
        TCGA-CG-4300         TCGA-CG-4301         TCGA-CG-4304 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-CG-4305         TCGA-CG-4306         TCGA-CG-4436 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE"   "12P LOSS MUTATED" 
        TCGA-CG-4437         TCGA-CG-4438         TCGA-CG-4440 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-CG-4441         TCGA-CG-4443         TCGA-CG-4444 
"12P LOSS WILD-TYPE"   "12P LOSS MUTATED" "12P LOSS WILD-TYPE" 
        TCGA-CG-4449         TCGA-CG-4455         TCGA-CG-4460 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-CG-4462         TCGA-CG-4465         TCGA-CG-4466 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-CG-4469         TCGA-CG-4472         TCGA-CG-4474 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-CG-4477         TCGA-CG-5716         TCGA-CG-5717 
  "12P LOSS MUTATED" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-CG-5718         TCGA-CG-5719         TCGA-CG-5720 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-CG-5721         TCGA-CG-5722         TCGA-CG-5723 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-CG-5724         TCGA-CG-5725         TCGA-CG-5726 
"12P LOSS WILD-TYPE"   "12P LOSS MUTATED" "12P LOSS WILD-TYPE" 
        TCGA-CG-5727         TCGA-CG-5728         TCGA-CG-5730 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-CG-5732         TCGA-CG-5733         TCGA-CG-5734 
  "12P LOSS MUTATED" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-D7-5577         TCGA-D7-5578         TCGA-D7-5579 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-D7-6518         TCGA-D7-6519         TCGA-D7-6520 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-D7-6521         TCGA-D7-6522         TCGA-D7-6524 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-D7-6525         TCGA-D7-6526         TCGA-D7-6527 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-D7-6528         TCGA-D7-6815         TCGA-D7-6817 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-D7-6818         TCGA-D7-6820         TCGA-D7-6822 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE"   "12P LOSS MUTATED" 
        TCGA-EQ-5647         TCGA-EQ-8122         TCGA-F1-6177 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-F1-6874         TCGA-F1-6875         TCGA-FP-7735 
"12P LOSS WILD-TYPE"   "12P LOSS MUTATED" "12P LOSS WILD-TYPE" 
        TCGA-FP-7829         TCGA-FP-7916         TCGA-FP-7998 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-HJ-7597         TCGA-IN-7806         TCGA-IN-7808 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-IP-7968 
"12P LOSS WILD-TYPE" 
[1] "hr=" "3.8"
D58V2, continuous
D58V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED      3    8
  12P LOSS WILD-TYPE   62   88
        clus
vv       12P LOSS MUTATED 12P LOSS WILD-TYPE
  FEMALE                3                 62
  MALE                  8                 88
                    vv
clus                 STOMACH ADENOCARCINOMA - DIFFUSE TYPE
  12P LOSS MUTATED                                       0
  12P LOSS WILD-TYPE                                    19
                    vv
clus                 STOMACH ADENOCARCINOMA - NOT OTHERWISE SPECIFIED (NOS)
  12P LOSS MUTATED                                                        5
  12P LOSS WILD-TYPE                                                     74
                    vv
clus                 STOMACH ADENOCARCINOMA - SIGNET RING TYPE
  12P LOSS MUTATED                                           0
  12P LOSS WILD-TYPE                                         1
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - MUCINOUS TYPE
  12P LOSS MUTATED                                                   0
  12P LOSS WILD-TYPE                                                 9
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - PAPILLARY TYPE
  12P LOSS MUTATED                                                    1
  12P LOSS WILD-TYPE                                                  2
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - TUBULAR TYPE
  12P LOSS MUTATED                                                  1
  12P LOSS WILD-TYPE                                                9
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - TYPE NOT OTHERWISE SPECIFIED (NOS)
  12P LOSS MUTATED                                                                        4
  12P LOSS WILD-TYPE                                                                     31
D58V4, multiclass
                    vv
clus                 T1 T2 T3 T4
  12P LOSS MUTATED    1  7  3  0
  12P LOSS WILD-TYPE  5 46 56 33
D58V5, multiclass
                    vv
clus                 N0 N1 N2 N3
  12P LOSS MUTATED   10  0  0  1
  12P LOSS WILD-TYPE 40 57 24 18
D58V6, multiclass
                    vv
clus                  M0  M1  MX
  12P LOSS MUTATED    10   0   1
  12P LOSS WILD-TYPE 122  18  10
D58V7, multiclass
                    vv
clus                  I II III IV
  12P LOSS MUTATED    7  3   0  1
  12P LOSS WILD-TYPE 18 40  48 28
D58V8, multiclass
D58V9, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED      1   10
  12P LOSS WILD-TYPE    4  146
     clus
vv    12P LOSS MUTATED 12P LOSS WILD-TYPE
  NO                 1                  4
  YES               10                146

Clustering(59) Variable = 12q loss mutation analysis
D59V1, survival
                    sevent
clus2                  0   1
  12Q LOSS MUTATED     5   1
  12Q LOSS WILD-TYPE 103  15
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                 6                118 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                 1                 15 
$`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-BR-7958 TCGA-BR-7959 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
        0.69         0.16         1.08         0.82         1.32         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
        0.95         0.49         0.46         0.72         0.26         0.43 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-CD-5798 
        0.26         1.18         1.55         1.48         0.76         0.82 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5803 TCGA-CG-4300 TCGA-CG-4301 
        0.69         0.36         0.49         0.07        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       27.02        15.95         1.02         8.05        54.05         4.01 
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-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-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-D7-6822 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6177 
        4.04         2.93         4.27         0.62         7.79         6.54 
TCGA-F1-6874 TCGA-F1-6875 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
        2.01        72.23         0.39         0.20         3.02         3.58 
TCGA-HJ-7597 TCGA-IN-7806 TCGA-IN-7808 TCGA-IP-7968 
       26.43         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               1.48 
[1] "0.3 - 55.0 (22.5)" "0.1 - 72.2 (1.5)" 
        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-BR-7958 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-BR-7959         TCGA-BR-8059         TCGA-BR-8060 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-BR-8077         TCGA-BR-8078         TCGA-BR-8080 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-BR-8081         TCGA-BR-8284         TCGA-BR-8285 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-BR-8286         TCGA-BR-8289         TCGA-BR-8291 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-BR-8295         TCGA-BR-8296         TCGA-BR-8297 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-CD-5798         TCGA-CD-5799         TCGA-CD-5800 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-CD-5801         TCGA-CD-5802         TCGA-CD-5803 
"12Q LOSS WILD-TYPE"   "12Q LOSS MUTATED" "12Q LOSS WILD-TYPE" 
        TCGA-CG-4300         TCGA-CG-4301         TCGA-CG-4304 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-CG-4305         TCGA-CG-4306         TCGA-CG-4436 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE"   "12Q LOSS MUTATED" 
        TCGA-CG-4437         TCGA-CG-4438         TCGA-CG-4440 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-CG-4441         TCGA-CG-4443         TCGA-CG-4444 
"12Q LOSS WILD-TYPE"   "12Q LOSS MUTATED" "12Q LOSS WILD-TYPE" 
        TCGA-CG-4449         TCGA-CG-4455         TCGA-CG-4460 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-CG-4462         TCGA-CG-4465         TCGA-CG-4466 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-CG-4469         TCGA-CG-4472         TCGA-CG-4474 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-CG-4477         TCGA-CG-5716         TCGA-CG-5717 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-CG-5718         TCGA-CG-5719         TCGA-CG-5720 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-CG-5721         TCGA-CG-5722         TCGA-CG-5723 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-CG-5724         TCGA-CG-5725         TCGA-CG-5726 
"12Q LOSS WILD-TYPE"   "12Q LOSS MUTATED" "12Q LOSS WILD-TYPE" 
        TCGA-CG-5727         TCGA-CG-5728         TCGA-CG-5730 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-CG-5732         TCGA-CG-5733         TCGA-CG-5734 
  "12Q LOSS MUTATED" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-D7-5577         TCGA-D7-5578         TCGA-D7-5579 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-D7-6518         TCGA-D7-6519         TCGA-D7-6520 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-D7-6521         TCGA-D7-6522         TCGA-D7-6524 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-D7-6525         TCGA-D7-6526         TCGA-D7-6527 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-D7-6528         TCGA-D7-6815         TCGA-D7-6817 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-D7-6818         TCGA-D7-6820         TCGA-D7-6822 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-EQ-5647         TCGA-EQ-8122         TCGA-F1-6177 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-F1-6874         TCGA-F1-6875         TCGA-FP-7735 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-FP-7829         TCGA-FP-7916         TCGA-FP-7998 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-HJ-7597         TCGA-IN-7806         TCGA-IN-7808 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-IP-7968 
"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-BR-7958 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-BR-7959         TCGA-BR-8059         TCGA-BR-8060 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-BR-8077         TCGA-BR-8078         TCGA-BR-8080 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-BR-8081         TCGA-BR-8284         TCGA-BR-8285 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-BR-8286         TCGA-BR-8289         TCGA-BR-8291 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-BR-8295         TCGA-BR-8296         TCGA-BR-8297 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-CD-5798         TCGA-CD-5799         TCGA-CD-5800 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-CD-5801         TCGA-CD-5802         TCGA-CD-5803 
"12Q LOSS WILD-TYPE"   "12Q LOSS MUTATED" "12Q LOSS WILD-TYPE" 
        TCGA-CG-4300         TCGA-CG-4301         TCGA-CG-4304 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-CG-4305         TCGA-CG-4306         TCGA-CG-4436 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE"   "12Q LOSS MUTATED" 
        TCGA-CG-4437         TCGA-CG-4438         TCGA-CG-4440 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-CG-4441         TCGA-CG-4443         TCGA-CG-4444 
"12Q LOSS WILD-TYPE"   "12Q LOSS MUTATED" "12Q LOSS WILD-TYPE" 
        TCGA-CG-4449         TCGA-CG-4455         TCGA-CG-4460 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-CG-4462         TCGA-CG-4465         TCGA-CG-4466 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-CG-4469         TCGA-CG-4472         TCGA-CG-4474 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-CG-4477         TCGA-CG-5716         TCGA-CG-5717 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-CG-5718         TCGA-CG-5719         TCGA-CG-5720 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-CG-5721         TCGA-CG-5722         TCGA-CG-5723 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-CG-5724         TCGA-CG-5725         TCGA-CG-5726 
"12Q LOSS WILD-TYPE"   "12Q LOSS MUTATED" "12Q LOSS WILD-TYPE" 
        TCGA-CG-5727         TCGA-CG-5728         TCGA-CG-5730 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-CG-5732         TCGA-CG-5733         TCGA-CG-5734 
  "12Q LOSS MUTATED" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-D7-5577         TCGA-D7-5578         TCGA-D7-5579 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-D7-6518         TCGA-D7-6519         TCGA-D7-6520 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-D7-6521         TCGA-D7-6522         TCGA-D7-6524 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-D7-6525         TCGA-D7-6526         TCGA-D7-6527 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-D7-6528         TCGA-D7-6815         TCGA-D7-6817 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-D7-6818         TCGA-D7-6820         TCGA-D7-6822 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-EQ-5647         TCGA-EQ-8122         TCGA-F1-6177 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-F1-6874         TCGA-F1-6875         TCGA-FP-7735 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-FP-7829         TCGA-FP-7916         TCGA-FP-7998 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-HJ-7597         TCGA-IN-7806         TCGA-IN-7808 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-IP-7968 
"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-BR-7958 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-BR-7959         TCGA-BR-8059         TCGA-BR-8060 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-BR-8077         TCGA-BR-8078         TCGA-BR-8080 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-BR-8081         TCGA-BR-8284         TCGA-BR-8285 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-BR-8286         TCGA-BR-8289         TCGA-BR-8291 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-BR-8295         TCGA-BR-8296         TCGA-BR-8297 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-CD-5798         TCGA-CD-5799         TCGA-CD-5800 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-CD-5801         TCGA-CD-5802         TCGA-CD-5803 
"12Q LOSS WILD-TYPE"   "12Q LOSS MUTATED" "12Q LOSS WILD-TYPE" 
        TCGA-CG-4300         TCGA-CG-4301         TCGA-CG-4304 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-CG-4305         TCGA-CG-4306         TCGA-CG-4436 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE"   "12Q LOSS MUTATED" 
        TCGA-CG-4437         TCGA-CG-4438         TCGA-CG-4440 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-CG-4441         TCGA-CG-4443         TCGA-CG-4444 
"12Q LOSS WILD-TYPE"   "12Q LOSS MUTATED" "12Q LOSS WILD-TYPE" 
        TCGA-CG-4449         TCGA-CG-4455         TCGA-CG-4460 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-CG-4462         TCGA-CG-4465         TCGA-CG-4466 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-CG-4469         TCGA-CG-4472         TCGA-CG-4474 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-CG-4477         TCGA-CG-5716         TCGA-CG-5717 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-CG-5718         TCGA-CG-5719         TCGA-CG-5720 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-CG-5721         TCGA-CG-5722         TCGA-CG-5723 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-CG-5724         TCGA-CG-5725         TCGA-CG-5726 
"12Q LOSS WILD-TYPE"   "12Q LOSS MUTATED" "12Q LOSS WILD-TYPE" 
        TCGA-CG-5727         TCGA-CG-5728         TCGA-CG-5730 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-CG-5732         TCGA-CG-5733         TCGA-CG-5734 
  "12Q LOSS MUTATED" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-D7-5577         TCGA-D7-5578         TCGA-D7-5579 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-D7-6518         TCGA-D7-6519         TCGA-D7-6520 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-D7-6521         TCGA-D7-6522         TCGA-D7-6524 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-D7-6525         TCGA-D7-6526         TCGA-D7-6527 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-D7-6528         TCGA-D7-6815         TCGA-D7-6817 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-D7-6818         TCGA-D7-6820         TCGA-D7-6822 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-EQ-5647         TCGA-EQ-8122         TCGA-F1-6177 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-F1-6874         TCGA-F1-6875         TCGA-FP-7735 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-FP-7829         TCGA-FP-7916         TCGA-FP-7998 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-HJ-7597         TCGA-IN-7806         TCGA-IN-7808 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-IP-7968 
"12Q LOSS WILD-TYPE" 
[1] "hr=" "2.6"
D59V2, continuous
D59V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED      0    6
  12Q LOSS WILD-TYPE   65   90
        clus
vv       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  FEMALE                0                 65
  MALE                  6                 90
                    vv
clus                 STOMACH ADENOCARCINOMA - DIFFUSE TYPE
  12Q LOSS MUTATED                                       0
  12Q LOSS WILD-TYPE                                    19
                    vv
clus                 STOMACH ADENOCARCINOMA - NOT OTHERWISE SPECIFIED (NOS)
  12Q LOSS MUTATED                                                        3
  12Q LOSS WILD-TYPE                                                     76
                    vv
clus                 STOMACH ADENOCARCINOMA - SIGNET RING TYPE
  12Q LOSS MUTATED                                           0
  12Q LOSS WILD-TYPE                                         1
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - MUCINOUS TYPE
  12Q LOSS MUTATED                                                   0
  12Q LOSS WILD-TYPE                                                 9
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - PAPILLARY TYPE
  12Q LOSS MUTATED                                                    0
  12Q LOSS WILD-TYPE                                                  3
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - TUBULAR TYPE
  12Q LOSS MUTATED                                                  0
  12Q LOSS WILD-TYPE                                               10
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - TYPE NOT OTHERWISE SPECIFIED (NOS)
  12Q LOSS MUTATED                                                                        3
  12Q LOSS WILD-TYPE                                                                     32
D59V4, multiclass
                    vv
clus                 T1 T2 T3 T4
  12Q LOSS MUTATED    1  3  2  0
  12Q LOSS WILD-TYPE  5 50 57 33
D59V5, multiclass
                    vv
clus                 N0 N1 N2 N3
  12Q LOSS MUTATED    5  0  0  1
  12Q LOSS WILD-TYPE 45 57 24 18
D59V6, multiclass
                    vv
clus                  M0  M1  MX
  12Q LOSS MUTATED     6   0   0
  12Q LOSS WILD-TYPE 126  18  11
D59V7, multiclass
                    vv
clus                  I II III IV
  12Q LOSS MUTATED    3  2   0  1
  12Q LOSS WILD-TYPE 22 41  48 28
D59V8, multiclass
D59V9, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED      0    6
  12Q LOSS WILD-TYPE    5  150
     clus
vv    12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  NO                 0                  5
  YES                6                150

Clustering(60) Variable = 13q loss mutation analysis
D60V1, survival
                    sevent
clus2                  0   1
  13Q LOSS MUTATED     2   0
  13Q LOSS WILD-TYPE 106  16
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                 2                122 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                 0                 16 
$`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-BR-7958 TCGA-BR-7959 TCGA-BR-8059 TCGA-BR-8060 
        0.95         0.69         0.16         1.08         0.82         1.32 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
        0.69         0.95         0.49         0.46         0.72         0.26 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
        0.43         0.26         1.18         1.55         1.48         0.76 
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-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-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6526 
       15.65         9.63         8.19         6.90         0.69         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-EQ-8122 TCGA-F1-6177 TCGA-F1-6874 TCGA-F1-6875 
        4.27         0.62         7.79         6.54         2.01        72.23 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-HJ-7597 TCGA-IN-7806 
        0.39         0.20         3.02         3.58        26.43         6.87 
TCGA-IN-7808 TCGA-IP-7968 
        3.55         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              1.480 
[1] "3.0 - 6.0 (4.5)"  "0.1 - 72.2 (1.5)"
        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-BR-7958 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BR-7959         TCGA-BR-8059         TCGA-BR-8060 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BR-8077         TCGA-BR-8078         TCGA-BR-8080 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BR-8081         TCGA-BR-8284         TCGA-BR-8285 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BR-8286         TCGA-BR-8289         TCGA-BR-8291 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BR-8295         TCGA-BR-8296         TCGA-BR-8297 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CD-5798         TCGA-CD-5799         TCGA-CD-5800 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CD-5801         TCGA-CD-5802         TCGA-CD-5803 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CG-4300         TCGA-CG-4301         TCGA-CG-4304 
"13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" 
        TCGA-CG-4305         TCGA-CG-4306         TCGA-CG-4436 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CG-4437         TCGA-CG-4438         TCGA-CG-4440 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CG-4441         TCGA-CG-4443         TCGA-CG-4444 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CG-4449         TCGA-CG-4455         TCGA-CG-4460 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CG-4462         TCGA-CG-4465         TCGA-CG-4466 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CG-4469         TCGA-CG-4472         TCGA-CG-4474 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CG-4477         TCGA-CG-5716         TCGA-CG-5717 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CG-5718         TCGA-CG-5719         TCGA-CG-5720 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CG-5721         TCGA-CG-5722         TCGA-CG-5723 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CG-5724         TCGA-CG-5725         TCGA-CG-5726 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CG-5727         TCGA-CG-5728         TCGA-CG-5730 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CG-5732         TCGA-CG-5733         TCGA-CG-5734 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-D7-5577         TCGA-D7-5578         TCGA-D7-5579 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-D7-6518         TCGA-D7-6519         TCGA-D7-6520 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-D7-6521         TCGA-D7-6522         TCGA-D7-6524 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-D7-6525         TCGA-D7-6526         TCGA-D7-6527 
  "13Q LOSS MUTATED" "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-EQ-8122         TCGA-F1-6177 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-F1-6874         TCGA-F1-6875         TCGA-FP-7735 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-FP-7829         TCGA-FP-7916         TCGA-FP-7998 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-HJ-7597         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" 
        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-BR-7958 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BR-7959         TCGA-BR-8059         TCGA-BR-8060 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BR-8077         TCGA-BR-8078         TCGA-BR-8080 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BR-8081         TCGA-BR-8284         TCGA-BR-8285 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BR-8286         TCGA-BR-8289         TCGA-BR-8291 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BR-8295         TCGA-BR-8296         TCGA-BR-8297 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CD-5798         TCGA-CD-5799         TCGA-CD-5800 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CD-5801         TCGA-CD-5802         TCGA-CD-5803 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CG-4300         TCGA-CG-4301         TCGA-CG-4304 
"13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" 
        TCGA-CG-4305         TCGA-CG-4306         TCGA-CG-4436 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CG-4437         TCGA-CG-4438         TCGA-CG-4440 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CG-4441         TCGA-CG-4443         TCGA-CG-4444 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CG-4449         TCGA-CG-4455         TCGA-CG-4460 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CG-4462         TCGA-CG-4465         TCGA-CG-4466 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CG-4469         TCGA-CG-4472         TCGA-CG-4474 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CG-4477         TCGA-CG-5716         TCGA-CG-5717 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CG-5718         TCGA-CG-5719         TCGA-CG-5720 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CG-5721         TCGA-CG-5722         TCGA-CG-5723 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CG-5724         TCGA-CG-5725         TCGA-CG-5726 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CG-5727         TCGA-CG-5728         TCGA-CG-5730 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CG-5732         TCGA-CG-5733         TCGA-CG-5734 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-D7-5577         TCGA-D7-5578         TCGA-D7-5579 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-D7-6518         TCGA-D7-6519         TCGA-D7-6520 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-D7-6521         TCGA-D7-6522         TCGA-D7-6524 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-D7-6525         TCGA-D7-6526         TCGA-D7-6527 
  "13Q LOSS MUTATED" "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-EQ-8122         TCGA-F1-6177 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-F1-6874         TCGA-F1-6875         TCGA-FP-7735 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-FP-7829         TCGA-FP-7916         TCGA-FP-7998 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-HJ-7597         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" 
        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-BR-7958 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BR-7959         TCGA-BR-8059         TCGA-BR-8060 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BR-8077         TCGA-BR-8078         TCGA-BR-8080 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BR-8081         TCGA-BR-8284         TCGA-BR-8285 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BR-8286         TCGA-BR-8289         TCGA-BR-8291 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BR-8295         TCGA-BR-8296         TCGA-BR-8297 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CD-5798         TCGA-CD-5799         TCGA-CD-5800 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CD-5801         TCGA-CD-5802         TCGA-CD-5803 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CG-4300         TCGA-CG-4301         TCGA-CG-4304 
"13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" 
        TCGA-CG-4305         TCGA-CG-4306         TCGA-CG-4436 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CG-4437         TCGA-CG-4438         TCGA-CG-4440 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CG-4441         TCGA-CG-4443         TCGA-CG-4444 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CG-4449         TCGA-CG-4455         TCGA-CG-4460 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CG-4462         TCGA-CG-4465         TCGA-CG-4466 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CG-4469         TCGA-CG-4472         TCGA-CG-4474 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CG-4477         TCGA-CG-5716         TCGA-CG-5717 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CG-5718         TCGA-CG-5719         TCGA-CG-5720 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CG-5721         TCGA-CG-5722         TCGA-CG-5723 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CG-5724         TCGA-CG-5725         TCGA-CG-5726 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CG-5727         TCGA-CG-5728         TCGA-CG-5730 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CG-5732         TCGA-CG-5733         TCGA-CG-5734 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-D7-5577         TCGA-D7-5578         TCGA-D7-5579 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-D7-6518         TCGA-D7-6519         TCGA-D7-6520 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-D7-6521         TCGA-D7-6522         TCGA-D7-6524 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-D7-6525         TCGA-D7-6526         TCGA-D7-6527 
  "13Q LOSS MUTATED" "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-EQ-8122         TCGA-F1-6177 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-F1-6874         TCGA-F1-6875         TCGA-FP-7735 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-FP-7829         TCGA-FP-7916         TCGA-FP-7998 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-HJ-7597         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" 
[1] "Remove cluster labels:" "13Q LOSS MUTATED"      
clus
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                 2                122 
        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-BR-7958 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BR-7959         TCGA-BR-8059         TCGA-BR-8060 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BR-8077         TCGA-BR-8078         TCGA-BR-8080 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BR-8081         TCGA-BR-8284         TCGA-BR-8285 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BR-8286         TCGA-BR-8289         TCGA-BR-8291 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BR-8295         TCGA-BR-8296         TCGA-BR-8297 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CD-5798         TCGA-CD-5799         TCGA-CD-5800 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CD-5801         TCGA-CD-5802         TCGA-CD-5803 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CG-4300         TCGA-CG-4304         TCGA-CG-4305 
"13Q LOSS WILD-TYPE" "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-D7-6526 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-D7-6527         TCGA-D7-6528         TCGA-D7-6815 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-D7-6817         TCGA-D7-6818         TCGA-D7-6820 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-D7-6822         TCGA-EQ-5647         TCGA-EQ-8122 
"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-7916 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-FP-7998         TCGA-HJ-7597         TCGA-IN-7806 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-IN-7808         TCGA-IP-7968 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
D60V2, continuous
D60V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED      2    3
  13Q LOSS WILD-TYPE   63   93
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  FEMALE                2                 63
  MALE                  3                 93
                    vv
clus                 STOMACH ADENOCARCINOMA - DIFFUSE TYPE
  13Q LOSS MUTATED                                       1
  13Q LOSS WILD-TYPE                                    18
                    vv
clus                 STOMACH ADENOCARCINOMA - NOT OTHERWISE SPECIFIED (NOS)
  13Q LOSS MUTATED                                                        1
  13Q LOSS WILD-TYPE                                                     78
                    vv
clus                 STOMACH ADENOCARCINOMA - SIGNET RING TYPE
  13Q LOSS MUTATED                                           0
  13Q LOSS WILD-TYPE                                         1
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - MUCINOUS TYPE
  13Q LOSS MUTATED                                                   1
  13Q LOSS WILD-TYPE                                                 8
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - PAPILLARY TYPE
  13Q LOSS MUTATED                                                    0
  13Q LOSS WILD-TYPE                                                  3
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - TUBULAR TYPE
  13Q LOSS MUTATED                                                  1
  13Q LOSS WILD-TYPE                                                9
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - TYPE NOT OTHERWISE SPECIFIED (NOS)
  13Q LOSS MUTATED                                                                        0
  13Q LOSS WILD-TYPE                                                                     35
D60V4, multiclass
                    vv
clus                 T1 T2 T3 T4
  13Q LOSS MUTATED    0  3  1  1
  13Q LOSS WILD-TYPE  6 50 58 32
D60V5, multiclass
                    vv
clus                 N0 N1 N2 N3
  13Q LOSS MUTATED    0  2  1  1
  13Q LOSS WILD-TYPE 50 55 23 18
D60V6, multiclass
                    vv
clus                  M0  M1  MX
  13Q LOSS MUTATED     4   1   0
  13Q LOSS WILD-TYPE 128  17  11
D60V7, multiclass
                    vv
clus                  I II III IV
  13Q LOSS MUTATED    0  1   1  2
  13Q LOSS WILD-TYPE 25 42  47 27
D60V8, multiclass
D60V9, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED      1    4
  13Q LOSS WILD-TYPE    4  152
     clus
vv    13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  NO                 1                  4
  YES                4                152

Clustering(61) Variable = 14q loss mutation analysis
D61V1, survival
                    sevent
clus2                  0   1
  14Q LOSS MUTATED     8   0
  14Q LOSS WILD-TYPE 100  16
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                 8                116 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                 0                 16 
$`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-EQ-8122 TCGA-IN-7806 
        7.79         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-BR-7958 TCGA-BR-7959 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 
        0.16         1.08         0.82         1.32         0.69         0.95 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
        0.49         0.46         0.72         0.26         0.43         0.26 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-CD-5798 TCGA-CD-5799 
        1.18         1.55         1.48         0.76         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-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-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
        3.58         4.54         9.80         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-7916 TCGA-FP-7998 TCGA-HJ-7597 
       72.23         0.39         0.20         3.02         3.58        26.43 
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 
              7.33               1.48 
[1] "1.0 - 54.0 (7.3)" "0.1 - 72.2 (1.5)"
        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-BR-7958 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-BR-7959         TCGA-BR-8059         TCGA-BR-8060 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-BR-8077         TCGA-BR-8078         TCGA-BR-8080 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-BR-8081         TCGA-BR-8284         TCGA-BR-8285 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-BR-8286         TCGA-BR-8289         TCGA-BR-8291 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-BR-8295         TCGA-BR-8296         TCGA-BR-8297 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-CD-5798         TCGA-CD-5799         TCGA-CD-5800 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-CD-5801         TCGA-CD-5802         TCGA-CD-5803 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-CG-4300         TCGA-CG-4301         TCGA-CG-4304 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-CG-4305         TCGA-CG-4306         TCGA-CG-4436 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-CG-4437         TCGA-CG-4438         TCGA-CG-4440 
"14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" 
        TCGA-CG-4441         TCGA-CG-4443         TCGA-CG-4444 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-CG-4449         TCGA-CG-4455         TCGA-CG-4460 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-CG-4462         TCGA-CG-4465         TCGA-CG-4466 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-CG-4469         TCGA-CG-4472         TCGA-CG-4474 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-CG-4477         TCGA-CG-5716         TCGA-CG-5717 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-CG-5718         TCGA-CG-5719         TCGA-CG-5720 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-CG-5721         TCGA-CG-5722         TCGA-CG-5723 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-CG-5724         TCGA-CG-5725         TCGA-CG-5726 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-CG-5727         TCGA-CG-5728         TCGA-CG-5730 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-CG-5732         TCGA-CG-5733         TCGA-CG-5734 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-D7-5577         TCGA-D7-5578         TCGA-D7-5579 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-D7-6518         TCGA-D7-6519         TCGA-D7-6520 
"14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED"   "14Q LOSS MUTATED" 
        TCGA-D7-6521         TCGA-D7-6522         TCGA-D7-6524 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-D7-6525         TCGA-D7-6526         TCGA-D7-6527 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-D7-6528         TCGA-D7-6815         TCGA-D7-6817 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-D7-6818         TCGA-D7-6820         TCGA-D7-6822 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-EQ-5647         TCGA-EQ-8122         TCGA-F1-6177 
"14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" 
        TCGA-F1-6874         TCGA-F1-6875         TCGA-FP-7735 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-FP-7829         TCGA-FP-7916         TCGA-FP-7998 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-HJ-7597         TCGA-IN-7806         TCGA-IN-7808 
"14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" 
        TCGA-IP-7968 
"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-BR-7958 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-BR-7959         TCGA-BR-8059         TCGA-BR-8060 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-BR-8077         TCGA-BR-8078         TCGA-BR-8080 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-BR-8081         TCGA-BR-8284         TCGA-BR-8285 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-BR-8286         TCGA-BR-8289         TCGA-BR-8291 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-BR-8295         TCGA-BR-8296         TCGA-BR-8297 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-CD-5798         TCGA-CD-5799         TCGA-CD-5800 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-CD-5801         TCGA-CD-5802         TCGA-CD-5803 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-CG-4300         TCGA-CG-4301         TCGA-CG-4304 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-CG-4305         TCGA-CG-4306         TCGA-CG-4436 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-CG-4437         TCGA-CG-4438         TCGA-CG-4440 
"14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" 
        TCGA-CG-4441         TCGA-CG-4443         TCGA-CG-4444 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-CG-4449         TCGA-CG-4455         TCGA-CG-4460 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-CG-4462         TCGA-CG-4465         TCGA-CG-4466 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-CG-4469         TCGA-CG-4472         TCGA-CG-4474 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-CG-4477         TCGA-CG-5716         TCGA-CG-5717 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-CG-5718         TCGA-CG-5719         TCGA-CG-5720 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-CG-5721         TCGA-CG-5722         TCGA-CG-5723 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-CG-5724         TCGA-CG-5725         TCGA-CG-5726 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-CG-5727         TCGA-CG-5728         TCGA-CG-5730 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-CG-5732         TCGA-CG-5733         TCGA-CG-5734 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-D7-5577         TCGA-D7-5578         TCGA-D7-5579 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-D7-6518         TCGA-D7-6519         TCGA-D7-6520 
"14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED"   "14Q LOSS MUTATED" 
        TCGA-D7-6521         TCGA-D7-6522         TCGA-D7-6524 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-D7-6525         TCGA-D7-6526         TCGA-D7-6527 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-D7-6528         TCGA-D7-6815         TCGA-D7-6817 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-D7-6818         TCGA-D7-6820         TCGA-D7-6822 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-EQ-5647         TCGA-EQ-8122         TCGA-F1-6177 
"14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" 
        TCGA-F1-6874         TCGA-F1-6875         TCGA-FP-7735 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-FP-7829         TCGA-FP-7916         TCGA-FP-7998 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-HJ-7597         TCGA-IN-7806         TCGA-IN-7808 
"14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" 
        TCGA-IP-7968 
"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-BR-7958 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-BR-7959         TCGA-BR-8059         TCGA-BR-8060 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-BR-8077         TCGA-BR-8078         TCGA-BR-8080 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-BR-8081         TCGA-BR-8284         TCGA-BR-8285 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-BR-8286         TCGA-BR-8289         TCGA-BR-8291 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-BR-8295         TCGA-BR-8296         TCGA-BR-8297 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-CD-5798         TCGA-CD-5799         TCGA-CD-5800 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-CD-5801         TCGA-CD-5802         TCGA-CD-5803 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-CG-4300         TCGA-CG-4301         TCGA-CG-4304 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-CG-4305         TCGA-CG-4306         TCGA-CG-4436 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-CG-4437         TCGA-CG-4438         TCGA-CG-4440 
"14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" 
        TCGA-CG-4441         TCGA-CG-4443         TCGA-CG-4444 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-CG-4449         TCGA-CG-4455         TCGA-CG-4460 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-CG-4462         TCGA-CG-4465         TCGA-CG-4466 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-CG-4469         TCGA-CG-4472         TCGA-CG-4474 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-CG-4477         TCGA-CG-5716         TCGA-CG-5717 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-CG-5718         TCGA-CG-5719         TCGA-CG-5720 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-CG-5721         TCGA-CG-5722         TCGA-CG-5723 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-CG-5724         TCGA-CG-5725         TCGA-CG-5726 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-CG-5727         TCGA-CG-5728         TCGA-CG-5730 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-CG-5732         TCGA-CG-5733         TCGA-CG-5734 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-D7-5577         TCGA-D7-5578         TCGA-D7-5579 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-D7-6518         TCGA-D7-6519         TCGA-D7-6520 
"14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED"   "14Q LOSS MUTATED" 
        TCGA-D7-6521         TCGA-D7-6522         TCGA-D7-6524 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-D7-6525         TCGA-D7-6526         TCGA-D7-6527 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-D7-6528         TCGA-D7-6815         TCGA-D7-6817 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-D7-6818         TCGA-D7-6820         TCGA-D7-6822 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-EQ-5647         TCGA-EQ-8122         TCGA-F1-6177 
"14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" 
        TCGA-F1-6874         TCGA-F1-6875         TCGA-FP-7735 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-FP-7829         TCGA-FP-7916         TCGA-FP-7998 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-HJ-7597         TCGA-IN-7806         TCGA-IN-7808 
"14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" 
        TCGA-IP-7968 
"14Q LOSS WILD-TYPE" 
[1] "hr="     "7.7e+07"
D61V2, continuous
D61V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED      4    6
  14Q LOSS WILD-TYPE   61   90
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  FEMALE                4                 61
  MALE                  6                 90
                    vv
clus                 STOMACH ADENOCARCINOMA - DIFFUSE TYPE
  14Q LOSS MUTATED                                       2
  14Q LOSS WILD-TYPE                                    17
                    vv
clus                 STOMACH ADENOCARCINOMA - NOT OTHERWISE SPECIFIED (NOS)
  14Q LOSS MUTATED                                                        4
  14Q LOSS WILD-TYPE                                                     75
                    vv
clus                 STOMACH ADENOCARCINOMA - SIGNET RING TYPE
  14Q LOSS MUTATED                                           0
  14Q LOSS WILD-TYPE                                         1
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - MUCINOUS TYPE
  14Q LOSS MUTATED                                                   0
  14Q LOSS WILD-TYPE                                                 9
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - PAPILLARY TYPE
  14Q LOSS MUTATED                                                    0
  14Q LOSS WILD-TYPE                                                  3
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - TUBULAR TYPE
  14Q LOSS MUTATED                                                  1
  14Q LOSS WILD-TYPE                                                9
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - TYPE NOT OTHERWISE SPECIFIED (NOS)
  14Q LOSS MUTATED                                                                        3
  14Q LOSS WILD-TYPE                                                                     32
D61V4, multiclass
                    vv
clus                 T1 T2 T3 T4
  14Q LOSS MUTATED    0  4  4  1
  14Q LOSS WILD-TYPE  6 49 55 32
D61V5, multiclass
                    vv
clus                 N0 N1 N2 N3
  14Q LOSS MUTATED    2  5  2  0
  14Q LOSS WILD-TYPE 48 52 22 19
D61V6, multiclass
                    vv
clus                  M0  M1  MX
  14Q LOSS MUTATED     9   0   1
  14Q LOSS WILD-TYPE 123  18  10
D61V7, multiclass
                    vv
clus                  I II III IV
  14Q LOSS MUTATED    1  4   3  1
  14Q LOSS WILD-TYPE 24 39  45 28
D61V8, multiclass
D61V9, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED      0   10
  14Q LOSS WILD-TYPE    5  146
     clus
vv    14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  NO                 0                  5
  YES               10                146

Clustering(62) Variable = 15q loss mutation analysis
D62V1, survival
                    sevent
clus2                  0   1
  15Q LOSS MUTATED     6   1
  15Q LOSS WILD-TYPE 102  15
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                 7                117 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                 1                 15 
$`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-BR-7958 TCGA-BR-7959 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
        0.69         0.16         1.08         0.82         1.32         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
        0.95         0.49         0.46         0.72         0.26         0.43 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-CD-5798 
        0.26         1.18         1.55         1.48         0.76         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-4469 TCGA-CG-4472 TCGA-CG-4474 
       21.99         1.02         8.98         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-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-D7-6528 TCGA-D7-6815 TCGA-D7-6818 
        0.69         5.95         6.61         1.68         3.65         4.04 
TCGA-D7-6820 TCGA-D7-6822 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6177 TCGA-F1-6874 
        2.93         4.27         0.62         7.79         6.54         2.01 
TCGA-F1-6875 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-HJ-7597 
       72.23         0.39         0.20         3.02         3.58        26.43 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IP-7968 
        6.87         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               1.41 
[1] "1.2 - 53.0 (12.0)" "0.1 - 72.2 (1.4)" 
        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-BR-7958 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BR-7959         TCGA-BR-8059         TCGA-BR-8060 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BR-8077         TCGA-BR-8078         TCGA-BR-8080 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BR-8081         TCGA-BR-8284         TCGA-BR-8285 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BR-8286         TCGA-BR-8289         TCGA-BR-8291 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BR-8295         TCGA-BR-8296         TCGA-BR-8297 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-CD-5798         TCGA-CD-5799         TCGA-CD-5800 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-CD-5801         TCGA-CD-5802         TCGA-CD-5803 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-CG-4300         TCGA-CG-4301         TCGA-CG-4304 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-CG-4305         TCGA-CG-4306         TCGA-CG-4436 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" 
        TCGA-CG-4437         TCGA-CG-4438         TCGA-CG-4440 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-CG-4441         TCGA-CG-4443         TCGA-CG-4444 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-CG-4449         TCGA-CG-4455         TCGA-CG-4460 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-CG-4462         TCGA-CG-4465         TCGA-CG-4466 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" 
        TCGA-CG-4469         TCGA-CG-4472         TCGA-CG-4474 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-CG-4477         TCGA-CG-5716         TCGA-CG-5717 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-CG-5718         TCGA-CG-5719         TCGA-CG-5720 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-CG-5721         TCGA-CG-5722         TCGA-CG-5723 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-CG-5724         TCGA-CG-5725         TCGA-CG-5726 
  "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-CG-5727         TCGA-CG-5728         TCGA-CG-5730 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-CG-5732         TCGA-CG-5733         TCGA-CG-5734 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-D7-5577         TCGA-D7-5578         TCGA-D7-5579 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-D7-6518         TCGA-D7-6519         TCGA-D7-6520 
"15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" 
        TCGA-D7-6521         TCGA-D7-6522         TCGA-D7-6524 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-D7-6525         TCGA-D7-6526         TCGA-D7-6527 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" 
        TCGA-D7-6528         TCGA-D7-6815         TCGA-D7-6817 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" 
        TCGA-D7-6818         TCGA-D7-6820         TCGA-D7-6822 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-EQ-5647         TCGA-EQ-8122         TCGA-F1-6177 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-F1-6874         TCGA-F1-6875         TCGA-FP-7735 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-FP-7829         TCGA-FP-7916         TCGA-FP-7998 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-HJ-7597         TCGA-IN-7806         TCGA-IN-7808 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-IP-7968 
"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-BR-7958 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BR-7959         TCGA-BR-8059         TCGA-BR-8060 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BR-8077         TCGA-BR-8078         TCGA-BR-8080 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BR-8081         TCGA-BR-8284         TCGA-BR-8285 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BR-8286         TCGA-BR-8289         TCGA-BR-8291 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BR-8295         TCGA-BR-8296         TCGA-BR-8297 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-CD-5798         TCGA-CD-5799         TCGA-CD-5800 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-CD-5801         TCGA-CD-5802         TCGA-CD-5803 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-CG-4300         TCGA-CG-4301         TCGA-CG-4304 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-CG-4305         TCGA-CG-4306         TCGA-CG-4436 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" 
        TCGA-CG-4437         TCGA-CG-4438         TCGA-CG-4440 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-CG-4441         TCGA-CG-4443         TCGA-CG-4444 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-CG-4449         TCGA-CG-4455         TCGA-CG-4460 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-CG-4462         TCGA-CG-4465         TCGA-CG-4466 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" 
        TCGA-CG-4469         TCGA-CG-4472         TCGA-CG-4474 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-CG-4477         TCGA-CG-5716         TCGA-CG-5717 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-CG-5718         TCGA-CG-5719         TCGA-CG-5720 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-CG-5721         TCGA-CG-5722         TCGA-CG-5723 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-CG-5724         TCGA-CG-5725         TCGA-CG-5726 
  "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-CG-5727         TCGA-CG-5728         TCGA-CG-5730 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-CG-5732         TCGA-CG-5733         TCGA-CG-5734 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-D7-5577         TCGA-D7-5578         TCGA-D7-5579 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-D7-6518         TCGA-D7-6519         TCGA-D7-6520 
"15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" 
        TCGA-D7-6521         TCGA-D7-6522         TCGA-D7-6524 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-D7-6525         TCGA-D7-6526         TCGA-D7-6527 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" 
        TCGA-D7-6528         TCGA-D7-6815         TCGA-D7-6817 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" 
        TCGA-D7-6818         TCGA-D7-6820         TCGA-D7-6822 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-EQ-5647         TCGA-EQ-8122         TCGA-F1-6177 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-F1-6874         TCGA-F1-6875         TCGA-FP-7735 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-FP-7829         TCGA-FP-7916         TCGA-FP-7998 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-HJ-7597         TCGA-IN-7806         TCGA-IN-7808 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-IP-7968 
"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-BR-7958 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BR-7959         TCGA-BR-8059         TCGA-BR-8060 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BR-8077         TCGA-BR-8078         TCGA-BR-8080 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BR-8081         TCGA-BR-8284         TCGA-BR-8285 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BR-8286         TCGA-BR-8289         TCGA-BR-8291 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BR-8295         TCGA-BR-8296         TCGA-BR-8297 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-CD-5798         TCGA-CD-5799         TCGA-CD-5800 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-CD-5801         TCGA-CD-5802         TCGA-CD-5803 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-CG-4300         TCGA-CG-4301         TCGA-CG-4304 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-CG-4305         TCGA-CG-4306         TCGA-CG-4436 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" 
        TCGA-CG-4437         TCGA-CG-4438         TCGA-CG-4440 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-CG-4441         TCGA-CG-4443         TCGA-CG-4444 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-CG-4449         TCGA-CG-4455         TCGA-CG-4460 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-CG-4462         TCGA-CG-4465         TCGA-CG-4466 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" 
        TCGA-CG-4469         TCGA-CG-4472         TCGA-CG-4474 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-CG-4477         TCGA-CG-5716         TCGA-CG-5717 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-CG-5718         TCGA-CG-5719         TCGA-CG-5720 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-CG-5721         TCGA-CG-5722         TCGA-CG-5723 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-CG-5724         TCGA-CG-5725         TCGA-CG-5726 
  "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-CG-5727         TCGA-CG-5728         TCGA-CG-5730 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-CG-5732         TCGA-CG-5733         TCGA-CG-5734 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-D7-5577         TCGA-D7-5578         TCGA-D7-5579 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-D7-6518         TCGA-D7-6519         TCGA-D7-6520 
"15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" 
        TCGA-D7-6521         TCGA-D7-6522         TCGA-D7-6524 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-D7-6525         TCGA-D7-6526         TCGA-D7-6527 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" 
        TCGA-D7-6528         TCGA-D7-6815         TCGA-D7-6817 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" 
        TCGA-D7-6818         TCGA-D7-6820         TCGA-D7-6822 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-EQ-5647         TCGA-EQ-8122         TCGA-F1-6177 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-F1-6874         TCGA-F1-6875         TCGA-FP-7735 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-FP-7829         TCGA-FP-7916         TCGA-FP-7998 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-HJ-7597         TCGA-IN-7806         TCGA-IN-7808 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-IP-7968 
"15Q LOSS WILD-TYPE" 
[1] "hr=" "1.8"
D62V2, continuous
D62V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED      4    6
  15Q LOSS WILD-TYPE   61   90
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  FEMALE                4                 61
  MALE                  6                 90
                    vv
clus                 STOMACH ADENOCARCINOMA - DIFFUSE TYPE
  15Q LOSS MUTATED                                       2
  15Q LOSS WILD-TYPE                                    17
                    vv
clus                 STOMACH ADENOCARCINOMA - NOT OTHERWISE SPECIFIED (NOS)
  15Q LOSS MUTATED                                                        2
  15Q LOSS WILD-TYPE                                                     77
                    vv
clus                 STOMACH ADENOCARCINOMA - SIGNET RING TYPE
  15Q LOSS MUTATED                                           0
  15Q LOSS WILD-TYPE                                         1
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - MUCINOUS TYPE
  15Q LOSS MUTATED                                                   0
  15Q LOSS WILD-TYPE                                                 9
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - PAPILLARY TYPE
  15Q LOSS MUTATED                                                    1
  15Q LOSS WILD-TYPE                                                  2
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - TUBULAR TYPE
  15Q LOSS MUTATED                                                  2
  15Q LOSS WILD-TYPE                                                8
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - TYPE NOT OTHERWISE SPECIFIED (NOS)
  15Q LOSS MUTATED                                                                        3
  15Q LOSS WILD-TYPE                                                                     32
D62V4, multiclass
                    vv
clus                 T1 T2 T3 T4
  15Q LOSS MUTATED    0  7  3  0
  15Q LOSS WILD-TYPE  6 46 56 33
D62V5, multiclass
                    vv
clus                 N0 N1 N2 N3
  15Q LOSS MUTATED    4  3  0  2
  15Q LOSS WILD-TYPE 46 54 24 17
D62V6, multiclass
                    vv
clus                  M0  M1  MX
  15Q LOSS MUTATED     8   1   1
  15Q LOSS WILD-TYPE 124  17  10
D62V7, multiclass
                    vv
clus                  I II III IV
  15Q LOSS MUTATED    3  2   3  1
  15Q LOSS WILD-TYPE 22 41  45 28
D62V8, multiclass
D62V9, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED      2    8
  15Q LOSS WILD-TYPE    3  148
     clus
vv    15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  NO                 2                  3
  YES                8                148

Clustering(63) Variable = 16p loss mutation analysis
D63V1, survival
                    sevent
clus2                  0   1
  16P LOSS MUTATED     5   1
  16P LOSS WILD-TYPE 103  15
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                 6                118 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                 1                 15 
$`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-BR-7958 TCGA-BR-7959 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
        0.69         0.16         1.08         0.82         1.32         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
        0.95         0.49         0.46         0.72         0.26         0.43 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-CD-5798 
        0.26         1.18         1.55         1.48         0.76         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-4444 TCGA-CG-4455 TCGA-CG-4460 
       54.05         4.01        14.01        47.05        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-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-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6177 
        4.70         4.04         2.93         0.62         7.79         6.54 
TCGA-F1-6874 TCGA-F1-6875 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
        2.01        72.23         0.39         0.20         3.02         3.58 
TCGA-HJ-7597 TCGA-IN-7806 TCGA-IN-7808 TCGA-IP-7968 
       26.43         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 
            13.840              1.445 
[1] "1.1 - 30.0 (13.8)" "0.1 - 72.2 (1.4)" 
        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-BR-7958 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BR-7959         TCGA-BR-8059         TCGA-BR-8060 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BR-8077         TCGA-BR-8078         TCGA-BR-8080 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BR-8081         TCGA-BR-8284         TCGA-BR-8285 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BR-8286         TCGA-BR-8289         TCGA-BR-8291 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BR-8295         TCGA-BR-8296         TCGA-BR-8297 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-CD-5798         TCGA-CD-5799         TCGA-CD-5800 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-CD-5801         TCGA-CD-5802         TCGA-CD-5803 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-CG-4300         TCGA-CG-4301         TCGA-CG-4304 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-CG-4305         TCGA-CG-4306         TCGA-CG-4436 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-CG-4437         TCGA-CG-4438         TCGA-CG-4440 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-CG-4441         TCGA-CG-4443         TCGA-CG-4444 
"16P LOSS WILD-TYPE"   "16P LOSS MUTATED" "16P LOSS WILD-TYPE" 
        TCGA-CG-4449         TCGA-CG-4455         TCGA-CG-4460 
  "16P LOSS MUTATED" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-CG-4462         TCGA-CG-4465         TCGA-CG-4466 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-CG-4469         TCGA-CG-4472         TCGA-CG-4474 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-CG-4477         TCGA-CG-5716         TCGA-CG-5717 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-CG-5718         TCGA-CG-5719         TCGA-CG-5720 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-CG-5721         TCGA-CG-5722         TCGA-CG-5723 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-CG-5724         TCGA-CG-5725         TCGA-CG-5726 
  "16P LOSS MUTATED" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-CG-5727         TCGA-CG-5728         TCGA-CG-5730 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-CG-5732         TCGA-CG-5733         TCGA-CG-5734 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-D7-5577         TCGA-D7-5578         TCGA-D7-5579 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-D7-6518         TCGA-D7-6519         TCGA-D7-6520 
"16P LOSS WILD-TYPE"   "16P LOSS MUTATED" "16P LOSS WILD-TYPE" 
        TCGA-D7-6521         TCGA-D7-6522         TCGA-D7-6524 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-D7-6525         TCGA-D7-6526         TCGA-D7-6527 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-D7-6528         TCGA-D7-6815         TCGA-D7-6817 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-D7-6818         TCGA-D7-6820         TCGA-D7-6822 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE"   "16P LOSS MUTATED" 
        TCGA-EQ-5647         TCGA-EQ-8122         TCGA-F1-6177 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-F1-6874         TCGA-F1-6875         TCGA-FP-7735 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-FP-7829         TCGA-FP-7916         TCGA-FP-7998 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-HJ-7597         TCGA-IN-7806         TCGA-IN-7808 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-IP-7968 
"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-BR-7958 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BR-7959         TCGA-BR-8059         TCGA-BR-8060 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BR-8077         TCGA-BR-8078         TCGA-BR-8080 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BR-8081         TCGA-BR-8284         TCGA-BR-8285 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BR-8286         TCGA-BR-8289         TCGA-BR-8291 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BR-8295         TCGA-BR-8296         TCGA-BR-8297 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-CD-5798         TCGA-CD-5799         TCGA-CD-5800 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-CD-5801         TCGA-CD-5802         TCGA-CD-5803 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-CG-4300         TCGA-CG-4301         TCGA-CG-4304 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-CG-4305         TCGA-CG-4306         TCGA-CG-4436 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-CG-4437         TCGA-CG-4438         TCGA-CG-4440 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-CG-4441         TCGA-CG-4443         TCGA-CG-4444 
"16P LOSS WILD-TYPE"   "16P LOSS MUTATED" "16P LOSS WILD-TYPE" 
        TCGA-CG-4449         TCGA-CG-4455         TCGA-CG-4460 
  "16P LOSS MUTATED" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-CG-4462         TCGA-CG-4465         TCGA-CG-4466 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-CG-4469         TCGA-CG-4472         TCGA-CG-4474 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-CG-4477         TCGA-CG-5716         TCGA-CG-5717 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-CG-5718         TCGA-CG-5719         TCGA-CG-5720 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-CG-5721         TCGA-CG-5722         TCGA-CG-5723 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-CG-5724         TCGA-CG-5725         TCGA-CG-5726 
  "16P LOSS MUTATED" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-CG-5727         TCGA-CG-5728         TCGA-CG-5730 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-CG-5732         TCGA-CG-5733         TCGA-CG-5734 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-D7-5577         TCGA-D7-5578         TCGA-D7-5579 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-D7-6518         TCGA-D7-6519         TCGA-D7-6520 
"16P LOSS WILD-TYPE"   "16P LOSS MUTATED" "16P LOSS WILD-TYPE" 
        TCGA-D7-6521         TCGA-D7-6522         TCGA-D7-6524 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-D7-6525         TCGA-D7-6526         TCGA-D7-6527 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-D7-6528         TCGA-D7-6815         TCGA-D7-6817 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-D7-6818         TCGA-D7-6820         TCGA-D7-6822 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE"   "16P LOSS MUTATED" 
        TCGA-EQ-5647         TCGA-EQ-8122         TCGA-F1-6177 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-F1-6874         TCGA-F1-6875         TCGA-FP-7735 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-FP-7829         TCGA-FP-7916         TCGA-FP-7998 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-HJ-7597         TCGA-IN-7806         TCGA-IN-7808 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-IP-7968 
"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-BR-7958 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BR-7959         TCGA-BR-8059         TCGA-BR-8060 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BR-8077         TCGA-BR-8078         TCGA-BR-8080 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BR-8081         TCGA-BR-8284         TCGA-BR-8285 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BR-8286         TCGA-BR-8289         TCGA-BR-8291 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BR-8295         TCGA-BR-8296         TCGA-BR-8297 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-CD-5798         TCGA-CD-5799         TCGA-CD-5800 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-CD-5801         TCGA-CD-5802         TCGA-CD-5803 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-CG-4300         TCGA-CG-4301         TCGA-CG-4304 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-CG-4305         TCGA-CG-4306         TCGA-CG-4436 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-CG-4437         TCGA-CG-4438         TCGA-CG-4440 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-CG-4441         TCGA-CG-4443         TCGA-CG-4444 
"16P LOSS WILD-TYPE"   "16P LOSS MUTATED" "16P LOSS WILD-TYPE" 
        TCGA-CG-4449         TCGA-CG-4455         TCGA-CG-4460 
  "16P LOSS MUTATED" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-CG-4462         TCGA-CG-4465         TCGA-CG-4466 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-CG-4469         TCGA-CG-4472         TCGA-CG-4474 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-CG-4477         TCGA-CG-5716         TCGA-CG-5717 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-CG-5718         TCGA-CG-5719         TCGA-CG-5720 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-CG-5721         TCGA-CG-5722         TCGA-CG-5723 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-CG-5724         TCGA-CG-5725         TCGA-CG-5726 
  "16P LOSS MUTATED" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-CG-5727         TCGA-CG-5728         TCGA-CG-5730 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-CG-5732         TCGA-CG-5733         TCGA-CG-5734 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-D7-5577         TCGA-D7-5578         TCGA-D7-5579 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-D7-6518         TCGA-D7-6519         TCGA-D7-6520 
"16P LOSS WILD-TYPE"   "16P LOSS MUTATED" "16P LOSS WILD-TYPE" 
        TCGA-D7-6521         TCGA-D7-6522         TCGA-D7-6524 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-D7-6525         TCGA-D7-6526         TCGA-D7-6527 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-D7-6528         TCGA-D7-6815         TCGA-D7-6817 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-D7-6818         TCGA-D7-6820         TCGA-D7-6822 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE"   "16P LOSS MUTATED" 
        TCGA-EQ-5647         TCGA-EQ-8122         TCGA-F1-6177 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-F1-6874         TCGA-F1-6875         TCGA-FP-7735 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-FP-7829         TCGA-FP-7916         TCGA-FP-7998 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-HJ-7597         TCGA-IN-7806         TCGA-IN-7808 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-IP-7968 
"16P LOSS WILD-TYPE" 
[1] "hr=" "1.7"
D63V2, continuous
D63V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED      1    8
  16P LOSS WILD-TYPE   64   88
        clus
vv       16P LOSS MUTATED 16P LOSS WILD-TYPE
  FEMALE                1                 64
  MALE                  8                 88
                    vv
clus                 STOMACH ADENOCARCINOMA - DIFFUSE TYPE
  16P LOSS MUTATED                                       2
  16P LOSS WILD-TYPE                                    17
                    vv
clus                 STOMACH ADENOCARCINOMA - NOT OTHERWISE SPECIFIED (NOS)
  16P LOSS MUTATED                                                        3
  16P LOSS WILD-TYPE                                                     76
                    vv
clus                 STOMACH ADENOCARCINOMA - SIGNET RING TYPE
  16P LOSS MUTATED                                           0
  16P LOSS WILD-TYPE                                         1
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - MUCINOUS TYPE
  16P LOSS MUTATED                                                   1
  16P LOSS WILD-TYPE                                                 8
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - PAPILLARY TYPE
  16P LOSS MUTATED                                                    0
  16P LOSS WILD-TYPE                                                  3
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - TUBULAR TYPE
  16P LOSS MUTATED                                                  2
  16P LOSS WILD-TYPE                                                8
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - TYPE NOT OTHERWISE SPECIFIED (NOS)
  16P LOSS MUTATED                                                                        1
  16P LOSS WILD-TYPE                                                                     34
D63V4, multiclass
                    vv
clus                 T1 T2 T3 T4
  16P LOSS MUTATED    1  4  3  0
  16P LOSS WILD-TYPE  5 49 56 33
D63V5, multiclass
                    vv
clus                 N0 N1 N2 N3
  16P LOSS MUTATED    3  3  0  1
  16P LOSS WILD-TYPE 47 54 24 18
D63V6, multiclass
                    vv
clus                  M0  M1  MX
  16P LOSS MUTATED     8   1   0
  16P LOSS WILD-TYPE 124  17  11
D63V7, multiclass
                    vv
clus                  I II III IV
  16P LOSS MUTATED    2  2   2  1
  16P LOSS WILD-TYPE 23 41  46 28
D63V8, multiclass
D63V9, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED      0    9
  16P LOSS WILD-TYPE    5  147
     clus
vv    16P LOSS MUTATED 16P LOSS WILD-TYPE
  NO                 0                  5
  YES                9                147

Clustering(64) Variable = 16q loss mutation analysis
D64V1, survival
                    sevent
clus2                  0   1
  16Q LOSS MUTATED     8   1
  16Q LOSS WILD-TYPE 100  15
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                 9                115 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                 1                 15 
$`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 TCGA-EQ-8122 
       15.65         4.70         7.79 

$`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-BR-7958 TCGA-BR-7959 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
        0.69         0.16         1.08         0.82         1.32         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
        0.95         0.49         0.46         0.72         0.26         0.43 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-CD-5798 
        0.26         1.18         1.55         1.48         0.76         0.82 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5803 TCGA-CG-4300 TCGA-CG-4301 
        0.69         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-4438 
       27.02        15.95         1.02        52.96         8.05        54.05 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4444 TCGA-CG-4455 TCGA-CG-4460 TCGA-CG-4462 
        4.01        14.01        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-5716 
        8.98        18.94         7.07        12.00         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-D7-6520 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-D7-6818 TCGA-D7-6820 
        6.61         4.14         1.68         3.65         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-7916 TCGA-FP-7998 TCGA-HJ-7597 TCGA-IN-7806 TCGA-IN-7808 
        0.20         3.02         3.58        26.43         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 
              7.79               1.48 
[1] "0.3 - 30.0 (7.8)" "0.1 - 72.2 (1.5)"
        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-BR-7958 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BR-7959         TCGA-BR-8059         TCGA-BR-8060 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BR-8077         TCGA-BR-8078         TCGA-BR-8080 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BR-8081         TCGA-BR-8284         TCGA-BR-8285 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BR-8286         TCGA-BR-8289         TCGA-BR-8291 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BR-8295         TCGA-BR-8296         TCGA-BR-8297 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CD-5798         TCGA-CD-5799         TCGA-CD-5800 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CD-5801         TCGA-CD-5802         TCGA-CD-5803 
"16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" 
        TCGA-CG-4300         TCGA-CG-4301         TCGA-CG-4304 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CG-4305         TCGA-CG-4306         TCGA-CG-4436 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CG-4437         TCGA-CG-4438         TCGA-CG-4440 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CG-4441         TCGA-CG-4443         TCGA-CG-4444 
"16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" 
        TCGA-CG-4449         TCGA-CG-4455         TCGA-CG-4460 
  "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CG-4462         TCGA-CG-4465         TCGA-CG-4466 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CG-4469         TCGA-CG-4472         TCGA-CG-4474 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CG-4477         TCGA-CG-5716         TCGA-CG-5717 
  "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CG-5718         TCGA-CG-5719         TCGA-CG-5720 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CG-5721         TCGA-CG-5722         TCGA-CG-5723 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CG-5724         TCGA-CG-5725         TCGA-CG-5726 
  "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CG-5727         TCGA-CG-5728         TCGA-CG-5730 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CG-5732         TCGA-CG-5733         TCGA-CG-5734 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-D7-5577         TCGA-D7-5578         TCGA-D7-5579 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-D7-6518         TCGA-D7-6519         TCGA-D7-6520 
"16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" 
        TCGA-D7-6521         TCGA-D7-6522         TCGA-D7-6524 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-D7-6525         TCGA-D7-6526         TCGA-D7-6527 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-D7-6528         TCGA-D7-6815         TCGA-D7-6817 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" 
        TCGA-D7-6818         TCGA-D7-6820         TCGA-D7-6822 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EQ-5647         TCGA-EQ-8122         TCGA-F1-6177 
"16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" 
        TCGA-F1-6874         TCGA-F1-6875         TCGA-FP-7735 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-FP-7829         TCGA-FP-7916         TCGA-FP-7998 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-HJ-7597         TCGA-IN-7806         TCGA-IN-7808 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-IP-7968 
"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-BR-7958 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BR-7959         TCGA-BR-8059         TCGA-BR-8060 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BR-8077         TCGA-BR-8078         TCGA-BR-8080 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BR-8081         TCGA-BR-8284         TCGA-BR-8285 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BR-8286         TCGA-BR-8289         TCGA-BR-8291 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BR-8295         TCGA-BR-8296         TCGA-BR-8297 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CD-5798         TCGA-CD-5799         TCGA-CD-5800 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CD-5801         TCGA-CD-5802         TCGA-CD-5803 
"16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" 
        TCGA-CG-4300         TCGA-CG-4301         TCGA-CG-4304 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CG-4305         TCGA-CG-4306         TCGA-CG-4436 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CG-4437         TCGA-CG-4438         TCGA-CG-4440 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CG-4441         TCGA-CG-4443         TCGA-CG-4444 
"16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" 
        TCGA-CG-4449         TCGA-CG-4455         TCGA-CG-4460 
  "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CG-4462         TCGA-CG-4465         TCGA-CG-4466 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CG-4469         TCGA-CG-4472         TCGA-CG-4474 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CG-4477         TCGA-CG-5716         TCGA-CG-5717 
  "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CG-5718         TCGA-CG-5719         TCGA-CG-5720 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CG-5721         TCGA-CG-5722         TCGA-CG-5723 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CG-5724         TCGA-CG-5725         TCGA-CG-5726 
  "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CG-5727         TCGA-CG-5728         TCGA-CG-5730 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CG-5732         TCGA-CG-5733         TCGA-CG-5734 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-D7-5577         TCGA-D7-5578         TCGA-D7-5579 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-D7-6518         TCGA-D7-6519         TCGA-D7-6520 
"16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" 
        TCGA-D7-6521         TCGA-D7-6522         TCGA-D7-6524 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-D7-6525         TCGA-D7-6526         TCGA-D7-6527 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-D7-6528         TCGA-D7-6815         TCGA-D7-6817 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" 
        TCGA-D7-6818         TCGA-D7-6820         TCGA-D7-6822 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EQ-5647         TCGA-EQ-8122         TCGA-F1-6177 
"16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" 
        TCGA-F1-6874         TCGA-F1-6875         TCGA-FP-7735 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-FP-7829         TCGA-FP-7916         TCGA-FP-7998 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-HJ-7597         TCGA-IN-7806         TCGA-IN-7808 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-IP-7968 
"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-BR-7958 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BR-7959         TCGA-BR-8059         TCGA-BR-8060 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BR-8077         TCGA-BR-8078         TCGA-BR-8080 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BR-8081         TCGA-BR-8284         TCGA-BR-8285 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BR-8286         TCGA-BR-8289         TCGA-BR-8291 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BR-8295         TCGA-BR-8296         TCGA-BR-8297 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CD-5798         TCGA-CD-5799         TCGA-CD-5800 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CD-5801         TCGA-CD-5802         TCGA-CD-5803 
"16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" 
        TCGA-CG-4300         TCGA-CG-4301         TCGA-CG-4304 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CG-4305         TCGA-CG-4306         TCGA-CG-4436 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CG-4437         TCGA-CG-4438         TCGA-CG-4440 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CG-4441         TCGA-CG-4443         TCGA-CG-4444 
"16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" 
        TCGA-CG-4449         TCGA-CG-4455         TCGA-CG-4460 
  "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CG-4462         TCGA-CG-4465         TCGA-CG-4466 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CG-4469         TCGA-CG-4472         TCGA-CG-4474 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CG-4477         TCGA-CG-5716         TCGA-CG-5717 
  "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CG-5718         TCGA-CG-5719         TCGA-CG-5720 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CG-5721         TCGA-CG-5722         TCGA-CG-5723 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CG-5724         TCGA-CG-5725         TCGA-CG-5726 
  "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CG-5727         TCGA-CG-5728         TCGA-CG-5730 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CG-5732         TCGA-CG-5733         TCGA-CG-5734 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-D7-5577         TCGA-D7-5578         TCGA-D7-5579 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-D7-6518         TCGA-D7-6519         TCGA-D7-6520 
"16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" 
        TCGA-D7-6521         TCGA-D7-6522         TCGA-D7-6524 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-D7-6525         TCGA-D7-6526         TCGA-D7-6527 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-D7-6528         TCGA-D7-6815         TCGA-D7-6817 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" 
        TCGA-D7-6818         TCGA-D7-6820         TCGA-D7-6822 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EQ-5647         TCGA-EQ-8122         TCGA-F1-6177 
"16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" 
        TCGA-F1-6874         TCGA-F1-6875         TCGA-FP-7735 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-FP-7829         TCGA-FP-7916         TCGA-FP-7998 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-HJ-7597         TCGA-IN-7806         TCGA-IN-7808 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-IP-7968 
"16Q LOSS WILD-TYPE" 
[1] "hr=" "1.9"
D64V2, continuous
D64V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED      4   10
  16Q LOSS WILD-TYPE   61   86
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  FEMALE                4                 61
  MALE                 10                 86
                    vv
clus                 STOMACH ADENOCARCINOMA - DIFFUSE TYPE
  16Q LOSS MUTATED                                       2
  16Q LOSS WILD-TYPE                                    17
                    vv
clus                 STOMACH ADENOCARCINOMA - NOT OTHERWISE SPECIFIED (NOS)
  16Q LOSS MUTATED                                                        4
  16Q LOSS WILD-TYPE                                                     75
                    vv
clus                 STOMACH ADENOCARCINOMA - SIGNET RING TYPE
  16Q LOSS MUTATED                                           0
  16Q LOSS WILD-TYPE                                         1
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - MUCINOUS TYPE
  16Q LOSS MUTATED                                                   2
  16Q LOSS WILD-TYPE                                                 7
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - PAPILLARY TYPE
  16Q LOSS MUTATED                                                    0
  16Q LOSS WILD-TYPE                                                  3
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - TUBULAR TYPE
  16Q LOSS MUTATED                                                  2
  16Q LOSS WILD-TYPE                                                8
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - TYPE NOT OTHERWISE SPECIFIED (NOS)
  16Q LOSS MUTATED                                                                        3
  16Q LOSS WILD-TYPE                                                                     32
D64V4, multiclass
                    vv
clus                 T1 T2 T3 T4
  16Q LOSS MUTATED    1  6  6  0
  16Q LOSS WILD-TYPE  5 47 53 33
D64V5, multiclass
                    vv
clus                 N0 N1 N2 N3
  16Q LOSS MUTATED    4  5  0  3
  16Q LOSS WILD-TYPE 46 52 24 16
D64V6, multiclass
                    vv
clus                  M0  M1  MX
  16Q LOSS MUTATED    12   1   1
  16Q LOSS WILD-TYPE 120  17  10
D64V7, multiclass
                    vv
clus                  I II III IV
  16Q LOSS MUTATED    2  5   3  2
  16Q LOSS WILD-TYPE 23 38  45 27
D64V8, multiclass
D64V9, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED      1   13
  16Q LOSS WILD-TYPE    4  143
     clus
vv    16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  NO                 1                  4
  YES               13                143

Clustering(65) Variable = 17p loss mutation analysis
D65V1, survival
                    sevent
clus2                 0  1
  17P LOSS MUTATED   23  3
  17P LOSS WILD-TYPE 85 13
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                26                 98 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                 3                 13 
$`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-BR-7958 
        0.16         4.54         0.99         0.95         0.69         0.16 
TCGA-BR-7959 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
        1.08         0.82         1.32         0.69         0.95         0.49 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
        0.46         0.72         0.26         0.43         0.26         1.18 
TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-CD-5798 TCGA-CD-5801 TCGA-CD-5802 
        1.55         1.48         0.76         0.82         0.49         0.30 
TCGA-CD-5803 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4441 TCGA-CG-4444 
        0.07        15.95         1.02        52.96        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-4472 TCGA-CG-4474 TCGA-CG-5716 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5720 
       12.00         1.02         1.02         6.94         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5728 
        5.98         0.95        70.06        12.03        28.96        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-D7-6518 TCGA-D7-6519 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6527 
        9.80        15.65         6.90         0.69         5.95         4.14 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6822 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6177 
        4.70         4.04         4.27         0.62         7.79         6.54 
TCGA-F1-6874 TCGA-F1-6875 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
        2.01        72.23         0.39         0.20         3.02         3.58 
TCGA-HJ-7597 TCGA-IN-7808 
       26.43         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 
             4.010              1.235 
[1] "0.1 - 54.0 (4.0)" "0.1 - 72.2 (1.2)"
        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-BR-7958 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-BR-7959         TCGA-BR-8059         TCGA-BR-8060 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-BR-8077         TCGA-BR-8078         TCGA-BR-8080 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-BR-8081         TCGA-BR-8284         TCGA-BR-8285 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-BR-8286         TCGA-BR-8289         TCGA-BR-8291 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-BR-8295         TCGA-BR-8296         TCGA-BR-8297 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-CD-5798         TCGA-CD-5799         TCGA-CD-5800 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED"   "17P LOSS MUTATED" 
        TCGA-CD-5801         TCGA-CD-5802         TCGA-CD-5803 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-CG-4300         TCGA-CG-4301         TCGA-CG-4304 
  "17P LOSS MUTATED"   "17P LOSS MUTATED"   "17P LOSS MUTATED" 
        TCGA-CG-4305         TCGA-CG-4306         TCGA-CG-4436 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-CG-4437         TCGA-CG-4438         TCGA-CG-4440 
  "17P LOSS MUTATED"   "17P LOSS MUTATED"   "17P LOSS MUTATED" 
        TCGA-CG-4441         TCGA-CG-4443         TCGA-CG-4444 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-CG-4449         TCGA-CG-4455         TCGA-CG-4460 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-CG-4462         TCGA-CG-4465         TCGA-CG-4466 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-CG-4469         TCGA-CG-4472         TCGA-CG-4474 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-CG-4477         TCGA-CG-5716         TCGA-CG-5717 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-CG-5718         TCGA-CG-5719         TCGA-CG-5720 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-CG-5721         TCGA-CG-5722         TCGA-CG-5723 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-CG-5724         TCGA-CG-5725         TCGA-CG-5726 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-CG-5727         TCGA-CG-5728         TCGA-CG-5730 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-CG-5732         TCGA-CG-5733         TCGA-CG-5734 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-D7-5577         TCGA-D7-5578         TCGA-D7-5579 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-D7-6518         TCGA-D7-6519         TCGA-D7-6520 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-D7-6521         TCGA-D7-6522         TCGA-D7-6524 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-D7-6525         TCGA-D7-6526         TCGA-D7-6527 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-D7-6528         TCGA-D7-6815         TCGA-D7-6817 
  "17P LOSS MUTATED"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-D7-6818         TCGA-D7-6820         TCGA-D7-6822 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-EQ-5647         TCGA-EQ-8122         TCGA-F1-6177 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-F1-6874         TCGA-F1-6875         TCGA-FP-7735 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-FP-7829         TCGA-FP-7916         TCGA-FP-7998 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-HJ-7597         TCGA-IN-7806         TCGA-IN-7808 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-IP-7968 
  "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-BR-7958 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-BR-7959         TCGA-BR-8059         TCGA-BR-8060 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-BR-8077         TCGA-BR-8078         TCGA-BR-8080 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-BR-8081         TCGA-BR-8284         TCGA-BR-8285 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-BR-8286         TCGA-BR-8289         TCGA-BR-8291 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-BR-8295         TCGA-BR-8296         TCGA-BR-8297 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-CD-5798         TCGA-CD-5799         TCGA-CD-5800 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED"   "17P LOSS MUTATED" 
        TCGA-CD-5801         TCGA-CD-5802         TCGA-CD-5803 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-CG-4300         TCGA-CG-4301         TCGA-CG-4304 
  "17P LOSS MUTATED"   "17P LOSS MUTATED"   "17P LOSS MUTATED" 
        TCGA-CG-4305         TCGA-CG-4306         TCGA-CG-4436 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-CG-4437         TCGA-CG-4438         TCGA-CG-4440 
  "17P LOSS MUTATED"   "17P LOSS MUTATED"   "17P LOSS MUTATED" 
        TCGA-CG-4441         TCGA-CG-4443         TCGA-CG-4444 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-CG-4449         TCGA-CG-4455         TCGA-CG-4460 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-CG-4462         TCGA-CG-4465         TCGA-CG-4466 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-CG-4469         TCGA-CG-4472         TCGA-CG-4474 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-CG-4477         TCGA-CG-5716         TCGA-CG-5717 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-CG-5718         TCGA-CG-5719         TCGA-CG-5720 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-CG-5721         TCGA-CG-5722         TCGA-CG-5723 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-CG-5724         TCGA-CG-5725         TCGA-CG-5726 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-CG-5727         TCGA-CG-5728         TCGA-CG-5730 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-CG-5732         TCGA-CG-5733         TCGA-CG-5734 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-D7-5577         TCGA-D7-5578         TCGA-D7-5579 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-D7-6518         TCGA-D7-6519         TCGA-D7-6520 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-D7-6521         TCGA-D7-6522         TCGA-D7-6524 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-D7-6525         TCGA-D7-6526         TCGA-D7-6527 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-D7-6528         TCGA-D7-6815         TCGA-D7-6817 
  "17P LOSS MUTATED"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-D7-6818         TCGA-D7-6820         TCGA-D7-6822 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-EQ-5647         TCGA-EQ-8122         TCGA-F1-6177 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-F1-6874         TCGA-F1-6875         TCGA-FP-7735 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-FP-7829         TCGA-FP-7916         TCGA-FP-7998 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-HJ-7597         TCGA-IN-7806         TCGA-IN-7808 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-IP-7968 
  "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-BR-7958 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-BR-7959         TCGA-BR-8059         TCGA-BR-8060 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-BR-8077         TCGA-BR-8078         TCGA-BR-8080 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-BR-8081         TCGA-BR-8284         TCGA-BR-8285 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-BR-8286         TCGA-BR-8289         TCGA-BR-8291 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-BR-8295         TCGA-BR-8296         TCGA-BR-8297 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-CD-5798         TCGA-CD-5799         TCGA-CD-5800 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED"   "17P LOSS MUTATED" 
        TCGA-CD-5801         TCGA-CD-5802         TCGA-CD-5803 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-CG-4300         TCGA-CG-4301         TCGA-CG-4304 
  "17P LOSS MUTATED"   "17P LOSS MUTATED"   "17P LOSS MUTATED" 
        TCGA-CG-4305         TCGA-CG-4306         TCGA-CG-4436 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-CG-4437         TCGA-CG-4438         TCGA-CG-4440 
  "17P LOSS MUTATED"   "17P LOSS MUTATED"   "17P LOSS MUTATED" 
        TCGA-CG-4441         TCGA-CG-4443         TCGA-CG-4444 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-CG-4449         TCGA-CG-4455         TCGA-CG-4460 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-CG-4462         TCGA-CG-4465         TCGA-CG-4466 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-CG-4469         TCGA-CG-4472         TCGA-CG-4474 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-CG-4477         TCGA-CG-5716         TCGA-CG-5717 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-CG-5718         TCGA-CG-5719         TCGA-CG-5720 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-CG-5721         TCGA-CG-5722         TCGA-CG-5723 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-CG-5724         TCGA-CG-5725         TCGA-CG-5726 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-CG-5727         TCGA-CG-5728         TCGA-CG-5730 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-CG-5732         TCGA-CG-5733         TCGA-CG-5734 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-D7-5577         TCGA-D7-5578         TCGA-D7-5579 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-D7-6518         TCGA-D7-6519         TCGA-D7-6520 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-D7-6521         TCGA-D7-6522         TCGA-D7-6524 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-D7-6525         TCGA-D7-6526         TCGA-D7-6527 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-D7-6528         TCGA-D7-6815         TCGA-D7-6817 
  "17P LOSS MUTATED"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-D7-6818         TCGA-D7-6820         TCGA-D7-6822 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-EQ-5647         TCGA-EQ-8122         TCGA-F1-6177 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-F1-6874         TCGA-F1-6875         TCGA-FP-7735 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-FP-7829         TCGA-FP-7916         TCGA-FP-7998 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-HJ-7597         TCGA-IN-7806         TCGA-IN-7808 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-IP-7968 
  "17P LOSS MUTATED" 
[1] "hr=" "1.6"
D65V2, continuous
D65V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED     11   21
  17P LOSS WILD-TYPE   54   75
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  FEMALE               11                 54
  MALE                 21                 75
                    vv
clus                 STOMACH ADENOCARCINOMA - DIFFUSE TYPE
  17P LOSS MUTATED                                       3
  17P LOSS WILD-TYPE                                    16
                    vv
clus                 STOMACH ADENOCARCINOMA - NOT OTHERWISE SPECIFIED (NOS)
  17P LOSS MUTATED                                                       10
  17P LOSS WILD-TYPE                                                     69
                    vv
clus                 STOMACH ADENOCARCINOMA - SIGNET RING TYPE
  17P LOSS MUTATED                                           0
  17P LOSS WILD-TYPE                                         1
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - MUCINOUS TYPE
  17P LOSS MUTATED                                                   2
  17P LOSS WILD-TYPE                                                 7
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - PAPILLARY TYPE
  17P LOSS MUTATED                                                    1
  17P LOSS WILD-TYPE                                                  2
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - TUBULAR TYPE
  17P LOSS MUTATED                                                  6
  17P LOSS WILD-TYPE                                                4
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - TYPE NOT OTHERWISE SPECIFIED (NOS)
  17P LOSS MUTATED                                                                       10
  17P LOSS WILD-TYPE                                                                     25
D65V4, multiclass
                    vv
clus                 T1 T2 T3 T4
  17P LOSS MUTATED    1 17 11  3
  17P LOSS WILD-TYPE  5 36 48 30
D65V5, multiclass
                    vv
clus                 N0 N1 N2 N3
  17P LOSS MUTATED   13  8  7  3
  17P LOSS WILD-TYPE 37 49 17 16
D65V6, multiclass
                    vv
clus                  M0  M1  MX
  17P LOSS MUTATED    26   4   2
  17P LOSS WILD-TYPE 106  14   9
D65V7, multiclass
                    vv
clus                  I II III IV
  17P LOSS MUTATED    8  8   8  7
  17P LOSS WILD-TYPE 17 35  40 22
D65V8, multiclass
D65V9, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED      3   29
  17P LOSS WILD-TYPE    2  127
     clus
vv    17P LOSS MUTATED 17P LOSS WILD-TYPE
  NO                 3                  2
  YES               29                127

Clustering(66) Variable = 17q loss mutation analysis
D66V1, survival
                    sevent
clus2                  0   1
  17Q LOSS MUTATED     6   1
  17Q LOSS WILD-TYPE 102  15
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                 7                117 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                 1                 15 
$`17Q LOSS MUTATED`
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4477 TCGA-D7-6526 
       20.02         3.02        54.05         4.01         1.02         6.61 
TCGA-D7-6820 
        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-BR-7958 TCGA-BR-7959 TCGA-BR-8059 TCGA-BR-8060 
        0.95         0.69         0.16         1.08         0.82         1.32 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
        0.69         0.95         0.49         0.46         0.72         0.26 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
        0.43         0.26         1.18         1.55         1.48         0.76 
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-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-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-5716 
        8.98        18.94         7.07        12.00         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-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
        0.69         5.95         4.14         1.68         3.65         4.70 
TCGA-D7-6818 TCGA-D7-6822 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6177 TCGA-F1-6874 
        4.04         4.27         0.62         7.79         6.54         2.01 
TCGA-F1-6875 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-HJ-7597 
       72.23         0.39         0.20         3.02         3.58        26.43 
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 
              4.01               1.41 
[1] "1.0 - 54.0 (4.0)" "0.1 - 72.2 (1.4)"
        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-BR-7958 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-BR-7959         TCGA-BR-8059         TCGA-BR-8060 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-BR-8077         TCGA-BR-8078         TCGA-BR-8080 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-BR-8081         TCGA-BR-8284         TCGA-BR-8285 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-BR-8286         TCGA-BR-8289         TCGA-BR-8291 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-BR-8295         TCGA-BR-8296         TCGA-BR-8297 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-CD-5798         TCGA-CD-5799         TCGA-CD-5800 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-CD-5801         TCGA-CD-5802         TCGA-CD-5803 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-CG-4300         TCGA-CG-4301         TCGA-CG-4304 
  "17Q LOSS MUTATED"   "17Q LOSS MUTATED" "17Q LOSS WILD-TYPE" 
        TCGA-CG-4305         TCGA-CG-4306         TCGA-CG-4436 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-CG-4437         TCGA-CG-4438         TCGA-CG-4440 
"17Q LOSS WILD-TYPE"   "17Q LOSS MUTATED"   "17Q LOSS MUTATED" 
        TCGA-CG-4441         TCGA-CG-4443         TCGA-CG-4444 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-CG-4449         TCGA-CG-4455         TCGA-CG-4460 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-CG-4462         TCGA-CG-4465         TCGA-CG-4466 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-CG-4469         TCGA-CG-4472         TCGA-CG-4474 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-CG-4477         TCGA-CG-5716         TCGA-CG-5717 
  "17Q LOSS MUTATED" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-CG-5718         TCGA-CG-5719         TCGA-CG-5720 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-CG-5721         TCGA-CG-5722         TCGA-CG-5723 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-CG-5724         TCGA-CG-5725         TCGA-CG-5726 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-CG-5727         TCGA-CG-5728         TCGA-CG-5730 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-CG-5732         TCGA-CG-5733         TCGA-CG-5734 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-D7-5577         TCGA-D7-5578         TCGA-D7-5579 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-D7-6518         TCGA-D7-6519         TCGA-D7-6520 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-D7-6521         TCGA-D7-6522         TCGA-D7-6524 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-D7-6525         TCGA-D7-6526         TCGA-D7-6527 
"17Q LOSS WILD-TYPE"   "17Q LOSS MUTATED" "17Q LOSS WILD-TYPE" 
        TCGA-D7-6528         TCGA-D7-6815         TCGA-D7-6817 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-D7-6818         TCGA-D7-6820         TCGA-D7-6822 
"17Q LOSS WILD-TYPE"   "17Q LOSS MUTATED" "17Q LOSS WILD-TYPE" 
        TCGA-EQ-5647         TCGA-EQ-8122         TCGA-F1-6177 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-F1-6874         TCGA-F1-6875         TCGA-FP-7735 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-FP-7829         TCGA-FP-7916         TCGA-FP-7998 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-HJ-7597         TCGA-IN-7806         TCGA-IN-7808 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-IP-7968 
"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-BR-7958 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-BR-7959         TCGA-BR-8059         TCGA-BR-8060 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-BR-8077         TCGA-BR-8078         TCGA-BR-8080 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-BR-8081         TCGA-BR-8284         TCGA-BR-8285 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-BR-8286         TCGA-BR-8289         TCGA-BR-8291 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-BR-8295         TCGA-BR-8296         TCGA-BR-8297 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-CD-5798         TCGA-CD-5799         TCGA-CD-5800 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-CD-5801         TCGA-CD-5802         TCGA-CD-5803 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-CG-4300         TCGA-CG-4301         TCGA-CG-4304 
  "17Q LOSS MUTATED"   "17Q LOSS MUTATED" "17Q LOSS WILD-TYPE" 
        TCGA-CG-4305         TCGA-CG-4306         TCGA-CG-4436 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-CG-4437         TCGA-CG-4438         TCGA-CG-4440 
"17Q LOSS WILD-TYPE"   "17Q LOSS MUTATED"   "17Q LOSS MUTATED" 
        TCGA-CG-4441         TCGA-CG-4443         TCGA-CG-4444 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-CG-4449         TCGA-CG-4455         TCGA-CG-4460 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-CG-4462         TCGA-CG-4465         TCGA-CG-4466 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-CG-4469         TCGA-CG-4472         TCGA-CG-4474 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-CG-4477         TCGA-CG-5716         TCGA-CG-5717 
  "17Q LOSS MUTATED" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-CG-5718         TCGA-CG-5719         TCGA-CG-5720 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-CG-5721         TCGA-CG-5722         TCGA-CG-5723 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-CG-5724         TCGA-CG-5725         TCGA-CG-5726 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-CG-5727         TCGA-CG-5728         TCGA-CG-5730 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-CG-5732         TCGA-CG-5733         TCGA-CG-5734 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-D7-5577         TCGA-D7-5578         TCGA-D7-5579 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-D7-6518         TCGA-D7-6519         TCGA-D7-6520 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-D7-6521         TCGA-D7-6522         TCGA-D7-6524 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-D7-6525         TCGA-D7-6526         TCGA-D7-6527 
"17Q LOSS WILD-TYPE"   "17Q LOSS MUTATED" "17Q LOSS WILD-TYPE" 
        TCGA-D7-6528         TCGA-D7-6815         TCGA-D7-6817 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-D7-6818         TCGA-D7-6820         TCGA-D7-6822 
"17Q LOSS WILD-TYPE"   "17Q LOSS MUTATED" "17Q LOSS WILD-TYPE" 
        TCGA-EQ-5647         TCGA-EQ-8122         TCGA-F1-6177 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-F1-6874         TCGA-F1-6875         TCGA-FP-7735 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-FP-7829         TCGA-FP-7916         TCGA-FP-7998 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-HJ-7597         TCGA-IN-7806         TCGA-IN-7808 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-IP-7968 
"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-BR-7958 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-BR-7959         TCGA-BR-8059         TCGA-BR-8060 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-BR-8077         TCGA-BR-8078         TCGA-BR-8080 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-BR-8081         TCGA-BR-8284         TCGA-BR-8285 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-BR-8286         TCGA-BR-8289         TCGA-BR-8291 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-BR-8295         TCGA-BR-8296         TCGA-BR-8297 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-CD-5798         TCGA-CD-5799         TCGA-CD-5800 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-CD-5801         TCGA-CD-5802         TCGA-CD-5803 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-CG-4300         TCGA-CG-4301         TCGA-CG-4304 
  "17Q LOSS MUTATED"   "17Q LOSS MUTATED" "17Q LOSS WILD-TYPE" 
        TCGA-CG-4305         TCGA-CG-4306         TCGA-CG-4436 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-CG-4437         TCGA-CG-4438         TCGA-CG-4440 
"17Q LOSS WILD-TYPE"   "17Q LOSS MUTATED"   "17Q LOSS MUTATED" 
        TCGA-CG-4441         TCGA-CG-4443         TCGA-CG-4444 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-CG-4449         TCGA-CG-4455         TCGA-CG-4460 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-CG-4462         TCGA-CG-4465         TCGA-CG-4466 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-CG-4469         TCGA-CG-4472         TCGA-CG-4474 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-CG-4477         TCGA-CG-5716         TCGA-CG-5717 
  "17Q LOSS MUTATED" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-CG-5718         TCGA-CG-5719         TCGA-CG-5720 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-CG-5721         TCGA-CG-5722         TCGA-CG-5723 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-CG-5724         TCGA-CG-5725         TCGA-CG-5726 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-CG-5727         TCGA-CG-5728         TCGA-CG-5730 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-CG-5732         TCGA-CG-5733         TCGA-CG-5734 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-D7-5577         TCGA-D7-5578         TCGA-D7-5579 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-D7-6518         TCGA-D7-6519         TCGA-D7-6520 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-D7-6521         TCGA-D7-6522         TCGA-D7-6524 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-D7-6525         TCGA-D7-6526         TCGA-D7-6527 
"17Q LOSS WILD-TYPE"   "17Q LOSS MUTATED" "17Q LOSS WILD-TYPE" 
        TCGA-D7-6528         TCGA-D7-6815         TCGA-D7-6817 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-D7-6818         TCGA-D7-6820         TCGA-D7-6822 
"17Q LOSS WILD-TYPE"   "17Q LOSS MUTATED" "17Q LOSS WILD-TYPE" 
        TCGA-EQ-5647         TCGA-EQ-8122         TCGA-F1-6177 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-F1-6874         TCGA-F1-6875         TCGA-FP-7735 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-FP-7829         TCGA-FP-7916         TCGA-FP-7998 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-HJ-7597         TCGA-IN-7806         TCGA-IN-7808 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-IP-7968 
"17Q LOSS WILD-TYPE" 
[1] "hr=" "1.2"
D66V2, continuous
D66V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED      5    4
  17Q LOSS WILD-TYPE   60   92
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  FEMALE                5                 60
  MALE                  4                 92
                    vv
clus                 STOMACH ADENOCARCINOMA - DIFFUSE TYPE
  17Q LOSS MUTATED                                       0
  17Q LOSS WILD-TYPE                                    19
                    vv
clus                 STOMACH ADENOCARCINOMA - NOT OTHERWISE SPECIFIED (NOS)
  17Q LOSS MUTATED                                                        3
  17Q LOSS WILD-TYPE                                                     76
                    vv
clus                 STOMACH ADENOCARCINOMA - SIGNET RING TYPE
  17Q LOSS MUTATED                                           0
  17Q LOSS WILD-TYPE                                         1
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - MUCINOUS TYPE
  17Q LOSS MUTATED                                                   0
  17Q LOSS WILD-TYPE                                                 9
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - PAPILLARY TYPE
  17Q LOSS MUTATED                                                    0
  17Q LOSS WILD-TYPE                                                  3
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - TUBULAR TYPE
  17Q LOSS MUTATED                                                  3
  17Q LOSS WILD-TYPE                                                7
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - TYPE NOT OTHERWISE SPECIFIED (NOS)
  17Q LOSS MUTATED                                                                        3
  17Q LOSS WILD-TYPE                                                                     32
D66V4, multiclass
                    vv
clus                 T1 T2 T3 T4
  17Q LOSS MUTATED    0  4  3  2
  17Q LOSS WILD-TYPE  6 49 56 31
D66V5, multiclass
                    vv
clus                 N0 N1 N2 N3
  17Q LOSS MUTATED    2  2  3  1
  17Q LOSS WILD-TYPE 48 55 21 18
D66V6, multiclass
                    vv
clus                  M0  M1  MX
  17Q LOSS MUTATED     6   2   1
  17Q LOSS WILD-TYPE 126  16  10
D66V7, multiclass
                    vv
clus                  I II III IV
  17Q LOSS MUTATED    2  1   2  3
  17Q LOSS WILD-TYPE 23 42  46 26
D66V8, multiclass
D66V9, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED      1    8
  17Q LOSS WILD-TYPE    4  148
     clus
vv    17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  NO                 1                  4
  YES                8                148

Clustering(67) Variable = 18p loss mutation analysis
D67V1, survival
                    sevent
clus2                  0   1
  18P LOSS MUTATED     5   4
  18P LOSS WILD-TYPE 103  12
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                 9                115 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                 4                 12 
$`18P LOSS MUTATED`
TCGA-BR-7723 TCGA-CG-4440 TCGA-CG-4449 TCGA-CG-4469 TCGA-CG-4477 TCGA-D7-6519 
        4.54         4.01        19.07         7.07         1.02        15.65 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6875 
        0.62         7.79        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-BR-7958 TCGA-BR-7959 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
        0.69         0.16         1.08         0.82         1.32         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
        0.95         0.49         0.46         0.72         0.26         0.43 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-CD-5798 
        0.26         1.18         1.55         1.48         0.76         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-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4455 TCGA-CG-4460 
       54.05        14.01        29.98        47.05        12.03        21.99 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4472 TCGA-CG-4474 TCGA-CG-5716 
        1.02         8.98        18.94        12.00         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-FP-7735 
        4.04         2.93         4.27         6.54         2.01         0.39 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-HJ-7597 TCGA-IN-7806 TCGA-IN-7808 
        0.20         3.02         3.58        26.43         6.87         3.55 
TCGA-IP-7968 
        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 
              7.07               1.41 
[1] "0.6 - 72.2 (7.1)" "0.1 - 70.1 (1.4)"
        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-BR-7958 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BR-7959         TCGA-BR-8059         TCGA-BR-8060 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BR-8077         TCGA-BR-8078         TCGA-BR-8080 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BR-8081         TCGA-BR-8284         TCGA-BR-8285 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BR-8286         TCGA-BR-8289         TCGA-BR-8291 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BR-8295         TCGA-BR-8296         TCGA-BR-8297 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-CD-5798         TCGA-CD-5799         TCGA-CD-5800 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-CD-5801         TCGA-CD-5802         TCGA-CD-5803 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-CG-4300         TCGA-CG-4301         TCGA-CG-4304 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-CG-4305         TCGA-CG-4306         TCGA-CG-4436 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-CG-4437         TCGA-CG-4438         TCGA-CG-4440 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE"   "18P LOSS MUTATED" 
        TCGA-CG-4441         TCGA-CG-4443         TCGA-CG-4444 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-CG-4449         TCGA-CG-4455         TCGA-CG-4460 
  "18P LOSS MUTATED" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-CG-4462         TCGA-CG-4465         TCGA-CG-4466 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-CG-4469         TCGA-CG-4472         TCGA-CG-4474 
  "18P LOSS MUTATED" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-CG-4477         TCGA-CG-5716         TCGA-CG-5717 
  "18P LOSS MUTATED" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-CG-5718         TCGA-CG-5719         TCGA-CG-5720 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-CG-5721         TCGA-CG-5722         TCGA-CG-5723 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-CG-5724         TCGA-CG-5725         TCGA-CG-5726 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-CG-5727         TCGA-CG-5728         TCGA-CG-5730 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-CG-5732         TCGA-CG-5733         TCGA-CG-5734 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-D7-5577         TCGA-D7-5578         TCGA-D7-5579 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-D7-6518         TCGA-D7-6519         TCGA-D7-6520 
"18P LOSS WILD-TYPE"   "18P LOSS MUTATED" "18P LOSS WILD-TYPE" 
        TCGA-D7-6521         TCGA-D7-6522         TCGA-D7-6524 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-D7-6525         TCGA-D7-6526         TCGA-D7-6527 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-D7-6528         TCGA-D7-6815         TCGA-D7-6817 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-D7-6818         TCGA-D7-6820         TCGA-D7-6822 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EQ-5647         TCGA-EQ-8122         TCGA-F1-6177 
  "18P LOSS MUTATED"   "18P LOSS MUTATED" "18P LOSS WILD-TYPE" 
        TCGA-F1-6874         TCGA-F1-6875         TCGA-FP-7735 
"18P LOSS WILD-TYPE"   "18P LOSS MUTATED" "18P LOSS WILD-TYPE" 
        TCGA-FP-7829         TCGA-FP-7916         TCGA-FP-7998 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-HJ-7597         TCGA-IN-7806         TCGA-IN-7808 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-IP-7968 
"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-BR-7958 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BR-7959         TCGA-BR-8059         TCGA-BR-8060 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BR-8077         TCGA-BR-8078         TCGA-BR-8080 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BR-8081         TCGA-BR-8284         TCGA-BR-8285 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BR-8286         TCGA-BR-8289         TCGA-BR-8291 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BR-8295         TCGA-BR-8296         TCGA-BR-8297 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-CD-5798         TCGA-CD-5799         TCGA-CD-5800 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-CD-5801         TCGA-CD-5802         TCGA-CD-5803 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-CG-4300         TCGA-CG-4301         TCGA-CG-4304 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-CG-4305         TCGA-CG-4306         TCGA-CG-4436 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-CG-4437         TCGA-CG-4438         TCGA-CG-4440 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE"   "18P LOSS MUTATED" 
        TCGA-CG-4441         TCGA-CG-4443         TCGA-CG-4444 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-CG-4449         TCGA-CG-4455         TCGA-CG-4460 
  "18P LOSS MUTATED" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-CG-4462         TCGA-CG-4465         TCGA-CG-4466 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-CG-4469         TCGA-CG-4472         TCGA-CG-4474 
  "18P LOSS MUTATED" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-CG-4477         TCGA-CG-5716         TCGA-CG-5717 
  "18P LOSS MUTATED" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-CG-5718         TCGA-CG-5719         TCGA-CG-5720 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-CG-5721         TCGA-CG-5722         TCGA-CG-5723 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-CG-5724         TCGA-CG-5725         TCGA-CG-5726 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-CG-5727         TCGA-CG-5728         TCGA-CG-5730 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-CG-5732         TCGA-CG-5733         TCGA-CG-5734 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-D7-5577         TCGA-D7-5578         TCGA-D7-5579 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-D7-6518         TCGA-D7-6519         TCGA-D7-6520 
"18P LOSS WILD-TYPE"   "18P LOSS MUTATED" "18P LOSS WILD-TYPE" 
        TCGA-D7-6521         TCGA-D7-6522         TCGA-D7-6524 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-D7-6525         TCGA-D7-6526         TCGA-D7-6527 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-D7-6528         TCGA-D7-6815         TCGA-D7-6817 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-D7-6818         TCGA-D7-6820         TCGA-D7-6822 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EQ-5647         TCGA-EQ-8122         TCGA-F1-6177 
  "18P LOSS MUTATED"   "18P LOSS MUTATED" "18P LOSS WILD-TYPE" 
        TCGA-F1-6874         TCGA-F1-6875         TCGA-FP-7735 
"18P LOSS WILD-TYPE"   "18P LOSS MUTATED" "18P LOSS WILD-TYPE" 
        TCGA-FP-7829         TCGA-FP-7916         TCGA-FP-7998 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-HJ-7597         TCGA-IN-7806         TCGA-IN-7808 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-IP-7968 
"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-BR-7958 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BR-7959         TCGA-BR-8059         TCGA-BR-8060 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BR-8077         TCGA-BR-8078         TCGA-BR-8080 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BR-8081         TCGA-BR-8284         TCGA-BR-8285 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BR-8286         TCGA-BR-8289         TCGA-BR-8291 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BR-8295         TCGA-BR-8296         TCGA-BR-8297 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-CD-5798         TCGA-CD-5799         TCGA-CD-5800 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-CD-5801         TCGA-CD-5802         TCGA-CD-5803 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-CG-4300         TCGA-CG-4301         TCGA-CG-4304 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-CG-4305         TCGA-CG-4306         TCGA-CG-4436 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-CG-4437         TCGA-CG-4438         TCGA-CG-4440 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE"   "18P LOSS MUTATED" 
        TCGA-CG-4441         TCGA-CG-4443         TCGA-CG-4444 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-CG-4449         TCGA-CG-4455         TCGA-CG-4460 
  "18P LOSS MUTATED" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-CG-4462         TCGA-CG-4465         TCGA-CG-4466 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-CG-4469         TCGA-CG-4472         TCGA-CG-4474 
  "18P LOSS MUTATED" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-CG-4477         TCGA-CG-5716         TCGA-CG-5717 
  "18P LOSS MUTATED" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-CG-5718         TCGA-CG-5719         TCGA-CG-5720 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-CG-5721         TCGA-CG-5722         TCGA-CG-5723 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-CG-5724         TCGA-CG-5725         TCGA-CG-5726 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-CG-5727         TCGA-CG-5728         TCGA-CG-5730 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-CG-5732         TCGA-CG-5733         TCGA-CG-5734 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-D7-5577         TCGA-D7-5578         TCGA-D7-5579 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-D7-6518         TCGA-D7-6519         TCGA-D7-6520 
"18P LOSS WILD-TYPE"   "18P LOSS MUTATED" "18P LOSS WILD-TYPE" 
        TCGA-D7-6521         TCGA-D7-6522         TCGA-D7-6524 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-D7-6525         TCGA-D7-6526         TCGA-D7-6527 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-D7-6528         TCGA-D7-6815         TCGA-D7-6817 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-D7-6818         TCGA-D7-6820         TCGA-D7-6822 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EQ-5647         TCGA-EQ-8122         TCGA-F1-6177 
  "18P LOSS MUTATED"   "18P LOSS MUTATED" "18P LOSS WILD-TYPE" 
        TCGA-F1-6874         TCGA-F1-6875         TCGA-FP-7735 
"18P LOSS WILD-TYPE"   "18P LOSS MUTATED" "18P LOSS WILD-TYPE" 
        TCGA-FP-7829         TCGA-FP-7916         TCGA-FP-7998 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-HJ-7597         TCGA-IN-7806         TCGA-IN-7808 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-IP-7968 
"18P LOSS WILD-TYPE" 
[1] "hr=" "2"  
D67V2, continuous
D67V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED      5    7
  18P LOSS WILD-TYPE   60   89
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  FEMALE                5                 60
  MALE                  7                 89
                    vv
clus                 STOMACH ADENOCARCINOMA - DIFFUSE TYPE
  18P LOSS MUTATED                                       1
  18P LOSS WILD-TYPE                                    18
                    vv
clus                 STOMACH ADENOCARCINOMA - NOT OTHERWISE SPECIFIED (NOS)
  18P LOSS MUTATED                                                        5
  18P LOSS WILD-TYPE                                                     74
                    vv
clus                 STOMACH ADENOCARCINOMA - SIGNET RING TYPE
  18P LOSS MUTATED                                           0
  18P LOSS WILD-TYPE                                         1
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - MUCINOUS TYPE
  18P LOSS MUTATED                                                   1
  18P LOSS WILD-TYPE                                                 8
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - PAPILLARY TYPE
  18P LOSS MUTATED                                                    0
  18P LOSS WILD-TYPE                                                  3
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - TUBULAR TYPE
  18P LOSS MUTATED                                                  1
  18P LOSS WILD-TYPE                                                9
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - TYPE NOT OTHERWISE SPECIFIED (NOS)
  18P LOSS MUTATED                                                                        4
  18P LOSS WILD-TYPE                                                                     31
D67V4, multiclass
                    vv
clus                 T1 T2 T3 T4
  18P LOSS MUTATED    0  6  4  1
  18P LOSS WILD-TYPE  6 47 55 32
D67V5, multiclass
                    vv
clus                 N0 N1 N2 N3
  18P LOSS MUTATED    2  4  1  3
  18P LOSS WILD-TYPE 48 53 23 16
D67V6, multiclass
                    vv
clus                  M0  M1  MX
  18P LOSS MUTATED     9   2   1
  18P LOSS WILD-TYPE 123  16  10
D67V7, multiclass
                    vv
clus                  I II III IV
  18P LOSS MUTATED    2  4   1  3
  18P LOSS WILD-TYPE 23 39  47 26
D67V8, multiclass
D67V9, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED      0   12
  18P LOSS WILD-TYPE    5  144
     clus
vv    18P LOSS MUTATED 18P LOSS WILD-TYPE
  NO                 0                  5
  YES               12                144

Clustering(68) Variable = 18q loss mutation analysis
D68V1, survival
                    sevent
clus2                 0  1
  18Q LOSS MUTATED   13  4
  18Q LOSS WILD-TYPE 95 12
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                17                107 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                 4                 12 
$`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-5724 TCGA-CG-5730 TCGA-D7-5577 
       19.07         7.07         1.02        12.03         4.01         8.65 
TCGA-D7-6519 TCGA-D7-6521 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-FP-7829 
       15.65         8.19         0.62         7.79         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-BR-7958 TCGA-BR-7959 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 
        0.16         1.08         0.82         1.32         0.69         0.95 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
        0.49         0.46         0.72         0.26         0.43         0.26 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-CD-5798 TCGA-CD-5799 
        1.18         1.55         1.48         0.76         0.82         0.69 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5803 TCGA-CG-4300 TCGA-CG-4304 TCGA-CG-4305 
        0.36         0.49         0.07        20.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 
        1.02        52.96         8.05        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-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-D7-5578 TCGA-D7-5579 
       65.10        55.04        21.07         7.99         3.58         4.54 
TCGA-D7-6518 TCGA-D7-6520 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
        9.80         9.63         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-F1-6875 TCGA-FP-7735 TCGA-FP-7916 
        4.27         6.54         2.01        72.23         0.39         3.02 
TCGA-FP-7998 TCGA-HJ-7597 TCGA-IN-7806 TCGA-IN-7808 TCGA-IP-7968 
        3.58        26.43         6.87         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               1.35 
[1] "0.1 - 54.0 (4.5)" "0.1 - 72.2 (1.4)"
        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-BR-7958 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BR-7959         TCGA-BR-8059         TCGA-BR-8060 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BR-8077         TCGA-BR-8078         TCGA-BR-8080 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BR-8081         TCGA-BR-8284         TCGA-BR-8285 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BR-8286         TCGA-BR-8289         TCGA-BR-8291 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BR-8295         TCGA-BR-8296         TCGA-BR-8297 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-CD-5798         TCGA-CD-5799         TCGA-CD-5800 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-CD-5801         TCGA-CD-5802         TCGA-CD-5803 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" 
        TCGA-CG-4300         TCGA-CG-4301         TCGA-CG-4304 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" 
        TCGA-CG-4305         TCGA-CG-4306         TCGA-CG-4436 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-CG-4437         TCGA-CG-4438         TCGA-CG-4440 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED"   "18Q LOSS MUTATED" 
        TCGA-CG-4441         TCGA-CG-4443         TCGA-CG-4444 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-CG-4449         TCGA-CG-4455         TCGA-CG-4460 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-CG-4462         TCGA-CG-4465         TCGA-CG-4466 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-CG-4469         TCGA-CG-4472         TCGA-CG-4474 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-CG-4477         TCGA-CG-5716         TCGA-CG-5717 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-CG-5718         TCGA-CG-5719         TCGA-CG-5720 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-CG-5721         TCGA-CG-5722         TCGA-CG-5723 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-CG-5724         TCGA-CG-5725         TCGA-CG-5726 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-CG-5727         TCGA-CG-5728         TCGA-CG-5730 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" 
        TCGA-CG-5732         TCGA-CG-5733         TCGA-CG-5734 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-D7-5577         TCGA-D7-5578         TCGA-D7-5579 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-D7-6518         TCGA-D7-6519         TCGA-D7-6520 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" 
        TCGA-D7-6521         TCGA-D7-6522         TCGA-D7-6524 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-D7-6525         TCGA-D7-6526         TCGA-D7-6527 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-D7-6528         TCGA-D7-6815         TCGA-D7-6817 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-D7-6818         TCGA-D7-6820         TCGA-D7-6822 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EQ-5647         TCGA-EQ-8122         TCGA-F1-6177 
  "18Q LOSS MUTATED"   "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" 
        TCGA-F1-6874         TCGA-F1-6875         TCGA-FP-7735 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-FP-7829         TCGA-FP-7916         TCGA-FP-7998 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-HJ-7597         TCGA-IN-7806         TCGA-IN-7808 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-IP-7968 
"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-BR-7958 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BR-7959         TCGA-BR-8059         TCGA-BR-8060 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BR-8077         TCGA-BR-8078         TCGA-BR-8080 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BR-8081         TCGA-BR-8284         TCGA-BR-8285 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BR-8286         TCGA-BR-8289         TCGA-BR-8291 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BR-8295         TCGA-BR-8296         TCGA-BR-8297 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-CD-5798         TCGA-CD-5799         TCGA-CD-5800 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-CD-5801         TCGA-CD-5802         TCGA-CD-5803 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" 
        TCGA-CG-4300         TCGA-CG-4301         TCGA-CG-4304 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" 
        TCGA-CG-4305         TCGA-CG-4306         TCGA-CG-4436 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-CG-4437         TCGA-CG-4438         TCGA-CG-4440 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED"   "18Q LOSS MUTATED" 
        TCGA-CG-4441         TCGA-CG-4443         TCGA-CG-4444 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-CG-4449         TCGA-CG-4455         TCGA-CG-4460 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-CG-4462         TCGA-CG-4465         TCGA-CG-4466 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-CG-4469         TCGA-CG-4472         TCGA-CG-4474 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-CG-4477         TCGA-CG-5716         TCGA-CG-5717 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-CG-5718         TCGA-CG-5719         TCGA-CG-5720 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-CG-5721         TCGA-CG-5722         TCGA-CG-5723 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-CG-5724         TCGA-CG-5725         TCGA-CG-5726 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-CG-5727         TCGA-CG-5728         TCGA-CG-5730 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" 
        TCGA-CG-5732         TCGA-CG-5733         TCGA-CG-5734 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-D7-5577         TCGA-D7-5578         TCGA-D7-5579 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-D7-6518         TCGA-D7-6519         TCGA-D7-6520 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" 
        TCGA-D7-6521         TCGA-D7-6522         TCGA-D7-6524 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-D7-6525         TCGA-D7-6526         TCGA-D7-6527 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-D7-6528         TCGA-D7-6815         TCGA-D7-6817 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-D7-6818         TCGA-D7-6820         TCGA-D7-6822 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EQ-5647         TCGA-EQ-8122         TCGA-F1-6177 
  "18Q LOSS MUTATED"   "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" 
        TCGA-F1-6874         TCGA-F1-6875         TCGA-FP-7735 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-FP-7829         TCGA-FP-7916         TCGA-FP-7998 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-HJ-7597         TCGA-IN-7806         TCGA-IN-7808 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-IP-7968 
"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-BR-7958 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BR-7959         TCGA-BR-8059         TCGA-BR-8060 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BR-8077         TCGA-BR-8078         TCGA-BR-8080 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BR-8081         TCGA-BR-8284         TCGA-BR-8285 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BR-8286         TCGA-BR-8289         TCGA-BR-8291 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BR-8295         TCGA-BR-8296         TCGA-BR-8297 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-CD-5798         TCGA-CD-5799         TCGA-CD-5800 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-CD-5801         TCGA-CD-5802         TCGA-CD-5803 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" 
        TCGA-CG-4300         TCGA-CG-4301         TCGA-CG-4304 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" 
        TCGA-CG-4305         TCGA-CG-4306         TCGA-CG-4436 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-CG-4437         TCGA-CG-4438         TCGA-CG-4440 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED"   "18Q LOSS MUTATED" 
        TCGA-CG-4441         TCGA-CG-4443         TCGA-CG-4444 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-CG-4449         TCGA-CG-4455         TCGA-CG-4460 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-CG-4462         TCGA-CG-4465         TCGA-CG-4466 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-CG-4469         TCGA-CG-4472         TCGA-CG-4474 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-CG-4477         TCGA-CG-5716         TCGA-CG-5717 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-CG-5718         TCGA-CG-5719         TCGA-CG-5720 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-CG-5721         TCGA-CG-5722         TCGA-CG-5723 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-CG-5724         TCGA-CG-5725         TCGA-CG-5726 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-CG-5727         TCGA-CG-5728         TCGA-CG-5730 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" 
        TCGA-CG-5732         TCGA-CG-5733         TCGA-CG-5734 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-D7-5577         TCGA-D7-5578         TCGA-D7-5579 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-D7-6518         TCGA-D7-6519         TCGA-D7-6520 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" 
        TCGA-D7-6521         TCGA-D7-6522         TCGA-D7-6524 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-D7-6525         TCGA-D7-6526         TCGA-D7-6527 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-D7-6528         TCGA-D7-6815         TCGA-D7-6817 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-D7-6818         TCGA-D7-6820         TCGA-D7-6822 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EQ-5647         TCGA-EQ-8122         TCGA-F1-6177 
  "18Q LOSS MUTATED"   "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" 
        TCGA-F1-6874         TCGA-F1-6875         TCGA-FP-7735 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-FP-7829         TCGA-FP-7916         TCGA-FP-7998 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-HJ-7597         TCGA-IN-7806         TCGA-IN-7808 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-IP-7968 
"18Q LOSS WILD-TYPE" 
[1] "hr=" "2.1"
D68V2, continuous
D68V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED      8   16
  18Q LOSS WILD-TYPE   57   80
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  FEMALE                8                 57
  MALE                 16                 80
                    vv
clus                 STOMACH ADENOCARCINOMA - DIFFUSE TYPE
  18Q LOSS MUTATED                                       4
  18Q LOSS WILD-TYPE                                    15
                    vv
clus                 STOMACH ADENOCARCINOMA - NOT OTHERWISE SPECIFIED (NOS)
  18Q LOSS MUTATED                                                        9
  18Q LOSS WILD-TYPE                                                     70
                    vv
clus                 STOMACH ADENOCARCINOMA - SIGNET RING TYPE
  18Q LOSS MUTATED                                           0
  18Q LOSS WILD-TYPE                                         1
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - MUCINOUS TYPE
  18Q LOSS MUTATED                                                   2
  18Q LOSS WILD-TYPE                                                 7
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - PAPILLARY TYPE
  18Q LOSS MUTATED                                                    0
  18Q LOSS WILD-TYPE                                                  3
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - TUBULAR TYPE
  18Q LOSS MUTATED                                                  2
  18Q LOSS WILD-TYPE                                                8
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - TYPE NOT OTHERWISE SPECIFIED (NOS)
  18Q LOSS MUTATED                                                                        6
  18Q LOSS WILD-TYPE                                                                     29
D68V4, multiclass
                    vv
clus                 T1 T2 T3 T4
  18Q LOSS MUTATED    0 10  9  3
  18Q LOSS WILD-TYPE  6 43 50 30
D68V5, multiclass
                    vv
clus                 N0 N1 N2 N3
  18Q LOSS MUTATED    4 10  3  5
  18Q LOSS WILD-TYPE 46 47 21 14
D68V6, multiclass
                    vv
clus                  M0  M1  MX
  18Q LOSS MUTATED    18   5   1
  18Q LOSS WILD-TYPE 114  13  10
D68V7, multiclass
                    vv
clus                  I II III IV
  18Q LOSS MUTATED    3  6   5  7
  18Q LOSS WILD-TYPE 22 37  43 22
D68V8, multiclass
D68V9, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED      0   24
  18Q LOSS WILD-TYPE    5  132
     clus
vv    18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  NO                 0                  5
  YES               24                132

Clustering(69) Variable = 19p loss mutation analysis
D69V1, survival
                    sevent
clus2                 0  1
  19P LOSS MUTATED   11  3
  19P LOSS WILD-TYPE 97 13
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                14                110 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                 3                 13 
$`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-BR-7958 
        0.69         0.16         0.99         0.95         0.69         0.16 
TCGA-BR-7959 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
        1.08         0.82         1.32         0.69         0.95         0.49 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
        0.46         0.72         0.26         0.43         0.26         1.18 
TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
        1.55         1.48         0.76         0.82         0.69         0.36 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
        0.49         0.30         0.07        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4437 TCGA-CG-4441 TCGA-CG-4444 TCGA-CG-4449 
       15.95         1.02         8.05        14.01        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-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-D7-6521 TCGA-D7-6522 
        3.58         4.54         9.80        15.65         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-D7-6822 TCGA-EQ-8122 TCGA-F1-6177 TCGA-F1-6874 TCGA-F1-6875 
        4.04         4.27         7.79         6.54         2.01        72.23 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-HJ-7597 TCGA-IN-7806 
        0.39         0.20         3.02         3.58        26.43         6.87 
TCGA-IN-7808 TCGA-IP-7968 
        3.55         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 
             7.790              1.335 
[1] "0.6 - 55.0 (7.8)" "0.1 - 72.2 (1.3)"
        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-BR-7958 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BR-7959         TCGA-BR-8059         TCGA-BR-8060 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BR-8077         TCGA-BR-8078         TCGA-BR-8080 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BR-8081         TCGA-BR-8284         TCGA-BR-8285 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BR-8286         TCGA-BR-8289         TCGA-BR-8291 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BR-8295         TCGA-BR-8296         TCGA-BR-8297 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-CD-5798         TCGA-CD-5799         TCGA-CD-5800 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-CD-5801         TCGA-CD-5802         TCGA-CD-5803 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-CG-4300         TCGA-CG-4301         TCGA-CG-4304 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-CG-4305         TCGA-CG-4306         TCGA-CG-4436 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE"   "19P LOSS MUTATED" 
        TCGA-CG-4437         TCGA-CG-4438         TCGA-CG-4440 
"19P LOSS WILD-TYPE"   "19P LOSS MUTATED"   "19P LOSS MUTATED" 
        TCGA-CG-4441         TCGA-CG-4443         TCGA-CG-4444 
"19P LOSS WILD-TYPE"   "19P LOSS MUTATED" "19P LOSS WILD-TYPE" 
        TCGA-CG-4449         TCGA-CG-4455         TCGA-CG-4460 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-CG-4462         TCGA-CG-4465         TCGA-CG-4466 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE"   "19P LOSS MUTATED" 
        TCGA-CG-4469         TCGA-CG-4472         TCGA-CG-4474 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-CG-4477         TCGA-CG-5716         TCGA-CG-5717 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-CG-5718         TCGA-CG-5719         TCGA-CG-5720 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-CG-5721         TCGA-CG-5722         TCGA-CG-5723 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-CG-5724         TCGA-CG-5725         TCGA-CG-5726 
"19P LOSS WILD-TYPE"   "19P LOSS MUTATED" "19P LOSS WILD-TYPE" 
        TCGA-CG-5727         TCGA-CG-5728         TCGA-CG-5730 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-CG-5732         TCGA-CG-5733         TCGA-CG-5734 
  "19P LOSS MUTATED" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-D7-5577         TCGA-D7-5578         TCGA-D7-5579 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-D7-6518         TCGA-D7-6519         TCGA-D7-6520 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE"   "19P LOSS MUTATED" 
        TCGA-D7-6521         TCGA-D7-6522         TCGA-D7-6524 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-D7-6525         TCGA-D7-6526         TCGA-D7-6527 
  "19P LOSS MUTATED" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-D7-6528         TCGA-D7-6815         TCGA-D7-6817 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-D7-6818         TCGA-D7-6820         TCGA-D7-6822 
"19P LOSS WILD-TYPE"   "19P LOSS MUTATED" "19P LOSS WILD-TYPE" 
        TCGA-EQ-5647         TCGA-EQ-8122         TCGA-F1-6177 
  "19P LOSS MUTATED" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-F1-6874         TCGA-F1-6875         TCGA-FP-7735 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-FP-7829         TCGA-FP-7916         TCGA-FP-7998 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-HJ-7597         TCGA-IN-7806         TCGA-IN-7808 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-IP-7968 
"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-BR-7958 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BR-7959         TCGA-BR-8059         TCGA-BR-8060 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BR-8077         TCGA-BR-8078         TCGA-BR-8080 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BR-8081         TCGA-BR-8284         TCGA-BR-8285 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BR-8286         TCGA-BR-8289         TCGA-BR-8291 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BR-8295         TCGA-BR-8296         TCGA-BR-8297 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-CD-5798         TCGA-CD-5799         TCGA-CD-5800 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-CD-5801         TCGA-CD-5802         TCGA-CD-5803 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-CG-4300         TCGA-CG-4301         TCGA-CG-4304 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-CG-4305         TCGA-CG-4306         TCGA-CG-4436 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE"   "19P LOSS MUTATED" 
        TCGA-CG-4437         TCGA-CG-4438         TCGA-CG-4440 
"19P LOSS WILD-TYPE"   "19P LOSS MUTATED"   "19P LOSS MUTATED" 
        TCGA-CG-4441         TCGA-CG-4443         TCGA-CG-4444 
"19P LOSS WILD-TYPE"   "19P LOSS MUTATED" "19P LOSS WILD-TYPE" 
        TCGA-CG-4449         TCGA-CG-4455         TCGA-CG-4460 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-CG-4462         TCGA-CG-4465         TCGA-CG-4466 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE"   "19P LOSS MUTATED" 
        TCGA-CG-4469         TCGA-CG-4472         TCGA-CG-4474 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-CG-4477         TCGA-CG-5716         TCGA-CG-5717 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-CG-5718         TCGA-CG-5719         TCGA-CG-5720 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-CG-5721         TCGA-CG-5722         TCGA-CG-5723 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-CG-5724         TCGA-CG-5725         TCGA-CG-5726 
"19P LOSS WILD-TYPE"   "19P LOSS MUTATED" "19P LOSS WILD-TYPE" 
        TCGA-CG-5727         TCGA-CG-5728         TCGA-CG-5730 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-CG-5732         TCGA-CG-5733         TCGA-CG-5734 
  "19P LOSS MUTATED" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-D7-5577         TCGA-D7-5578         TCGA-D7-5579 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-D7-6518         TCGA-D7-6519         TCGA-D7-6520 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE"   "19P LOSS MUTATED" 
        TCGA-D7-6521         TCGA-D7-6522         TCGA-D7-6524 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-D7-6525         TCGA-D7-6526         TCGA-D7-6527 
  "19P LOSS MUTATED" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-D7-6528         TCGA-D7-6815         TCGA-D7-6817 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-D7-6818         TCGA-D7-6820         TCGA-D7-6822 
"19P LOSS WILD-TYPE"   "19P LOSS MUTATED" "19P LOSS WILD-TYPE" 
        TCGA-EQ-5647         TCGA-EQ-8122         TCGA-F1-6177 
  "19P LOSS MUTATED" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-F1-6874         TCGA-F1-6875         TCGA-FP-7735 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-FP-7829         TCGA-FP-7916         TCGA-FP-7998 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-HJ-7597         TCGA-IN-7806         TCGA-IN-7808 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-IP-7968 
"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-BR-7958 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BR-7959         TCGA-BR-8059         TCGA-BR-8060 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BR-8077         TCGA-BR-8078         TCGA-BR-8080 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BR-8081         TCGA-BR-8284         TCGA-BR-8285 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BR-8286         TCGA-BR-8289         TCGA-BR-8291 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BR-8295         TCGA-BR-8296         TCGA-BR-8297 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-CD-5798         TCGA-CD-5799         TCGA-CD-5800 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-CD-5801         TCGA-CD-5802         TCGA-CD-5803 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-CG-4300         TCGA-CG-4301         TCGA-CG-4304 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-CG-4305         TCGA-CG-4306         TCGA-CG-4436 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE"   "19P LOSS MUTATED" 
        TCGA-CG-4437         TCGA-CG-4438         TCGA-CG-4440 
"19P LOSS WILD-TYPE"   "19P LOSS MUTATED"   "19P LOSS MUTATED" 
        TCGA-CG-4441         TCGA-CG-4443         TCGA-CG-4444 
"19P LOSS WILD-TYPE"   "19P LOSS MUTATED" "19P LOSS WILD-TYPE" 
        TCGA-CG-4449         TCGA-CG-4455         TCGA-CG-4460 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-CG-4462         TCGA-CG-4465         TCGA-CG-4466 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE"   "19P LOSS MUTATED" 
        TCGA-CG-4469         TCGA-CG-4472         TCGA-CG-4474 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-CG-4477         TCGA-CG-5716         TCGA-CG-5717 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-CG-5718         TCGA-CG-5719         TCGA-CG-5720 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-CG-5721         TCGA-CG-5722         TCGA-CG-5723 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-CG-5724         TCGA-CG-5725         TCGA-CG-5726 
"19P LOSS WILD-TYPE"   "19P LOSS MUTATED" "19P LOSS WILD-TYPE" 
        TCGA-CG-5727         TCGA-CG-5728         TCGA-CG-5730 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-CG-5732         TCGA-CG-5733         TCGA-CG-5734 
  "19P LOSS MUTATED" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-D7-5577         TCGA-D7-5578         TCGA-D7-5579 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-D7-6518         TCGA-D7-6519         TCGA-D7-6520 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE"   "19P LOSS MUTATED" 
        TCGA-D7-6521         TCGA-D7-6522         TCGA-D7-6524 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-D7-6525         TCGA-D7-6526         TCGA-D7-6527 
  "19P LOSS MUTATED" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-D7-6528         TCGA-D7-6815         TCGA-D7-6817 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-D7-6818         TCGA-D7-6820         TCGA-D7-6822 
"19P LOSS WILD-TYPE"   "19P LOSS MUTATED" "19P LOSS WILD-TYPE" 
        TCGA-EQ-5647         TCGA-EQ-8122         TCGA-F1-6177 
  "19P LOSS MUTATED" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-F1-6874         TCGA-F1-6875         TCGA-FP-7735 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-FP-7829         TCGA-FP-7916         TCGA-FP-7998 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-HJ-7597         TCGA-IN-7806         TCGA-IN-7808 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-IP-7968 
"19P LOSS WILD-TYPE" 
[1] "hr=" "1.3"
D69V2, continuous
D69V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED      4   12
  19P LOSS WILD-TYPE   61   84
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  FEMALE                4                 61
  MALE                 12                 84
                    vv
clus                 STOMACH ADENOCARCINOMA - DIFFUSE TYPE
  19P LOSS MUTATED                                       1
  19P LOSS WILD-TYPE                                    18
                    vv
clus                 STOMACH ADENOCARCINOMA - NOT OTHERWISE SPECIFIED (NOS)
  19P LOSS MUTATED                                                        7
  19P LOSS WILD-TYPE                                                     72
                    vv
clus                 STOMACH ADENOCARCINOMA - SIGNET RING TYPE
  19P LOSS MUTATED                                           0
  19P LOSS WILD-TYPE                                         1
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - MUCINOUS TYPE
  19P LOSS MUTATED                                                   0
  19P LOSS WILD-TYPE                                                 9
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - PAPILLARY TYPE
  19P LOSS MUTATED                                                    0
  19P LOSS WILD-TYPE                                                  3
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - TUBULAR TYPE
  19P LOSS MUTATED                                                  2
  19P LOSS WILD-TYPE                                                8
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - TYPE NOT OTHERWISE SPECIFIED (NOS)
  19P LOSS MUTATED                                                                        6
  19P LOSS WILD-TYPE                                                                     29
D69V4, multiclass
                    vv
clus                 T1 T2 T3 T4
  19P LOSS MUTATED    1  7  5  2
  19P LOSS WILD-TYPE  5 46 54 31
D69V5, multiclass
                    vv
clus                 N0 N1 N2 N3
  19P LOSS MUTATED    5  3  4  3
  19P LOSS WILD-TYPE 45 54 20 16
D69V6, multiclass
                    vv
clus                  M0  M1  MX
  19P LOSS MUTATED    14   2   0
  19P LOSS WILD-TYPE 118  16  11
D69V7, multiclass
                    vv
clus                  I II III IV
  19P LOSS MUTATED    4  4   3  4
  19P LOSS WILD-TYPE 21 39  45 25
D69V8, multiclass
D69V9, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED      0   16
  19P LOSS WILD-TYPE    5  140
     clus
vv    19P LOSS MUTATED 19P LOSS WILD-TYPE
  NO                 0                  5
  YES               16                140

Clustering(70) Variable = 19q loss mutation analysis
D70V1, survival
                    sevent
clus2                  0   1
  19Q LOSS MUTATED     7   3
  19Q LOSS WILD-TYPE 101  13
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                10                114 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                 3                 13 
$`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-BR-7958 TCGA-BR-7959 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 
        0.16         1.08         0.82         1.32         0.69         0.95 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
        0.49         0.46         0.72         0.26         0.43         0.26 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-CD-5798 TCGA-CD-5799 
        1.18         1.55         1.48         0.76         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-4437 TCGA-CG-4438 TCGA-CG-4441 
       27.02        15.95         1.02         8.05        54.05        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-D7-6520 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-D7-6822 
        4.14         1.68         3.65         4.70         4.04         4.27 
TCGA-EQ-8122 TCGA-F1-6177 TCGA-F1-6874 TCGA-F1-6875 TCGA-FP-7735 TCGA-FP-7829 
        7.79         6.54         2.01        72.23         0.39         0.20 
TCGA-FP-7916 TCGA-FP-7998 TCGA-HJ-7597 TCGA-IN-7806 TCGA-IN-7808 TCGA-IP-7968 
        3.02         3.58        26.43         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               1.38 
[1] "0.6 - 55.0 (9.8)" "0.1 - 72.2 (1.4)"
        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-BR-7958 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BR-7959         TCGA-BR-8059         TCGA-BR-8060 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BR-8077         TCGA-BR-8078         TCGA-BR-8080 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BR-8081         TCGA-BR-8284         TCGA-BR-8285 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BR-8286         TCGA-BR-8289         TCGA-BR-8291 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BR-8295         TCGA-BR-8296         TCGA-BR-8297 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-CD-5798         TCGA-CD-5799         TCGA-CD-5800 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-CD-5801         TCGA-CD-5802         TCGA-CD-5803 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-CG-4300         TCGA-CG-4301         TCGA-CG-4304 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-CG-4305         TCGA-CG-4306         TCGA-CG-4436 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE"   "19Q LOSS MUTATED" 
        TCGA-CG-4437         TCGA-CG-4438         TCGA-CG-4440 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE"   "19Q LOSS MUTATED" 
        TCGA-CG-4441         TCGA-CG-4443         TCGA-CG-4444 
"19Q LOSS WILD-TYPE"   "19Q LOSS MUTATED" "19Q LOSS WILD-TYPE" 
        TCGA-CG-4449         TCGA-CG-4455         TCGA-CG-4460 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-CG-4462         TCGA-CG-4465         TCGA-CG-4466 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE"   "19Q LOSS MUTATED" 
        TCGA-CG-4469         TCGA-CG-4472         TCGA-CG-4474 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-CG-4477         TCGA-CG-5716         TCGA-CG-5717 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-CG-5718         TCGA-CG-5719         TCGA-CG-5720 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-CG-5721         TCGA-CG-5722         TCGA-CG-5723 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-CG-5724         TCGA-CG-5725         TCGA-CG-5726 
"19Q LOSS WILD-TYPE"   "19Q LOSS MUTATED" "19Q LOSS WILD-TYPE" 
        TCGA-CG-5727         TCGA-CG-5728         TCGA-CG-5730 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-CG-5732         TCGA-CG-5733         TCGA-CG-5734 
  "19Q LOSS MUTATED" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-D7-5577         TCGA-D7-5578         TCGA-D7-5579 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-D7-6518         TCGA-D7-6519         TCGA-D7-6520 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-D7-6521         TCGA-D7-6522         TCGA-D7-6524 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-D7-6525         TCGA-D7-6526         TCGA-D7-6527 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-D7-6528         TCGA-D7-6815         TCGA-D7-6817 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-D7-6818         TCGA-D7-6820         TCGA-D7-6822 
"19Q LOSS WILD-TYPE"   "19Q LOSS MUTATED" "19Q LOSS WILD-TYPE" 
        TCGA-EQ-5647         TCGA-EQ-8122         TCGA-F1-6177 
  "19Q LOSS MUTATED" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-F1-6874         TCGA-F1-6875         TCGA-FP-7735 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-FP-7829         TCGA-FP-7916         TCGA-FP-7998 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-HJ-7597         TCGA-IN-7806         TCGA-IN-7808 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-IP-7968 
"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-BR-7958 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BR-7959         TCGA-BR-8059         TCGA-BR-8060 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BR-8077         TCGA-BR-8078         TCGA-BR-8080 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BR-8081         TCGA-BR-8284         TCGA-BR-8285 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BR-8286         TCGA-BR-8289         TCGA-BR-8291 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BR-8295         TCGA-BR-8296         TCGA-BR-8297 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-CD-5798         TCGA-CD-5799         TCGA-CD-5800 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-CD-5801         TCGA-CD-5802         TCGA-CD-5803 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-CG-4300         TCGA-CG-4301         TCGA-CG-4304 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-CG-4305         TCGA-CG-4306         TCGA-CG-4436 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE"   "19Q LOSS MUTATED" 
        TCGA-CG-4437         TCGA-CG-4438         TCGA-CG-4440 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE"   "19Q LOSS MUTATED" 
        TCGA-CG-4441         TCGA-CG-4443         TCGA-CG-4444 
"19Q LOSS WILD-TYPE"   "19Q LOSS MUTATED" "19Q LOSS WILD-TYPE" 
        TCGA-CG-4449         TCGA-CG-4455         TCGA-CG-4460 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-CG-4462         TCGA-CG-4465         TCGA-CG-4466 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE"   "19Q LOSS MUTATED" 
        TCGA-CG-4469         TCGA-CG-4472         TCGA-CG-4474 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-CG-4477         TCGA-CG-5716         TCGA-CG-5717 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-CG-5718         TCGA-CG-5719         TCGA-CG-5720 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-CG-5721         TCGA-CG-5722         TCGA-CG-5723 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-CG-5724         TCGA-CG-5725         TCGA-CG-5726 
"19Q LOSS WILD-TYPE"   "19Q LOSS MUTATED" "19Q LOSS WILD-TYPE" 
        TCGA-CG-5727         TCGA-CG-5728         TCGA-CG-5730 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-CG-5732         TCGA-CG-5733         TCGA-CG-5734 
  "19Q LOSS MUTATED" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-D7-5577         TCGA-D7-5578         TCGA-D7-5579 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-D7-6518         TCGA-D7-6519         TCGA-D7-6520 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-D7-6521         TCGA-D7-6522         TCGA-D7-6524 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-D7-6525         TCGA-D7-6526         TCGA-D7-6527 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-D7-6528         TCGA-D7-6815         TCGA-D7-6817 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-D7-6818         TCGA-D7-6820         TCGA-D7-6822 
"19Q LOSS WILD-TYPE"   "19Q LOSS MUTATED" "19Q LOSS WILD-TYPE" 
        TCGA-EQ-5647         TCGA-EQ-8122         TCGA-F1-6177 
  "19Q LOSS MUTATED" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-F1-6874         TCGA-F1-6875         TCGA-FP-7735 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-FP-7829         TCGA-FP-7916         TCGA-FP-7998 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-HJ-7597         TCGA-IN-7806         TCGA-IN-7808 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-IP-7968 
"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-BR-7958 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BR-7959         TCGA-BR-8059         TCGA-BR-8060 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BR-8077         TCGA-BR-8078         TCGA-BR-8080 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BR-8081         TCGA-BR-8284         TCGA-BR-8285 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BR-8286         TCGA-BR-8289         TCGA-BR-8291 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BR-8295         TCGA-BR-8296         TCGA-BR-8297 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-CD-5798         TCGA-CD-5799         TCGA-CD-5800 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-CD-5801         TCGA-CD-5802         TCGA-CD-5803 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-CG-4300         TCGA-CG-4301         TCGA-CG-4304 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-CG-4305         TCGA-CG-4306         TCGA-CG-4436 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE"   "19Q LOSS MUTATED" 
        TCGA-CG-4437         TCGA-CG-4438         TCGA-CG-4440 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE"   "19Q LOSS MUTATED" 
        TCGA-CG-4441         TCGA-CG-4443         TCGA-CG-4444 
"19Q LOSS WILD-TYPE"   "19Q LOSS MUTATED" "19Q LOSS WILD-TYPE" 
        TCGA-CG-4449         TCGA-CG-4455         TCGA-CG-4460 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-CG-4462         TCGA-CG-4465         TCGA-CG-4466 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE"   "19Q LOSS MUTATED" 
        TCGA-CG-4469         TCGA-CG-4472         TCGA-CG-4474 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-CG-4477         TCGA-CG-5716         TCGA-CG-5717 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-CG-5718         TCGA-CG-5719         TCGA-CG-5720 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-CG-5721         TCGA-CG-5722         TCGA-CG-5723 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-CG-5724         TCGA-CG-5725         TCGA-CG-5726 
"19Q LOSS WILD-TYPE"   "19Q LOSS MUTATED" "19Q LOSS WILD-TYPE" 
        TCGA-CG-5727         TCGA-CG-5728         TCGA-CG-5730 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-CG-5732         TCGA-CG-5733         TCGA-CG-5734 
  "19Q LOSS MUTATED" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-D7-5577         TCGA-D7-5578         TCGA-D7-5579 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-D7-6518         TCGA-D7-6519         TCGA-D7-6520 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-D7-6521         TCGA-D7-6522         TCGA-D7-6524 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-D7-6525         TCGA-D7-6526         TCGA-D7-6527 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-D7-6528         TCGA-D7-6815         TCGA-D7-6817 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-D7-6818         TCGA-D7-6820         TCGA-D7-6822 
"19Q LOSS WILD-TYPE"   "19Q LOSS MUTATED" "19Q LOSS WILD-TYPE" 
        TCGA-EQ-5647         TCGA-EQ-8122         TCGA-F1-6177 
  "19Q LOSS MUTATED" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-F1-6874         TCGA-F1-6875         TCGA-FP-7735 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-FP-7829         TCGA-FP-7916         TCGA-FP-7998 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-HJ-7597         TCGA-IN-7806         TCGA-IN-7808 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-IP-7968 
"19Q LOSS WILD-TYPE" 
[1] "hr=" "1.1"
D70V2, continuous
D70V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED      3    9
  19Q LOSS WILD-TYPE   62   87
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  FEMALE                3                 62
  MALE                  9                 87
                    vv
clus                 STOMACH ADENOCARCINOMA - DIFFUSE TYPE
  19Q LOSS MUTATED                                       0
  19Q LOSS WILD-TYPE                                    19
                    vv
clus                 STOMACH ADENOCARCINOMA - NOT OTHERWISE SPECIFIED (NOS)
  19Q LOSS MUTATED                                                        6
  19Q LOSS WILD-TYPE                                                     73
                    vv
clus                 STOMACH ADENOCARCINOMA - SIGNET RING TYPE
  19Q LOSS MUTATED                                           0
  19Q LOSS WILD-TYPE                                         1
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - MUCINOUS TYPE
  19Q LOSS MUTATED                                                   0
  19Q LOSS WILD-TYPE                                                 9
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - PAPILLARY TYPE
  19Q LOSS MUTATED                                                    0
  19Q LOSS WILD-TYPE                                                  3
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - TUBULAR TYPE
  19Q LOSS MUTATED                                                  1
  19Q LOSS WILD-TYPE                                                9
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - TYPE NOT OTHERWISE SPECIFIED (NOS)
  19Q LOSS MUTATED                                                                        5
  19Q LOSS WILD-TYPE                                                                     30
D70V4, multiclass
                    vv
clus                 T1 T2 T3 T4
  19Q LOSS MUTATED    1  5  4  1
  19Q LOSS WILD-TYPE  5 48 55 32
D70V5, multiclass
                    vv
clus                 N0 N1 N2 N3
  19Q LOSS MUTATED    5  2  1  3
  19Q LOSS WILD-TYPE 45 55 23 16
D70V6, multiclass
                    vv
clus                  M0  M1  MX
  19Q LOSS MUTATED    10   2   0
  19Q LOSS WILD-TYPE 122  16  11
D70V7, multiclass
                    vv
clus                  I II III IV
  19Q LOSS MUTATED    4  3   1  3
  19Q LOSS WILD-TYPE 21 40  47 26
D70V8, multiclass
D70V9, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED      0   12
  19Q LOSS WILD-TYPE    5  144
     clus
vv    19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  NO                 0                  5
  YES               12                144

Clustering(71) Variable = 20p loss mutation analysis
D71V1, survival
                    sevent
clus2                  0   1
  20P LOSS MUTATED     2   1
  20P LOSS WILD-TYPE 106  15
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                 3                121 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                 1                 15 
$`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-BR-7958 TCGA-BR-7959 TCGA-BR-8059 TCGA-BR-8060 
        0.95         0.69         0.16         1.08         0.82         1.32 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
        0.69         0.95         0.49         0.46         0.72         0.26 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
        0.43         0.26         1.18         1.55         1.48         0.76 
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-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-D7-6520 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-8122 TCGA-F1-6177 TCGA-F1-6874 TCGA-F1-6875 TCGA-FP-7735 
        4.27         7.79         6.54         2.01        72.23         0.39 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-HJ-7597 TCGA-IN-7806 TCGA-IN-7808 
        0.20         3.02         3.58        26.43         6.87         3.55 
TCGA-IP-7968 
        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               1.48 
[1] "0.6 - 15.7 (3.0)" "0.1 - 72.2 (1.5)"
        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-BR-7958 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-BR-7959         TCGA-BR-8059         TCGA-BR-8060 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-BR-8077         TCGA-BR-8078         TCGA-BR-8080 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-BR-8081         TCGA-BR-8284         TCGA-BR-8285 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-BR-8286         TCGA-BR-8289         TCGA-BR-8291 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-BR-8295         TCGA-BR-8296         TCGA-BR-8297 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CD-5798         TCGA-CD-5799         TCGA-CD-5800 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CD-5801         TCGA-CD-5802         TCGA-CD-5803 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CG-4300         TCGA-CG-4301         TCGA-CG-4304 
"20P LOSS WILD-TYPE"   "20P LOSS MUTATED" "20P LOSS WILD-TYPE" 
        TCGA-CG-4305         TCGA-CG-4306         TCGA-CG-4436 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CG-4437         TCGA-CG-4438         TCGA-CG-4440 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CG-4441         TCGA-CG-4443         TCGA-CG-4444 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CG-4449         TCGA-CG-4455         TCGA-CG-4460 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CG-4462         TCGA-CG-4465         TCGA-CG-4466 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CG-4469         TCGA-CG-4472         TCGA-CG-4474 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CG-4477         TCGA-CG-5716         TCGA-CG-5717 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CG-5718         TCGA-CG-5719         TCGA-CG-5720 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CG-5721         TCGA-CG-5722         TCGA-CG-5723 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CG-5724         TCGA-CG-5725         TCGA-CG-5726 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CG-5727         TCGA-CG-5728         TCGA-CG-5730 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CG-5732         TCGA-CG-5733         TCGA-CG-5734 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-D7-5577         TCGA-D7-5578         TCGA-D7-5579 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-D7-6518         TCGA-D7-6519         TCGA-D7-6520 
"20P LOSS WILD-TYPE"   "20P LOSS MUTATED" "20P LOSS WILD-TYPE" 
        TCGA-D7-6521         TCGA-D7-6522         TCGA-D7-6524 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-D7-6525         TCGA-D7-6526         TCGA-D7-6527 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-D7-6528         TCGA-D7-6815         TCGA-D7-6817 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-D7-6818         TCGA-D7-6820         TCGA-D7-6822 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EQ-5647         TCGA-EQ-8122         TCGA-F1-6177 
  "20P LOSS MUTATED" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-F1-6874         TCGA-F1-6875         TCGA-FP-7735 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-FP-7829         TCGA-FP-7916         TCGA-FP-7998 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-HJ-7597         TCGA-IN-7806         TCGA-IN-7808 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-IP-7968 
"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-BR-7958 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-BR-7959         TCGA-BR-8059         TCGA-BR-8060 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-BR-8077         TCGA-BR-8078         TCGA-BR-8080 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-BR-8081         TCGA-BR-8284         TCGA-BR-8285 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-BR-8286         TCGA-BR-8289         TCGA-BR-8291 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-BR-8295         TCGA-BR-8296         TCGA-BR-8297 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CD-5798         TCGA-CD-5799         TCGA-CD-5800 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CD-5801         TCGA-CD-5802         TCGA-CD-5803 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CG-4300         TCGA-CG-4301         TCGA-CG-4304 
"20P LOSS WILD-TYPE"   "20P LOSS MUTATED" "20P LOSS WILD-TYPE" 
        TCGA-CG-4305         TCGA-CG-4306         TCGA-CG-4436 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CG-4437         TCGA-CG-4438         TCGA-CG-4440 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CG-4441         TCGA-CG-4443         TCGA-CG-4444 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CG-4449         TCGA-CG-4455         TCGA-CG-4460 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CG-4462         TCGA-CG-4465         TCGA-CG-4466 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CG-4469         TCGA-CG-4472         TCGA-CG-4474 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CG-4477         TCGA-CG-5716         TCGA-CG-5717 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CG-5718         TCGA-CG-5719         TCGA-CG-5720 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CG-5721         TCGA-CG-5722         TCGA-CG-5723 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CG-5724         TCGA-CG-5725         TCGA-CG-5726 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CG-5727         TCGA-CG-5728         TCGA-CG-5730 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CG-5732         TCGA-CG-5733         TCGA-CG-5734 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-D7-5577         TCGA-D7-5578         TCGA-D7-5579 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-D7-6518         TCGA-D7-6519         TCGA-D7-6520 
"20P LOSS WILD-TYPE"   "20P LOSS MUTATED" "20P LOSS WILD-TYPE" 
        TCGA-D7-6521         TCGA-D7-6522         TCGA-D7-6524 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-D7-6525         TCGA-D7-6526         TCGA-D7-6527 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-D7-6528         TCGA-D7-6815         TCGA-D7-6817 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-D7-6818         TCGA-D7-6820         TCGA-D7-6822 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EQ-5647         TCGA-EQ-8122         TCGA-F1-6177 
  "20P LOSS MUTATED" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-F1-6874         TCGA-F1-6875         TCGA-FP-7735 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-FP-7829         TCGA-FP-7916         TCGA-FP-7998 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-HJ-7597         TCGA-IN-7806         TCGA-IN-7808 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-IP-7968 
"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-BR-7958 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-BR-7959         TCGA-BR-8059         TCGA-BR-8060 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-BR-8077         TCGA-BR-8078         TCGA-BR-8080 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-BR-8081         TCGA-BR-8284         TCGA-BR-8285 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-BR-8286         TCGA-BR-8289         TCGA-BR-8291 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-BR-8295         TCGA-BR-8296         TCGA-BR-8297 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CD-5798         TCGA-CD-5799         TCGA-CD-5800 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CD-5801         TCGA-CD-5802         TCGA-CD-5803 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CG-4300         TCGA-CG-4301         TCGA-CG-4304 
"20P LOSS WILD-TYPE"   "20P LOSS MUTATED" "20P LOSS WILD-TYPE" 
        TCGA-CG-4305         TCGA-CG-4306         TCGA-CG-4436 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CG-4437         TCGA-CG-4438         TCGA-CG-4440 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CG-4441         TCGA-CG-4443         TCGA-CG-4444 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CG-4449         TCGA-CG-4455         TCGA-CG-4460 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CG-4462         TCGA-CG-4465         TCGA-CG-4466 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CG-4469         TCGA-CG-4472         TCGA-CG-4474 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CG-4477         TCGA-CG-5716         TCGA-CG-5717 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CG-5718         TCGA-CG-5719         TCGA-CG-5720 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CG-5721         TCGA-CG-5722         TCGA-CG-5723 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CG-5724         TCGA-CG-5725         TCGA-CG-5726 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CG-5727         TCGA-CG-5728         TCGA-CG-5730 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CG-5732         TCGA-CG-5733         TCGA-CG-5734 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-D7-5577         TCGA-D7-5578         TCGA-D7-5579 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-D7-6518         TCGA-D7-6519         TCGA-D7-6520 
"20P LOSS WILD-TYPE"   "20P LOSS MUTATED" "20P LOSS WILD-TYPE" 
        TCGA-D7-6521         TCGA-D7-6522         TCGA-D7-6524 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-D7-6525         TCGA-D7-6526         TCGA-D7-6527 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-D7-6528         TCGA-D7-6815         TCGA-D7-6817 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-D7-6818         TCGA-D7-6820         TCGA-D7-6822 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EQ-5647         TCGA-EQ-8122         TCGA-F1-6177 
  "20P LOSS MUTATED" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-F1-6874         TCGA-F1-6875         TCGA-FP-7735 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-FP-7829         TCGA-FP-7916         TCGA-FP-7998 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-HJ-7597         TCGA-IN-7806         TCGA-IN-7808 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-IP-7968 
"20P LOSS WILD-TYPE" 
[1] "hr=" "2.9"
D71V2, continuous
D71V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED      3    1
  20P LOSS WILD-TYPE   62   95
        clus
vv       20P LOSS MUTATED 20P LOSS WILD-TYPE
  FEMALE                3                 62
  MALE                  1                 95
                    vv
clus                 STOMACH ADENOCARCINOMA - DIFFUSE TYPE
  20P LOSS MUTATED                                       1
  20P LOSS WILD-TYPE                                    18
                    vv
clus                 STOMACH ADENOCARCINOMA - NOT OTHERWISE SPECIFIED (NOS)
  20P LOSS MUTATED                                                        3
  20P LOSS WILD-TYPE                                                     76
                    vv
clus                 STOMACH ADENOCARCINOMA - SIGNET RING TYPE
  20P LOSS MUTATED                                           0
  20P LOSS WILD-TYPE                                         1
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - MUCINOUS TYPE
  20P LOSS MUTATED                                                   0
  20P LOSS WILD-TYPE                                                 9
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - PAPILLARY TYPE
  20P LOSS MUTATED                                                    0
  20P LOSS WILD-TYPE                                                  3
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - TUBULAR TYPE
  20P LOSS MUTATED                                                  0
  20P LOSS WILD-TYPE                                               10
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - TYPE NOT OTHERWISE SPECIFIED (NOS)
  20P LOSS MUTATED                                                                        0
  20P LOSS WILD-TYPE                                                                     35
D71V4, multiclass
                    vv
clus                 T1 T2 T3 T4
  20P LOSS MUTATED    0  2  0  2
  20P LOSS WILD-TYPE  6 51 59 31
D71V5, multiclass
                    vv
clus                 N0 N1 N2 N3
  20P LOSS MUTATED    1  2  0  1
  20P LOSS WILD-TYPE 49 55 24 18
D71V6, multiclass
                    vv
clus                  M0  M1  MX
  20P LOSS MUTATED     2   2   0
  20P LOSS WILD-TYPE 130  16  11
D71V7, multiclass
                    vv
clus                  I II III IV
  20P LOSS MUTATED    1  0   1  2
  20P LOSS WILD-TYPE 24 43  47 27
D71V8, multiclass
D71V9, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED      0    4
  20P LOSS WILD-TYPE    5  152
     clus
vv    20P LOSS MUTATED 20P LOSS WILD-TYPE
  NO                 0                  5
  YES                4                152

Clustering(72) Variable = 21q loss mutation analysis
D72V1, survival
                    sevent
clus2                 0  1
  21Q LOSS MUTATED   17  3
  21Q LOSS WILD-TYPE 91 13
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                20                104 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                 3                 13 
$`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-BR-7958 TCGA-BR-7959 
        4.54         0.99         0.95         0.69         0.16         1.08 
TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
        0.82         1.32         0.69         0.95         0.49         0.46 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
        0.72         0.26         0.43         0.26         1.18         1.55 
TCGA-BR-8296 TCGA-BR-8297 TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
        1.48         0.76         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-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-5716 TCGA-CG-5717 TCGA-CG-5718 
        7.07        12.00         1.02         1.02         6.94         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5726 TCGA-CG-5727 
        0.99         5.98         0.95        70.06        28.96        31.04 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-6518 
       55.04        21.07         7.99         8.65         3.58         9.80 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6527 TCGA-D7-6528 
        9.63         8.19         6.90         0.69         4.14         1.68 
TCGA-D7-6815 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-EQ-8122 TCGA-F1-6177 
        3.65         4.04         2.93         4.27         7.79         6.54 
TCGA-F1-6874 TCGA-F1-6875 TCGA-FP-7735 TCGA-FP-7916 TCGA-FP-7998 TCGA-HJ-7597 
        2.01        72.23         0.39         3.02         3.58        26.43 
TCGA-IN-7808 TCGA-IP-7968 
        3.55         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 
             4.620              1.445 
[1] "0.1 - 65.1 (4.6)" "0.1 - 72.2 (1.4)"
        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-BR-7958 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-BR-7959         TCGA-BR-8059         TCGA-BR-8060 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-BR-8077         TCGA-BR-8078         TCGA-BR-8080 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-BR-8081         TCGA-BR-8284         TCGA-BR-8285 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-BR-8286         TCGA-BR-8289         TCGA-BR-8291 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-BR-8295         TCGA-BR-8296         TCGA-BR-8297 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-CD-5798         TCGA-CD-5799         TCGA-CD-5800 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-CD-5801         TCGA-CD-5802         TCGA-CD-5803 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-CG-4300         TCGA-CG-4301         TCGA-CG-4304 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-CG-4305         TCGA-CG-4306         TCGA-CG-4436 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-CG-4437         TCGA-CG-4438         TCGA-CG-4440 
"21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-CG-4441         TCGA-CG-4443         TCGA-CG-4444 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-CG-4449         TCGA-CG-4455         TCGA-CG-4460 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-CG-4462         TCGA-CG-4465         TCGA-CG-4466 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" 
        TCGA-CG-4469         TCGA-CG-4472         TCGA-CG-4474 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-CG-4477         TCGA-CG-5716         TCGA-CG-5717 
  "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-CG-5718         TCGA-CG-5719         TCGA-CG-5720 
"21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-CG-5721         TCGA-CG-5722         TCGA-CG-5723 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-CG-5724         TCGA-CG-5725         TCGA-CG-5726 
  "21Q LOSS MUTATED"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-CG-5727         TCGA-CG-5728         TCGA-CG-5730 
"21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED"   "21Q LOSS MUTATED" 
        TCGA-CG-5732         TCGA-CG-5733         TCGA-CG-5734 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-D7-5577         TCGA-D7-5578         TCGA-D7-5579 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" 
        TCGA-D7-6518         TCGA-D7-6519         TCGA-D7-6520 
"21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-D7-6521         TCGA-D7-6522         TCGA-D7-6524 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-D7-6525         TCGA-D7-6526         TCGA-D7-6527 
  "21Q LOSS MUTATED"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-D7-6528         TCGA-D7-6815         TCGA-D7-6817 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" 
        TCGA-D7-6818         TCGA-D7-6820         TCGA-D7-6822 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-EQ-5647         TCGA-EQ-8122         TCGA-F1-6177 
  "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-F1-6874         TCGA-F1-6875         TCGA-FP-7735 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-FP-7829         TCGA-FP-7916         TCGA-FP-7998 
  "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-HJ-7597         TCGA-IN-7806         TCGA-IN-7808 
"21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-IP-7968 
"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-BR-7958 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-BR-7959         TCGA-BR-8059         TCGA-BR-8060 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-BR-8077         TCGA-BR-8078         TCGA-BR-8080 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-BR-8081         TCGA-BR-8284         TCGA-BR-8285 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-BR-8286         TCGA-BR-8289         TCGA-BR-8291 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-BR-8295         TCGA-BR-8296         TCGA-BR-8297 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-CD-5798         TCGA-CD-5799         TCGA-CD-5800 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-CD-5801         TCGA-CD-5802         TCGA-CD-5803 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-CG-4300         TCGA-CG-4301         TCGA-CG-4304 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-CG-4305         TCGA-CG-4306         TCGA-CG-4436 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-CG-4437         TCGA-CG-4438         TCGA-CG-4440 
"21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-CG-4441         TCGA-CG-4443         TCGA-CG-4444 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-CG-4449         TCGA-CG-4455         TCGA-CG-4460 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-CG-4462         TCGA-CG-4465         TCGA-CG-4466 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" 
        TCGA-CG-4469         TCGA-CG-4472         TCGA-CG-4474 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-CG-4477         TCGA-CG-5716         TCGA-CG-5717 
  "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-CG-5718         TCGA-CG-5719         TCGA-CG-5720 
"21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-CG-5721         TCGA-CG-5722         TCGA-CG-5723 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-CG-5724         TCGA-CG-5725         TCGA-CG-5726 
  "21Q LOSS MUTATED"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-CG-5727         TCGA-CG-5728         TCGA-CG-5730 
"21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED"   "21Q LOSS MUTATED" 
        TCGA-CG-5732         TCGA-CG-5733         TCGA-CG-5734 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-D7-5577         TCGA-D7-5578         TCGA-D7-5579 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" 
        TCGA-D7-6518         TCGA-D7-6519         TCGA-D7-6520 
"21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-D7-6521         TCGA-D7-6522         TCGA-D7-6524 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-D7-6525         TCGA-D7-6526         TCGA-D7-6527 
  "21Q LOSS MUTATED"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-D7-6528         TCGA-D7-6815         TCGA-D7-6817 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" 
        TCGA-D7-6818         TCGA-D7-6820         TCGA-D7-6822 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-EQ-5647         TCGA-EQ-8122         TCGA-F1-6177 
  "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-F1-6874         TCGA-F1-6875         TCGA-FP-7735 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-FP-7829         TCGA-FP-7916         TCGA-FP-7998 
  "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-HJ-7597         TCGA-IN-7806         TCGA-IN-7808 
"21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-IP-7968 
"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-BR-7958 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-BR-7959         TCGA-BR-8059         TCGA-BR-8060 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-BR-8077         TCGA-BR-8078         TCGA-BR-8080 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-BR-8081         TCGA-BR-8284         TCGA-BR-8285 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-BR-8286         TCGA-BR-8289         TCGA-BR-8291 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-BR-8295         TCGA-BR-8296         TCGA-BR-8297 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-CD-5798         TCGA-CD-5799         TCGA-CD-5800 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-CD-5801         TCGA-CD-5802         TCGA-CD-5803 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-CG-4300         TCGA-CG-4301         TCGA-CG-4304 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-CG-4305         TCGA-CG-4306         TCGA-CG-4436 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-CG-4437         TCGA-CG-4438         TCGA-CG-4440 
"21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-CG-4441         TCGA-CG-4443         TCGA-CG-4444 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-CG-4449         TCGA-CG-4455         TCGA-CG-4460 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-CG-4462         TCGA-CG-4465         TCGA-CG-4466 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" 
        TCGA-CG-4469         TCGA-CG-4472         TCGA-CG-4474 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-CG-4477         TCGA-CG-5716         TCGA-CG-5717 
  "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-CG-5718         TCGA-CG-5719         TCGA-CG-5720 
"21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-CG-5721         TCGA-CG-5722         TCGA-CG-5723 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-CG-5724         TCGA-CG-5725         TCGA-CG-5726 
  "21Q LOSS MUTATED"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-CG-5727         TCGA-CG-5728         TCGA-CG-5730 
"21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED"   "21Q LOSS MUTATED" 
        TCGA-CG-5732         TCGA-CG-5733         TCGA-CG-5734 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-D7-5577         TCGA-D7-5578         TCGA-D7-5579 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" 
        TCGA-D7-6518         TCGA-D7-6519         TCGA-D7-6520 
"21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-D7-6521         TCGA-D7-6522         TCGA-D7-6524 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-D7-6525         TCGA-D7-6526         TCGA-D7-6527 
  "21Q LOSS MUTATED"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-D7-6528         TCGA-D7-6815         TCGA-D7-6817 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" 
        TCGA-D7-6818         TCGA-D7-6820         TCGA-D7-6822 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-EQ-5647         TCGA-EQ-8122         TCGA-F1-6177 
  "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-F1-6874         TCGA-F1-6875         TCGA-FP-7735 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-FP-7829         TCGA-FP-7916         TCGA-FP-7998 
  "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-HJ-7597         TCGA-IN-7806         TCGA-IN-7808 
"21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-IP-7968 
"21Q LOSS WILD-TYPE" 
[1] "hr=" "1"  
D72V2, continuous
D72V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED     12   17
  21Q LOSS WILD-TYPE   53   79
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  FEMALE               12                 53
  MALE                 17                 79
                    vv
clus                 STOMACH ADENOCARCINOMA - DIFFUSE TYPE
  21Q LOSS MUTATED                                       5
  21Q LOSS WILD-TYPE                                    14
                    vv
clus                 STOMACH ADENOCARCINOMA - NOT OTHERWISE SPECIFIED (NOS)
  21Q LOSS MUTATED                                                       11
  21Q LOSS WILD-TYPE                                                     68
                    vv
clus                 STOMACH ADENOCARCINOMA - SIGNET RING TYPE
  21Q LOSS MUTATED                                           0
  21Q LOSS WILD-TYPE                                         1
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - MUCINOUS TYPE
  21Q LOSS MUTATED                                                   3
  21Q LOSS WILD-TYPE                                                 6
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - PAPILLARY TYPE
  21Q LOSS MUTATED                                                    0
  21Q LOSS WILD-TYPE                                                  3
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - TUBULAR TYPE
  21Q LOSS MUTATED                                                  2
  21Q LOSS WILD-TYPE                                                8
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - TYPE NOT OTHERWISE SPECIFIED (NOS)
  21Q LOSS MUTATED                                                                        7
  21Q LOSS WILD-TYPE                                                                     28
D72V4, multiclass
                    vv
clus                 T1 T2 T3 T4
  21Q LOSS MUTATED    0 10 12  3
  21Q LOSS WILD-TYPE  6 43 47 30
D72V5, multiclass
                    vv
clus                 N0 N1 N2 N3
  21Q LOSS MUTATED    8 10  4  4
  21Q LOSS WILD-TYPE 42 47 20 15
D72V6, multiclass
                    vv
clus                  M0  M1  MX
  21Q LOSS MUTATED    23   4   2
  21Q LOSS WILD-TYPE 109  14   9
D72V7, multiclass
                    vv
clus                  I II III IV
  21Q LOSS MUTATED    5  5   8  6
  21Q LOSS WILD-TYPE 20 38  40 23
D72V8, multiclass
D72V9, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED      1   28
  21Q LOSS WILD-TYPE    4  128
     clus
vv    21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  NO                 1                  4
  YES               28                128

Clustering(73) Variable = 22q loss mutation analysis
D73V1, survival
                    sevent
clus2                 0  1
  22Q LOSS MUTATED   12  4
  22Q LOSS WILD-TYPE 96 12
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                16                108 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                 4                 12 
$`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 TCGA-EQ-8122 
        4.70         2.93         0.62         7.79 

$`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-BR-7958 TCGA-BR-7959 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 
        0.16         1.08         0.82         1.32         0.69         0.95 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
        0.49         0.46         0.72         0.26         0.43         0.26 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-CD-5798 TCGA-CD-5799 
        1.18         1.55         1.48         0.76         0.82         0.69 
TCGA-CD-5801 TCGA-CD-5803 TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
        0.49         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-4469 
       47.05        19.07        12.03         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-5726 
        1.02         0.99         5.98         0.95        70.06        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-D7-5579 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-D7-6818 
        5.95         6.61         4.14         1.68         3.65         4.04 
TCGA-D7-6822 TCGA-F1-6177 TCGA-F1-6874 TCGA-F1-6875 TCGA-FP-7735 TCGA-FP-7829 
        4.27         6.54         2.01        72.23         0.39         0.20 
TCGA-FP-7916 TCGA-FP-7998 TCGA-HJ-7597 TCGA-IN-7806 TCGA-IN-7808 TCGA-IP-7968 
        3.02         3.58        26.43         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 
             6.245              1.380 
[1] "0.3 - 55.0 (6.2)" "0.1 - 72.2 (1.4)"
        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-BR-7958 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-BR-7959         TCGA-BR-8059         TCGA-BR-8060 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-BR-8077         TCGA-BR-8078         TCGA-BR-8080 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-BR-8081         TCGA-BR-8284         TCGA-BR-8285 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-BR-8286         TCGA-BR-8289         TCGA-BR-8291 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-BR-8295         TCGA-BR-8296         TCGA-BR-8297 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-CD-5798         TCGA-CD-5799         TCGA-CD-5800 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" 
        TCGA-CD-5801         TCGA-CD-5802         TCGA-CD-5803 
"22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" 
        TCGA-CG-4300         TCGA-CG-4301         TCGA-CG-4304 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-CG-4305         TCGA-CG-4306         TCGA-CG-4436 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-CG-4437         TCGA-CG-4438         TCGA-CG-4440 
"22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" 
        TCGA-CG-4441         TCGA-CG-4443         TCGA-CG-4444 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-CG-4449         TCGA-CG-4455         TCGA-CG-4460 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" 
        TCGA-CG-4462         TCGA-CG-4465         TCGA-CG-4466 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" 
        TCGA-CG-4469         TCGA-CG-4472         TCGA-CG-4474 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-CG-4477         TCGA-CG-5716         TCGA-CG-5717 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-CG-5718         TCGA-CG-5719         TCGA-CG-5720 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-CG-5721         TCGA-CG-5722         TCGA-CG-5723 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-CG-5724         TCGA-CG-5725         TCGA-CG-5726 
  "22Q LOSS MUTATED"   "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" 
        TCGA-CG-5727         TCGA-CG-5728         TCGA-CG-5730 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-CG-5732         TCGA-CG-5733         TCGA-CG-5734 
  "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-D7-5577         TCGA-D7-5578         TCGA-D7-5579 
"22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" 
        TCGA-D7-6518         TCGA-D7-6519         TCGA-D7-6520 
"22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" 
        TCGA-D7-6521         TCGA-D7-6522         TCGA-D7-6524 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-D7-6525         TCGA-D7-6526         TCGA-D7-6527 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-D7-6528         TCGA-D7-6815         TCGA-D7-6817 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" 
        TCGA-D7-6818         TCGA-D7-6820         TCGA-D7-6822 
"22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" 
        TCGA-EQ-5647         TCGA-EQ-8122         TCGA-F1-6177 
  "22Q LOSS MUTATED"   "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" 
        TCGA-F1-6874         TCGA-F1-6875         TCGA-FP-7735 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-FP-7829         TCGA-FP-7916         TCGA-FP-7998 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-HJ-7597         TCGA-IN-7806         TCGA-IN-7808 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-IP-7968 
"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-BR-7958 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-BR-7959         TCGA-BR-8059         TCGA-BR-8060 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-BR-8077         TCGA-BR-8078         TCGA-BR-8080 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-BR-8081         TCGA-BR-8284         TCGA-BR-8285 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-BR-8286         TCGA-BR-8289         TCGA-BR-8291 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-BR-8295         TCGA-BR-8296         TCGA-BR-8297 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-CD-5798         TCGA-CD-5799         TCGA-CD-5800 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" 
        TCGA-CD-5801         TCGA-CD-5802         TCGA-CD-5803 
"22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" 
        TCGA-CG-4300         TCGA-CG-4301         TCGA-CG-4304 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-CG-4305         TCGA-CG-4306         TCGA-CG-4436 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-CG-4437         TCGA-CG-4438         TCGA-CG-4440 
"22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" 
        TCGA-CG-4441         TCGA-CG-4443         TCGA-CG-4444 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-CG-4449         TCGA-CG-4455         TCGA-CG-4460 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" 
        TCGA-CG-4462         TCGA-CG-4465         TCGA-CG-4466 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" 
        TCGA-CG-4469         TCGA-CG-4472         TCGA-CG-4474 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-CG-4477         TCGA-CG-5716         TCGA-CG-5717 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-CG-5718         TCGA-CG-5719         TCGA-CG-5720 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-CG-5721         TCGA-CG-5722         TCGA-CG-5723 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-CG-5724         TCGA-CG-5725         TCGA-CG-5726 
  "22Q LOSS MUTATED"   "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" 
        TCGA-CG-5727         TCGA-CG-5728         TCGA-CG-5730 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-CG-5732         TCGA-CG-5733         TCGA-CG-5734 
  "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-D7-5577         TCGA-D7-5578         TCGA-D7-5579 
"22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" 
        TCGA-D7-6518         TCGA-D7-6519         TCGA-D7-6520 
"22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" 
        TCGA-D7-6521         TCGA-D7-6522         TCGA-D7-6524 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-D7-6525         TCGA-D7-6526         TCGA-D7-6527 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-D7-6528         TCGA-D7-6815         TCGA-D7-6817 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" 
        TCGA-D7-6818         TCGA-D7-6820         TCGA-D7-6822 
"22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" 
        TCGA-EQ-5647         TCGA-EQ-8122         TCGA-F1-6177 
  "22Q LOSS MUTATED"   "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" 
        TCGA-F1-6874         TCGA-F1-6875         TCGA-FP-7735 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-FP-7829         TCGA-FP-7916         TCGA-FP-7998 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-HJ-7597         TCGA-IN-7806         TCGA-IN-7808 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-IP-7968 
"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-BR-7958 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-BR-7959         TCGA-BR-8059         TCGA-BR-8060 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-BR-8077         TCGA-BR-8078         TCGA-BR-8080 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-BR-8081         TCGA-BR-8284         TCGA-BR-8285 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-BR-8286         TCGA-BR-8289         TCGA-BR-8291 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-BR-8295         TCGA-BR-8296         TCGA-BR-8297 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-CD-5798         TCGA-CD-5799         TCGA-CD-5800 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" 
        TCGA-CD-5801         TCGA-CD-5802         TCGA-CD-5803 
"22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" 
        TCGA-CG-4300         TCGA-CG-4301         TCGA-CG-4304 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-CG-4305         TCGA-CG-4306         TCGA-CG-4436 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-CG-4437         TCGA-CG-4438         TCGA-CG-4440 
"22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" 
        TCGA-CG-4441         TCGA-CG-4443         TCGA-CG-4444 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-CG-4449         TCGA-CG-4455         TCGA-CG-4460 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" 
        TCGA-CG-4462         TCGA-CG-4465         TCGA-CG-4466 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" 
        TCGA-CG-4469         TCGA-CG-4472         TCGA-CG-4474 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-CG-4477         TCGA-CG-5716         TCGA-CG-5717 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-CG-5718         TCGA-CG-5719         TCGA-CG-5720 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-CG-5721         TCGA-CG-5722         TCGA-CG-5723 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-CG-5724         TCGA-CG-5725         TCGA-CG-5726 
  "22Q LOSS MUTATED"   "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" 
        TCGA-CG-5727         TCGA-CG-5728         TCGA-CG-5730 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-CG-5732         TCGA-CG-5733         TCGA-CG-5734 
  "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-D7-5577         TCGA-D7-5578         TCGA-D7-5579 
"22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" 
        TCGA-D7-6518         TCGA-D7-6519         TCGA-D7-6520 
"22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" 
        TCGA-D7-6521         TCGA-D7-6522         TCGA-D7-6524 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-D7-6525         TCGA-D7-6526         TCGA-D7-6527 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-D7-6528         TCGA-D7-6815         TCGA-D7-6817 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" 
        TCGA-D7-6818         TCGA-D7-6820         TCGA-D7-6822 
"22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" 
        TCGA-EQ-5647         TCGA-EQ-8122         TCGA-F1-6177 
  "22Q LOSS MUTATED"   "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" 
        TCGA-F1-6874         TCGA-F1-6875         TCGA-FP-7735 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-FP-7829         TCGA-FP-7916         TCGA-FP-7998 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-HJ-7597         TCGA-IN-7806         TCGA-IN-7808 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-IP-7968 
"22Q LOSS WILD-TYPE" 
[1] "hr=" "1.3"
D73V2, continuous
D73V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED      9   13
  22Q LOSS WILD-TYPE   56   83
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  FEMALE                9                 56
  MALE                 13                 83
                    vv
clus                 STOMACH ADENOCARCINOMA - DIFFUSE TYPE
  22Q LOSS MUTATED                                       2
  22Q LOSS WILD-TYPE                                    17
                    vv
clus                 STOMACH ADENOCARCINOMA - NOT OTHERWISE SPECIFIED (NOS)
  22Q LOSS MUTATED                                                       10
  22Q LOSS WILD-TYPE                                                     69
                    vv
clus                 STOMACH ADENOCARCINOMA - SIGNET RING TYPE
  22Q LOSS MUTATED                                           0
  22Q LOSS WILD-TYPE                                         1
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - MUCINOUS TYPE
  22Q LOSS MUTATED                                                   0
  22Q LOSS WILD-TYPE                                                 9
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - PAPILLARY TYPE
  22Q LOSS MUTATED                                                    1
  22Q LOSS WILD-TYPE                                                  2
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - TUBULAR TYPE
  22Q LOSS MUTATED                                                  4
  22Q LOSS WILD-TYPE                                                6
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - TYPE NOT OTHERWISE SPECIFIED (NOS)
  22Q LOSS MUTATED                                                                        5
  22Q LOSS WILD-TYPE                                                                     30
D73V4, multiclass
                    vv
clus                 T1 T2 T3 T4
  22Q LOSS MUTATED    0  9  9  3
  22Q LOSS WILD-TYPE  6 44 50 30
D73V5, multiclass
                    vv
clus                 N0 N1 N2 N3
  22Q LOSS MUTATED    7  8  2  4
  22Q LOSS WILD-TYPE 43 49 22 15
D73V6, multiclass
                    vv
clus                  M0  M1  MX
  22Q LOSS MUTATED    17   3   2
  22Q LOSS WILD-TYPE 115  15   9
D73V7, multiclass
                    vv
clus                  I II III IV
  22Q LOSS MUTATED    4  7   4  5
  22Q LOSS WILD-TYPE 21 36  44 24
D73V8, multiclass
D73V9, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED      1   21
  22Q LOSS WILD-TYPE    4  135
     clus
vv    22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  NO                 1                  4
  YES               21                135

Clustering(74) Variable = Xq loss mutation analysis
D74V1, survival
                   sevent
clus2                 0   1
  XQ LOSS MUTATED     2   2
  XQ LOSS WILD-TYPE 106  14
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
                4               120 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
                2                14 
$`XQ LOSS MUTATED`
TCGA-BR-7703 TCGA-CG-4469 TCGA-CG-5725 TCGA-D7-6519 
        0.46         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-7704 TCGA-BR-7707 TCGA-BR-7715 
        0.26         1.22         1.48         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-BR-7958 TCGA-BR-7959 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
        0.69         0.16         1.08         0.82         1.32         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
        0.95         0.49         0.46         0.72         0.26         0.43 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-CD-5798 
        0.26         1.18         1.55         1.48         0.76         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-4472 
       12.03        21.99         1.02         8.98        18.94        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-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-D7-6520 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-D7-6527 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-EQ-8122 TCGA-F1-6177 TCGA-F1-6874 TCGA-F1-6875 TCGA-FP-7735 TCGA-FP-7829 
        7.79         6.54         2.01        72.23         0.39         0.20 
TCGA-FP-7916 TCGA-FP-7998 TCGA-HJ-7597 TCGA-IN-7806 TCGA-IN-7808 TCGA-IP-7968 
        3.02         3.58        26.43         6.87         3.55         2.53 

  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
             0.46              0.07 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
            15.65             72.23 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
           11.045             1.480 
[1] "0.5 - 15.7 (11.0)" "0.1 - 72.2 (1.5)" 
       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 MUTATED" "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-BR-7958        TCGA-BR-7959        TCGA-BR-8059        TCGA-BR-8060 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BR-8077        TCGA-BR-8078        TCGA-BR-8080        TCGA-BR-8081 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BR-8284        TCGA-BR-8285        TCGA-BR-8286        TCGA-BR-8289 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BR-8291        TCGA-BR-8295        TCGA-BR-8296        TCGA-BR-8297 
"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-EQ-8122        TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-FP-7735        TCGA-FP-7829        TCGA-FP-7916        TCGA-FP-7998 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-HJ-7597        TCGA-IN-7806        TCGA-IN-7808        TCGA-IP-7968 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "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 MUTATED" "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-BR-7958        TCGA-BR-7959        TCGA-BR-8059        TCGA-BR-8060 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BR-8077        TCGA-BR-8078        TCGA-BR-8080        TCGA-BR-8081 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BR-8284        TCGA-BR-8285        TCGA-BR-8286        TCGA-BR-8289 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BR-8291        TCGA-BR-8295        TCGA-BR-8296        TCGA-BR-8297 
"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-EQ-8122        TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-FP-7735        TCGA-FP-7829        TCGA-FP-7916        TCGA-FP-7998 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-HJ-7597        TCGA-IN-7806        TCGA-IN-7808        TCGA-IP-7968 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "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 MUTATED" "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-BR-7958        TCGA-BR-7959        TCGA-BR-8059        TCGA-BR-8060 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BR-8077        TCGA-BR-8078        TCGA-BR-8080        TCGA-BR-8081 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BR-8284        TCGA-BR-8285        TCGA-BR-8286        TCGA-BR-8289 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BR-8291        TCGA-BR-8295        TCGA-BR-8296        TCGA-BR-8297 
"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-EQ-8122        TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-FP-7735        TCGA-FP-7829        TCGA-FP-7916        TCGA-FP-7998 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-HJ-7597        TCGA-IN-7806        TCGA-IN-7808        TCGA-IP-7968 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
[1] "hr=" "3"  
D74V2, continuous
D74V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED      2    5
  XQ LOSS WILD-TYPE   63   91
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  FEMALE               2                63
  MALE                 5                91
                   vv
clus                STOMACH ADENOCARCINOMA - DIFFUSE TYPE
  XQ LOSS MUTATED                                       1
  XQ LOSS WILD-TYPE                                    18
                   vv
clus                STOMACH ADENOCARCINOMA - NOT OTHERWISE SPECIFIED (NOS)
  XQ LOSS MUTATED                                                        2
  XQ LOSS WILD-TYPE                                                     77
                   vv
clus                STOMACH ADENOCARCINOMA - SIGNET RING TYPE
  XQ LOSS MUTATED                                           0
  XQ LOSS WILD-TYPE                                         1
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - MUCINOUS TYPE
  XQ LOSS MUTATED                                                   1
  XQ LOSS WILD-TYPE                                                 8
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - PAPILLARY TYPE
  XQ LOSS MUTATED                                                    1
  XQ LOSS WILD-TYPE                                                  2
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - TUBULAR TYPE
  XQ LOSS MUTATED                                                  1
  XQ LOSS WILD-TYPE                                                9
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - TYPE NOT OTHERWISE SPECIFIED (NOS)
  XQ LOSS MUTATED                                                                        1
  XQ LOSS WILD-TYPE                                                                     34
D74V4, multiclass
                   vv
clus                T1 T2 T3 T4
  XQ LOSS MUTATED    1  4  1  0
  XQ LOSS WILD-TYPE  5 49 58 33
D74V5, multiclass
                   vv
clus                N0 N1 N2 N3
  XQ LOSS MUTATED    2  2  0  2
  XQ LOSS WILD-TYPE 48 55 24 17
D74V6, multiclass
                   vv
clus                 M0  M1  MX
  XQ LOSS MUTATED     7   0   0
  XQ LOSS WILD-TYPE 125  18  11
D74V7, multiclass
                   vv
clus                 I II III IV
  XQ LOSS MUTATED    2  0   1  2
  XQ LOSS WILD-TYPE 23 43  47 27
D74V8, multiclass
D74V9, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED      1    6
  XQ LOSS WILD-TYPE    4  150
     clus
vv    XQ LOSS MUTATED XQ LOSS WILD-TYPE
  NO                1                 4
  YES               6               150
                                    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" 
> q(save="no")
