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

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

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

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

> source("/xchip/tcga/gdac_prod/applications/process_mgmt/firehose_task_registry/tcga-gdac/Correlate_Clinical_Cnvsarms_onlysig/broadinstitute.org/cancer.genome.analysis/00498/19/CNV2ClinicalAnalysis_nozzle_onlysig_arm.R")
> result <- main("/xchip/tcga/gdac_prod/applications/process_mgmt/firehose_task_registry/tcga-gdac/Correlate_Clinical_Cnvsarms_onlysig/broadinstitute.org/cancer.genome.analysis/00498/19/", "-nF=/xchip/tcga/Tools/Nozzle/v1.current", "-iD=/xchip/cga/gdac-prod/tcga-gdac/jobResults/cnvarms2cluster/STAD-TP/2861352/broad_values_by_arm.mutsig.cluster.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPickerPipeline/STAD-TP/2844303/1.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=MUTSIG", "-iT=", "-iX=")
[1] "nver"          "-nV=Nozzle.R1"
[1] "nfn"                                 "/xchip/tcga/Tools/Nozzle/v1.current"
[1] "Nozzle.R1"
[1] "successfully load Nozzle.R1"
[1] "ofn"         "-oT=STAD-TP"
[1] "opt"        "-OP=MUTSIG"
[1] "tl"   "-iT="
[1] "dx"   "-iX="
[1] "opt"    "MUTSIG"
[1] "dx" ""  

nPatients in clinical file=178, in cluster file=306, common to both=177
[1] "Reduce the number of clustering variables from 80 to 74."
[1]  74 177
[1] "1p gain mutation analysis"
[1] 3
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
                9               168 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
                9               168 
[1] "1q gain mutation analysis"
[1] 3
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               24               153 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               24               153 
[1] "2p gain mutation analysis"
[1] 3
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               11               166 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               11               166 
[1] "2q gain mutation analysis"
[1] 3
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               13               164 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               13               164 
[1] "3p gain mutation analysis"
[1] 3
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
                3               174 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
                3               174 
[1] "3q gain mutation analysis"
[1] 3
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               14               163 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               14               163 
[1] "4p gain mutation analysis"
[1] 3
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                3               174 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                3               174 
[1] "5p gain mutation analysis"
[1] 3
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               26               151 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               26               151 
[1] "5q gain mutation analysis"
[1] 3
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
                7               170 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
                7               170 
[1] "6p gain mutation analysis"
[1] 3
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               13               164 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               13               164 
[1] "6q gain mutation analysis"
[1] 3
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               13               164 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               13               164 
[1] "7p gain mutation analysis"
[1] 3
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               53               124 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               53               124 
[1] "7q gain mutation analysis"
[1] 3
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               48               129 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               48               129 
[1] "8p gain mutation analysis"
[1] 3
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               49               128 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               49               128 
[1] "8q gain mutation analysis"
[1] 3
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               69               108 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               69               108 
[1] "9p gain mutation analysis"
[1] 3
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               14               163 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               14               163 
[1] "9q gain mutation analysis"
[1] 3
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               18               159 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               18               159 
[1] "10p gain mutation analysis"
[1] 3
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                26                151 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                26                151 
[1] "10q gain mutation analysis"
[1] 3
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                14                163 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                14                163 
[1] "11p gain mutation analysis"
[1] 3
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 5                172 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 5                172 
[1] "11q gain mutation analysis"
[1] 3
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 9                168 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 9                168 
[1] "12p gain mutation analysis"
[1] 3
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                17                160 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                17                160 
[1] "12q gain mutation analysis"
[1] 3
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                12                165 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                12                165 
[1] "13q gain mutation analysis"
[1] 3
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                34                143 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                34                143 
[1] "15q gain mutation analysis"
[1] 3
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                 7                170 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                 7                170 
[1] "16p gain mutation analysis"
[1] 3
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                12                165 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                12                165 
[1] "16q gain mutation analysis"
[1] 3
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                 8                169 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                 8                169 
[1] "17p gain mutation analysis"
[1] 3
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                 5                172 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                 5                172 
[1] "17q gain mutation analysis"
[1] 3
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                10                167 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                10                167 
[1] "18p gain mutation analysis"
[1] 3
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                16                161 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                16                161 
[1] "18q gain mutation analysis"
[1] 3
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 9                168 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 9                168 
[1] "19p gain mutation analysis"
[1] 3
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                10                167 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                10                167 
[1] "19q gain mutation analysis"
[1] 3
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                17                160 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                17                160 
[1] "20p gain mutation analysis"
[1] 3
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                67                110 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                67                110 
[1] "20q gain mutation analysis"
[1] 3
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                81                 96 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                81                 96 
[1] "22q gain mutation analysis"
[1] 3
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                 3                174 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                 3                174 
[1] "1p loss mutation analysis"
[1] 3
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
                8               169 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
                8               169 
[1] "1q loss mutation analysis"
[1] 3
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
                3               174 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
                3               174 
[1] "2q loss mutation analysis"
[1] 3
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
                3               174 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
                3               174 
[1] "3p loss mutation analysis"
[1] 3
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               15               162 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               15               162 
[1] "3q loss mutation analysis"
[1] 3
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
                9               168 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
                9               168 
[1] "4p loss mutation analysis"
[1] 3
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               27               150 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               27               150 
[1] "4q loss mutation analysis"
[1] 3
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               25               152 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               25               152 
[1] "5p loss mutation analysis"
[1] 3
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
                8               169 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
                8               169 
[1] "5q loss mutation analysis"
[1] 3
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               17               160 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               17               160 
[1] "6p loss mutation analysis"
[1] 3
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               10               167 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               10               167 
[1] "6q loss mutation analysis"
[1] 3
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               15               162 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               15               162 
[1] "7p loss mutation analysis"
[1] 3
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
                3               174 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
                3               174 
[1] "7q loss mutation analysis"
[1] 3
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
                6               171 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
                6               171 
[1] "8p loss mutation analysis"
[1] 3
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               15               162 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               15               162 
[1] "8q loss mutation analysis"
[1] 3
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                3               174 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                3               174 
[1] "9p loss mutation analysis"
[1] 3
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               30               147 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               30               147 
[1] "9q loss mutation analysis"
[1] 3
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               13               164 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               13               164 
[1] "10p loss mutation analysis"
[1] 3
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                12                165 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                12                165 
[1] "10q loss mutation analysis"
[1] 3
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                10                167 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                10                167 
[1] "11p loss mutation analysis"
[1] 3
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                13                164 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                13                164 
[1] "11q loss mutation analysis"
[1] 3
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                11                166 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                11                166 
[1] "12p loss mutation analysis"
[1] 3
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                12                165 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                12                165 
[1] "12q loss mutation analysis"
[1] 3
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                 8                169 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                 8                169 
[1] "13q loss mutation analysis"
[1] 3
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                 5                172 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                 5                172 
[1] "14q loss mutation analysis"
[1] 3
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                14                163 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                14                163 
[1] "15q loss mutation analysis"
[1] 3
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                12                165 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                12                165 
[1] "16p loss mutation analysis"
[1] 3
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                11                166 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                11                166 
[1] "16q loss mutation analysis"
[1] 3
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                15                162 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                15                162 
[1] "17p loss mutation analysis"
[1] 3
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                32                145 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                32                145 
[1] "17q loss mutation analysis"
[1] 3
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                11                166 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                11                166 
[1] "18p loss mutation analysis"
[1] 3
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                14                163 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                14                163 
[1] "18q loss mutation analysis"
[1] 3
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                27                150 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                27                150 
[1] "19p loss mutation analysis"
[1] 3
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                18                159 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                18                159 
[1] "19q loss mutation analysis"
[1] 3
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                13                164 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                13                164 
[1] "20p loss mutation analysis"
[1] 3
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                 5                172 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                 5                172 
[1] "21q loss mutation analysis"
[1] 3
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                30                147 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                30                147 
[1] "22q loss mutation analysis"
[1] 3
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                25                152 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                25                152 
[1] "Xq loss mutation analysis"
[1] 3
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
                6               171 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
                6               171 
[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] "COMPLETENESS.OF.RESECTION"             
[16] "NUMBER.OF.LYMPH.NODES"                 
[17] "BATCHNUMBER"                           

Input Data has 17 rows and 177 columns.

[1] "Batch" "17"   
[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-BR-8592 TCGA-BR-A4IU 
          36           47           45           23            6           18 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
          28           12           24           NA           24           16 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PF TCGA-CD-5798 
          13            4            7            3           22           25 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 
          21           11           15            9            2           NA 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
         609           92          822          485           31         1611 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4442 TCGA-CG-4443 
         245         1644          122          426           NA          912 
TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4460 TCGA-CG-4462 TCGA-CG-4465 
        1431          580          366          669           31          273 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4474 TCGA-CG-4475 TCGA-CG-4476 
         576          215          365           31           NA           NA 
TCGA-CG-4477 TCGA-CG-5716 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
          31           31          211           31           31           30 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 
         182           29         2131          366          457          881 
TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
         944         1980          122         1674          641          243 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
         263          109          138          298          476          293 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
         249          210           21          181          201          126 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
          51          111          143          123           89          130 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6177 TCGA-F1-6874 TCGA-F1-6875 TCGA-FP-7735 
          19          237          199           61           NA           12 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8631 
           6           92          109           31           NA           17 
TCGA-HF-7131 TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-7136 TCGA-HJ-7597 
          NA           NA           NA           NA           NA           NA 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IP-7968 
         209          108           77 
Variable 1:'AGE':	nDistinctValues=47,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'DAYSTODEATH':	nDistinctValues=18,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 3:'DAYSTOLASTFOLLOWUP':	nDistinctValues=94,	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:'COMPLETENESS.OF.RESECTION':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 16:'NUMBER.OF.LYMPH.NODES':	nDistinctValues=27,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 17:'BATCH.NUMBER':	nDistinctValues=11,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
 [1] "AGE"                                   
 [2] "GENDER"                                
 [3] "HISTOLOGICAL.TYPE"                     
 [4] "PATHOLOGY.T"                           
 [5] "PATHOLOGY.N"                           
 [6] "PATHOLOGICSPREAD(M)"                   
 [7] "TUMOR.STAGE"                           
 [8] "RADIATIONS.RADIATION.REGIMENINDICATION"
 [9] "COMPLETENESS.OF.RESECTION"             
[10] "NUMBER.OF.LYMPH.NODES"                 
[1] "TUMOR.?STAGE" "7"           
[1] "stage2"
vv
 1  2  3  4 
26 48 58 29 
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T" "4"          
[1] "PATHOLOGY.N" "5"          
Output Data has 177 columns, 1 survival variables, and 10 non-survival variables.
AGE, nv=47, 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 54 64 43 
[1] "table(vv)"
vv
T1 T2 T3 T4 
 6 54 64 43 
$ClinVariableName
[1] "PATHOLOGY.T"

$Table
vv
T1 T2 T3 T4 
 6 54 64 43 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


T1 T2 T3 T4 
 6 54 64 43 
PATHOLOGY.N, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.N',vnm)"
vv
N0 N1 N2 N3 
56 61 29 20 
[1] "table(vv)"
vv
N0 N1 N2 N3 
56 61 29 20 
$ClinVariableName
[1] "PATHOLOGY.N"

$Table
vv
N0 N1 N2 N3 
56 61 29 20 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


N0 N1 N2 N3 
56 61 29 20 
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 
 26  48  58  29 
[1] "table(vv)"
vv
  I  II III  IV 
 26  48  58  29 
$ClinVariableName
[1] "TUMOR.STAGE"

$Table
vv
  I  II III  IV 
 26  48  58  29 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


  I  II III  IV 
 26  48  58  29 
RADIATIONS.RADIATION.REGIMENINDICATION, nv=2, binary=FALSE, numeric=FALSE
COMPLETENESS.OF.RESECTION, nv=4, binary=FALSE, numeric=FALSE
NUMBER.OF.LYMPH.NODES, nv=27, binary=FALSE, numeric=TRUE

Clustering(1) Variable = 1p gain mutation analysis
D1V1, survival
                   sevent
clus2                 0   1
  1P GAIN MUTATED     3   0
  1P GAIN WILD-TYPE 119  18
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
                3               137 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
                0                18 
$`1P GAIN MUTATED`
TCGA-BR-7717 TCGA-BR-A4J8 TCGA-D7-6521 
        0.69         0.23         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-BR-8592 
        0.26         1.18         1.55         1.48         0.76         0.20 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
        0.59         0.92         0.39         0.79         0.72         0.79 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J9 TCGA-BR-A4PF TCGA-CD-5798 
        0.53         0.43         0.13         0.10         0.72         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-FP-8099 TCGA-FP-8209 
        0.39         0.20         3.02         3.58         1.02        59.05 
TCGA-FP-8631 TCGA-HJ-7597 TCGA-IN-7806 TCGA-IN-7808 TCGA-IP-7968 
        0.56        26.43         6.87         3.55         2.53 

  1P GAIN MUTATED 1P GAIN WILD-TYPE 
             0.23              0.07 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
             8.19             72.23 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
             0.69              1.25 
[1] "0.2 - 8.2 (0.7)"  "0.1 - 72.2 (1.2)"
       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-BR-8592        TCGA-BR-A4IU        TCGA-BR-A4IV        TCGA-BR-A4IY 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-BR-A4IZ        TCGA-BR-A4J1        TCGA-BR-A4J2        TCGA-BR-A4J4 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-BR-A4J5        TCGA-BR-A4J6        TCGA-BR-A4J8        TCGA-BR-A4J9 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE"   "1P GAIN MUTATED" "1P GAIN WILD-TYPE" 
       TCGA-BR-A4PF        TCGA-CD-5798        TCGA-CD-5799        TCGA-CD-5800 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CD-5801        TCGA-CD-5802        TCGA-CD-5803        TCGA-CG-4300 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CG-4301        TCGA-CG-4304        TCGA-CG-4305        TCGA-CG-4306 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CG-4436        TCGA-CG-4437        TCGA-CG-4438        TCGA-CG-4440 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CG-4441        TCGA-CG-4443        TCGA-CG-4444        TCGA-CG-4449 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CG-4455        TCGA-CG-4460        TCGA-CG-4462        TCGA-CG-4465 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CG-4466        TCGA-CG-4469        TCGA-CG-4472        TCGA-CG-4474 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CG-4477        TCGA-CG-5716        TCGA-CG-5717        TCGA-CG-5718 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CG-5719        TCGA-CG-5720        TCGA-CG-5721        TCGA-CG-5722 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CG-5723        TCGA-CG-5724        TCGA-CG-5725        TCGA-CG-5726 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CG-5727        TCGA-CG-5728        TCGA-CG-5730        TCGA-CG-5732 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CG-5733        TCGA-CG-5734        TCGA-D7-5577        TCGA-D7-5578 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-D7-5579        TCGA-D7-6518        TCGA-D7-6519        TCGA-D7-6520 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-D7-6521        TCGA-D7-6522        TCGA-D7-6524        TCGA-D7-6525 
  "1P GAIN MUTATED" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-D7-6526        TCGA-D7-6527        TCGA-D7-6528        TCGA-D7-6815 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-D7-6817        TCGA-D7-6818        TCGA-D7-6820        TCGA-D7-6822 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-EQ-5647        TCGA-EQ-8122        TCGA-F1-6177        TCGA-F1-6874 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-F1-6875        TCGA-FP-7735        TCGA-FP-7829        TCGA-FP-7916 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-FP-7998        TCGA-FP-8099        TCGA-FP-8209        TCGA-FP-8631 
"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-BR-8592        TCGA-BR-A4IU        TCGA-BR-A4IV        TCGA-BR-A4IY 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-BR-A4IZ        TCGA-BR-A4J1        TCGA-BR-A4J2        TCGA-BR-A4J4 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-BR-A4J5        TCGA-BR-A4J6        TCGA-BR-A4J8        TCGA-BR-A4J9 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE"   "1P GAIN MUTATED" "1P GAIN WILD-TYPE" 
       TCGA-BR-A4PF        TCGA-CD-5798        TCGA-CD-5799        TCGA-CD-5800 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CD-5801        TCGA-CD-5802        TCGA-CD-5803        TCGA-CG-4300 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CG-4301        TCGA-CG-4304        TCGA-CG-4305        TCGA-CG-4306 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CG-4436        TCGA-CG-4437        TCGA-CG-4438        TCGA-CG-4440 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CG-4441        TCGA-CG-4443        TCGA-CG-4444        TCGA-CG-4449 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CG-4455        TCGA-CG-4460        TCGA-CG-4462        TCGA-CG-4465 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CG-4466        TCGA-CG-4469        TCGA-CG-4472        TCGA-CG-4474 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CG-4477        TCGA-CG-5716        TCGA-CG-5717        TCGA-CG-5718 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CG-5719        TCGA-CG-5720        TCGA-CG-5721        TCGA-CG-5722 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CG-5723        TCGA-CG-5724        TCGA-CG-5725        TCGA-CG-5726 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CG-5727        TCGA-CG-5728        TCGA-CG-5730        TCGA-CG-5732 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CG-5733        TCGA-CG-5734        TCGA-D7-5577        TCGA-D7-5578 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-D7-5579        TCGA-D7-6518        TCGA-D7-6519        TCGA-D7-6520 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-D7-6521        TCGA-D7-6522        TCGA-D7-6524        TCGA-D7-6525 
  "1P GAIN MUTATED" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-D7-6526        TCGA-D7-6527        TCGA-D7-6528        TCGA-D7-6815 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-D7-6817        TCGA-D7-6818        TCGA-D7-6820        TCGA-D7-6822 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-EQ-5647        TCGA-EQ-8122        TCGA-F1-6177        TCGA-F1-6874 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-F1-6875        TCGA-FP-7735        TCGA-FP-7829        TCGA-FP-7916 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-FP-7998        TCGA-FP-8099        TCGA-FP-8209        TCGA-FP-8631 
"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-BR-8592        TCGA-BR-A4IU        TCGA-BR-A4IV        TCGA-BR-A4IY 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-BR-A4IZ        TCGA-BR-A4J1        TCGA-BR-A4J2        TCGA-BR-A4J4 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-BR-A4J5        TCGA-BR-A4J6        TCGA-BR-A4J8        TCGA-BR-A4J9 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE"   "1P GAIN MUTATED" "1P GAIN WILD-TYPE" 
       TCGA-BR-A4PF        TCGA-CD-5798        TCGA-CD-5799        TCGA-CD-5800 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CD-5801        TCGA-CD-5802        TCGA-CD-5803        TCGA-CG-4300 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CG-4301        TCGA-CG-4304        TCGA-CG-4305        TCGA-CG-4306 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CG-4436        TCGA-CG-4437        TCGA-CG-4438        TCGA-CG-4440 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CG-4441        TCGA-CG-4443        TCGA-CG-4444        TCGA-CG-4449 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CG-4455        TCGA-CG-4460        TCGA-CG-4462        TCGA-CG-4465 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CG-4466        TCGA-CG-4469        TCGA-CG-4472        TCGA-CG-4474 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CG-4477        TCGA-CG-5716        TCGA-CG-5717        TCGA-CG-5718 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CG-5719        TCGA-CG-5720        TCGA-CG-5721        TCGA-CG-5722 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CG-5723        TCGA-CG-5724        TCGA-CG-5725        TCGA-CG-5726 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CG-5727        TCGA-CG-5728        TCGA-CG-5730        TCGA-CG-5732 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CG-5733        TCGA-CG-5734        TCGA-D7-5577        TCGA-D7-5578 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-D7-5579        TCGA-D7-6518        TCGA-D7-6519        TCGA-D7-6520 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-D7-6521        TCGA-D7-6522        TCGA-D7-6524        TCGA-D7-6525 
  "1P GAIN MUTATED" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-D7-6526        TCGA-D7-6527        TCGA-D7-6528        TCGA-D7-6815 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-D7-6817        TCGA-D7-6818        TCGA-D7-6820        TCGA-D7-6822 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-EQ-5647        TCGA-EQ-8122        TCGA-F1-6177        TCGA-F1-6874 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-F1-6875        TCGA-FP-7735        TCGA-FP-7829        TCGA-FP-7916 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-FP-7998        TCGA-FP-8099        TCGA-FP-8209        TCGA-FP-8631 
"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] "hr="     "9200000"
D1V2, continuous
D1V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED      2    7
  1P GAIN WILD-TYPE   68  100
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  FEMALE               2                68
  MALE                 7               100
                   vv
clus                STOMACH ADENOCARCINOMA - DIFFUSE TYPE
  1P GAIN MUTATED                                       1
  1P GAIN WILD-TYPE                                    24
                   vv
clus                STOMACH ADENOCARCINOMA - NOT OTHERWISE SPECIFIED (NOS)
  1P GAIN MUTATED                                                        8
  1P GAIN WILD-TYPE                                                     79
                   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                                                10
                   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                                                                     36
D1V4, multiclass
                   vv
clus                T1 T2 T3 T4
  1P GAIN MUTATED    0  1  4  1
  1P GAIN WILD-TYPE  6 53 60 42
D1V5, multiclass
    clus
vv   1P GAIN MUTATED 1P GAIN WILD-TYPE
  T1               0                 6
  T2               1                53
  T3               4                60
  T4               1                42
                   vv
clus                N0 N1 N2 N3
  1P GAIN MUTATED    1  3  1  1
  1P GAIN WILD-TYPE 55 58 28 19
D1V6, multiclass
    clus
vv   1P GAIN MUTATED 1P GAIN WILD-TYPE
  N0               1                55
  N1               3                58
  N2               1                28
  N3               1                19
                   vv
clus                 M0  M1  MX
  1P GAIN MUTATED     8   0   1
  1P GAIN WILD-TYPE 138  18  12
D1V7, multiclass
    clus
vv   1P GAIN MUTATED 1P GAIN WILD-TYPE
  M0               8               138
  M1               0                18
  MX               1                12
                   vv
clus                 I II III IV
  1P GAIN MUTATED    0  1   3  1
  1P GAIN WILD-TYPE 26 47  55 28
D1V8, multiclass
     clus
vv    1P GAIN MUTATED 1P GAIN WILD-TYPE
  I                 0                26
  II                1                47
  III               3                55
  IV                1                28
D1V9, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED      0    9
  1P GAIN WILD-TYPE    5  163
     clus
vv    1P GAIN MUTATED 1P GAIN WILD-TYPE
  NO                0                 5
  YES               9               163
                   vv
clus                 R0  R1  R2  RX
  1P GAIN MUTATED     5   0   0   4
  1P GAIN WILD-TYPE 118   7  12  21
D1V10, multiclass
    clus
vv   1P GAIN MUTATED 1P GAIN WILD-TYPE
  R0               5               118
  R1               0                 7
  R2               0                12
  RX               4                21
D1V11, continuous

Clustering(2) Variable = 1q gain mutation analysis
D2V1, survival
                   sevent
clus2                 0   1
  1Q GAIN MUTATED    13   3
  1Q GAIN WILD-TYPE 109  15
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               16               124 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
                3                15 
$`1Q GAIN MUTATED`
TCGA-BR-7717 TCGA-BR-7723 TCGA-BR-A4J8 TCGA-CG-4460 TCGA-D7-6521 TCGA-D7-6526 
        0.69         4.54         0.23        21.99         8.19         6.61 
TCGA-D7-6527 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6822 TCGA-EQ-5647 TCGA-F1-6875 
        4.14         4.70         4.04         4.27         0.62        72.23 
TCGA-FP-7735 TCGA-FP-8099 TCGA-FP-8631 TCGA-IN-7808 
        0.39         1.02         0.56         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-BR-8592 TCGA-BR-A4IU 
        1.18         1.55         1.48         0.76         0.20         0.59 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
        0.92         0.39         0.79         0.72         0.79         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J9 TCGA-BR-A4PF TCGA-CD-5798 TCGA-CD-5799 
        0.43         0.13         0.10         0.72         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-FP-8209 TCGA-HJ-7597 TCGA-IN-7806 TCGA-IP-7968 
       59.05        26.43         6.87         2.53 

  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
             0.23              0.07 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
            72.23             70.06 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
             4.09              1.20 
[1] "0.2 - 72.2 (4.1)" "0.1 - 70.1 (1.2)"
       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-BR-8592        TCGA-BR-A4IU        TCGA-BR-A4IV        TCGA-BR-A4IY 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-BR-A4IZ        TCGA-BR-A4J1        TCGA-BR-A4J2        TCGA-BR-A4J4 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-BR-A4J5        TCGA-BR-A4J6        TCGA-BR-A4J8        TCGA-BR-A4J9 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" 
       TCGA-BR-A4PF        TCGA-CD-5798        TCGA-CD-5799        TCGA-CD-5800 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-CD-5801        TCGA-CD-5802        TCGA-CD-5803        TCGA-CG-4300 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-CG-4301        TCGA-CG-4304        TCGA-CG-4305        TCGA-CG-4306 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-CG-4436        TCGA-CG-4437        TCGA-CG-4438        TCGA-CG-4440 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-CG-4441        TCGA-CG-4443        TCGA-CG-4444        TCGA-CG-4449 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-CG-4455        TCGA-CG-4460        TCGA-CG-4462        TCGA-CG-4465 
"1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-CG-4466        TCGA-CG-4469        TCGA-CG-4472        TCGA-CG-4474 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-CG-4477        TCGA-CG-5716        TCGA-CG-5717        TCGA-CG-5718 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-CG-5719        TCGA-CG-5720        TCGA-CG-5721        TCGA-CG-5722 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-CG-5723        TCGA-CG-5724        TCGA-CG-5725        TCGA-CG-5726 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-CG-5727        TCGA-CG-5728        TCGA-CG-5730        TCGA-CG-5732 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-CG-5733        TCGA-CG-5734        TCGA-D7-5577        TCGA-D7-5578 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-D7-5579        TCGA-D7-6518        TCGA-D7-6519        TCGA-D7-6520 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-D7-6521        TCGA-D7-6522        TCGA-D7-6524        TCGA-D7-6525 
  "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-D7-6526        TCGA-D7-6527        TCGA-D7-6528        TCGA-D7-6815 
  "1Q GAIN MUTATED"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-D7-6817        TCGA-D7-6818        TCGA-D7-6820        TCGA-D7-6822 
  "1Q GAIN MUTATED"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" 
       TCGA-EQ-5647        TCGA-EQ-8122        TCGA-F1-6177        TCGA-F1-6874 
  "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-F1-6875        TCGA-FP-7735        TCGA-FP-7829        TCGA-FP-7916 
  "1Q GAIN MUTATED"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-FP-7998        TCGA-FP-8099        TCGA-FP-8209        TCGA-FP-8631 
"1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" 
       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-BR-8592        TCGA-BR-A4IU        TCGA-BR-A4IV        TCGA-BR-A4IY 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-BR-A4IZ        TCGA-BR-A4J1        TCGA-BR-A4J2        TCGA-BR-A4J4 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-BR-A4J5        TCGA-BR-A4J6        TCGA-BR-A4J8        TCGA-BR-A4J9 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" 
       TCGA-BR-A4PF        TCGA-CD-5798        TCGA-CD-5799        TCGA-CD-5800 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-CD-5801        TCGA-CD-5802        TCGA-CD-5803        TCGA-CG-4300 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-CG-4301        TCGA-CG-4304        TCGA-CG-4305        TCGA-CG-4306 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-CG-4436        TCGA-CG-4437        TCGA-CG-4438        TCGA-CG-4440 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-CG-4441        TCGA-CG-4443        TCGA-CG-4444        TCGA-CG-4449 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-CG-4455        TCGA-CG-4460        TCGA-CG-4462        TCGA-CG-4465 
"1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-CG-4466        TCGA-CG-4469        TCGA-CG-4472        TCGA-CG-4474 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-CG-4477        TCGA-CG-5716        TCGA-CG-5717        TCGA-CG-5718 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-CG-5719        TCGA-CG-5720        TCGA-CG-5721        TCGA-CG-5722 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-CG-5723        TCGA-CG-5724        TCGA-CG-5725        TCGA-CG-5726 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-CG-5727        TCGA-CG-5728        TCGA-CG-5730        TCGA-CG-5732 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-CG-5733        TCGA-CG-5734        TCGA-D7-5577        TCGA-D7-5578 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-D7-5579        TCGA-D7-6518        TCGA-D7-6519        TCGA-D7-6520 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-D7-6521        TCGA-D7-6522        TCGA-D7-6524        TCGA-D7-6525 
  "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-D7-6526        TCGA-D7-6527        TCGA-D7-6528        TCGA-D7-6815 
  "1Q GAIN MUTATED"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-D7-6817        TCGA-D7-6818        TCGA-D7-6820        TCGA-D7-6822 
  "1Q GAIN MUTATED"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" 
       TCGA-EQ-5647        TCGA-EQ-8122        TCGA-F1-6177        TCGA-F1-6874 
  "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-F1-6875        TCGA-FP-7735        TCGA-FP-7829        TCGA-FP-7916 
  "1Q GAIN MUTATED"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-FP-7998        TCGA-FP-8099        TCGA-FP-8209        TCGA-FP-8631 
"1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" 
       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-BR-8592        TCGA-BR-A4IU        TCGA-BR-A4IV        TCGA-BR-A4IY 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-BR-A4IZ        TCGA-BR-A4J1        TCGA-BR-A4J2        TCGA-BR-A4J4 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-BR-A4J5        TCGA-BR-A4J6        TCGA-BR-A4J8        TCGA-BR-A4J9 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" 
       TCGA-BR-A4PF        TCGA-CD-5798        TCGA-CD-5799        TCGA-CD-5800 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-CD-5801        TCGA-CD-5802        TCGA-CD-5803        TCGA-CG-4300 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-CG-4301        TCGA-CG-4304        TCGA-CG-4305        TCGA-CG-4306 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-CG-4436        TCGA-CG-4437        TCGA-CG-4438        TCGA-CG-4440 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-CG-4441        TCGA-CG-4443        TCGA-CG-4444        TCGA-CG-4449 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-CG-4455        TCGA-CG-4460        TCGA-CG-4462        TCGA-CG-4465 
"1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-CG-4466        TCGA-CG-4469        TCGA-CG-4472        TCGA-CG-4474 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-CG-4477        TCGA-CG-5716        TCGA-CG-5717        TCGA-CG-5718 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-CG-5719        TCGA-CG-5720        TCGA-CG-5721        TCGA-CG-5722 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-CG-5723        TCGA-CG-5724        TCGA-CG-5725        TCGA-CG-5726 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-CG-5727        TCGA-CG-5728        TCGA-CG-5730        TCGA-CG-5732 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-CG-5733        TCGA-CG-5734        TCGA-D7-5577        TCGA-D7-5578 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-D7-5579        TCGA-D7-6518        TCGA-D7-6519        TCGA-D7-6520 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-D7-6521        TCGA-D7-6522        TCGA-D7-6524        TCGA-D7-6525 
  "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-D7-6526        TCGA-D7-6527        TCGA-D7-6528        TCGA-D7-6815 
  "1Q GAIN MUTATED"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-D7-6817        TCGA-D7-6818        TCGA-D7-6820        TCGA-D7-6822 
  "1Q GAIN MUTATED"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" 
       TCGA-EQ-5647        TCGA-EQ-8122        TCGA-F1-6177        TCGA-F1-6874 
  "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-F1-6875        TCGA-FP-7735        TCGA-FP-7829        TCGA-FP-7916 
  "1Q GAIN MUTATED"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-FP-7998        TCGA-FP-8099        TCGA-FP-8209        TCGA-FP-8631 
"1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" 
       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"  
D2V2, continuous
D2V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED      6   18
  1Q GAIN WILD-TYPE   64   89
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  FEMALE               6                64
  MALE                18                89
                   vv
clus                STOMACH ADENOCARCINOMA - DIFFUSE TYPE
  1Q GAIN MUTATED                                       3
  1Q GAIN WILD-TYPE                                    22
                   vv
clus                STOMACH ADENOCARCINOMA - NOT OTHERWISE SPECIFIED (NOS)
  1Q GAIN MUTATED                                                       14
  1Q GAIN WILD-TYPE                                                     73
                   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                                                10
                   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                                                                        3
  1Q GAIN WILD-TYPE                                                                     33
D2V4, multiclass
                   vv
clus                T1 T2 T3 T4
  1Q GAIN MUTATED    1  8  9  3
  1Q GAIN WILD-TYPE  5 46 55 40
D2V5, multiclass
    clus
vv   1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  T1               1                 5
  T2               8                46
  T3               9                55
  T4               3                40
                   vv
clus                N0 N1 N2 N3
  1Q GAIN MUTATED    6  5  4  5
  1Q GAIN WILD-TYPE 50 56 25 15
D2V6, multiclass
    clus
vv   1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  N0               6                50
  N1               5                56
  N2               4                25
  N3               5                15
                   vv
clus                 M0  M1  MX
  1Q GAIN MUTATED    17   3   4
  1Q GAIN WILD-TYPE 129  15   9
D2V7, multiclass
    clus
vv   1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  M0              17               129
  M1               3                15
  MX               4                 9
                   vv
clus                 I II III IV
  1Q GAIN MUTATED    4  4   7  4
  1Q GAIN WILD-TYPE 22 44  51 25
D2V8, multiclass
     clus
vv    1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  I                 4                22
  II                4                44
  III               7                51
  IV                4                25
D2V9, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED      2   22
  1Q GAIN WILD-TYPE    3  150
     clus
vv    1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  NO                2                 3
  YES              22               150
                   vv
clus                 R0  R1  R2  RX
  1Q GAIN MUTATED    16   0   2   5
  1Q GAIN WILD-TYPE 107   7  10  20
D2V10, multiclass
    clus
vv   1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  R0              16               107
  R1               0                 7
  R2               2                10
  RX               5                20
D2V11, continuous

Clustering(3) Variable = 2p gain mutation analysis
D3V1, survival
                   sevent
clus2                 0   1
  2P GAIN MUTATED    10   1
  2P GAIN WILD-TYPE 112  17
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               11               129 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
                1                17 
$`2P GAIN MUTATED`
TCGA-BR-7197 TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7717 TCGA-BR-A4IY TCGA-CD-5801 
        1.48         1.25         1.05         0.69         0.39         0.49 
TCGA-CD-5802 TCGA-CG-4460 TCGA-CG-4472 TCGA-CG-5718 TCGA-CG-5727 
        0.30        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-BR-8592 TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IZ 
        1.48         0.76         0.20         0.59         0.92         0.79 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J8 
        0.72         0.79         0.53         0.43         0.13         0.23 
TCGA-BR-A4J9 TCGA-BR-A4PF TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5803 
        0.10         0.72         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-FP-8099 TCGA-FP-8209 TCGA-FP-8631 TCGA-HJ-7597 
        3.02         3.58         1.02        59.05         0.56        26.43 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IP-7968 
        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 
             1.05              1.32 
[1] "0.3 - 31.0 (1.1)" "0.1 - 72.2 (1.3)"
       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-BR-8592        TCGA-BR-A4IU        TCGA-BR-A4IV        TCGA-BR-A4IY 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE"   "2P GAIN MUTATED" 
       TCGA-BR-A4IZ        TCGA-BR-A4J1        TCGA-BR-A4J2        TCGA-BR-A4J4 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-BR-A4J5        TCGA-BR-A4J6        TCGA-BR-A4J8        TCGA-BR-A4J9 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-BR-A4PF        TCGA-CD-5798        TCGA-CD-5799        TCGA-CD-5800 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-CD-5801        TCGA-CD-5802        TCGA-CD-5803        TCGA-CG-4300 
  "2P GAIN MUTATED"   "2P GAIN MUTATED" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-CG-4301        TCGA-CG-4304        TCGA-CG-4305        TCGA-CG-4306 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-CG-4436        TCGA-CG-4437        TCGA-CG-4438        TCGA-CG-4440 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-CG-4441        TCGA-CG-4443        TCGA-CG-4444        TCGA-CG-4449 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-CG-4455        TCGA-CG-4460        TCGA-CG-4462        TCGA-CG-4465 
"2P GAIN WILD-TYPE"   "2P GAIN MUTATED" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-CG-4466        TCGA-CG-4469        TCGA-CG-4472        TCGA-CG-4474 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE"   "2P GAIN MUTATED" "2P GAIN WILD-TYPE" 
       TCGA-CG-4477        TCGA-CG-5716        TCGA-CG-5717        TCGA-CG-5718 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE"   "2P GAIN MUTATED" 
       TCGA-CG-5719        TCGA-CG-5720        TCGA-CG-5721        TCGA-CG-5722 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-CG-5723        TCGA-CG-5724        TCGA-CG-5725        TCGA-CG-5726 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-CG-5727        TCGA-CG-5728        TCGA-CG-5730        TCGA-CG-5732 
  "2P GAIN MUTATED" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-CG-5733        TCGA-CG-5734        TCGA-D7-5577        TCGA-D7-5578 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-D7-5579        TCGA-D7-6518        TCGA-D7-6519        TCGA-D7-6520 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-D7-6521        TCGA-D7-6522        TCGA-D7-6524        TCGA-D7-6525 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-D7-6526        TCGA-D7-6527        TCGA-D7-6528        TCGA-D7-6815 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-D7-6817        TCGA-D7-6818        TCGA-D7-6820        TCGA-D7-6822 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-EQ-5647        TCGA-EQ-8122        TCGA-F1-6177        TCGA-F1-6874 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-F1-6875        TCGA-FP-7735        TCGA-FP-7829        TCGA-FP-7916 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-FP-7998        TCGA-FP-8099        TCGA-FP-8209        TCGA-FP-8631 
"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-BR-8592        TCGA-BR-A4IU        TCGA-BR-A4IV        TCGA-BR-A4IY 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE"   "2P GAIN MUTATED" 
       TCGA-BR-A4IZ        TCGA-BR-A4J1        TCGA-BR-A4J2        TCGA-BR-A4J4 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-BR-A4J5        TCGA-BR-A4J6        TCGA-BR-A4J8        TCGA-BR-A4J9 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-BR-A4PF        TCGA-CD-5798        TCGA-CD-5799        TCGA-CD-5800 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-CD-5801        TCGA-CD-5802        TCGA-CD-5803        TCGA-CG-4300 
  "2P GAIN MUTATED"   "2P GAIN MUTATED" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-CG-4301        TCGA-CG-4304        TCGA-CG-4305        TCGA-CG-4306 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-CG-4436        TCGA-CG-4437        TCGA-CG-4438        TCGA-CG-4440 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-CG-4441        TCGA-CG-4443        TCGA-CG-4444        TCGA-CG-4449 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-CG-4455        TCGA-CG-4460        TCGA-CG-4462        TCGA-CG-4465 
"2P GAIN WILD-TYPE"   "2P GAIN MUTATED" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-CG-4466        TCGA-CG-4469        TCGA-CG-4472        TCGA-CG-4474 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE"   "2P GAIN MUTATED" "2P GAIN WILD-TYPE" 
       TCGA-CG-4477        TCGA-CG-5716        TCGA-CG-5717        TCGA-CG-5718 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE"   "2P GAIN MUTATED" 
       TCGA-CG-5719        TCGA-CG-5720        TCGA-CG-5721        TCGA-CG-5722 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-CG-5723        TCGA-CG-5724        TCGA-CG-5725        TCGA-CG-5726 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-CG-5727        TCGA-CG-5728        TCGA-CG-5730        TCGA-CG-5732 
  "2P GAIN MUTATED" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-CG-5733        TCGA-CG-5734        TCGA-D7-5577        TCGA-D7-5578 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-D7-5579        TCGA-D7-6518        TCGA-D7-6519        TCGA-D7-6520 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-D7-6521        TCGA-D7-6522        TCGA-D7-6524        TCGA-D7-6525 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-D7-6526        TCGA-D7-6527        TCGA-D7-6528        TCGA-D7-6815 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-D7-6817        TCGA-D7-6818        TCGA-D7-6820        TCGA-D7-6822 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-EQ-5647        TCGA-EQ-8122        TCGA-F1-6177        TCGA-F1-6874 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-F1-6875        TCGA-FP-7735        TCGA-FP-7829        TCGA-FP-7916 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-FP-7998        TCGA-FP-8099        TCGA-FP-8209        TCGA-FP-8631 
"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-BR-8592        TCGA-BR-A4IU        TCGA-BR-A4IV        TCGA-BR-A4IY 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE"   "2P GAIN MUTATED" 
       TCGA-BR-A4IZ        TCGA-BR-A4J1        TCGA-BR-A4J2        TCGA-BR-A4J4 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-BR-A4J5        TCGA-BR-A4J6        TCGA-BR-A4J8        TCGA-BR-A4J9 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-BR-A4PF        TCGA-CD-5798        TCGA-CD-5799        TCGA-CD-5800 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-CD-5801        TCGA-CD-5802        TCGA-CD-5803        TCGA-CG-4300 
  "2P GAIN MUTATED"   "2P GAIN MUTATED" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-CG-4301        TCGA-CG-4304        TCGA-CG-4305        TCGA-CG-4306 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-CG-4436        TCGA-CG-4437        TCGA-CG-4438        TCGA-CG-4440 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-CG-4441        TCGA-CG-4443        TCGA-CG-4444        TCGA-CG-4449 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-CG-4455        TCGA-CG-4460        TCGA-CG-4462        TCGA-CG-4465 
"2P GAIN WILD-TYPE"   "2P GAIN MUTATED" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-CG-4466        TCGA-CG-4469        TCGA-CG-4472        TCGA-CG-4474 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE"   "2P GAIN MUTATED" "2P GAIN WILD-TYPE" 
       TCGA-CG-4477        TCGA-CG-5716        TCGA-CG-5717        TCGA-CG-5718 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE"   "2P GAIN MUTATED" 
       TCGA-CG-5719        TCGA-CG-5720        TCGA-CG-5721        TCGA-CG-5722 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-CG-5723        TCGA-CG-5724        TCGA-CG-5725        TCGA-CG-5726 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-CG-5727        TCGA-CG-5728        TCGA-CG-5730        TCGA-CG-5732 
  "2P GAIN MUTATED" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-CG-5733        TCGA-CG-5734        TCGA-D7-5577        TCGA-D7-5578 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-D7-5579        TCGA-D7-6518        TCGA-D7-6519        TCGA-D7-6520 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-D7-6521        TCGA-D7-6522        TCGA-D7-6524        TCGA-D7-6525 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-D7-6526        TCGA-D7-6527        TCGA-D7-6528        TCGA-D7-6815 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-D7-6817        TCGA-D7-6818        TCGA-D7-6820        TCGA-D7-6822 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-EQ-5647        TCGA-EQ-8122        TCGA-F1-6177        TCGA-F1-6874 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-F1-6875        TCGA-FP-7735        TCGA-FP-7829        TCGA-FP-7916 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-FP-7998        TCGA-FP-8099        TCGA-FP-8209        TCGA-FP-8631 
"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    8
  2P GAIN WILD-TYPE   67   99
        clus
vv       2P GAIN MUTATED 2P GAIN WILD-TYPE
  FEMALE               3                67
  MALE                 8                99
                   vv
clus                STOMACH ADENOCARCINOMA - DIFFUSE TYPE
  2P GAIN MUTATED                                       0
  2P GAIN WILD-TYPE                                    25
                   vv
clus                STOMACH ADENOCARCINOMA - NOT OTHERWISE SPECIFIED (NOS)
  2P GAIN MUTATED                                                        6
  2P GAIN WILD-TYPE                                                     81
                   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                                                10
                   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                                                                     32
D3V4, multiclass
                   vv
clus                T1 T2 T3 T4
  2P GAIN MUTATED    0  1  6  4
  2P GAIN WILD-TYPE  6 53 58 39
D3V5, multiclass
    clus
vv   2P GAIN MUTATED 2P GAIN WILD-TYPE
  T1               0                 6
  T2               1                53
  T3               6                58
  T4               4                39
                   vv
clus                N0 N1 N2 N3
  2P GAIN MUTATED    6  5  0  0
  2P GAIN WILD-TYPE 50 56 29 20
D3V6, multiclass
    clus
vv   2P GAIN MUTATED 2P GAIN WILD-TYPE
  N0               6                50
  N1               5                56
  N2               0                29
  N3               0                20
                   vv
clus                 M0  M1  MX
  2P GAIN MUTATED    10   1   0
  2P GAIN WILD-TYPE 136  17  13
D3V7, multiclass
    clus
vv   2P GAIN MUTATED 2P GAIN WILD-TYPE
  M0              10               136
  M1               1                17
  MX               0                13
                   vv
clus                 I II III IV
  2P GAIN MUTATED    0  7   1  3
  2P GAIN WILD-TYPE 26 41  57 26
D3V8, multiclass
     clus
vv    2P GAIN MUTATED 2P GAIN WILD-TYPE
  I                 0                26
  II                7                41
  III               1                57
  IV                3                26
D3V9, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED      0   11
  2P GAIN WILD-TYPE    5  161
     clus
vv    2P GAIN MUTATED 2P GAIN WILD-TYPE
  NO                0                 5
  YES              11               161
                   vv
clus                 R0  R1  R2  RX
  2P GAIN MUTATED     8   0   1   0
  2P GAIN WILD-TYPE 115   7  11  25
D3V10, multiclass
    clus
vv   2P GAIN MUTATED 2P GAIN WILD-TYPE
  R0               8               115
  R1               0                 7
  R2               1                11
  RX               0                25
D3V11, continuous

Clustering(4) Variable = 2q gain mutation analysis
D4V1, survival
                   sevent
clus2                 0   1
  2Q GAIN MUTATED    10   2
  2Q GAIN WILD-TYPE 112  16
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               12               128 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
                2                16 
$`2Q GAIN MUTATED`
TCGA-BR-7197 TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7717 TCGA-BR-A4IY TCGA-BR-A4J6 
        1.48         1.25         1.05         0.69         0.39         0.13 
TCGA-CD-5801 TCGA-CG-4460 TCGA-CG-4472 TCGA-CG-5718 TCGA-CG-5727 TCGA-F1-6875 
        0.49        21.99        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-BR-8592 TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IZ 
        1.48         0.76         0.20         0.59         0.92         0.79 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J8 TCGA-BR-A4J9 
        0.72         0.79         0.53         0.43         0.23         0.10 
TCGA-BR-A4PF TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5802 TCGA-CD-5803 
        0.72         0.82         0.69         0.36         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-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-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
        7.79         6.54         2.01         0.39         0.20         3.02 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8631 TCGA-HJ-7597 TCGA-IN-7806 
        3.58         1.02        59.05         0.56        26.43         6.87 
TCGA-IN-7808 TCGA-IP-7968 
        3.55         2.53 

  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
             0.13              0.07 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
            72.23             70.06 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
             1.15              1.27 
[1] "0.1 - 72.2 (1.1)" "0.1 - 70.1 (1.3)"
       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-BR-8592        TCGA-BR-A4IU        TCGA-BR-A4IV        TCGA-BR-A4IY 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" 
       TCGA-BR-A4IZ        TCGA-BR-A4J1        TCGA-BR-A4J2        TCGA-BR-A4J4 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-BR-A4J5        TCGA-BR-A4J6        TCGA-BR-A4J8        TCGA-BR-A4J9 
"2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-BR-A4PF        TCGA-CD-5798        TCGA-CD-5799        TCGA-CD-5800 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-CD-5801        TCGA-CD-5802        TCGA-CD-5803        TCGA-CG-4300 
  "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-CG-4301        TCGA-CG-4304        TCGA-CG-4305        TCGA-CG-4306 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-CG-4436        TCGA-CG-4437        TCGA-CG-4438        TCGA-CG-4440 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-CG-4441        TCGA-CG-4443        TCGA-CG-4444        TCGA-CG-4449 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-CG-4455        TCGA-CG-4460        TCGA-CG-4462        TCGA-CG-4465 
"2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-CG-4466        TCGA-CG-4469        TCGA-CG-4472        TCGA-CG-4474 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" 
       TCGA-CG-4477        TCGA-CG-5716        TCGA-CG-5717        TCGA-CG-5718 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" 
       TCGA-CG-5719        TCGA-CG-5720        TCGA-CG-5721        TCGA-CG-5722 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-CG-5723        TCGA-CG-5724        TCGA-CG-5725        TCGA-CG-5726 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-CG-5727        TCGA-CG-5728        TCGA-CG-5730        TCGA-CG-5732 
  "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-CG-5733        TCGA-CG-5734        TCGA-D7-5577        TCGA-D7-5578 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-D7-5579        TCGA-D7-6518        TCGA-D7-6519        TCGA-D7-6520 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-D7-6521        TCGA-D7-6522        TCGA-D7-6524        TCGA-D7-6525 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-D7-6526        TCGA-D7-6527        TCGA-D7-6528        TCGA-D7-6815 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-D7-6817        TCGA-D7-6818        TCGA-D7-6820        TCGA-D7-6822 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-EQ-5647        TCGA-EQ-8122        TCGA-F1-6177        TCGA-F1-6874 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-F1-6875        TCGA-FP-7735        TCGA-FP-7829        TCGA-FP-7916 
  "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-FP-7998        TCGA-FP-8099        TCGA-FP-8209        TCGA-FP-8631 
"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-BR-8592        TCGA-BR-A4IU        TCGA-BR-A4IV        TCGA-BR-A4IY 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" 
       TCGA-BR-A4IZ        TCGA-BR-A4J1        TCGA-BR-A4J2        TCGA-BR-A4J4 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-BR-A4J5        TCGA-BR-A4J6        TCGA-BR-A4J8        TCGA-BR-A4J9 
"2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-BR-A4PF        TCGA-CD-5798        TCGA-CD-5799        TCGA-CD-5800 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-CD-5801        TCGA-CD-5802        TCGA-CD-5803        TCGA-CG-4300 
  "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-CG-4301        TCGA-CG-4304        TCGA-CG-4305        TCGA-CG-4306 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-CG-4436        TCGA-CG-4437        TCGA-CG-4438        TCGA-CG-4440 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-CG-4441        TCGA-CG-4443        TCGA-CG-4444        TCGA-CG-4449 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-CG-4455        TCGA-CG-4460        TCGA-CG-4462        TCGA-CG-4465 
"2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-CG-4466        TCGA-CG-4469        TCGA-CG-4472        TCGA-CG-4474 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" 
       TCGA-CG-4477        TCGA-CG-5716        TCGA-CG-5717        TCGA-CG-5718 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" 
       TCGA-CG-5719        TCGA-CG-5720        TCGA-CG-5721        TCGA-CG-5722 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-CG-5723        TCGA-CG-5724        TCGA-CG-5725        TCGA-CG-5726 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-CG-5727        TCGA-CG-5728        TCGA-CG-5730        TCGA-CG-5732 
  "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-CG-5733        TCGA-CG-5734        TCGA-D7-5577        TCGA-D7-5578 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-D7-5579        TCGA-D7-6518        TCGA-D7-6519        TCGA-D7-6520 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-D7-6521        TCGA-D7-6522        TCGA-D7-6524        TCGA-D7-6525 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-D7-6526        TCGA-D7-6527        TCGA-D7-6528        TCGA-D7-6815 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-D7-6817        TCGA-D7-6818        TCGA-D7-6820        TCGA-D7-6822 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-EQ-5647        TCGA-EQ-8122        TCGA-F1-6177        TCGA-F1-6874 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-F1-6875        TCGA-FP-7735        TCGA-FP-7829        TCGA-FP-7916 
  "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-FP-7998        TCGA-FP-8099        TCGA-FP-8209        TCGA-FP-8631 
"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-BR-8592        TCGA-BR-A4IU        TCGA-BR-A4IV        TCGA-BR-A4IY 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" 
       TCGA-BR-A4IZ        TCGA-BR-A4J1        TCGA-BR-A4J2        TCGA-BR-A4J4 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-BR-A4J5        TCGA-BR-A4J6        TCGA-BR-A4J8        TCGA-BR-A4J9 
"2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-BR-A4PF        TCGA-CD-5798        TCGA-CD-5799        TCGA-CD-5800 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-CD-5801        TCGA-CD-5802        TCGA-CD-5803        TCGA-CG-4300 
  "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-CG-4301        TCGA-CG-4304        TCGA-CG-4305        TCGA-CG-4306 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-CG-4436        TCGA-CG-4437        TCGA-CG-4438        TCGA-CG-4440 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-CG-4441        TCGA-CG-4443        TCGA-CG-4444        TCGA-CG-4449 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-CG-4455        TCGA-CG-4460        TCGA-CG-4462        TCGA-CG-4465 
"2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-CG-4466        TCGA-CG-4469        TCGA-CG-4472        TCGA-CG-4474 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" 
       TCGA-CG-4477        TCGA-CG-5716        TCGA-CG-5717        TCGA-CG-5718 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" 
       TCGA-CG-5719        TCGA-CG-5720        TCGA-CG-5721        TCGA-CG-5722 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-CG-5723        TCGA-CG-5724        TCGA-CG-5725        TCGA-CG-5726 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-CG-5727        TCGA-CG-5728        TCGA-CG-5730        TCGA-CG-5732 
  "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-CG-5733        TCGA-CG-5734        TCGA-D7-5577        TCGA-D7-5578 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-D7-5579        TCGA-D7-6518        TCGA-D7-6519        TCGA-D7-6520 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-D7-6521        TCGA-D7-6522        TCGA-D7-6524        TCGA-D7-6525 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-D7-6526        TCGA-D7-6527        TCGA-D7-6528        TCGA-D7-6815 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-D7-6817        TCGA-D7-6818        TCGA-D7-6820        TCGA-D7-6822 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-EQ-5647        TCGA-EQ-8122        TCGA-F1-6177        TCGA-F1-6874 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-F1-6875        TCGA-FP-7735        TCGA-FP-7829        TCGA-FP-7916 
  "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-FP-7998        TCGA-FP-8099        TCGA-FP-8209        TCGA-FP-8631 
"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=" "2.6"
D4V2, continuous
D4V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED      4    9
  2Q GAIN WILD-TYPE   66   98
        clus
vv       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  FEMALE               4                66
  MALE                 9                98
                   vv
clus                STOMACH ADENOCARCINOMA - DIFFUSE TYPE
  2Q GAIN MUTATED                                       0
  2Q GAIN WILD-TYPE                                    25
                   vv
clus                STOMACH ADENOCARCINOMA - NOT OTHERWISE SPECIFIED (NOS)
  2Q GAIN MUTATED                                                        8
  2Q GAIN WILD-TYPE                                                     79
                   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                                                10
                   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                                                                     32
D4V4, multiclass
                   vv
clus                T1 T2 T3 T4
  2Q GAIN MUTATED    0  2  7  4
  2Q GAIN WILD-TYPE  6 52 57 39
D4V5, multiclass
    clus
vv   2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  T1               0                 6
  T2               2                52
  T3               7                57
  T4               4                39
                   vv
clus                N0 N1 N2 N3
  2Q GAIN MUTATED    7  5  0  0
  2Q GAIN WILD-TYPE 49 56 29 20
D4V6, multiclass
    clus
vv   2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  N0               7                49
  N1               5                56
  N2               0                29
  N3               0                20
                   vv
clus                 M0  M1  MX
  2Q GAIN MUTATED    11   1   1
  2Q GAIN WILD-TYPE 135  17  12
D4V7, multiclass
    clus
vv   2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  M0              11               135
  M1               1                17
  MX               1                12
                   vv
clus                 I II III IV
  2Q GAIN MUTATED    1  7   1  3
  2Q GAIN WILD-TYPE 25 41  57 26
D4V8, multiclass
     clus
vv    2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  I                 1                25
  II                7                41
  III               1                57
  IV                3                26
D4V9, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED      0   13
  2Q GAIN WILD-TYPE    5  159
     clus
vv    2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  NO                0                 5
  YES              13               159
                   vv
clus                 R0  R1  R2  RX
  2Q GAIN MUTATED    10   0   1   1
  2Q GAIN WILD-TYPE 113   7  11  24
D4V10, multiclass
    clus
vv   2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  R0              10               113
  R1               0                 7
  R2               1                11
  RX               1                24
D4V11, continuous

Clustering(5) Variable = 3p gain mutation analysis
D5V1, survival
                   sevent
clus2                 0   1
  3P GAIN MUTATED     1   0
  3P GAIN WILD-TYPE 121  18
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
                1               139 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
                0                18 
$`3P GAIN MUTATED`
TCGA-BR-7722 
        0.16 

$`3P GAIN WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-6452 TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6458 
        5.62         0.10         0.95         1.41         1.35         1.35 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
        0.85         0.82         0.62         0.62         1.71         2.17 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
        0.99         1.22         0.66         1.12         0.76         0.66 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
        0.26         1.22         1.48         0.46         1.25         0.13 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 
        1.05         0.82         0.69         4.54         0.99         0.95 
TCGA-BR-7957 TCGA-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-BR-8592 
        0.26         1.18         1.55         1.48         0.76         0.20 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
        0.59         0.92         0.39         0.79         0.72         0.79 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PF 
        0.53         0.43         0.13         0.23         0.10         0.72 
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-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-FP-8099 TCGA-FP-8209 TCGA-FP-8631 TCGA-HJ-7597 TCGA-IN-7806 TCGA-IN-7808 
        1.02        59.05         0.56        26.43         6.87         3.55 
TCGA-IP-7968 
        2.53 

  3P GAIN MUTATED 3P GAIN WILD-TYPE 
             0.16              0.07 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
             0.16             72.23 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
             0.16              1.25 
[1] "0.2 - 0.2 (0.2)"  "0.1 - 72.2 (1.2)"
       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-BR-8592        TCGA-BR-A4IU        TCGA-BR-A4IV        TCGA-BR-A4IY 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BR-A4IZ        TCGA-BR-A4J1        TCGA-BR-A4J2        TCGA-BR-A4J4 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BR-A4J5        TCGA-BR-A4J6        TCGA-BR-A4J8        TCGA-BR-A4J9 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BR-A4PF        TCGA-CD-5798        TCGA-CD-5799        TCGA-CD-5800 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-CD-5801        TCGA-CD-5802        TCGA-CD-5803        TCGA-CG-4300 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-CG-4301        TCGA-CG-4304        TCGA-CG-4305        TCGA-CG-4306 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-CG-4436        TCGA-CG-4437        TCGA-CG-4438        TCGA-CG-4440 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-CG-4441        TCGA-CG-4443        TCGA-CG-4444        TCGA-CG-4449 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-CG-4455        TCGA-CG-4460        TCGA-CG-4462        TCGA-CG-4465 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-CG-4466        TCGA-CG-4469        TCGA-CG-4472        TCGA-CG-4474 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-CG-4477        TCGA-CG-5716        TCGA-CG-5717        TCGA-CG-5718 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-CG-5719        TCGA-CG-5720        TCGA-CG-5721        TCGA-CG-5722 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-CG-5723        TCGA-CG-5724        TCGA-CG-5725        TCGA-CG-5726 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-CG-5727        TCGA-CG-5728        TCGA-CG-5730        TCGA-CG-5732 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-CG-5733        TCGA-CG-5734        TCGA-D7-5577        TCGA-D7-5578 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-D7-5579        TCGA-D7-6518        TCGA-D7-6519        TCGA-D7-6520 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-D7-6521        TCGA-D7-6522        TCGA-D7-6524        TCGA-D7-6525 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-D7-6526        TCGA-D7-6527        TCGA-D7-6528        TCGA-D7-6815 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-D7-6817        TCGA-D7-6818        TCGA-D7-6820        TCGA-D7-6822 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EQ-5647        TCGA-EQ-8122        TCGA-F1-6177        TCGA-F1-6874 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-F1-6875        TCGA-FP-7735        TCGA-FP-7829        TCGA-FP-7916 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-FP-7998        TCGA-FP-8099        TCGA-FP-8209        TCGA-FP-8631 
"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-BR-8592        TCGA-BR-A4IU        TCGA-BR-A4IV        TCGA-BR-A4IY 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BR-A4IZ        TCGA-BR-A4J1        TCGA-BR-A4J2        TCGA-BR-A4J4 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BR-A4J5        TCGA-BR-A4J6        TCGA-BR-A4J8        TCGA-BR-A4J9 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BR-A4PF        TCGA-CD-5798        TCGA-CD-5799        TCGA-CD-5800 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-CD-5801        TCGA-CD-5802        TCGA-CD-5803        TCGA-CG-4300 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-CG-4301        TCGA-CG-4304        TCGA-CG-4305        TCGA-CG-4306 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-CG-4436        TCGA-CG-4437        TCGA-CG-4438        TCGA-CG-4440 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-CG-4441        TCGA-CG-4443        TCGA-CG-4444        TCGA-CG-4449 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-CG-4455        TCGA-CG-4460        TCGA-CG-4462        TCGA-CG-4465 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-CG-4466        TCGA-CG-4469        TCGA-CG-4472        TCGA-CG-4474 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-CG-4477        TCGA-CG-5716        TCGA-CG-5717        TCGA-CG-5718 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-CG-5719        TCGA-CG-5720        TCGA-CG-5721        TCGA-CG-5722 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-CG-5723        TCGA-CG-5724        TCGA-CG-5725        TCGA-CG-5726 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-CG-5727        TCGA-CG-5728        TCGA-CG-5730        TCGA-CG-5732 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-CG-5733        TCGA-CG-5734        TCGA-D7-5577        TCGA-D7-5578 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-D7-5579        TCGA-D7-6518        TCGA-D7-6519        TCGA-D7-6520 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-D7-6521        TCGA-D7-6522        TCGA-D7-6524        TCGA-D7-6525 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-D7-6526        TCGA-D7-6527        TCGA-D7-6528        TCGA-D7-6815 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-D7-6817        TCGA-D7-6818        TCGA-D7-6820        TCGA-D7-6822 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EQ-5647        TCGA-EQ-8122        TCGA-F1-6177        TCGA-F1-6874 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-F1-6875        TCGA-FP-7735        TCGA-FP-7829        TCGA-FP-7916 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-FP-7998        TCGA-FP-8099        TCGA-FP-8209        TCGA-FP-8631 
"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-BR-8592        TCGA-BR-A4IU        TCGA-BR-A4IV        TCGA-BR-A4IY 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BR-A4IZ        TCGA-BR-A4J1        TCGA-BR-A4J2        TCGA-BR-A4J4 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BR-A4J5        TCGA-BR-A4J6        TCGA-BR-A4J8        TCGA-BR-A4J9 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BR-A4PF        TCGA-CD-5798        TCGA-CD-5799        TCGA-CD-5800 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-CD-5801        TCGA-CD-5802        TCGA-CD-5803        TCGA-CG-4300 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-CG-4301        TCGA-CG-4304        TCGA-CG-4305        TCGA-CG-4306 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-CG-4436        TCGA-CG-4437        TCGA-CG-4438        TCGA-CG-4440 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-CG-4441        TCGA-CG-4443        TCGA-CG-4444        TCGA-CG-4449 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-CG-4455        TCGA-CG-4460        TCGA-CG-4462        TCGA-CG-4465 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-CG-4466        TCGA-CG-4469        TCGA-CG-4472        TCGA-CG-4474 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-CG-4477        TCGA-CG-5716        TCGA-CG-5717        TCGA-CG-5718 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-CG-5719        TCGA-CG-5720        TCGA-CG-5721        TCGA-CG-5722 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-CG-5723        TCGA-CG-5724        TCGA-CG-5725        TCGA-CG-5726 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-CG-5727        TCGA-CG-5728        TCGA-CG-5730        TCGA-CG-5732 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-CG-5733        TCGA-CG-5734        TCGA-D7-5577        TCGA-D7-5578 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-D7-5579        TCGA-D7-6518        TCGA-D7-6519        TCGA-D7-6520 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-D7-6521        TCGA-D7-6522        TCGA-D7-6524        TCGA-D7-6525 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-D7-6526        TCGA-D7-6527        TCGA-D7-6528        TCGA-D7-6815 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-D7-6817        TCGA-D7-6818        TCGA-D7-6820        TCGA-D7-6822 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EQ-5647        TCGA-EQ-8122        TCGA-F1-6177        TCGA-F1-6874 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-F1-6875        TCGA-FP-7735        TCGA-FP-7829        TCGA-FP-7916 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-FP-7998        TCGA-FP-8099        TCGA-FP-8209        TCGA-FP-8631 
"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 
                1               139 
       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-BR-8592 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BR-A4IU        TCGA-BR-A4IV        TCGA-BR-A4IY        TCGA-BR-A4IZ 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BR-A4J1        TCGA-BR-A4J2        TCGA-BR-A4J4        TCGA-BR-A4J5 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BR-A4J6        TCGA-BR-A4J8        TCGA-BR-A4J9        TCGA-BR-A4PF 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-CD-5798        TCGA-CD-5799        TCGA-CD-5800        TCGA-CD-5801 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-CD-5802        TCGA-CD-5803        TCGA-CG-4300        TCGA-CG-4301 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-CG-4304        TCGA-CG-4305        TCGA-CG-4306        TCGA-CG-4436 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-CG-4437        TCGA-CG-4438        TCGA-CG-4440        TCGA-CG-4441 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-CG-4443        TCGA-CG-4444        TCGA-CG-4449        TCGA-CG-4455 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-CG-4460        TCGA-CG-4462        TCGA-CG-4465        TCGA-CG-4466 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-CG-4469        TCGA-CG-4472        TCGA-CG-4474        TCGA-CG-4477 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-CG-5716        TCGA-CG-5717        TCGA-CG-5718        TCGA-CG-5719 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-CG-5720        TCGA-CG-5721        TCGA-CG-5722        TCGA-CG-5723 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-CG-5724        TCGA-CG-5725        TCGA-CG-5726        TCGA-CG-5727 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-CG-5728        TCGA-CG-5730        TCGA-CG-5732        TCGA-CG-5733 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-CG-5734        TCGA-D7-5577        TCGA-D7-5578        TCGA-D7-5579 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-D7-6518        TCGA-D7-6519        TCGA-D7-6520        TCGA-D7-6521 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-D7-6522        TCGA-D7-6524        TCGA-D7-6525        TCGA-D7-6526 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-D7-6527        TCGA-D7-6528        TCGA-D7-6815        TCGA-D7-6817 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-D7-6818        TCGA-D7-6820        TCGA-D7-6822        TCGA-EQ-5647 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-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-FP-8099        TCGA-FP-8209        TCGA-FP-8631        TCGA-HJ-7597 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-IN-7806        TCGA-IN-7808        TCGA-IP-7968 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
D5V2, continuous
D5V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED      1    2
  3P GAIN WILD-TYPE   69  105
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  FEMALE               1                69
  MALE                 2               105
                   vv
clus                STOMACH ADENOCARCINOMA - DIFFUSE TYPE
  3P GAIN MUTATED                                       0
  3P GAIN WILD-TYPE                                    25
                   vv
clus                STOMACH ADENOCARCINOMA - NOT OTHERWISE SPECIFIED (NOS)
  3P GAIN MUTATED                                                        3
  3P GAIN WILD-TYPE                                                     84
                   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                                                10
                   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                                                                     36
D5V4, multiclass
                   vv
clus                T1 T2 T3 T4
  3P GAIN MUTATED    0  1  1  1
  3P GAIN WILD-TYPE  6 53 63 42
D5V5, multiclass
    clus
vv   3P GAIN MUTATED 3P GAIN WILD-TYPE
  T1               0                 6
  T2               1                53
  T3               1                63
  T4               1                42
                   vv
clus                N0 N1 N2 N3
  3P GAIN MUTATED    1  1  1  0
  3P GAIN WILD-TYPE 55 60 28 20
D5V6, multiclass
    clus
vv   3P GAIN MUTATED 3P GAIN WILD-TYPE
  N0               1                55
  N1               1                60
  N2               1                28
  N3               0                20
                   vv
clus                 M0  M1  MX
  3P GAIN MUTATED     3   0   0
  3P GAIN WILD-TYPE 143  18  13
D5V7, multiclass
    clus
vv   3P GAIN MUTATED 3P GAIN WILD-TYPE
  M0               3               143
  M1               0                18
  MX               0                13
                   vv
clus                 I II III IV
  3P GAIN MUTATED    1  0   1  1
  3P GAIN WILD-TYPE 25 48  57 28
D5V8, multiclass
     clus
vv    3P GAIN MUTATED 3P GAIN WILD-TYPE
  I                 1                25
  II                0                48
  III               1                57
  IV                1                28
D5V9, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED      0    3
  3P GAIN WILD-TYPE    5  169
     clus
vv    3P GAIN MUTATED 3P GAIN WILD-TYPE
  NO                0                 5
  YES               3               169
                   vv
clus                 R0  R1  R2  RX
  3P GAIN MUTATED     1   0   0   2
  3P GAIN WILD-TYPE 122   7  12  23
D5V10, multiclass
    clus
vv   3P GAIN MUTATED 3P GAIN WILD-TYPE
  R0               1               122
  R1               0                 7
  R2               0                12
  RX               2                23
D5V11, continuous

Clustering(6) Variable = 3q gain mutation analysis
D6V1, survival
                   sevent
clus2                 0   1
  3Q GAIN MUTATED    10   0
  3Q GAIN WILD-TYPE 112  18
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               10               130 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
                0                18 
$`3Q GAIN MUTATED`
TCGA-B7-5818 TCGA-BR-6565 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-A4J4 TCGA-CD-5799 
        0.10         0.62         0.16         4.54         0.53         0.69 
TCGA-CD-5801 TCGA-CG-4305 TCGA-CG-4472 TCGA-D7-6521 
        0.49        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-BR-8592 TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        1.48         0.76         0.20         0.59         0.92         0.39 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J8 
        0.79         0.72         0.79         0.43         0.13         0.23 
TCGA-BR-A4J9 TCGA-BR-A4PF TCGA-CD-5798 TCGA-CD-5800 TCGA-CD-5802 TCGA-CD-5803 
        0.10         0.72         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-FP-8099 TCGA-FP-8209 TCGA-FP-8631 
        0.20         3.02         3.58         1.02        59.05         0.56 
TCGA-HJ-7597 TCGA-IN-7806 TCGA-IN-7808 TCGA-IP-7968 
       26.43         6.87         3.55         2.53 

  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
             0.10              0.07 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
            15.95             72.23 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
            0.655             1.285 
[1] "0.1 - 15.9 (0.7)" "0.1 - 72.2 (1.3)"
       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-BR-8592        TCGA-BR-A4IU        TCGA-BR-A4IV        TCGA-BR-A4IY 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-BR-A4IZ        TCGA-BR-A4J1        TCGA-BR-A4J2        TCGA-BR-A4J4 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" 
       TCGA-BR-A4J5        TCGA-BR-A4J6        TCGA-BR-A4J8        TCGA-BR-A4J9 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-BR-A4PF        TCGA-CD-5798        TCGA-CD-5799        TCGA-CD-5800 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" 
       TCGA-CD-5801        TCGA-CD-5802        TCGA-CD-5803        TCGA-CG-4300 
  "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-CG-4301        TCGA-CG-4304        TCGA-CG-4305        TCGA-CG-4306 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" 
       TCGA-CG-4436        TCGA-CG-4437        TCGA-CG-4438        TCGA-CG-4440 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-CG-4441        TCGA-CG-4443        TCGA-CG-4444        TCGA-CG-4449 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-CG-4455        TCGA-CG-4460        TCGA-CG-4462        TCGA-CG-4465 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-CG-4466        TCGA-CG-4469        TCGA-CG-4472        TCGA-CG-4474 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" 
       TCGA-CG-4477        TCGA-CG-5716        TCGA-CG-5717        TCGA-CG-5718 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-CG-5719        TCGA-CG-5720        TCGA-CG-5721        TCGA-CG-5722 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-CG-5723        TCGA-CG-5724        TCGA-CG-5725        TCGA-CG-5726 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-CG-5727        TCGA-CG-5728        TCGA-CG-5730        TCGA-CG-5732 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-CG-5733        TCGA-CG-5734        TCGA-D7-5577        TCGA-D7-5578 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-D7-5579        TCGA-D7-6518        TCGA-D7-6519        TCGA-D7-6520 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-D7-6521        TCGA-D7-6522        TCGA-D7-6524        TCGA-D7-6525 
  "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-D7-6526        TCGA-D7-6527        TCGA-D7-6528        TCGA-D7-6815 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-D7-6817        TCGA-D7-6818        TCGA-D7-6820        TCGA-D7-6822 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-EQ-5647        TCGA-EQ-8122        TCGA-F1-6177        TCGA-F1-6874 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-F1-6875        TCGA-FP-7735        TCGA-FP-7829        TCGA-FP-7916 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-FP-7998        TCGA-FP-8099        TCGA-FP-8209        TCGA-FP-8631 
"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-BR-8592        TCGA-BR-A4IU        TCGA-BR-A4IV        TCGA-BR-A4IY 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-BR-A4IZ        TCGA-BR-A4J1        TCGA-BR-A4J2        TCGA-BR-A4J4 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" 
       TCGA-BR-A4J5        TCGA-BR-A4J6        TCGA-BR-A4J8        TCGA-BR-A4J9 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-BR-A4PF        TCGA-CD-5798        TCGA-CD-5799        TCGA-CD-5800 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" 
       TCGA-CD-5801        TCGA-CD-5802        TCGA-CD-5803        TCGA-CG-4300 
  "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-CG-4301        TCGA-CG-4304        TCGA-CG-4305        TCGA-CG-4306 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" 
       TCGA-CG-4436        TCGA-CG-4437        TCGA-CG-4438        TCGA-CG-4440 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-CG-4441        TCGA-CG-4443        TCGA-CG-4444        TCGA-CG-4449 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-CG-4455        TCGA-CG-4460        TCGA-CG-4462        TCGA-CG-4465 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-CG-4466        TCGA-CG-4469        TCGA-CG-4472        TCGA-CG-4474 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" 
       TCGA-CG-4477        TCGA-CG-5716        TCGA-CG-5717        TCGA-CG-5718 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-CG-5719        TCGA-CG-5720        TCGA-CG-5721        TCGA-CG-5722 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-CG-5723        TCGA-CG-5724        TCGA-CG-5725        TCGA-CG-5726 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-CG-5727        TCGA-CG-5728        TCGA-CG-5730        TCGA-CG-5732 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-CG-5733        TCGA-CG-5734        TCGA-D7-5577        TCGA-D7-5578 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-D7-5579        TCGA-D7-6518        TCGA-D7-6519        TCGA-D7-6520 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-D7-6521        TCGA-D7-6522        TCGA-D7-6524        TCGA-D7-6525 
  "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-D7-6526        TCGA-D7-6527        TCGA-D7-6528        TCGA-D7-6815 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-D7-6817        TCGA-D7-6818        TCGA-D7-6820        TCGA-D7-6822 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-EQ-5647        TCGA-EQ-8122        TCGA-F1-6177        TCGA-F1-6874 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-F1-6875        TCGA-FP-7735        TCGA-FP-7829        TCGA-FP-7916 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-FP-7998        TCGA-FP-8099        TCGA-FP-8209        TCGA-FP-8631 
"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-BR-8592        TCGA-BR-A4IU        TCGA-BR-A4IV        TCGA-BR-A4IY 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-BR-A4IZ        TCGA-BR-A4J1        TCGA-BR-A4J2        TCGA-BR-A4J4 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" 
       TCGA-BR-A4J5        TCGA-BR-A4J6        TCGA-BR-A4J8        TCGA-BR-A4J9 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-BR-A4PF        TCGA-CD-5798        TCGA-CD-5799        TCGA-CD-5800 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" 
       TCGA-CD-5801        TCGA-CD-5802        TCGA-CD-5803        TCGA-CG-4300 
  "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-CG-4301        TCGA-CG-4304        TCGA-CG-4305        TCGA-CG-4306 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" 
       TCGA-CG-4436        TCGA-CG-4437        TCGA-CG-4438        TCGA-CG-4440 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-CG-4441        TCGA-CG-4443        TCGA-CG-4444        TCGA-CG-4449 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-CG-4455        TCGA-CG-4460        TCGA-CG-4462        TCGA-CG-4465 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-CG-4466        TCGA-CG-4469        TCGA-CG-4472        TCGA-CG-4474 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" 
       TCGA-CG-4477        TCGA-CG-5716        TCGA-CG-5717        TCGA-CG-5718 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-CG-5719        TCGA-CG-5720        TCGA-CG-5721        TCGA-CG-5722 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-CG-5723        TCGA-CG-5724        TCGA-CG-5725        TCGA-CG-5726 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-CG-5727        TCGA-CG-5728        TCGA-CG-5730        TCGA-CG-5732 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-CG-5733        TCGA-CG-5734        TCGA-D7-5577        TCGA-D7-5578 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-D7-5579        TCGA-D7-6518        TCGA-D7-6519        TCGA-D7-6520 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-D7-6521        TCGA-D7-6522        TCGA-D7-6524        TCGA-D7-6525 
  "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-D7-6526        TCGA-D7-6527        TCGA-D7-6528        TCGA-D7-6815 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-D7-6817        TCGA-D7-6818        TCGA-D7-6820        TCGA-D7-6822 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-EQ-5647        TCGA-EQ-8122        TCGA-F1-6177        TCGA-F1-6874 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-F1-6875        TCGA-FP-7735        TCGA-FP-7829        TCGA-FP-7916 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-FP-7998        TCGA-FP-8099        TCGA-FP-8209        TCGA-FP-8631 
"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   13
  3Q GAIN WILD-TYPE   69   94
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  FEMALE               1                69
  MALE                13                94
                   vv
clus                STOMACH ADENOCARCINOMA - DIFFUSE TYPE
  3Q GAIN MUTATED                                       3
  3Q GAIN WILD-TYPE                                    22
                   vv
clus                STOMACH ADENOCARCINOMA - NOT OTHERWISE SPECIFIED (NOS)
  3Q GAIN MUTATED                                                        9
  3Q GAIN WILD-TYPE                                                     78
                   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                                                10
                   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                                                                     35
D6V4, multiclass
                   vv
clus                T1 T2 T3 T4
  3Q GAIN MUTATED    0  5  5  4
  3Q GAIN WILD-TYPE  6 49 59 39
D6V5, multiclass
    clus
vv   3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  T1               0                 6
  T2               5                49
  T3               5                59
  T4               4                39
                   vv
clus                N0 N1 N2 N3
  3Q GAIN MUTATED    3  5  4  1
  3Q GAIN WILD-TYPE 53 56 25 19
D6V6, multiclass
    clus
vv   3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  N0               3                53
  N1               5                56
  N2               4                25
  N3               1                19
                   vv
clus                 M0  M1  MX
  3Q GAIN MUTATED    13   0   1
  3Q GAIN WILD-TYPE 133  18  12
D6V7, multiclass
    clus
vv   3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  M0              13               133
  M1               0                18
  MX               1                12
                   vv
clus                 I II III IV
  3Q GAIN MUTATED    2  4   5  2
  3Q GAIN WILD-TYPE 24 44  53 27
D6V8, multiclass
     clus
vv    3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  I                 2                24
  II                4                44
  III               5                53
  IV                2                27
D6V9, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED      0   14
  3Q GAIN WILD-TYPE    5  158
     clus
vv    3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  NO                0                 5
  YES              14               158
                   vv
clus                 R0  R1  R2  RX
  3Q GAIN MUTATED     9   0   0   3
  3Q GAIN WILD-TYPE 114   7  12  22
D6V10, multiclass
    clus
vv   3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  R0               9               114
  R1               0                 7
  R2               0                12
  RX               3                22
D6V11, continuous

Clustering(7) Variable = 4p gain mutation analysis
D7V1, survival
                   sevent
clus2                 0   1
  4P GAIN MUTATED     2   0
  4P GAIN WILD-TYPE 120  18
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                2               138 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                0                18 
$`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-BR-8592 TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        0.20         0.59         0.92         0.39         0.79         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J8 TCGA-BR-A4J9 
        0.79         0.53         0.43         0.13         0.23         0.10 
TCGA-BR-A4PF TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        0.72         0.82         0.69         0.36         0.49         0.30 
TCGA-CD-5803 TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
        0.07        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4444 
       52.96         8.05        54.05         4.01        14.01        47.05 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4460 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       19.07        12.03        21.99         1.02         8.98        18.94 
TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4474 TCGA-CG-4477 TCGA-CG-5716 TCGA-CG-5717 
        7.07        12.00         1.02         1.02         1.02         6.94 
TCGA-CG-5718 TCGA-CG-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-D7-6518 
       55.04        21.07         7.99         8.65         3.58         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-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-FP-8099 
       72.23         0.39         0.20         3.02         3.58         1.02 
TCGA-FP-8209 TCGA-FP-8631 TCGA-HJ-7597 TCGA-IN-7806 TCGA-IN-7808 TCGA-IP-7968 
       59.05         0.56        26.43         6.87         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              1.22 
[1] "4.5 - 30.0 (17.3)" "0.1 - 72.2 (1.2)" 
       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-BR-8592        TCGA-BR-A4IU        TCGA-BR-A4IV        TCGA-BR-A4IY 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BR-A4IZ        TCGA-BR-A4J1        TCGA-BR-A4J2        TCGA-BR-A4J4 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BR-A4J5        TCGA-BR-A4J6        TCGA-BR-A4J8        TCGA-BR-A4J9 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BR-A4PF        TCGA-CD-5798        TCGA-CD-5799        TCGA-CD-5800 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-CD-5801        TCGA-CD-5802        TCGA-CD-5803        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-4443        TCGA-CG-4444        TCGA-CG-4449 
"4P GAIN WILD-TYPE"   "4P GAIN MUTATED" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-CG-4455        TCGA-CG-4460        TCGA-CG-4462        TCGA-CG-4465 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-CG-4466        TCGA-CG-4469        TCGA-CG-4472        TCGA-CG-4474 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-CG-4477        TCGA-CG-5716        TCGA-CG-5717        TCGA-CG-5718 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-CG-5719        TCGA-CG-5720        TCGA-CG-5721        TCGA-CG-5722 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-CG-5723        TCGA-CG-5724        TCGA-CG-5725        TCGA-CG-5726 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-CG-5727        TCGA-CG-5728        TCGA-CG-5730        TCGA-CG-5732 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-CG-5733        TCGA-CG-5734        TCGA-D7-5577        TCGA-D7-5578 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-D7-5579        TCGA-D7-6518        TCGA-D7-6519        TCGA-D7-6520 
  "4P GAIN MUTATED" "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-FP-8099        TCGA-FP-8209        TCGA-FP-8631 
"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-BR-8592        TCGA-BR-A4IU        TCGA-BR-A4IV        TCGA-BR-A4IY 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BR-A4IZ        TCGA-BR-A4J1        TCGA-BR-A4J2        TCGA-BR-A4J4 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BR-A4J5        TCGA-BR-A4J6        TCGA-BR-A4J8        TCGA-BR-A4J9 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BR-A4PF        TCGA-CD-5798        TCGA-CD-5799        TCGA-CD-5800 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-CD-5801        TCGA-CD-5802        TCGA-CD-5803        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-4443        TCGA-CG-4444        TCGA-CG-4449 
"4P GAIN WILD-TYPE"   "4P GAIN MUTATED" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-CG-4455        TCGA-CG-4460        TCGA-CG-4462        TCGA-CG-4465 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-CG-4466        TCGA-CG-4469        TCGA-CG-4472        TCGA-CG-4474 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-CG-4477        TCGA-CG-5716        TCGA-CG-5717        TCGA-CG-5718 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-CG-5719        TCGA-CG-5720        TCGA-CG-5721        TCGA-CG-5722 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-CG-5723        TCGA-CG-5724        TCGA-CG-5725        TCGA-CG-5726 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-CG-5727        TCGA-CG-5728        TCGA-CG-5730        TCGA-CG-5732 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-CG-5733        TCGA-CG-5734        TCGA-D7-5577        TCGA-D7-5578 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-D7-5579        TCGA-D7-6518        TCGA-D7-6519        TCGA-D7-6520 
  "4P GAIN MUTATED" "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-FP-8099        TCGA-FP-8209        TCGA-FP-8631 
"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-BR-8592        TCGA-BR-A4IU        TCGA-BR-A4IV        TCGA-BR-A4IY 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BR-A4IZ        TCGA-BR-A4J1        TCGA-BR-A4J2        TCGA-BR-A4J4 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BR-A4J5        TCGA-BR-A4J6        TCGA-BR-A4J8        TCGA-BR-A4J9 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BR-A4PF        TCGA-CD-5798        TCGA-CD-5799        TCGA-CD-5800 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-CD-5801        TCGA-CD-5802        TCGA-CD-5803        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-4443        TCGA-CG-4444        TCGA-CG-4449 
"4P GAIN WILD-TYPE"   "4P GAIN MUTATED" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-CG-4455        TCGA-CG-4460        TCGA-CG-4462        TCGA-CG-4465 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-CG-4466        TCGA-CG-4469        TCGA-CG-4472        TCGA-CG-4474 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-CG-4477        TCGA-CG-5716        TCGA-CG-5717        TCGA-CG-5718 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-CG-5719        TCGA-CG-5720        TCGA-CG-5721        TCGA-CG-5722 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-CG-5723        TCGA-CG-5724        TCGA-CG-5725        TCGA-CG-5726 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-CG-5727        TCGA-CG-5728        TCGA-CG-5730        TCGA-CG-5732 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-CG-5733        TCGA-CG-5734        TCGA-D7-5577        TCGA-D7-5578 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-D7-5579        TCGA-D7-6518        TCGA-D7-6519        TCGA-D7-6520 
  "4P GAIN MUTATED" "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-FP-8099        TCGA-FP-8209        TCGA-FP-8631 
"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               138 
       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-BR-8592        TCGA-BR-A4IU        TCGA-BR-A4IV        TCGA-BR-A4IY 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BR-A4IZ        TCGA-BR-A4J1        TCGA-BR-A4J2        TCGA-BR-A4J4 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BR-A4J5        TCGA-BR-A4J6        TCGA-BR-A4J8        TCGA-BR-A4J9 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BR-A4PF        TCGA-CD-5798        TCGA-CD-5799        TCGA-CD-5800 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-CD-5801        TCGA-CD-5802        TCGA-CD-5803        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-4444        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-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-D7-6518 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-D7-6519        TCGA-D7-6520        TCGA-D7-6521        TCGA-D7-6522 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-D7-6524        TCGA-D7-6525        TCGA-D7-6526        TCGA-D7-6527 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-D7-6528        TCGA-D7-6815        TCGA-D7-6817        TCGA-D7-6818 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-D7-6820        TCGA-D7-6822        TCGA-EQ-5647        TCGA-EQ-8122 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875        TCGA-FP-7735 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-FP-7829        TCGA-FP-7916        TCGA-FP-7998        TCGA-FP-8099 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-FP-8209        TCGA-FP-8631        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   70  104
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  FEMALE               0                70
  MALE                 3               104
                   vv
clus                STOMACH ADENOCARCINOMA - DIFFUSE TYPE
  4P GAIN MUTATED                                       0
  4P GAIN WILD-TYPE                                    25
                   vv
clus                STOMACH ADENOCARCINOMA - NOT OTHERWISE SPECIFIED (NOS)
  4P GAIN MUTATED                                                        0
  4P GAIN WILD-TYPE                                                     87
                   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                                                 9
                   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                                                                     35
D7V4, multiclass
[1] "Remove cluster labels:" "4P GAIN MUTATED"       
clus
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                2               170 
       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-BR-8592        TCGA-BR-A4IU        TCGA-BR-A4IV        TCGA-BR-A4IY 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BR-A4IZ        TCGA-BR-A4J1        TCGA-BR-A4J2        TCGA-BR-A4J4 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BR-A4J5        TCGA-BR-A4J6        TCGA-BR-A4J8        TCGA-BR-A4J9 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BR-A4PF        TCGA-CD-5798        TCGA-CD-5799        TCGA-CD-5800 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-CD-5801        TCGA-CD-5802        TCGA-CD-5803        TCGA-CD-5804 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-CG-4300        TCGA-CG-4301        TCGA-CG-4304        TCGA-CG-4305 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-CG-4306        TCGA-CG-4436        TCGA-CG-4437        TCGA-CG-4438 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-CG-4440        TCGA-CG-4441        TCGA-CG-4442        TCGA-CG-4449 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-CG-4455        TCGA-CG-4460        TCGA-CG-4466        TCGA-CG-4469 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-CG-4474        TCGA-CG-4476        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-FP-8099        TCGA-FP-8209 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-FP-8631        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 54 62 43
D7V5, multiclass
    clus
vv   4P GAIN MUTATED 4P GAIN WILD-TYPE
  T1               1                 5
  T2               0                54
  T3               2                62
  T4               0                43
                   vv
clus                N0 N1 N2 N3
  4P GAIN MUTATED    1  1  1  0
  4P GAIN WILD-TYPE 55 60 28 20
D7V6, multiclass
    clus
vv   4P GAIN MUTATED 4P GAIN WILD-TYPE
  N0               1                55
  N1               1                60
  N2               1                28
  N3               0                20
                   vv
clus                 M0  M1  MX
  4P GAIN MUTATED     3   0   0
  4P GAIN WILD-TYPE 143  18  13
D7V7, multiclass
    clus
vv   4P GAIN MUTATED 4P GAIN WILD-TYPE
  M0               3               143
  M1               0                18
  MX               0                13
                   vv
clus                 I II III IV
  4P GAIN MUTATED    1  2   0  0
  4P GAIN WILD-TYPE 25 46  58 29
D7V8, multiclass
     clus
vv    4P GAIN MUTATED 4P GAIN WILD-TYPE
  I                 1                25
  II                2                46
  III               0                58
  IV                0                29
D7V9, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED      0    3
  4P GAIN WILD-TYPE    5  169
     clus
vv    4P GAIN MUTATED 4P GAIN WILD-TYPE
  NO                0                 5
  YES               3               169
                   vv
clus                 R0  R1  R2  RX
  4P GAIN MUTATED     2   1   0   0
  4P GAIN WILD-TYPE 121   6  12  25
D7V10, multiclass
    clus
vv   4P GAIN MUTATED 4P GAIN WILD-TYPE
  R0               2               121
  R1               1                 6
  R2               0                12
  RX               0                25
D7V11, continuous
[1] "Remove cluster labels:" "4P GAIN MUTATED"       
clus
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                1               132 
       TCGA-B7-5816        TCGA-BR-4183        TCGA-BR-4184        TCGA-BR-4188 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BR-4191        TCGA-BR-4253        TCGA-BR-4255        TCGA-BR-4256 
"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-4361 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BR-4362        TCGA-BR-4367        TCGA-BR-4368        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-BR-8592        TCGA-BR-A4IU        TCGA-BR-A4IV        TCGA-BR-A4IY 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BR-A4IZ        TCGA-BR-A4J1        TCGA-BR-A4J2        TCGA-BR-A4J4 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BR-A4J5        TCGA-BR-A4J6        TCGA-BR-A4J8        TCGA-BR-A4J9 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BR-A4PF        TCGA-CD-5804        TCGA-CG-5717        TCGA-CG-5718 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-CG-5719        TCGA-CG-5720        TCGA-CG-5721        TCGA-CG-5722 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-CG-5723        TCGA-CG-5724        TCGA-CG-5725        TCGA-CG-5726 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-CG-5727        TCGA-CG-5728        TCGA-CG-5730        TCGA-CG-5732 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-CG-5733        TCGA-CG-5734        TCGA-D7-5577        TCGA-D7-5578 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       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-FP-8099        TCGA-FP-8209        TCGA-FP-8631        TCGA-HF-7131 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-HF-7132        TCGA-HF-7133        TCGA-HF-7134        TCGA-HF-7136 
"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" 

Clustering(8) Variable = 5p gain mutation analysis
D8V1, survival
                   sevent
clus2                 0   1
  5P GAIN MUTATED    18   4
  5P GAIN WILD-TYPE 104  14
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               22               118 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
                4                14 
$`5P GAIN MUTATED`
TCGA-BR-7197 TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7717 TCGA-CD-5801 TCGA-CG-4436 
        1.48         1.25         1.05         0.69         0.49        52.96 
TCGA-CG-4438 TCGA-CG-4444 TCGA-CG-4455 TCGA-CG-4460 TCGA-CG-4466 TCGA-CG-4472 
       54.05        47.05        12.03        21.99        18.94        12.00 
TCGA-CG-5718 TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5725 TCGA-D7-5579 TCGA-D7-6527 
        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-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-BR-8592 TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        1.48         0.76         0.20         0.59         0.92         0.39 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
        0.79         0.72         0.79         0.53         0.43         0.13 
TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PF TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
        0.23         0.10         0.72         0.82         0.69         0.36 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
        0.30         0.07        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4437 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        1.02         8.05         4.01        14.01        29.98        19.07 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4469 TCGA-CG-4474 TCGA-CG-4477 TCGA-CG-5716 
        1.02         8.98         7.07         1.02         1.02         1.02 
TCGA-CG-5717 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5723 TCGA-CG-5726 
        6.94         1.02         0.99         5.98        70.06        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-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
        8.65         3.58         9.80        15.65         9.63         8.19 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6528 TCGA-D7-6815 
        6.90         0.69         5.95         6.61         1.68         3.65 
TCGA-D7-6817 TCGA-D7-6822 TCGA-EQ-8122 TCGA-F1-6177 TCGA-F1-6874 TCGA-F1-6875 
        4.70         4.27         7.79         6.54         2.01        72.23 
TCGA-FP-7735 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8631 
        0.39         3.02         3.58         1.02        59.05         0.56 
TCGA-HJ-7597 TCGA-IN-7806 TCGA-IN-7808 TCGA-IP-7968 
       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 
             4.09              1.10 
[1] "0.2 - 54.0 (4.1)" "0.1 - 72.2 (1.1)"
       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 MUTATED" "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 WILD-TYPE" "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-BR-8592        TCGA-BR-A4IU        TCGA-BR-A4IV        TCGA-BR-A4IY 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-BR-A4IZ        TCGA-BR-A4J1        TCGA-BR-A4J2        TCGA-BR-A4J4 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-BR-A4J5        TCGA-BR-A4J6        TCGA-BR-A4J8        TCGA-BR-A4J9 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-BR-A4PF        TCGA-CD-5798        TCGA-CD-5799        TCGA-CD-5800 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-CD-5801        TCGA-CD-5802        TCGA-CD-5803        TCGA-CG-4300 
  "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-CG-4301        TCGA-CG-4304        TCGA-CG-4305        TCGA-CG-4306 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-CG-4436        TCGA-CG-4437        TCGA-CG-4438        TCGA-CG-4440 
  "5P GAIN MUTATED" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" 
       TCGA-CG-4441        TCGA-CG-4443        TCGA-CG-4444        TCGA-CG-4449 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" 
       TCGA-CG-4455        TCGA-CG-4460        TCGA-CG-4462        TCGA-CG-4465 
  "5P GAIN MUTATED"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-CG-4466        TCGA-CG-4469        TCGA-CG-4472        TCGA-CG-4474 
  "5P GAIN MUTATED" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" 
       TCGA-CG-4477        TCGA-CG-5716        TCGA-CG-5717        TCGA-CG-5718 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" 
       TCGA-CG-5719        TCGA-CG-5720        TCGA-CG-5721        TCGA-CG-5722 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" 
       TCGA-CG-5723        TCGA-CG-5724        TCGA-CG-5725        TCGA-CG-5726 
"5P GAIN WILD-TYPE"   "5P GAIN MUTATED"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" 
       TCGA-CG-5727        TCGA-CG-5728        TCGA-CG-5730        TCGA-CG-5732 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-CG-5733        TCGA-CG-5734        TCGA-D7-5577        TCGA-D7-5578 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-D7-5579        TCGA-D7-6518        TCGA-D7-6519        TCGA-D7-6520 
  "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-D7-6521        TCGA-D7-6522        TCGA-D7-6524        TCGA-D7-6525 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-D7-6526        TCGA-D7-6527        TCGA-D7-6528        TCGA-D7-6815 
"5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-D7-6817        TCGA-D7-6818        TCGA-D7-6820        TCGA-D7-6822 
"5P GAIN WILD-TYPE"   "5P GAIN MUTATED"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" 
       TCGA-EQ-5647        TCGA-EQ-8122        TCGA-F1-6177        TCGA-F1-6874 
  "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-F1-6875        TCGA-FP-7735        TCGA-FP-7829        TCGA-FP-7916 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" 
       TCGA-FP-7998        TCGA-FP-8099        TCGA-FP-8209        TCGA-FP-8631 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "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 MUTATED" "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 WILD-TYPE" "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-BR-8592        TCGA-BR-A4IU        TCGA-BR-A4IV        TCGA-BR-A4IY 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-BR-A4IZ        TCGA-BR-A4J1        TCGA-BR-A4J2        TCGA-BR-A4J4 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-BR-A4J5        TCGA-BR-A4J6        TCGA-BR-A4J8        TCGA-BR-A4J9 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-BR-A4PF        TCGA-CD-5798        TCGA-CD-5799        TCGA-CD-5800 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-CD-5801        TCGA-CD-5802        TCGA-CD-5803        TCGA-CG-4300 
  "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-CG-4301        TCGA-CG-4304        TCGA-CG-4305        TCGA-CG-4306 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-CG-4436        TCGA-CG-4437        TCGA-CG-4438        TCGA-CG-4440 
  "5P GAIN MUTATED" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" 
       TCGA-CG-4441        TCGA-CG-4443        TCGA-CG-4444        TCGA-CG-4449 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" 
       TCGA-CG-4455        TCGA-CG-4460        TCGA-CG-4462        TCGA-CG-4465 
  "5P GAIN MUTATED"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-CG-4466        TCGA-CG-4469        TCGA-CG-4472        TCGA-CG-4474 
  "5P GAIN MUTATED" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" 
       TCGA-CG-4477        TCGA-CG-5716        TCGA-CG-5717        TCGA-CG-5718 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" 
       TCGA-CG-5719        TCGA-CG-5720        TCGA-CG-5721        TCGA-CG-5722 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" 
       TCGA-CG-5723        TCGA-CG-5724        TCGA-CG-5725        TCGA-CG-5726 
"5P GAIN WILD-TYPE"   "5P GAIN MUTATED"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" 
       TCGA-CG-5727        TCGA-CG-5728        TCGA-CG-5730        TCGA-CG-5732 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-CG-5733        TCGA-CG-5734        TCGA-D7-5577        TCGA-D7-5578 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-D7-5579        TCGA-D7-6518        TCGA-D7-6519        TCGA-D7-6520 
  "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-D7-6521        TCGA-D7-6522        TCGA-D7-6524        TCGA-D7-6525 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-D7-6526        TCGA-D7-6527        TCGA-D7-6528        TCGA-D7-6815 
"5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-D7-6817        TCGA-D7-6818        TCGA-D7-6820        TCGA-D7-6822 
"5P GAIN WILD-TYPE"   "5P GAIN MUTATED"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" 
       TCGA-EQ-5647        TCGA-EQ-8122        TCGA-F1-6177        TCGA-F1-6874 
  "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-F1-6875        TCGA-FP-7735        TCGA-FP-7829        TCGA-FP-7916 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" 
       TCGA-FP-7998        TCGA-FP-8099        TCGA-FP-8209        TCGA-FP-8631 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "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 MUTATED" "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 WILD-TYPE" "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-BR-8592        TCGA-BR-A4IU        TCGA-BR-A4IV        TCGA-BR-A4IY 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-BR-A4IZ        TCGA-BR-A4J1        TCGA-BR-A4J2        TCGA-BR-A4J4 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-BR-A4J5        TCGA-BR-A4J6        TCGA-BR-A4J8        TCGA-BR-A4J9 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-BR-A4PF        TCGA-CD-5798        TCGA-CD-5799        TCGA-CD-5800 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-CD-5801        TCGA-CD-5802        TCGA-CD-5803        TCGA-CG-4300 
  "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-CG-4301        TCGA-CG-4304        TCGA-CG-4305        TCGA-CG-4306 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-CG-4436        TCGA-CG-4437        TCGA-CG-4438        TCGA-CG-4440 
  "5P GAIN MUTATED" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" 
       TCGA-CG-4441        TCGA-CG-4443        TCGA-CG-4444        TCGA-CG-4449 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" 
       TCGA-CG-4455        TCGA-CG-4460        TCGA-CG-4462        TCGA-CG-4465 
  "5P GAIN MUTATED"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-CG-4466        TCGA-CG-4469        TCGA-CG-4472        TCGA-CG-4474 
  "5P GAIN MUTATED" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" 
       TCGA-CG-4477        TCGA-CG-5716        TCGA-CG-5717        TCGA-CG-5718 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" 
       TCGA-CG-5719        TCGA-CG-5720        TCGA-CG-5721        TCGA-CG-5722 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" 
       TCGA-CG-5723        TCGA-CG-5724        TCGA-CG-5725        TCGA-CG-5726 
"5P GAIN WILD-TYPE"   "5P GAIN MUTATED"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" 
       TCGA-CG-5727        TCGA-CG-5728        TCGA-CG-5730        TCGA-CG-5732 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-CG-5733        TCGA-CG-5734        TCGA-D7-5577        TCGA-D7-5578 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-D7-5579        TCGA-D7-6518        TCGA-D7-6519        TCGA-D7-6520 
  "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-D7-6521        TCGA-D7-6522        TCGA-D7-6524        TCGA-D7-6525 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-D7-6526        TCGA-D7-6527        TCGA-D7-6528        TCGA-D7-6815 
"5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-D7-6817        TCGA-D7-6818        TCGA-D7-6820        TCGA-D7-6822 
"5P GAIN WILD-TYPE"   "5P GAIN MUTATED"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" 
       TCGA-EQ-5647        TCGA-EQ-8122        TCGA-F1-6177        TCGA-F1-6874 
  "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-F1-6875        TCGA-FP-7735        TCGA-FP-7829        TCGA-FP-7916 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" 
       TCGA-FP-7998        TCGA-FP-8099        TCGA-FP-8209        TCGA-FP-8631 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "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   63   88
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  FEMALE               7                63
  MALE                19                88
                   vv
clus                STOMACH ADENOCARCINOMA - DIFFUSE TYPE
  5P GAIN MUTATED                                       2
  5P GAIN WILD-TYPE                                    23
                   vv
clus                STOMACH ADENOCARCINOMA - NOT OTHERWISE SPECIFIED (NOS)
  5P GAIN MUTATED                                                        9
  5P GAIN WILD-TYPE                                                     78
                   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                                                 7
                   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                                                                     29
D8V4, multiclass
                   vv
clus                T1 T2 T3 T4
  5P GAIN MUTATED    0  9 10  5
  5P GAIN WILD-TYPE  6 45 54 38
D8V5, multiclass
    clus
vv   5P GAIN MUTATED 5P GAIN WILD-TYPE
  T1               0                 6
  T2               9                45
  T3              10                54
  T4               5                38
                   vv
clus                N0 N1 N2 N3
  5P GAIN MUTATED    7 11  4  3
  5P GAIN WILD-TYPE 49 50 25 17
D8V6, multiclass
    clus
vv   5P GAIN MUTATED 5P GAIN WILD-TYPE
  N0               7                49
  N1              11                50
  N2               4                25
  N3               3                17
                   vv
clus                 M0  M1  MX
  5P GAIN MUTATED    22   4   0
  5P GAIN WILD-TYPE 124  14  13
D8V7, multiclass
    clus
vv   5P GAIN MUTATED 5P GAIN WILD-TYPE
  M0              22               124
  M1               4                14
  MX               0                13
                   vv
clus                 I II III IV
  5P GAIN MUTATED    3 10   3  8
  5P GAIN WILD-TYPE 23 38  55 21
D8V8, multiclass
     clus
vv    5P GAIN MUTATED 5P GAIN WILD-TYPE
  I                 3                23
  II               10                38
  III               3                55
  IV                8                21
D8V9, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED      2   24
  5P GAIN WILD-TYPE    3  148
     clus
vv    5P GAIN MUTATED 5P GAIN WILD-TYPE
  NO                2                 3
  YES              24               148
                   vv
clus                 R0  R1  R2  RX
  5P GAIN MUTATED    18   1   4   2
  5P GAIN WILD-TYPE 105   6   8  23
D8V10, multiclass
    clus
vv   5P GAIN MUTATED 5P GAIN WILD-TYPE
  R0              18               105
  R1               1                 6
  R2               4                 8
  RX               2                23
D8V11, continuous

Clustering(9) Variable = 5q gain mutation analysis
D9V1, survival
                   sevent
clus2                 0   1
  5Q GAIN MUTATED     6   0
  5Q GAIN WILD-TYPE 116  18
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
                6               134 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
                0                18 
$`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-BR-8592 
        0.26         1.18         1.55         1.48         0.76         0.20 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
        0.59         0.92         0.39         0.79         0.72         0.79 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PF 
        0.53         0.43         0.13         0.23         0.10         0.72 
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-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4460 
        4.01        14.01        29.98        47.05        19.07        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-5725 TCGA-CG-5726 TCGA-CG-5727 
        0.95        70.06        12.03        15.02        28.96        31.04 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        55.04        21.07         7.99         8.65 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
        3.58         4.54         9.80        15.65         9.63         8.19 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
        6.90         0.69         5.95         6.61         4.14         1.68 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-EQ-5647 
        3.65         4.70         4.04         2.93         4.27         0.62 
TCGA-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-FP-8099 TCGA-FP-8209 TCGA-FP-8631 TCGA-HJ-7597 TCGA-IN-7806 
        3.58         1.02        59.05         0.56        26.43         6.87 
TCGA-IN-7808 TCGA-IP-7968 
        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             1.220 
[1] "0.2 - 54.0 (15.5)" "0.1 - 72.2 (1.2)" 
       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-BR-8592        TCGA-BR-A4IU        TCGA-BR-A4IV        TCGA-BR-A4IY 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-BR-A4IZ        TCGA-BR-A4J1        TCGA-BR-A4J2        TCGA-BR-A4J4 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-BR-A4J5        TCGA-BR-A4J6        TCGA-BR-A4J8        TCGA-BR-A4J9 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-BR-A4PF        TCGA-CD-5798        TCGA-CD-5799        TCGA-CD-5800 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-CD-5801        TCGA-CD-5802        TCGA-CD-5803        TCGA-CG-4300 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-CG-4301        TCGA-CG-4304        TCGA-CG-4305        TCGA-CG-4306 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-CG-4436        TCGA-CG-4437        TCGA-CG-4438        TCGA-CG-4440 
  "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE" 
       TCGA-CG-4441        TCGA-CG-4443        TCGA-CG-4444        TCGA-CG-4449 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-CG-4455        TCGA-CG-4460        TCGA-CG-4462        TCGA-CG-4465 
  "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-CG-4466        TCGA-CG-4469        TCGA-CG-4472        TCGA-CG-4474 
  "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-CG-4477        TCGA-CG-5716        TCGA-CG-5717        TCGA-CG-5718 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-CG-5719        TCGA-CG-5720        TCGA-CG-5721        TCGA-CG-5722 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-CG-5723        TCGA-CG-5724        TCGA-CG-5725        TCGA-CG-5726 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-CG-5727        TCGA-CG-5728        TCGA-CG-5730        TCGA-CG-5732 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-CG-5733        TCGA-CG-5734        TCGA-D7-5577        TCGA-D7-5578 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-D7-5579        TCGA-D7-6518        TCGA-D7-6519        TCGA-D7-6520 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-D7-6521        TCGA-D7-6522        TCGA-D7-6524        TCGA-D7-6525 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-D7-6526        TCGA-D7-6527        TCGA-D7-6528        TCGA-D7-6815 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-D7-6817        TCGA-D7-6818        TCGA-D7-6820        TCGA-D7-6822 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-EQ-5647        TCGA-EQ-8122        TCGA-F1-6177        TCGA-F1-6874 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-F1-6875        TCGA-FP-7735        TCGA-FP-7829        TCGA-FP-7916 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE" 
       TCGA-FP-7998        TCGA-FP-8099        TCGA-FP-8209        TCGA-FP-8631 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "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-BR-8592        TCGA-BR-A4IU        TCGA-BR-A4IV        TCGA-BR-A4IY 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-BR-A4IZ        TCGA-BR-A4J1        TCGA-BR-A4J2        TCGA-BR-A4J4 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-BR-A4J5        TCGA-BR-A4J6        TCGA-BR-A4J8        TCGA-BR-A4J9 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-BR-A4PF        TCGA-CD-5798        TCGA-CD-5799        TCGA-CD-5800 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-CD-5801        TCGA-CD-5802        TCGA-CD-5803        TCGA-CG-4300 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-CG-4301        TCGA-CG-4304        TCGA-CG-4305        TCGA-CG-4306 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-CG-4436        TCGA-CG-4437        TCGA-CG-4438        TCGA-CG-4440 
  "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE" 
       TCGA-CG-4441        TCGA-CG-4443        TCGA-CG-4444        TCGA-CG-4449 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-CG-4455        TCGA-CG-4460        TCGA-CG-4462        TCGA-CG-4465 
  "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-CG-4466        TCGA-CG-4469        TCGA-CG-4472        TCGA-CG-4474 
  "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-CG-4477        TCGA-CG-5716        TCGA-CG-5717        TCGA-CG-5718 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-CG-5719        TCGA-CG-5720        TCGA-CG-5721        TCGA-CG-5722 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-CG-5723        TCGA-CG-5724        TCGA-CG-5725        TCGA-CG-5726 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-CG-5727        TCGA-CG-5728        TCGA-CG-5730        TCGA-CG-5732 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-CG-5733        TCGA-CG-5734        TCGA-D7-5577        TCGA-D7-5578 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-D7-5579        TCGA-D7-6518        TCGA-D7-6519        TCGA-D7-6520 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-D7-6521        TCGA-D7-6522        TCGA-D7-6524        TCGA-D7-6525 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-D7-6526        TCGA-D7-6527        TCGA-D7-6528        TCGA-D7-6815 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-D7-6817        TCGA-D7-6818        TCGA-D7-6820        TCGA-D7-6822 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-EQ-5647        TCGA-EQ-8122        TCGA-F1-6177        TCGA-F1-6874 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-F1-6875        TCGA-FP-7735        TCGA-FP-7829        TCGA-FP-7916 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE" 
       TCGA-FP-7998        TCGA-FP-8099        TCGA-FP-8209        TCGA-FP-8631 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "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-BR-8592        TCGA-BR-A4IU        TCGA-BR-A4IV        TCGA-BR-A4IY 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-BR-A4IZ        TCGA-BR-A4J1        TCGA-BR-A4J2        TCGA-BR-A4J4 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-BR-A4J5        TCGA-BR-A4J6        TCGA-BR-A4J8        TCGA-BR-A4J9 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-BR-A4PF        TCGA-CD-5798        TCGA-CD-5799        TCGA-CD-5800 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-CD-5801        TCGA-CD-5802        TCGA-CD-5803        TCGA-CG-4300 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-CG-4301        TCGA-CG-4304        TCGA-CG-4305        TCGA-CG-4306 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-CG-4436        TCGA-CG-4437        TCGA-CG-4438        TCGA-CG-4440 
  "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE" 
       TCGA-CG-4441        TCGA-CG-4443        TCGA-CG-4444        TCGA-CG-4449 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-CG-4455        TCGA-CG-4460        TCGA-CG-4462        TCGA-CG-4465 
  "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-CG-4466        TCGA-CG-4469        TCGA-CG-4472        TCGA-CG-4474 
  "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-CG-4477        TCGA-CG-5716        TCGA-CG-5717        TCGA-CG-5718 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-CG-5719        TCGA-CG-5720        TCGA-CG-5721        TCGA-CG-5722 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-CG-5723        TCGA-CG-5724        TCGA-CG-5725        TCGA-CG-5726 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-CG-5727        TCGA-CG-5728        TCGA-CG-5730        TCGA-CG-5732 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-CG-5733        TCGA-CG-5734        TCGA-D7-5577        TCGA-D7-5578 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-D7-5579        TCGA-D7-6518        TCGA-D7-6519        TCGA-D7-6520 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-D7-6521        TCGA-D7-6522        TCGA-D7-6524        TCGA-D7-6525 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-D7-6526        TCGA-D7-6527        TCGA-D7-6528        TCGA-D7-6815 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-D7-6817        TCGA-D7-6818        TCGA-D7-6820        TCGA-D7-6822 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-EQ-5647        TCGA-EQ-8122        TCGA-F1-6177        TCGA-F1-6874 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-F1-6875        TCGA-FP-7735        TCGA-FP-7829        TCGA-FP-7916 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE" 
       TCGA-FP-7998        TCGA-FP-8099        TCGA-FP-8209        TCGA-FP-8631 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "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="     "8.2e+07"
D9V2, continuous
D9V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED      1    6
  5Q GAIN WILD-TYPE   69  101
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  FEMALE               1                69
  MALE                 6               101
                   vv
clus                STOMACH ADENOCARCINOMA - DIFFUSE TYPE
  5Q GAIN MUTATED                                       0
  5Q GAIN WILD-TYPE                                    25
                   vv
clus                STOMACH ADENOCARCINOMA - NOT OTHERWISE SPECIFIED (NOS)
  5Q GAIN MUTATED                                                        2
  5Q GAIN WILD-TYPE                                                     85
                   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                                                 8
                   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                                                                     33
D9V4, multiclass
                   vv
clus                T1 T2 T3 T4
  5Q GAIN MUTATED    0  3  3  1
  5Q GAIN WILD-TYPE  6 51 61 42
D9V5, multiclass
    clus
vv   5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  T1               0                 6
  T2               3                51
  T3               3                61
  T4               1                42
                   vv
clus                N0 N1 N2 N3
  5Q GAIN MUTATED    4  2  1  0
  5Q GAIN WILD-TYPE 52 59 28 20
D9V6, multiclass
    clus
vv   5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  N0               4                52
  N1               2                59
  N2               1                28
  N3               0                20
                   vv
clus                 M0  M1  MX
  5Q GAIN MUTATED     7   0   0
  5Q GAIN WILD-TYPE 139  18  13
D9V7, multiclass
    clus
vv   5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  M0               7               139
  M1               0                18
  MX               0                13
                   vv
clus                 I II III IV
  5Q GAIN MUTATED    2  3   1  1
  5Q GAIN WILD-TYPE 24 45  57 28
D9V8, multiclass
     clus
vv    5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  I                 2                24
  II                3                45
  III               1                57
  IV                1                28
D9V9, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED      0    7
  5Q GAIN WILD-TYPE    5  165
     clus
vv    5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  NO                0                 5
  YES               7               165
                   vv
clus                 R0  R1  R2  RX
  5Q GAIN MUTATED     7   0   0   0
  5Q GAIN WILD-TYPE 116   7  12  25
D9V10, multiclass
    clus
vv   5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  R0               7               116
  R1               0                 7
  R2               0                12
  RX               0                25
D9V11, continuous

Clustering(10) Variable = 6p gain mutation analysis
D10V1, survival
                   sevent
clus2                 0   1
  6P GAIN MUTATED     7   1
  6P GAIN WILD-TYPE 115  17
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
                8               132 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
                1                17 
$`6P GAIN MUTATED`
TCGA-BR-7197 TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7717 TCGA-BR-7723 TCGA-CG-4438 
        1.48         1.25         1.05         0.69         4.54        54.05 
TCGA-CG-4460 TCGA-D7-6822 
       21.99         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-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8059 
        0.99         0.95         0.69         0.16         1.08         0.82 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
        1.32         0.69         0.95         0.49         0.46         0.72 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 
        0.26         0.43         0.26         1.18         1.55         1.48 
TCGA-BR-8297 TCGA-BR-8592 TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
        0.76         0.20         0.59         0.92         0.39         0.79 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J8 
        0.72         0.79         0.53         0.43         0.13         0.23 
TCGA-BR-A4J9 TCGA-BR-A4PF TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
        0.10         0.72         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-FP-8099 
       72.23         0.39         0.20         3.02         3.58         1.02 
TCGA-FP-8209 TCGA-FP-8631 TCGA-HJ-7597 TCGA-IN-7806 TCGA-IN-7808 TCGA-IP-7968 
       59.05         0.56        26.43         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 
            2.875             1.200 
[1] "0.7 - 54.0 (2.9)" "0.1 - 72.2 (1.2)"
       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 MUTATED" "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-BR-8592        TCGA-BR-A4IU        TCGA-BR-A4IV        TCGA-BR-A4IY 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-BR-A4IZ        TCGA-BR-A4J1        TCGA-BR-A4J2        TCGA-BR-A4J4 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-BR-A4J5        TCGA-BR-A4J6        TCGA-BR-A4J8        TCGA-BR-A4J9 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-BR-A4PF        TCGA-CD-5798        TCGA-CD-5799        TCGA-CD-5800 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-CD-5801        TCGA-CD-5802        TCGA-CD-5803        TCGA-CG-4300 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-CG-4301        TCGA-CG-4304        TCGA-CG-4305        TCGA-CG-4306 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-CG-4436        TCGA-CG-4437        TCGA-CG-4438        TCGA-CG-4440 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" 
       TCGA-CG-4441        TCGA-CG-4443        TCGA-CG-4444        TCGA-CG-4449 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-CG-4455        TCGA-CG-4460        TCGA-CG-4462        TCGA-CG-4465 
"6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-CG-4466        TCGA-CG-4469        TCGA-CG-4472        TCGA-CG-4474 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-CG-4477        TCGA-CG-5716        TCGA-CG-5717        TCGA-CG-5718 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-CG-5719        TCGA-CG-5720        TCGA-CG-5721        TCGA-CG-5722 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-CG-5723        TCGA-CG-5724        TCGA-CG-5725        TCGA-CG-5726 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-CG-5727        TCGA-CG-5728        TCGA-CG-5730        TCGA-CG-5732 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-CG-5733        TCGA-CG-5734        TCGA-D7-5577        TCGA-D7-5578 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-D7-5579        TCGA-D7-6518        TCGA-D7-6519        TCGA-D7-6520 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-D7-6521        TCGA-D7-6522        TCGA-D7-6524        TCGA-D7-6525 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-D7-6526        TCGA-D7-6527        TCGA-D7-6528        TCGA-D7-6815 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-D7-6817        TCGA-D7-6818        TCGA-D7-6820        TCGA-D7-6822 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" 
       TCGA-EQ-5647        TCGA-EQ-8122        TCGA-F1-6177        TCGA-F1-6874 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-F1-6875        TCGA-FP-7735        TCGA-FP-7829        TCGA-FP-7916 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-FP-7998        TCGA-FP-8099        TCGA-FP-8209        TCGA-FP-8631 
"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 MUTATED" "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-BR-8592        TCGA-BR-A4IU        TCGA-BR-A4IV        TCGA-BR-A4IY 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-BR-A4IZ        TCGA-BR-A4J1        TCGA-BR-A4J2        TCGA-BR-A4J4 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-BR-A4J5        TCGA-BR-A4J6        TCGA-BR-A4J8        TCGA-BR-A4J9 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-BR-A4PF        TCGA-CD-5798        TCGA-CD-5799        TCGA-CD-5800 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-CD-5801        TCGA-CD-5802        TCGA-CD-5803        TCGA-CG-4300 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-CG-4301        TCGA-CG-4304        TCGA-CG-4305        TCGA-CG-4306 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-CG-4436        TCGA-CG-4437        TCGA-CG-4438        TCGA-CG-4440 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" 
       TCGA-CG-4441        TCGA-CG-4443        TCGA-CG-4444        TCGA-CG-4449 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-CG-4455        TCGA-CG-4460        TCGA-CG-4462        TCGA-CG-4465 
"6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-CG-4466        TCGA-CG-4469        TCGA-CG-4472        TCGA-CG-4474 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-CG-4477        TCGA-CG-5716        TCGA-CG-5717        TCGA-CG-5718 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-CG-5719        TCGA-CG-5720        TCGA-CG-5721        TCGA-CG-5722 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-CG-5723        TCGA-CG-5724        TCGA-CG-5725        TCGA-CG-5726 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-CG-5727        TCGA-CG-5728        TCGA-CG-5730        TCGA-CG-5732 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-CG-5733        TCGA-CG-5734        TCGA-D7-5577        TCGA-D7-5578 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-D7-5579        TCGA-D7-6518        TCGA-D7-6519        TCGA-D7-6520 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-D7-6521        TCGA-D7-6522        TCGA-D7-6524        TCGA-D7-6525 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-D7-6526        TCGA-D7-6527        TCGA-D7-6528        TCGA-D7-6815 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-D7-6817        TCGA-D7-6818        TCGA-D7-6820        TCGA-D7-6822 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" 
       TCGA-EQ-5647        TCGA-EQ-8122        TCGA-F1-6177        TCGA-F1-6874 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-F1-6875        TCGA-FP-7735        TCGA-FP-7829        TCGA-FP-7916 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-FP-7998        TCGA-FP-8099        TCGA-FP-8209        TCGA-FP-8631 
"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 MUTATED" "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-BR-8592        TCGA-BR-A4IU        TCGA-BR-A4IV        TCGA-BR-A4IY 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-BR-A4IZ        TCGA-BR-A4J1        TCGA-BR-A4J2        TCGA-BR-A4J4 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-BR-A4J5        TCGA-BR-A4J6        TCGA-BR-A4J8        TCGA-BR-A4J9 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-BR-A4PF        TCGA-CD-5798        TCGA-CD-5799        TCGA-CD-5800 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-CD-5801        TCGA-CD-5802        TCGA-CD-5803        TCGA-CG-4300 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-CG-4301        TCGA-CG-4304        TCGA-CG-4305        TCGA-CG-4306 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-CG-4436        TCGA-CG-4437        TCGA-CG-4438        TCGA-CG-4440 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" 
       TCGA-CG-4441        TCGA-CG-4443        TCGA-CG-4444        TCGA-CG-4449 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-CG-4455        TCGA-CG-4460        TCGA-CG-4462        TCGA-CG-4465 
"6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-CG-4466        TCGA-CG-4469        TCGA-CG-4472        TCGA-CG-4474 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-CG-4477        TCGA-CG-5716        TCGA-CG-5717        TCGA-CG-5718 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-CG-5719        TCGA-CG-5720        TCGA-CG-5721        TCGA-CG-5722 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-CG-5723        TCGA-CG-5724        TCGA-CG-5725        TCGA-CG-5726 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-CG-5727        TCGA-CG-5728        TCGA-CG-5730        TCGA-CG-5732 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-CG-5733        TCGA-CG-5734        TCGA-D7-5577        TCGA-D7-5578 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-D7-5579        TCGA-D7-6518        TCGA-D7-6519        TCGA-D7-6520 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-D7-6521        TCGA-D7-6522        TCGA-D7-6524        TCGA-D7-6525 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-D7-6526        TCGA-D7-6527        TCGA-D7-6528        TCGA-D7-6815 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-D7-6817        TCGA-D7-6818        TCGA-D7-6820        TCGA-D7-6822 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" 
       TCGA-EQ-5647        TCGA-EQ-8122        TCGA-F1-6177        TCGA-F1-6874 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-F1-6875        TCGA-FP-7735        TCGA-FP-7829        TCGA-FP-7916 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-FP-7998        TCGA-FP-8099        TCGA-FP-8209        TCGA-FP-8631 
"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=" "1.4"
D10V2, continuous
D10V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED      6    7
  6P GAIN WILD-TYPE   64  100
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  FEMALE               6                64
  MALE                 7               100
                   vv
clus                STOMACH ADENOCARCINOMA - DIFFUSE TYPE
  6P GAIN MUTATED                                       0
  6P GAIN WILD-TYPE                                    25
                   vv
clus                STOMACH ADENOCARCINOMA - NOT OTHERWISE SPECIFIED (NOS)
  6P GAIN MUTATED                                                        9
  6P GAIN WILD-TYPE                                                     78
                   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                                                10
                   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                                                                     33
D10V4, multiclass
                   vv
clus                T1 T2 T3 T4
  6P GAIN MUTATED    0  2  6  4
  6P GAIN WILD-TYPE  6 52 58 39
D10V5, multiclass
    clus
vv   6P GAIN MUTATED 6P GAIN WILD-TYPE
  T1               0                 6
  T2               2                52
  T3               6                58
  T4               4                39
                   vv
clus                N0 N1 N2 N3
  6P GAIN MUTATED    5  5  3  0
  6P GAIN WILD-TYPE 51 56 26 20
D10V6, multiclass
    clus
vv   6P GAIN MUTATED 6P GAIN WILD-TYPE
  N0               5                51
  N1               5                56
  N2               3                26
  N3               0                20
                   vv
clus                 M0  M1  MX
  6P GAIN MUTATED    11   1   1
  6P GAIN WILD-TYPE 135  17  12
D10V7, multiclass
    clus
vv   6P GAIN MUTATED 6P GAIN WILD-TYPE
  M0              11               135
  M1               1                17
  MX               1                12
                   vv
clus                 I II III IV
  6P GAIN MUTATED    2  4   2  4
  6P GAIN WILD-TYPE 24 44  56 25
D10V8, multiclass
     clus
vv    6P GAIN MUTATED 6P GAIN WILD-TYPE
  I                 2                24
  II                4                44
  III               2                56
  IV                4                25
D10V9, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED      1   12
  6P GAIN WILD-TYPE    4  160
     clus
vv    6P GAIN MUTATED 6P GAIN WILD-TYPE
  NO                1                 4
  YES              12               160
                   vv
clus                 R0  R1  R2  RX
  6P GAIN MUTATED     8   1   1   3
  6P GAIN WILD-TYPE 115   6  11  22
D10V10, multiclass
    clus
vv   6P GAIN MUTATED 6P GAIN WILD-TYPE
  R0               8               115
  R1               1                 6
  R2               1                11
  RX               3                22
D10V11, continuous

Clustering(11) Variable = 6q gain mutation analysis
D11V1, survival
                   sevent
clus2                 0   1
  6Q GAIN MUTATED     7   1
  6Q GAIN WILD-TYPE 115  17
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
                8               132 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
                1                17 
$`6Q GAIN MUTATED`
TCGA-BR-7197 TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7717 TCGA-BR-7723 TCGA-CG-4438 
        1.48         1.25         1.05         0.69         4.54        54.05 
TCGA-CG-4460 TCGA-D7-6822 
       21.99         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-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8059 
        0.99         0.95         0.69         0.16         1.08         0.82 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
        1.32         0.69         0.95         0.49         0.46         0.72 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 
        0.26         0.43         0.26         1.18         1.55         1.48 
TCGA-BR-8297 TCGA-BR-8592 TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
        0.76         0.20         0.59         0.92         0.39         0.79 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J8 
        0.72         0.79         0.53         0.43         0.13         0.23 
TCGA-BR-A4J9 TCGA-BR-A4PF TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
        0.10         0.72         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-FP-8099 
       72.23         0.39         0.20         3.02         3.58         1.02 
TCGA-FP-8209 TCGA-FP-8631 TCGA-HJ-7597 TCGA-IN-7806 TCGA-IN-7808 TCGA-IP-7968 
       59.05         0.56        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 
            2.875             1.200 
[1] "0.7 - 54.0 (2.9)" "0.1 - 72.2 (1.2)"
       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 MUTATED" "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-BR-8592        TCGA-BR-A4IU        TCGA-BR-A4IV        TCGA-BR-A4IY 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-BR-A4IZ        TCGA-BR-A4J1        TCGA-BR-A4J2        TCGA-BR-A4J4 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-BR-A4J5        TCGA-BR-A4J6        TCGA-BR-A4J8        TCGA-BR-A4J9 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-BR-A4PF        TCGA-CD-5798        TCGA-CD-5799        TCGA-CD-5800 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-CD-5801        TCGA-CD-5802        TCGA-CD-5803        TCGA-CG-4300 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-CG-4301        TCGA-CG-4304        TCGA-CG-4305        TCGA-CG-4306 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-CG-4436        TCGA-CG-4437        TCGA-CG-4438        TCGA-CG-4440 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE"   "6Q GAIN MUTATED" "6Q GAIN WILD-TYPE" 
       TCGA-CG-4441        TCGA-CG-4443        TCGA-CG-4444        TCGA-CG-4449 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-CG-4455        TCGA-CG-4460        TCGA-CG-4462        TCGA-CG-4465 
"6Q GAIN WILD-TYPE"   "6Q GAIN MUTATED" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-CG-4466        TCGA-CG-4469        TCGA-CG-4472        TCGA-CG-4474 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-CG-4477        TCGA-CG-5716        TCGA-CG-5717        TCGA-CG-5718 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-CG-5719        TCGA-CG-5720        TCGA-CG-5721        TCGA-CG-5722 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-CG-5723        TCGA-CG-5724        TCGA-CG-5725        TCGA-CG-5726 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-CG-5727        TCGA-CG-5728        TCGA-CG-5730        TCGA-CG-5732 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-CG-5733        TCGA-CG-5734        TCGA-D7-5577        TCGA-D7-5578 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-D7-5579        TCGA-D7-6518        TCGA-D7-6519        TCGA-D7-6520 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-D7-6521        TCGA-D7-6522        TCGA-D7-6524        TCGA-D7-6525 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-D7-6526        TCGA-D7-6527        TCGA-D7-6528        TCGA-D7-6815 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-D7-6817        TCGA-D7-6818        TCGA-D7-6820        TCGA-D7-6822 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE"   "6Q GAIN MUTATED" 
       TCGA-EQ-5647        TCGA-EQ-8122        TCGA-F1-6177        TCGA-F1-6874 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-F1-6875        TCGA-FP-7735        TCGA-FP-7829        TCGA-FP-7916 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-FP-7998        TCGA-FP-8099        TCGA-FP-8209        TCGA-FP-8631 
"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 MUTATED" "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-BR-8592        TCGA-BR-A4IU        TCGA-BR-A4IV        TCGA-BR-A4IY 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-BR-A4IZ        TCGA-BR-A4J1        TCGA-BR-A4J2        TCGA-BR-A4J4 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-BR-A4J5        TCGA-BR-A4J6        TCGA-BR-A4J8        TCGA-BR-A4J9 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-BR-A4PF        TCGA-CD-5798        TCGA-CD-5799        TCGA-CD-5800 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-CD-5801        TCGA-CD-5802        TCGA-CD-5803        TCGA-CG-4300 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-CG-4301        TCGA-CG-4304        TCGA-CG-4305        TCGA-CG-4306 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-CG-4436        TCGA-CG-4437        TCGA-CG-4438        TCGA-CG-4440 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE"   "6Q GAIN MUTATED" "6Q GAIN WILD-TYPE" 
       TCGA-CG-4441        TCGA-CG-4443        TCGA-CG-4444        TCGA-CG-4449 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-CG-4455        TCGA-CG-4460        TCGA-CG-4462        TCGA-CG-4465 
"6Q GAIN WILD-TYPE"   "6Q GAIN MUTATED" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-CG-4466        TCGA-CG-4469        TCGA-CG-4472        TCGA-CG-4474 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-CG-4477        TCGA-CG-5716        TCGA-CG-5717        TCGA-CG-5718 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-CG-5719        TCGA-CG-5720        TCGA-CG-5721        TCGA-CG-5722 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-CG-5723        TCGA-CG-5724        TCGA-CG-5725        TCGA-CG-5726 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-CG-5727        TCGA-CG-5728        TCGA-CG-5730        TCGA-CG-5732 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-CG-5733        TCGA-CG-5734        TCGA-D7-5577        TCGA-D7-5578 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-D7-5579        TCGA-D7-6518        TCGA-D7-6519        TCGA-D7-6520 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-D7-6521        TCGA-D7-6522        TCGA-D7-6524        TCGA-D7-6525 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-D7-6526        TCGA-D7-6527        TCGA-D7-6528        TCGA-D7-6815 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-D7-6817        TCGA-D7-6818        TCGA-D7-6820        TCGA-D7-6822 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE"   "6Q GAIN MUTATED" 
       TCGA-EQ-5647        TCGA-EQ-8122        TCGA-F1-6177        TCGA-F1-6874 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-F1-6875        TCGA-FP-7735        TCGA-FP-7829        TCGA-FP-7916 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-FP-7998        TCGA-FP-8099        TCGA-FP-8209        TCGA-FP-8631 
"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 MUTATED" "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-BR-8592        TCGA-BR-A4IU        TCGA-BR-A4IV        TCGA-BR-A4IY 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-BR-A4IZ        TCGA-BR-A4J1        TCGA-BR-A4J2        TCGA-BR-A4J4 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-BR-A4J5        TCGA-BR-A4J6        TCGA-BR-A4J8        TCGA-BR-A4J9 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-BR-A4PF        TCGA-CD-5798        TCGA-CD-5799        TCGA-CD-5800 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-CD-5801        TCGA-CD-5802        TCGA-CD-5803        TCGA-CG-4300 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-CG-4301        TCGA-CG-4304        TCGA-CG-4305        TCGA-CG-4306 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-CG-4436        TCGA-CG-4437        TCGA-CG-4438        TCGA-CG-4440 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE"   "6Q GAIN MUTATED" "6Q GAIN WILD-TYPE" 
       TCGA-CG-4441        TCGA-CG-4443        TCGA-CG-4444        TCGA-CG-4449 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-CG-4455        TCGA-CG-4460        TCGA-CG-4462        TCGA-CG-4465 
"6Q GAIN WILD-TYPE"   "6Q GAIN MUTATED" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-CG-4466        TCGA-CG-4469        TCGA-CG-4472        TCGA-CG-4474 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-CG-4477        TCGA-CG-5716        TCGA-CG-5717        TCGA-CG-5718 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-CG-5719        TCGA-CG-5720        TCGA-CG-5721        TCGA-CG-5722 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-CG-5723        TCGA-CG-5724        TCGA-CG-5725        TCGA-CG-5726 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-CG-5727        TCGA-CG-5728        TCGA-CG-5730        TCGA-CG-5732 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-CG-5733        TCGA-CG-5734        TCGA-D7-5577        TCGA-D7-5578 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-D7-5579        TCGA-D7-6518        TCGA-D7-6519        TCGA-D7-6520 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-D7-6521        TCGA-D7-6522        TCGA-D7-6524        TCGA-D7-6525 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-D7-6526        TCGA-D7-6527        TCGA-D7-6528        TCGA-D7-6815 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-D7-6817        TCGA-D7-6818        TCGA-D7-6820        TCGA-D7-6822 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE"   "6Q GAIN MUTATED" 
       TCGA-EQ-5647        TCGA-EQ-8122        TCGA-F1-6177        TCGA-F1-6874 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-F1-6875        TCGA-FP-7735        TCGA-FP-7829        TCGA-FP-7916 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-FP-7998        TCGA-FP-8099        TCGA-FP-8209        TCGA-FP-8631 
"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=" "1.4"
D11V2, continuous
D11V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED      6    7
  6Q GAIN WILD-TYPE   64  100
        clus
vv       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  FEMALE               6                64
  MALE                 7               100
                   vv
clus                STOMACH ADENOCARCINOMA - DIFFUSE TYPE
  6Q GAIN MUTATED                                       0
  6Q GAIN WILD-TYPE                                    25
                   vv
clus                STOMACH ADENOCARCINOMA - NOT OTHERWISE SPECIFIED (NOS)
  6Q GAIN MUTATED                                                        9
  6Q GAIN WILD-TYPE                                                     78
                   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                                                10
                   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                                                                        3
  6Q GAIN WILD-TYPE                                                                     33
D11V4, multiclass
                   vv
clus                T1 T2 T3 T4
  6Q GAIN MUTATED    0  2  6  4
  6Q GAIN WILD-TYPE  6 52 58 39
D11V5, multiclass
    clus
vv   6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  T1               0                 6
  T2               2                52
  T3               6                58
  T4               4                39
                   vv
clus                N0 N1 N2 N3
  6Q GAIN MUTATED    5  5  3  0
  6Q GAIN WILD-TYPE 51 56 26 20
D11V6, multiclass
    clus
vv   6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  N0               5                51
  N1               5                56
  N2               3                26
  N3               0                20
                   vv
clus                 M0  M1  MX
  6Q GAIN MUTATED    11   1   1
  6Q GAIN WILD-TYPE 135  17  12
D11V7, multiclass
    clus
vv   6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  M0              11               135
  M1               1                17
  MX               1                12
                   vv
clus                 I II III IV
  6Q GAIN MUTATED    2  4   2  4
  6Q GAIN WILD-TYPE 24 44  56 25
D11V8, multiclass
     clus
vv    6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  I                 2                24
  II                4                44
  III               2                56
  IV                4                25
D11V9, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED      1   12
  6Q GAIN WILD-TYPE    4  160
     clus
vv    6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  NO                1                 4
  YES              12               160
                   vv
clus                 R0  R1  R2  RX
  6Q GAIN MUTATED     8   1   1   3
  6Q GAIN WILD-TYPE 115   6  11  22
D11V10, multiclass
    clus
vv   6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  R0               8               115
  R1               1                 6
  R2               1                11
  RX               3                22
D11V11, continuous

Clustering(12) Variable = 7p gain mutation analysis
D12V1, survival
                   sevent
clus2                0  1
  7P GAIN MUTATED   33  6
  7P GAIN WILD-TYPE 89 12
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               39               101 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
                6                12 
$`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-BR-A4IY TCGA-BR-A4J4 TCGA-BR-A4J8 
        1.05         0.69         0.95         0.39         0.53         0.23 
TCGA-CD-5801 TCGA-CG-4300 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4436 TCGA-CG-4460 
        0.49        20.02        27.02        15.95        52.96        21.99 
TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4474 TCGA-CG-5718 TCGA-CG-5724 TCGA-CG-5726 
        7.07        12.00         1.02         1.02        12.03        28.96 
TCGA-CG-5727 TCGA-CG-5733 TCGA-D7-6518 TCGA-D7-6521 TCGA-D7-6526 TCGA-D7-6528 
       31.04        21.07         9.80         8.19         6.61         1.68 
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-8099 TCGA-IN-7808 
        0.39         1.02         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-BR-8592 TCGA-BR-A4IU TCGA-BR-A4IV 
        1.55         1.48         0.76         0.20         0.59         0.92 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J9 
        0.79         0.72         0.79         0.43         0.13         0.10 
TCGA-BR-A4PF TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5802 TCGA-CD-5803 
        0.72         0.82         0.69         0.36         0.30         0.07 
TCGA-CG-4301 TCGA-CG-4306 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        3.02         1.02         8.05        54.05         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       29.98        47.05        19.07        12.03         1.02         8.98 
TCGA-CG-4466 TCGA-CG-4477 TCGA-CG-5716 TCGA-CG-5717 TCGA-CG-5719 TCGA-CG-5720 
       18.94         1.02         1.02         6.94         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5725 TCGA-CG-5728 TCGA-CG-5730 
        5.98         0.95        70.06        15.02        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6519 
       55.04         7.99         8.65         3.58         4.54        15.65 
TCGA-D7-6520 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6527 TCGA-D7-6815 
        9.63         6.90         0.69         5.95         4.14         3.65 
TCGA-D7-6817 TCGA-D7-6820 TCGA-EQ-5647 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
        4.70         2.93         0.62         0.20         3.02         3.58 
TCGA-FP-8209 TCGA-FP-8631 TCGA-HJ-7597 TCGA-IN-7806 TCGA-IP-7968 
       59.05         0.56        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 
             3.55              1.02 
[1] "0.1 - 72.2 (3.5)" "0.1 - 70.1 (1.0)"
       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-BR-8592        TCGA-BR-A4IU        TCGA-BR-A4IV        TCGA-BR-A4IY 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       TCGA-BR-A4IZ        TCGA-BR-A4J1        TCGA-BR-A4J2        TCGA-BR-A4J4 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       TCGA-BR-A4J5        TCGA-BR-A4J6        TCGA-BR-A4J8        TCGA-BR-A4J9 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-BR-A4PF        TCGA-CD-5798        TCGA-CD-5799        TCGA-CD-5800 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-CD-5801        TCGA-CD-5802        TCGA-CD-5803        TCGA-CG-4300 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       TCGA-CG-4301        TCGA-CG-4304        TCGA-CG-4305        TCGA-CG-4306 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-CG-4436        TCGA-CG-4437        TCGA-CG-4438        TCGA-CG-4440 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-CG-4441        TCGA-CG-4443        TCGA-CG-4444        TCGA-CG-4449 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-CG-4455        TCGA-CG-4460        TCGA-CG-4462        TCGA-CG-4465 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-CG-4466        TCGA-CG-4469        TCGA-CG-4472        TCGA-CG-4474 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-CG-4477        TCGA-CG-5716        TCGA-CG-5717        TCGA-CG-5718 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       TCGA-CG-5719        TCGA-CG-5720        TCGA-CG-5721        TCGA-CG-5722 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-CG-5723        TCGA-CG-5724        TCGA-CG-5725        TCGA-CG-5726 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       TCGA-CG-5727        TCGA-CG-5728        TCGA-CG-5730        TCGA-CG-5732 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-CG-5733        TCGA-CG-5734        TCGA-D7-5577        TCGA-D7-5578 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-D7-5579        TCGA-D7-6518        TCGA-D7-6519        TCGA-D7-6520 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-D7-6521        TCGA-D7-6522        TCGA-D7-6524        TCGA-D7-6525 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-D7-6526        TCGA-D7-6527        TCGA-D7-6528        TCGA-D7-6815 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-D7-6817        TCGA-D7-6818        TCGA-D7-6820        TCGA-D7-6822 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       TCGA-EQ-5647        TCGA-EQ-8122        TCGA-F1-6177        TCGA-F1-6874 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-F1-6875        TCGA-FP-7735        TCGA-FP-7829        TCGA-FP-7916 
  "7P GAIN MUTATED"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-FP-7998        TCGA-FP-8099        TCGA-FP-8209        TCGA-FP-8631 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "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-BR-8592        TCGA-BR-A4IU        TCGA-BR-A4IV        TCGA-BR-A4IY 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       TCGA-BR-A4IZ        TCGA-BR-A4J1        TCGA-BR-A4J2        TCGA-BR-A4J4 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       TCGA-BR-A4J5        TCGA-BR-A4J6        TCGA-BR-A4J8        TCGA-BR-A4J9 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-BR-A4PF        TCGA-CD-5798        TCGA-CD-5799        TCGA-CD-5800 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-CD-5801        TCGA-CD-5802        TCGA-CD-5803        TCGA-CG-4300 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       TCGA-CG-4301        TCGA-CG-4304        TCGA-CG-4305        TCGA-CG-4306 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-CG-4436        TCGA-CG-4437        TCGA-CG-4438        TCGA-CG-4440 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-CG-4441        TCGA-CG-4443        TCGA-CG-4444        TCGA-CG-4449 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-CG-4455        TCGA-CG-4460        TCGA-CG-4462        TCGA-CG-4465 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-CG-4466        TCGA-CG-4469        TCGA-CG-4472        TCGA-CG-4474 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-CG-4477        TCGA-CG-5716        TCGA-CG-5717        TCGA-CG-5718 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       TCGA-CG-5719        TCGA-CG-5720        TCGA-CG-5721        TCGA-CG-5722 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-CG-5723        TCGA-CG-5724        TCGA-CG-5725        TCGA-CG-5726 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       TCGA-CG-5727        TCGA-CG-5728        TCGA-CG-5730        TCGA-CG-5732 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-CG-5733        TCGA-CG-5734        TCGA-D7-5577        TCGA-D7-5578 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-D7-5579        TCGA-D7-6518        TCGA-D7-6519        TCGA-D7-6520 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-D7-6521        TCGA-D7-6522        TCGA-D7-6524        TCGA-D7-6525 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-D7-6526        TCGA-D7-6527        TCGA-D7-6528        TCGA-D7-6815 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-D7-6817        TCGA-D7-6818        TCGA-D7-6820        TCGA-D7-6822 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       TCGA-EQ-5647        TCGA-EQ-8122        TCGA-F1-6177        TCGA-F1-6874 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-F1-6875        TCGA-FP-7735        TCGA-FP-7829        TCGA-FP-7916 
  "7P GAIN MUTATED"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-FP-7998        TCGA-FP-8099        TCGA-FP-8209        TCGA-FP-8631 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "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-BR-8592        TCGA-BR-A4IU        TCGA-BR-A4IV        TCGA-BR-A4IY 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       TCGA-BR-A4IZ        TCGA-BR-A4J1        TCGA-BR-A4J2        TCGA-BR-A4J4 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       TCGA-BR-A4J5        TCGA-BR-A4J6        TCGA-BR-A4J8        TCGA-BR-A4J9 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-BR-A4PF        TCGA-CD-5798        TCGA-CD-5799        TCGA-CD-5800 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-CD-5801        TCGA-CD-5802        TCGA-CD-5803        TCGA-CG-4300 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       TCGA-CG-4301        TCGA-CG-4304        TCGA-CG-4305        TCGA-CG-4306 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-CG-4436        TCGA-CG-4437        TCGA-CG-4438        TCGA-CG-4440 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-CG-4441        TCGA-CG-4443        TCGA-CG-4444        TCGA-CG-4449 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-CG-4455        TCGA-CG-4460        TCGA-CG-4462        TCGA-CG-4465 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-CG-4466        TCGA-CG-4469        TCGA-CG-4472        TCGA-CG-4474 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-CG-4477        TCGA-CG-5716        TCGA-CG-5717        TCGA-CG-5718 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       TCGA-CG-5719        TCGA-CG-5720        TCGA-CG-5721        TCGA-CG-5722 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-CG-5723        TCGA-CG-5724        TCGA-CG-5725        TCGA-CG-5726 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       TCGA-CG-5727        TCGA-CG-5728        TCGA-CG-5730        TCGA-CG-5732 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-CG-5733        TCGA-CG-5734        TCGA-D7-5577        TCGA-D7-5578 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-D7-5579        TCGA-D7-6518        TCGA-D7-6519        TCGA-D7-6520 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-D7-6521        TCGA-D7-6522        TCGA-D7-6524        TCGA-D7-6525 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-D7-6526        TCGA-D7-6527        TCGA-D7-6528        TCGA-D7-6815 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-D7-6817        TCGA-D7-6818        TCGA-D7-6820        TCGA-D7-6822 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       TCGA-EQ-5647        TCGA-EQ-8122        TCGA-F1-6177        TCGA-F1-6874 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-F1-6875        TCGA-FP-7735        TCGA-FP-7829        TCGA-FP-7916 
  "7P GAIN MUTATED"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-FP-7998        TCGA-FP-8099        TCGA-FP-8209        TCGA-FP-8631 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "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=" "1.5"
D12V2, continuous
D12V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED     16   37
  7P GAIN WILD-TYPE   54   70
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  FEMALE              16                54
  MALE                37                70
                   vv
clus                STOMACH ADENOCARCINOMA - DIFFUSE TYPE
  7P GAIN MUTATED                                       8
  7P GAIN WILD-TYPE                                    17
                   vv
clus                STOMACH ADENOCARCINOMA - NOT OTHERWISE SPECIFIED (NOS)
  7P GAIN MUTATED                                                       29
  7P GAIN WILD-TYPE                                                     58
                   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                                                10
                   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                                                                     25
D12V4, multiclass
                   vv
clus                T1 T2 T3 T4
  7P GAIN MUTATED    3 16 21  9
  7P GAIN WILD-TYPE  3 38 43 34
D12V5, multiclass
    clus
vv   7P GAIN MUTATED 7P GAIN WILD-TYPE
  T1               3                 3
  T2              16                38
  T3              21                43
  T4               9                34
                   vv
clus                N0 N1 N2 N3
  7P GAIN MUTATED   21 15  7  7
  7P GAIN WILD-TYPE 35 46 22 13
D12V6, multiclass
    clus
vv   7P GAIN MUTATED 7P GAIN WILD-TYPE
  N0              21                35
  N1              15                46
  N2               7                22
  N3               7                13
                   vv
clus                 M0  M1  MX
  7P GAIN MUTATED    44   4   5
  7P GAIN WILD-TYPE 102  14   8
D12V7, multiclass
    clus
vv   7P GAIN MUTATED 7P GAIN WILD-TYPE
  M0              44               102
  M1               4                14
  MX               5                 8
                   vv
clus                 I II III IV
  7P GAIN MUTATED   12 14  13  9
  7P GAIN WILD-TYPE 14 34  45 20
D12V8, multiclass
     clus
vv    7P GAIN MUTATED 7P GAIN WILD-TYPE
  I                12                14
  II               14                34
  III              13                45
  IV                9                20
D12V9, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED      2   51
  7P GAIN WILD-TYPE    3  121
     clus
vv    7P GAIN MUTATED 7P GAIN WILD-TYPE
  NO                2                 3
  YES              51               121
                   vv
clus                R0 R1 R2 RX
  7P GAIN MUTATED   38  3  3  6
  7P GAIN WILD-TYPE 85  4  9 19
D12V10, multiclass
    clus
vv   7P GAIN MUTATED 7P GAIN WILD-TYPE
  R0              38                85
  R1               3                 4
  R2               3                 9
  RX               6                19
D12V11, continuous

Clustering(13) Variable = 7q gain mutation analysis
D13V1, survival
                   sevent
clus2                0  1
  7Q GAIN MUTATED   28  6
  7Q GAIN WILD-TYPE 94 12
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               34               106 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
                6                12 
$`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-BR-A4IY TCGA-BR-A4J4 TCGA-BR-A4J8 TCGA-CD-5801 TCGA-CG-4300 
        1.05         0.39         0.53         0.23         0.49        20.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4436 TCGA-CG-4440 TCGA-CG-4469 TCGA-CG-4472 
       27.02        15.95        52.96         4.01         7.07        12.00 
TCGA-CG-4474 TCGA-CG-5718 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5733 
        1.02         1.02        12.03        28.96        31.04        21.07 
TCGA-D7-6518 TCGA-D7-6521 TCGA-D7-6526 TCGA-D7-6528 TCGA-EQ-8122 TCGA-F1-6177 
        9.80         8.19         6.61         1.68         7.79         6.54 
TCGA-F1-6874 TCGA-F1-6875 TCGA-FP-7735 TCGA-FP-8099 
        2.01        72.23         0.39         1.02 

$`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-BR-8592 
        0.26         1.18         1.55         1.48         0.76         0.20 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J5 
        0.59         0.92         0.79         0.72         0.79         0.43 
TCGA-BR-A4J6 TCGA-BR-A4J9 TCGA-BR-A4PF TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
        0.13         0.10         0.72         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-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-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-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
        4.14         3.65         4.70         4.04         2.93         4.27 
TCGA-EQ-5647 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8209 TCGA-FP-8631 
        0.62         0.20         3.02         3.58        59.05         0.56 
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 
             3.01              1.05 
[1] "0.1 - 72.2 (3.0)" "0.1 - 70.1 (1.1)"
       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-BR-8592        TCGA-BR-A4IU        TCGA-BR-A4IV        TCGA-BR-A4IY 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-BR-A4IZ        TCGA-BR-A4J1        TCGA-BR-A4J2        TCGA-BR-A4J4 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-BR-A4J5        TCGA-BR-A4J6        TCGA-BR-A4J8        TCGA-BR-A4J9 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-BR-A4PF        TCGA-CD-5798        TCGA-CD-5799        TCGA-CD-5800 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-CD-5801        TCGA-CD-5802        TCGA-CD-5803        TCGA-CG-4300 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-CG-4301        TCGA-CG-4304        TCGA-CG-4305        TCGA-CG-4306 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-CG-4436        TCGA-CG-4437        TCGA-CG-4438        TCGA-CG-4440 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-CG-4441        TCGA-CG-4443        TCGA-CG-4444        TCGA-CG-4449 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-CG-4455        TCGA-CG-4460        TCGA-CG-4462        TCGA-CG-4465 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-CG-4466        TCGA-CG-4469        TCGA-CG-4472        TCGA-CG-4474 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" 
       TCGA-CG-4477        TCGA-CG-5716        TCGA-CG-5717        TCGA-CG-5718 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-CG-5719        TCGA-CG-5720        TCGA-CG-5721        TCGA-CG-5722 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-CG-5723        TCGA-CG-5724        TCGA-CG-5725        TCGA-CG-5726 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-CG-5727        TCGA-CG-5728        TCGA-CG-5730        TCGA-CG-5732 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-CG-5733        TCGA-CG-5734        TCGA-D7-5577        TCGA-D7-5578 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-D7-5579        TCGA-D7-6518        TCGA-D7-6519        TCGA-D7-6520 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-D7-6521        TCGA-D7-6522        TCGA-D7-6524        TCGA-D7-6525 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-D7-6526        TCGA-D7-6527        TCGA-D7-6528        TCGA-D7-6815 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-D7-6817        TCGA-D7-6818        TCGA-D7-6820        TCGA-D7-6822 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-EQ-5647        TCGA-EQ-8122        TCGA-F1-6177        TCGA-F1-6874 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" 
       TCGA-F1-6875        TCGA-FP-7735        TCGA-FP-7829        TCGA-FP-7916 
  "7Q GAIN MUTATED"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-FP-7998        TCGA-FP-8099        TCGA-FP-8209        TCGA-FP-8631 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "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-BR-8592        TCGA-BR-A4IU        TCGA-BR-A4IV        TCGA-BR-A4IY 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-BR-A4IZ        TCGA-BR-A4J1        TCGA-BR-A4J2        TCGA-BR-A4J4 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-BR-A4J5        TCGA-BR-A4J6        TCGA-BR-A4J8        TCGA-BR-A4J9 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-BR-A4PF        TCGA-CD-5798        TCGA-CD-5799        TCGA-CD-5800 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-CD-5801        TCGA-CD-5802        TCGA-CD-5803        TCGA-CG-4300 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-CG-4301        TCGA-CG-4304        TCGA-CG-4305        TCGA-CG-4306 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-CG-4436        TCGA-CG-4437        TCGA-CG-4438        TCGA-CG-4440 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-CG-4441        TCGA-CG-4443        TCGA-CG-4444        TCGA-CG-4449 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-CG-4455        TCGA-CG-4460        TCGA-CG-4462        TCGA-CG-4465 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-CG-4466        TCGA-CG-4469        TCGA-CG-4472        TCGA-CG-4474 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" 
       TCGA-CG-4477        TCGA-CG-5716        TCGA-CG-5717        TCGA-CG-5718 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-CG-5719        TCGA-CG-5720        TCGA-CG-5721        TCGA-CG-5722 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-CG-5723        TCGA-CG-5724        TCGA-CG-5725        TCGA-CG-5726 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-CG-5727        TCGA-CG-5728        TCGA-CG-5730        TCGA-CG-5732 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-CG-5733        TCGA-CG-5734        TCGA-D7-5577        TCGA-D7-5578 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-D7-5579        TCGA-D7-6518        TCGA-D7-6519        TCGA-D7-6520 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-D7-6521        TCGA-D7-6522        TCGA-D7-6524        TCGA-D7-6525 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-D7-6526        TCGA-D7-6527        TCGA-D7-6528        TCGA-D7-6815 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-D7-6817        TCGA-D7-6818        TCGA-D7-6820        TCGA-D7-6822 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-EQ-5647        TCGA-EQ-8122        TCGA-F1-6177        TCGA-F1-6874 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" 
       TCGA-F1-6875        TCGA-FP-7735        TCGA-FP-7829        TCGA-FP-7916 
  "7Q GAIN MUTATED"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-FP-7998        TCGA-FP-8099        TCGA-FP-8209        TCGA-FP-8631 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "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-BR-8592        TCGA-BR-A4IU        TCGA-BR-A4IV        TCGA-BR-A4IY 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-BR-A4IZ        TCGA-BR-A4J1        TCGA-BR-A4J2        TCGA-BR-A4J4 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-BR-A4J5        TCGA-BR-A4J6        TCGA-BR-A4J8        TCGA-BR-A4J9 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-BR-A4PF        TCGA-CD-5798        TCGA-CD-5799        TCGA-CD-5800 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-CD-5801        TCGA-CD-5802        TCGA-CD-5803        TCGA-CG-4300 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-CG-4301        TCGA-CG-4304        TCGA-CG-4305        TCGA-CG-4306 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-CG-4436        TCGA-CG-4437        TCGA-CG-4438        TCGA-CG-4440 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-CG-4441        TCGA-CG-4443        TCGA-CG-4444        TCGA-CG-4449 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-CG-4455        TCGA-CG-4460        TCGA-CG-4462        TCGA-CG-4465 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-CG-4466        TCGA-CG-4469        TCGA-CG-4472        TCGA-CG-4474 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" 
       TCGA-CG-4477        TCGA-CG-5716        TCGA-CG-5717        TCGA-CG-5718 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-CG-5719        TCGA-CG-5720        TCGA-CG-5721        TCGA-CG-5722 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-CG-5723        TCGA-CG-5724        TCGA-CG-5725        TCGA-CG-5726 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-CG-5727        TCGA-CG-5728        TCGA-CG-5730        TCGA-CG-5732 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-CG-5733        TCGA-CG-5734        TCGA-D7-5577        TCGA-D7-5578 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-D7-5579        TCGA-D7-6518        TCGA-D7-6519        TCGA-D7-6520 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-D7-6521        TCGA-D7-6522        TCGA-D7-6524        TCGA-D7-6525 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-D7-6526        TCGA-D7-6527        TCGA-D7-6528        TCGA-D7-6815 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-D7-6817        TCGA-D7-6818        TCGA-D7-6820        TCGA-D7-6822 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-EQ-5647        TCGA-EQ-8122        TCGA-F1-6177        TCGA-F1-6874 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" 
       TCGA-F1-6875        TCGA-FP-7735        TCGA-FP-7829        TCGA-FP-7916 
  "7Q GAIN MUTATED"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-FP-7998        TCGA-FP-8099        TCGA-FP-8209        TCGA-FP-8631 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "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=" "1.3"
D13V2, continuous
D13V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED     16   32
  7Q GAIN WILD-TYPE   54   75
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  FEMALE              16                54
  MALE                32                75
                   vv
clus                STOMACH ADENOCARCINOMA - DIFFUSE TYPE
  7Q GAIN MUTATED                                       6
  7Q GAIN WILD-TYPE                                    19
                   vv
clus                STOMACH ADENOCARCINOMA - NOT OTHERWISE SPECIFIED (NOS)
  7Q GAIN MUTATED                                                       27
  7Q GAIN WILD-TYPE                                                     60
                   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                                                10
                   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                                                                     25
D13V4, multiclass
                   vv
clus                T1 T2 T3 T4
  7Q GAIN MUTATED    3 14 20  7
  7Q GAIN WILD-TYPE  3 40 44 36
D13V5, multiclass
    clus
vv   7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  T1               3                 3
  T2              14                40
  T3              20                44
  T4               7                36
                   vv
clus                N0 N1 N2 N3
  7Q GAIN MUTATED   19 13  7  6
  7Q GAIN WILD-TYPE 37 48 22 14
D13V6, multiclass
    clus
vv   7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  N0              19                37
  N1              13                48
  N2               7                22
  N3               6                14
                   vv
clus                 M0  M1  MX
  7Q GAIN MUTATED    39   3   6
  7Q GAIN WILD-TYPE 107  15   7
D13V7, multiclass
    clus
vv   7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  M0              39               107
  M1               3                15
  MX               6                 7
                   vv
clus                 I II III IV
  7Q GAIN MUTATED   11 13  11  7
  7Q GAIN WILD-TYPE 15 35  47 22
D13V8, multiclass
     clus
vv    7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  I                11                15
  II               13                35
  III              11                47
  IV                7                22
D13V9, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED      1   47
  7Q GAIN WILD-TYPE    4  125
     clus
vv    7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  NO                1                 4
  YES              47               125
                   vv
clus                R0 R1 R2 RX
  7Q GAIN MUTATED   33  3  3  7
  7Q GAIN WILD-TYPE 90  4  9 18
D13V10, multiclass
    clus
vv   7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  R0              33                90
  R1               3                 4
  R2               3                 9
  RX               7                18
D13V11, continuous

Clustering(14) Variable = 8p gain mutation analysis
D14V1, survival
                   sevent
clus2                0  1
  8P GAIN MUTATED   25  7
  8P GAIN WILD-TYPE 97 11
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               32               108 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
                7                11 
$`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-D7-6818 TCGA-D7-6822 TCGA-EQ-5647 
        9.63         0.69         6.61         4.04         4.27         0.62 
TCGA-FP-7829 TCGA-IN-7808 
        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-BR-8592 TCGA-BR-A4IU 
        1.18         1.55         1.48         0.76         0.20         0.59 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
        0.92         0.39         0.79         0.72         0.79         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PF TCGA-CD-5798 
        0.43         0.13         0.23         0.10         0.72         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-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
        3.02        27.02         1.02        52.96         8.05        54.05 
TCGA-CG-4440 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4474 
        4.01        29.98        19.07         1.02         8.98         1.02 
TCGA-CG-4477 TCGA-CG-5716 TCGA-CG-5717 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
        1.02         1.02         6.94         1.02         0.99         5.98 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5734 
        0.95        70.06        12.03         4.01        55.04         7.99 
TCGA-D7-5577 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6525 
        8.65         9.80        15.65         8.19         6.90         5.95 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6820 TCGA-EQ-8122 
        4.14         1.68         3.65         4.70         2.93         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-FP-8099 TCGA-FP-8209 TCGA-FP-8631 TCGA-HJ-7597 TCGA-IN-7806 TCGA-IP-7968 
        1.02        59.05         0.56        26.43         6.87         2.53 

  8P GAIN MUTATED 8P GAIN WILD-TYPE 
             0.13              0.07 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
            65.10             72.23 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
             5.08              1.02 
[1] "0.1 - 65.1 (5.1)" "0.1 - 72.2 (1.0)"
       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-BR-8592        TCGA-BR-A4IU        TCGA-BR-A4IV        TCGA-BR-A4IY 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-BR-A4IZ        TCGA-BR-A4J1        TCGA-BR-A4J2        TCGA-BR-A4J4 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-BR-A4J5        TCGA-BR-A4J6        TCGA-BR-A4J8        TCGA-BR-A4J9 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-BR-A4PF        TCGA-CD-5798        TCGA-CD-5799        TCGA-CD-5800 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-CD-5801        TCGA-CD-5802        TCGA-CD-5803        TCGA-CG-4300 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-CG-4301        TCGA-CG-4304        TCGA-CG-4305        TCGA-CG-4306 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" 
       TCGA-CG-4436        TCGA-CG-4437        TCGA-CG-4438        TCGA-CG-4440 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-CG-4441        TCGA-CG-4443        TCGA-CG-4444        TCGA-CG-4449 
  "8P GAIN MUTATED" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" 
       TCGA-CG-4455        TCGA-CG-4460        TCGA-CG-4462        TCGA-CG-4465 
  "8P GAIN MUTATED"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-CG-4466        TCGA-CG-4469        TCGA-CG-4472        TCGA-CG-4474 
  "8P GAIN MUTATED"   "8P GAIN MUTATED"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" 
       TCGA-CG-4477        TCGA-CG-5716        TCGA-CG-5717        TCGA-CG-5718 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" 
       TCGA-CG-5719        TCGA-CG-5720        TCGA-CG-5721        TCGA-CG-5722 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-CG-5723        TCGA-CG-5724        TCGA-CG-5725        TCGA-CG-5726 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED"   "8P GAIN MUTATED" 
       TCGA-CG-5727        TCGA-CG-5728        TCGA-CG-5730        TCGA-CG-5732 
  "8P GAIN MUTATED"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-CG-5733        TCGA-CG-5734        TCGA-D7-5577        TCGA-D7-5578 
  "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" 
       TCGA-D7-5579        TCGA-D7-6518        TCGA-D7-6519        TCGA-D7-6520 
  "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" 
       TCGA-D7-6521        TCGA-D7-6522        TCGA-D7-6524        TCGA-D7-6525 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" 
       TCGA-D7-6526        TCGA-D7-6527        TCGA-D7-6528        TCGA-D7-6815 
  "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-D7-6817        TCGA-D7-6818        TCGA-D7-6820        TCGA-D7-6822 
"8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" 
       TCGA-EQ-5647        TCGA-EQ-8122        TCGA-F1-6177        TCGA-F1-6874 
  "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-F1-6875        TCGA-FP-7735        TCGA-FP-7829        TCGA-FP-7916 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" 
       TCGA-FP-7998        TCGA-FP-8099        TCGA-FP-8209        TCGA-FP-8631 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "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-BR-8592        TCGA-BR-A4IU        TCGA-BR-A4IV        TCGA-BR-A4IY 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-BR-A4IZ        TCGA-BR-A4J1        TCGA-BR-A4J2        TCGA-BR-A4J4 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-BR-A4J5        TCGA-BR-A4J6        TCGA-BR-A4J8        TCGA-BR-A4J9 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-BR-A4PF        TCGA-CD-5798        TCGA-CD-5799        TCGA-CD-5800 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-CD-5801        TCGA-CD-5802        TCGA-CD-5803        TCGA-CG-4300 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-CG-4301        TCGA-CG-4304        TCGA-CG-4305        TCGA-CG-4306 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" 
       TCGA-CG-4436        TCGA-CG-4437        TCGA-CG-4438        TCGA-CG-4440 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-CG-4441        TCGA-CG-4443        TCGA-CG-4444        TCGA-CG-4449 
  "8P GAIN MUTATED" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" 
       TCGA-CG-4455        TCGA-CG-4460        TCGA-CG-4462        TCGA-CG-4465 
  "8P GAIN MUTATED"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-CG-4466        TCGA-CG-4469        TCGA-CG-4472        TCGA-CG-4474 
  "8P GAIN MUTATED"   "8P GAIN MUTATED"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" 
       TCGA-CG-4477        TCGA-CG-5716        TCGA-CG-5717        TCGA-CG-5718 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" 
       TCGA-CG-5719        TCGA-CG-5720        TCGA-CG-5721        TCGA-CG-5722 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-CG-5723        TCGA-CG-5724        TCGA-CG-5725        TCGA-CG-5726 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED"   "8P GAIN MUTATED" 
       TCGA-CG-5727        TCGA-CG-5728        TCGA-CG-5730        TCGA-CG-5732 
  "8P GAIN MUTATED"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-CG-5733        TCGA-CG-5734        TCGA-D7-5577        TCGA-D7-5578 
  "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" 
       TCGA-D7-5579        TCGA-D7-6518        TCGA-D7-6519        TCGA-D7-6520 
  "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" 
       TCGA-D7-6521        TCGA-D7-6522        TCGA-D7-6524        TCGA-D7-6525 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" 
       TCGA-D7-6526        TCGA-D7-6527        TCGA-D7-6528        TCGA-D7-6815 
  "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-D7-6817        TCGA-D7-6818        TCGA-D7-6820        TCGA-D7-6822 
"8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" 
       TCGA-EQ-5647        TCGA-EQ-8122        TCGA-F1-6177        TCGA-F1-6874 
  "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-F1-6875        TCGA-FP-7735        TCGA-FP-7829        TCGA-FP-7916 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" 
       TCGA-FP-7998        TCGA-FP-8099        TCGA-FP-8209        TCGA-FP-8631 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "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-BR-8592        TCGA-BR-A4IU        TCGA-BR-A4IV        TCGA-BR-A4IY 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-BR-A4IZ        TCGA-BR-A4J1        TCGA-BR-A4J2        TCGA-BR-A4J4 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-BR-A4J5        TCGA-BR-A4J6        TCGA-BR-A4J8        TCGA-BR-A4J9 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-BR-A4PF        TCGA-CD-5798        TCGA-CD-5799        TCGA-CD-5800 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-CD-5801        TCGA-CD-5802        TCGA-CD-5803        TCGA-CG-4300 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-CG-4301        TCGA-CG-4304        TCGA-CG-4305        TCGA-CG-4306 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" 
       TCGA-CG-4436        TCGA-CG-4437        TCGA-CG-4438        TCGA-CG-4440 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-CG-4441        TCGA-CG-4443        TCGA-CG-4444        TCGA-CG-4449 
  "8P GAIN MUTATED" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" 
       TCGA-CG-4455        TCGA-CG-4460        TCGA-CG-4462        TCGA-CG-4465 
  "8P GAIN MUTATED"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-CG-4466        TCGA-CG-4469        TCGA-CG-4472        TCGA-CG-4474 
  "8P GAIN MUTATED"   "8P GAIN MUTATED"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" 
       TCGA-CG-4477        TCGA-CG-5716        TCGA-CG-5717        TCGA-CG-5718 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" 
       TCGA-CG-5719        TCGA-CG-5720        TCGA-CG-5721        TCGA-CG-5722 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-CG-5723        TCGA-CG-5724        TCGA-CG-5725        TCGA-CG-5726 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED"   "8P GAIN MUTATED" 
       TCGA-CG-5727        TCGA-CG-5728        TCGA-CG-5730        TCGA-CG-5732 
  "8P GAIN MUTATED"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-CG-5733        TCGA-CG-5734        TCGA-D7-5577        TCGA-D7-5578 
  "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" 
       TCGA-D7-5579        TCGA-D7-6518        TCGA-D7-6519        TCGA-D7-6520 
  "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" 
       TCGA-D7-6521        TCGA-D7-6522        TCGA-D7-6524        TCGA-D7-6525 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" 
       TCGA-D7-6526        TCGA-D7-6527        TCGA-D7-6528        TCGA-D7-6815 
  "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-D7-6817        TCGA-D7-6818        TCGA-D7-6820        TCGA-D7-6822 
"8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" 
       TCGA-EQ-5647        TCGA-EQ-8122        TCGA-F1-6177        TCGA-F1-6874 
  "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-F1-6875        TCGA-FP-7735        TCGA-FP-7829        TCGA-FP-7916 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" 
       TCGA-FP-7998        TCGA-FP-8099        TCGA-FP-8209        TCGA-FP-8631 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "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=" "1.2"
D14V2, continuous
D14V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED     23   26
  8P GAIN WILD-TYPE   47   81
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  FEMALE              23                47
  MALE                26                81
                   vv
clus                STOMACH ADENOCARCINOMA - DIFFUSE TYPE
  8P GAIN MUTATED                                       4
  8P GAIN WILD-TYPE                                    21
                   vv
clus                STOMACH ADENOCARCINOMA - NOT OTHERWISE SPECIFIED (NOS)
  8P GAIN MUTATED                                                       23
  8P GAIN WILD-TYPE                                                     64
                   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                                                 6
                   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                                                  4
  8P GAIN WILD-TYPE                                                6
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - TYPE NOT OTHERWISE SPECIFIED (NOS)
  8P GAIN MUTATED                                                                       12
  8P GAIN WILD-TYPE                                                                     24
D14V4, multiclass
                   vv
clus                T1 T2 T3 T4
  8P GAIN MUTATED    3 20 15  6
  8P GAIN WILD-TYPE  3 34 49 37
D14V5, multiclass
    clus
vv   8P GAIN MUTATED 8P GAIN WILD-TYPE
  T1               3                 3
  T2              20                34
  T3              15                49
  T4               6                37
                   vv
clus                N0 N1 N2 N3
  8P GAIN MUTATED   17 13  8  4
  8P GAIN WILD-TYPE 39 48 21 16
D14V6, multiclass
    clus
vv   8P GAIN MUTATED 8P GAIN WILD-TYPE
  N0              17                39
  N1              13                48
  N2               8                21
  N3               4                16
                   vv
clus                 M0  M1  MX
  8P GAIN MUTATED    45   3   1
  8P GAIN WILD-TYPE 101  15  12
D14V7, multiclass
    clus
vv   8P GAIN MUTATED 8P GAIN WILD-TYPE
  M0              45               101
  M1               3                15
  MX               1                12
                   vv
clus                 I II III IV
  8P GAIN MUTATED    9 14  12  6
  8P GAIN WILD-TYPE 17 34  46 23
D14V8, multiclass
     clus
vv    8P GAIN MUTATED 8P GAIN WILD-TYPE
  I                 9                17
  II               14                34
  III              12                46
  IV                6                23
D14V9, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED      3   46
  8P GAIN WILD-TYPE    2  126
     clus
vv    8P GAIN MUTATED 8P GAIN WILD-TYPE
  NO                3                 2
  YES              46               126
                   vv
clus                R0 R1 R2 RX
  8P GAIN MUTATED   31  3  2 12
  8P GAIN WILD-TYPE 92  4 10 13
D14V10, multiclass
    clus
vv   8P GAIN MUTATED 8P GAIN WILD-TYPE
  R0              31                92
  R1               3                 4
  R2               2                10
  RX              12                13
D14V11, continuous

Clustering(15) Variable = 8q gain mutation analysis
D15V1, survival
                   sevent
clus2                0  1
  8Q GAIN MUTATED   39  9
  8Q GAIN WILD-TYPE 83  9
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               48                92 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
                9                 9 
$`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-BR-A4J1 TCGA-CD-5800 TCGA-CG-4305 TCGA-CG-4436 TCGA-CG-4438 TCGA-CG-4441 
        0.72         0.36        15.95        52.96        54.05        14.01 
TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4455 TCGA-CG-4460 TCGA-CG-4466 TCGA-CG-4469 
       29.98        47.05        12.03        21.99        18.94         7.07 
TCGA-CG-4472 TCGA-CG-5718 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 
       12.00         1.02        15.02        28.96        31.04        65.10 
TCGA-CG-5730 TCGA-CG-5733 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6520 TCGA-D7-6524 
        4.01        21.07         3.58         4.54         9.63         0.69 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6815 TCGA-D7-6818 TCGA-D7-6822 TCGA-EQ-5647 
        5.95         6.61         3.65         4.04         4.27         0.62 
TCGA-F1-6177 TCGA-F1-6875 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-8631 TCGA-IN-7808 
        6.54        72.23         0.39         0.20         0.56         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-BR-8592 TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J2 
        0.20         0.59         0.92         0.39         0.79         0.79 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PF 
        0.53         0.43         0.13         0.23         0.10         0.72 
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-D7-6817 TCGA-D7-6820 TCGA-EQ-8122 
        6.90         4.14         1.68         4.70         2.93         7.79 
TCGA-F1-6874 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-HJ-7597 
        2.01         3.02         3.58         1.02        59.05        26.43 
TCGA-IN-7806 TCGA-IP-7968 
        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 
            4.155             1.020 
[1] "0.1 - 72.2 (4.2)" "0.1 - 70.1 (1.0)"
       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-BR-8592        TCGA-BR-A4IU        TCGA-BR-A4IV        TCGA-BR-A4IY 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-BR-A4IZ        TCGA-BR-A4J1        TCGA-BR-A4J2        TCGA-BR-A4J4 
"8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-BR-A4J5        TCGA-BR-A4J6        TCGA-BR-A4J8        TCGA-BR-A4J9 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-BR-A4PF        TCGA-CD-5798        TCGA-CD-5799        TCGA-CD-5800 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
       TCGA-CD-5801        TCGA-CD-5802        TCGA-CD-5803        TCGA-CG-4300 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-CG-4301        TCGA-CG-4304        TCGA-CG-4305        TCGA-CG-4306 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-CG-4436        TCGA-CG-4437        TCGA-CG-4438        TCGA-CG-4440 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-CG-4441        TCGA-CG-4443        TCGA-CG-4444        TCGA-CG-4449 
  "8Q GAIN MUTATED"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-CG-4455        TCGA-CG-4460        TCGA-CG-4462        TCGA-CG-4465 
  "8Q GAIN MUTATED"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-CG-4466        TCGA-CG-4469        TCGA-CG-4472        TCGA-CG-4474 
  "8Q GAIN MUTATED"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-CG-4477        TCGA-CG-5716        TCGA-CG-5717        TCGA-CG-5718 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
       TCGA-CG-5719        TCGA-CG-5720        TCGA-CG-5721        TCGA-CG-5722 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-CG-5723        TCGA-CG-5724        TCGA-CG-5725        TCGA-CG-5726 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" 
       TCGA-CG-5727        TCGA-CG-5728        TCGA-CG-5730        TCGA-CG-5732 
  "8Q GAIN MUTATED"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-CG-5733        TCGA-CG-5734        TCGA-D7-5577        TCGA-D7-5578 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
       TCGA-D7-5579        TCGA-D7-6518        TCGA-D7-6519        TCGA-D7-6520 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
       TCGA-D7-6521        TCGA-D7-6522        TCGA-D7-6524        TCGA-D7-6525 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" 
       TCGA-D7-6526        TCGA-D7-6527        TCGA-D7-6528        TCGA-D7-6815 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
       TCGA-D7-6817        TCGA-D7-6818        TCGA-D7-6820        TCGA-D7-6822 
"8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
       TCGA-EQ-5647        TCGA-EQ-8122        TCGA-F1-6177        TCGA-F1-6874 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-F1-6875        TCGA-FP-7735        TCGA-FP-7829        TCGA-FP-7916 
  "8Q GAIN MUTATED"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-FP-7998        TCGA-FP-8099        TCGA-FP-8209        TCGA-FP-8631 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
       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-BR-8592        TCGA-BR-A4IU        TCGA-BR-A4IV        TCGA-BR-A4IY 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-BR-A4IZ        TCGA-BR-A4J1        TCGA-BR-A4J2        TCGA-BR-A4J4 
"8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-BR-A4J5        TCGA-BR-A4J6        TCGA-BR-A4J8        TCGA-BR-A4J9 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-BR-A4PF        TCGA-CD-5798        TCGA-CD-5799        TCGA-CD-5800 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
       TCGA-CD-5801        TCGA-CD-5802        TCGA-CD-5803        TCGA-CG-4300 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-CG-4301        TCGA-CG-4304        TCGA-CG-4305        TCGA-CG-4306 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-CG-4436        TCGA-CG-4437        TCGA-CG-4438        TCGA-CG-4440 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-CG-4441        TCGA-CG-4443        TCGA-CG-4444        TCGA-CG-4449 
  "8Q GAIN MUTATED"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-CG-4455        TCGA-CG-4460        TCGA-CG-4462        TCGA-CG-4465 
  "8Q GAIN MUTATED"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-CG-4466        TCGA-CG-4469        TCGA-CG-4472        TCGA-CG-4474 
  "8Q GAIN MUTATED"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-CG-4477        TCGA-CG-5716        TCGA-CG-5717        TCGA-CG-5718 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
       TCGA-CG-5719        TCGA-CG-5720        TCGA-CG-5721        TCGA-CG-5722 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-CG-5723        TCGA-CG-5724        TCGA-CG-5725        TCGA-CG-5726 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" 
       TCGA-CG-5727        TCGA-CG-5728        TCGA-CG-5730        TCGA-CG-5732 
  "8Q GAIN MUTATED"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-CG-5733        TCGA-CG-5734        TCGA-D7-5577        TCGA-D7-5578 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
       TCGA-D7-5579        TCGA-D7-6518        TCGA-D7-6519        TCGA-D7-6520 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
       TCGA-D7-6521        TCGA-D7-6522        TCGA-D7-6524        TCGA-D7-6525 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" 
       TCGA-D7-6526        TCGA-D7-6527        TCGA-D7-6528        TCGA-D7-6815 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
       TCGA-D7-6817        TCGA-D7-6818        TCGA-D7-6820        TCGA-D7-6822 
"8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
       TCGA-EQ-5647        TCGA-EQ-8122        TCGA-F1-6177        TCGA-F1-6874 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-F1-6875        TCGA-FP-7735        TCGA-FP-7829        TCGA-FP-7916 
  "8Q GAIN MUTATED"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-FP-7998        TCGA-FP-8099        TCGA-FP-8209        TCGA-FP-8631 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
       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-BR-8592        TCGA-BR-A4IU        TCGA-BR-A4IV        TCGA-BR-A4IY 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-BR-A4IZ        TCGA-BR-A4J1        TCGA-BR-A4J2        TCGA-BR-A4J4 
"8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-BR-A4J5        TCGA-BR-A4J6        TCGA-BR-A4J8        TCGA-BR-A4J9 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-BR-A4PF        TCGA-CD-5798        TCGA-CD-5799        TCGA-CD-5800 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
       TCGA-CD-5801        TCGA-CD-5802        TCGA-CD-5803        TCGA-CG-4300 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-CG-4301        TCGA-CG-4304        TCGA-CG-4305        TCGA-CG-4306 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-CG-4436        TCGA-CG-4437        TCGA-CG-4438        TCGA-CG-4440 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-CG-4441        TCGA-CG-4443        TCGA-CG-4444        TCGA-CG-4449 
  "8Q GAIN MUTATED"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-CG-4455        TCGA-CG-4460        TCGA-CG-4462        TCGA-CG-4465 
  "8Q GAIN MUTATED"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-CG-4466        TCGA-CG-4469        TCGA-CG-4472        TCGA-CG-4474 
  "8Q GAIN MUTATED"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-CG-4477        TCGA-CG-5716        TCGA-CG-5717        TCGA-CG-5718 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
       TCGA-CG-5719        TCGA-CG-5720        TCGA-CG-5721        TCGA-CG-5722 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-CG-5723        TCGA-CG-5724        TCGA-CG-5725        TCGA-CG-5726 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" 
       TCGA-CG-5727        TCGA-CG-5728        TCGA-CG-5730        TCGA-CG-5732 
  "8Q GAIN MUTATED"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-CG-5733        TCGA-CG-5734        TCGA-D7-5577        TCGA-D7-5578 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
       TCGA-D7-5579        TCGA-D7-6518        TCGA-D7-6519        TCGA-D7-6520 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
       TCGA-D7-6521        TCGA-D7-6522        TCGA-D7-6524        TCGA-D7-6525 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" 
       TCGA-D7-6526        TCGA-D7-6527        TCGA-D7-6528        TCGA-D7-6815 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
       TCGA-D7-6817        TCGA-D7-6818        TCGA-D7-6820        TCGA-D7-6822 
"8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
       TCGA-EQ-5647        TCGA-EQ-8122        TCGA-F1-6177        TCGA-F1-6874 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-F1-6875        TCGA-FP-7735        TCGA-FP-7829        TCGA-FP-7916 
  "8Q GAIN MUTATED"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-FP-7998        TCGA-FP-8099        TCGA-FP-8209        TCGA-FP-8631 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
       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=" "1.4"
D15V2, continuous
D15V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED     30   39
  8Q GAIN WILD-TYPE   40   68
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  FEMALE              30                40
  MALE                39                68
                   vv
clus                STOMACH ADENOCARCINOMA - DIFFUSE TYPE
  8Q GAIN MUTATED                                       5
  8Q GAIN WILD-TYPE                                    20
                   vv
clus                STOMACH ADENOCARCINOMA - NOT OTHERWISE SPECIFIED (NOS)
  8Q GAIN MUTATED                                                       35
  8Q GAIN WILD-TYPE                                                     52
                   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                                                 6
                   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                                                  5
  8Q GAIN WILD-TYPE                                                5
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - TYPE NOT OTHERWISE SPECIFIED (NOS)
  8Q GAIN MUTATED                                                                       17
  8Q GAIN WILD-TYPE                                                                     19
D15V4, multiclass
                   vv
clus                T1 T2 T3 T4
  8Q GAIN MUTATED    5 26 23  9
  8Q GAIN WILD-TYPE  1 28 41 34
D15V5, multiclass
    clus
vv   8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  T1               5                 1
  T2              26                28
  T3              23                41
  T4               9                34
                   vv
clus                N0 N1 N2 N3
  8Q GAIN MUTATED   24 20 13  4
  8Q GAIN WILD-TYPE 32 41 16 16
D15V6, multiclass
    clus
vv   8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  N0              24                32
  N1              20                41
  N2              13                16
  N3               4                16
                   vv
clus                M0 M1 MX
  8Q GAIN MUTATED   60  4  5
  8Q GAIN WILD-TYPE 86 14  8
D15V7, multiclass
    clus
vv   8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  M0              60                86
  M1               4                14
  MX               5                 8
                   vv
clus                 I II III IV
  8Q GAIN MUTATED   14 18  18  9
  8Q GAIN WILD-TYPE 12 30  40 20
D15V8, multiclass
     clus
vv    8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  I                14                12
  II               18                30
  III              18                40
  IV                9                20
D15V9, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED      3   66
  8Q GAIN WILD-TYPE    2  106
     clus
vv    8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  NO                3                 2
  YES              66               106
                   vv
clus                R0 R1 R2 RX
  8Q GAIN MUTATED   45  5  3 14
  8Q GAIN WILD-TYPE 78  2  9 11
D15V10, multiclass
    clus
vv   8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  R0              45                78
  R1               5                 2
  R2               3                 9
  RX              14                11
D15V11, continuous

Clustering(16) Variable = 9p gain mutation analysis
D16V1, survival
                   sevent
clus2                 0   1
  9P GAIN MUTATED     8   2
  9P GAIN WILD-TYPE 114  16
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               10               130 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
                2                16 
$`9P GAIN MUTATED`
TCGA-BR-6707 TCGA-BR-7707 TCGA-BR-A4J4 TCGA-BR-A4J9 TCGA-CG-4436 TCGA-CG-4460 
        0.99         0.13         0.53         0.10        52.96        21.99 
TCGA-D7-6528 TCGA-D7-6818 TCGA-D7-6822 TCGA-EQ-5647 
        1.68         4.04         4.27         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-BR-8592 TCGA-BR-A4IU 
        1.18         1.55         1.48         0.76         0.20         0.59 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J5 
        0.92         0.39         0.79         0.72         0.79         0.43 
TCGA-BR-A4J6 TCGA-BR-A4J8 TCGA-BR-A4PF TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
        0.13         0.23         0.72         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-4462 TCGA-CG-4465 
       29.98        47.05        19.07        12.03         1.02         8.98 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4474 TCGA-CG-4477 TCGA-CG-5716 
       18.94         7.07        12.00         1.02         1.02         1.02 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.94         1.02         1.02         0.99         5.98         0.95 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 
       70.06        12.03        15.02        28.96        31.04        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        55.04        21.07         7.99         8.65         3.58 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
        4.54         9.80        15.65         9.63         8.19         6.90 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6815 TCGA-D7-6817 
        0.69         5.95         6.61         4.14         3.65         4.70 
TCGA-D7-6820 TCGA-EQ-8122 TCGA-F1-6177 TCGA-F1-6874 TCGA-F1-6875 TCGA-FP-7735 
        2.93         7.79         6.54         2.01        72.23         0.39 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8631 
        0.20         3.02         3.58         1.02        59.05         0.56 
TCGA-HJ-7597 TCGA-IN-7806 TCGA-IN-7808 TCGA-IP-7968 
       26.43         6.87         3.55         2.53 

  9P GAIN MUTATED 9P GAIN WILD-TYPE 
             0.10              0.07 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
            52.96             72.23 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
            1.335             1.235 
[1] "0.1 - 53.0 (1.3)" "0.1 - 72.2 (1.2)"
       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-BR-8592        TCGA-BR-A4IU        TCGA-BR-A4IV        TCGA-BR-A4IY 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-BR-A4IZ        TCGA-BR-A4J1        TCGA-BR-A4J2        TCGA-BR-A4J4 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE"   "9P GAIN MUTATED" 
       TCGA-BR-A4J5        TCGA-BR-A4J6        TCGA-BR-A4J8        TCGA-BR-A4J9 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE"   "9P GAIN MUTATED" 
       TCGA-BR-A4PF        TCGA-CD-5798        TCGA-CD-5799        TCGA-CD-5800 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-CD-5801        TCGA-CD-5802        TCGA-CD-5803        TCGA-CG-4300 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-CG-4301        TCGA-CG-4304        TCGA-CG-4305        TCGA-CG-4306 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-CG-4436        TCGA-CG-4437        TCGA-CG-4438        TCGA-CG-4440 
  "9P GAIN MUTATED" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-CG-4441        TCGA-CG-4443        TCGA-CG-4444        TCGA-CG-4449 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-CG-4455        TCGA-CG-4460        TCGA-CG-4462        TCGA-CG-4465 
"9P GAIN WILD-TYPE"   "9P GAIN MUTATED" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-CG-4466        TCGA-CG-4469        TCGA-CG-4472        TCGA-CG-4474 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-CG-4477        TCGA-CG-5716        TCGA-CG-5717        TCGA-CG-5718 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-CG-5719        TCGA-CG-5720        TCGA-CG-5721        TCGA-CG-5722 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-CG-5723        TCGA-CG-5724        TCGA-CG-5725        TCGA-CG-5726 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-CG-5727        TCGA-CG-5728        TCGA-CG-5730        TCGA-CG-5732 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-CG-5733        TCGA-CG-5734        TCGA-D7-5577        TCGA-D7-5578 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-D7-5579        TCGA-D7-6518        TCGA-D7-6519        TCGA-D7-6520 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-D7-6521        TCGA-D7-6522        TCGA-D7-6524        TCGA-D7-6525 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-D7-6526        TCGA-D7-6527        TCGA-D7-6528        TCGA-D7-6815 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE"   "9P GAIN MUTATED" "9P GAIN WILD-TYPE" 
       TCGA-D7-6817        TCGA-D7-6818        TCGA-D7-6820        TCGA-D7-6822 
"9P GAIN WILD-TYPE"   "9P GAIN MUTATED" "9P GAIN WILD-TYPE"   "9P GAIN MUTATED" 
       TCGA-EQ-5647        TCGA-EQ-8122        TCGA-F1-6177        TCGA-F1-6874 
  "9P GAIN MUTATED" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-F1-6875        TCGA-FP-7735        TCGA-FP-7829        TCGA-FP-7916 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-FP-7998        TCGA-FP-8099        TCGA-FP-8209        TCGA-FP-8631 
"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-BR-8592        TCGA-BR-A4IU        TCGA-BR-A4IV        TCGA-BR-A4IY 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-BR-A4IZ        TCGA-BR-A4J1        TCGA-BR-A4J2        TCGA-BR-A4J4 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE"   "9P GAIN MUTATED" 
       TCGA-BR-A4J5        TCGA-BR-A4J6        TCGA-BR-A4J8        TCGA-BR-A4J9 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE"   "9P GAIN MUTATED" 
       TCGA-BR-A4PF        TCGA-CD-5798        TCGA-CD-5799        TCGA-CD-5800 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-CD-5801        TCGA-CD-5802        TCGA-CD-5803        TCGA-CG-4300 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-CG-4301        TCGA-CG-4304        TCGA-CG-4305        TCGA-CG-4306 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-CG-4436        TCGA-CG-4437        TCGA-CG-4438        TCGA-CG-4440 
  "9P GAIN MUTATED" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-CG-4441        TCGA-CG-4443        TCGA-CG-4444        TCGA-CG-4449 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-CG-4455        TCGA-CG-4460        TCGA-CG-4462        TCGA-CG-4465 
"9P GAIN WILD-TYPE"   "9P GAIN MUTATED" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-CG-4466        TCGA-CG-4469        TCGA-CG-4472        TCGA-CG-4474 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-CG-4477        TCGA-CG-5716        TCGA-CG-5717        TCGA-CG-5718 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-CG-5719        TCGA-CG-5720        TCGA-CG-5721        TCGA-CG-5722 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-CG-5723        TCGA-CG-5724        TCGA-CG-5725        TCGA-CG-5726 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-CG-5727        TCGA-CG-5728        TCGA-CG-5730        TCGA-CG-5732 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-CG-5733        TCGA-CG-5734        TCGA-D7-5577        TCGA-D7-5578 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-D7-5579        TCGA-D7-6518        TCGA-D7-6519        TCGA-D7-6520 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-D7-6521        TCGA-D7-6522        TCGA-D7-6524        TCGA-D7-6525 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-D7-6526        TCGA-D7-6527        TCGA-D7-6528        TCGA-D7-6815 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE"   "9P GAIN MUTATED" "9P GAIN WILD-TYPE" 
       TCGA-D7-6817        TCGA-D7-6818        TCGA-D7-6820        TCGA-D7-6822 
"9P GAIN WILD-TYPE"   "9P GAIN MUTATED" "9P GAIN WILD-TYPE"   "9P GAIN MUTATED" 
       TCGA-EQ-5647        TCGA-EQ-8122        TCGA-F1-6177        TCGA-F1-6874 
  "9P GAIN MUTATED" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-F1-6875        TCGA-FP-7735        TCGA-FP-7829        TCGA-FP-7916 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-FP-7998        TCGA-FP-8099        TCGA-FP-8209        TCGA-FP-8631 
"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-BR-8592        TCGA-BR-A4IU        TCGA-BR-A4IV        TCGA-BR-A4IY 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-BR-A4IZ        TCGA-BR-A4J1        TCGA-BR-A4J2        TCGA-BR-A4J4 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE"   "9P GAIN MUTATED" 
       TCGA-BR-A4J5        TCGA-BR-A4J6        TCGA-BR-A4J8        TCGA-BR-A4J9 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE"   "9P GAIN MUTATED" 
       TCGA-BR-A4PF        TCGA-CD-5798        TCGA-CD-5799        TCGA-CD-5800 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-CD-5801        TCGA-CD-5802        TCGA-CD-5803        TCGA-CG-4300 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-CG-4301        TCGA-CG-4304        TCGA-CG-4305        TCGA-CG-4306 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-CG-4436        TCGA-CG-4437        TCGA-CG-4438        TCGA-CG-4440 
  "9P GAIN MUTATED" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-CG-4441        TCGA-CG-4443        TCGA-CG-4444        TCGA-CG-4449 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-CG-4455        TCGA-CG-4460        TCGA-CG-4462        TCGA-CG-4465 
"9P GAIN WILD-TYPE"   "9P GAIN MUTATED" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-CG-4466        TCGA-CG-4469        TCGA-CG-4472        TCGA-CG-4474 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-CG-4477        TCGA-CG-5716        TCGA-CG-5717        TCGA-CG-5718 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-CG-5719        TCGA-CG-5720        TCGA-CG-5721        TCGA-CG-5722 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-CG-5723        TCGA-CG-5724        TCGA-CG-5725        TCGA-CG-5726 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-CG-5727        TCGA-CG-5728        TCGA-CG-5730        TCGA-CG-5732 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-CG-5733        TCGA-CG-5734        TCGA-D7-5577        TCGA-D7-5578 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-D7-5579        TCGA-D7-6518        TCGA-D7-6519        TCGA-D7-6520 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-D7-6521        TCGA-D7-6522        TCGA-D7-6524        TCGA-D7-6525 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-D7-6526        TCGA-D7-6527        TCGA-D7-6528        TCGA-D7-6815 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE"   "9P GAIN MUTATED" "9P GAIN WILD-TYPE" 
       TCGA-D7-6817        TCGA-D7-6818        TCGA-D7-6820        TCGA-D7-6822 
"9P GAIN WILD-TYPE"   "9P GAIN MUTATED" "9P GAIN WILD-TYPE"   "9P GAIN MUTATED" 
       TCGA-EQ-5647        TCGA-EQ-8122        TCGA-F1-6177        TCGA-F1-6874 
  "9P GAIN MUTATED" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-F1-6875        TCGA-FP-7735        TCGA-FP-7829        TCGA-FP-7916 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-FP-7998        TCGA-FP-8099        TCGA-FP-8209        TCGA-FP-8631 
"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=" "1.6"
D16V2, continuous
D16V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED      7    7
  9P GAIN WILD-TYPE   63  100
        clus
vv       9P GAIN MUTATED 9P GAIN WILD-TYPE
  FEMALE               7                63
  MALE                 7               100
                   vv
clus                STOMACH ADENOCARCINOMA - DIFFUSE TYPE
  9P GAIN MUTATED                                       1
  9P GAIN WILD-TYPE                                    24
                   vv
clus                STOMACH ADENOCARCINOMA - NOT OTHERWISE SPECIFIED (NOS)
  9P GAIN MUTATED                                                        8
  9P GAIN WILD-TYPE                                                     79
                   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                                                10
                   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                                                                        3
  9P GAIN WILD-TYPE                                                                     33
D16V4, multiclass
                   vv
clus                T1 T2 T3 T4
  9P GAIN MUTATED    2  5  3  3
  9P GAIN WILD-TYPE  4 49 61 40
D16V5, multiclass
    clus
vv   9P GAIN MUTATED 9P GAIN WILD-TYPE
  T1               2                 4
  T2               5                49
  T3               3                61
  T4               3                40
                   vv
clus                N0 N1 N2 N3
  9P GAIN MUTATED    7  3  1  2
  9P GAIN WILD-TYPE 49 58 28 18
D16V6, multiclass
    clus
vv   9P GAIN MUTATED 9P GAIN WILD-TYPE
  N0               7                49
  N1               3                58
  N2               1                28
  N3               2                18
                   vv
clus                 M0  M1  MX
  9P GAIN MUTATED    12   2   0
  9P GAIN WILD-TYPE 134  16  13
D16V7, multiclass
    clus
vv   9P GAIN MUTATED 9P GAIN WILD-TYPE
  M0              12               134
  M1               2                16
  MX               0                13
                   vv
clus                 I II III IV
  9P GAIN MUTATED    5  3   1  3
  9P GAIN WILD-TYPE 21 45  57 26
D16V8, multiclass
     clus
vv    9P GAIN MUTATED 9P GAIN WILD-TYPE
  I                 5                21
  II                3                45
  III               1                57
  IV                3                26
D16V9, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED      1   13
  9P GAIN WILD-TYPE    4  159
     clus
vv    9P GAIN MUTATED 9P GAIN WILD-TYPE
  NO                1                 4
  YES              13               159
                   vv
clus                 R0  R1  R2  RX
  9P GAIN MUTATED    10   0   2   2
  9P GAIN WILD-TYPE 113   7  10  23
D16V10, multiclass
    clus
vv   9P GAIN MUTATED 9P GAIN WILD-TYPE
  R0              10               113
  R1               0                 7
  R2               2                10
  RX               2                23
D16V11, continuous

Clustering(17) Variable = 9q gain mutation analysis
D17V1, survival
                   sevent
clus2                 0   1
  9Q GAIN MUTATED    10   2
  9Q GAIN WILD-TYPE 112  16
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               12               128 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
                2                16 
$`9Q GAIN MUTATED`
TCGA-BR-6707 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-A4J4 TCGA-BR-A4J9 TCGA-CG-4436 
        0.99         1.25         0.13         0.53         0.10        52.96 
TCGA-CG-4460 TCGA-D7-6528 TCGA-D7-6818 TCGA-EQ-5647 TCGA-FP-7735 TCGA-IN-7808 
       21.99         1.68         4.04         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-BR-8592 TCGA-BR-A4IU TCGA-BR-A4IV 
        1.55         1.48         0.76         0.20         0.59         0.92 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J5 TCGA-BR-A4J6 
        0.39         0.79         0.72         0.79         0.43         0.13 
TCGA-BR-A4J8 TCGA-BR-A4PF TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
        0.23         0.72         0.82         0.69         0.36         0.49 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
        0.30         0.07        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        1.02         8.05        54.05         4.01        14.01        29.98 
TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-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-D7-6815 TCGA-D7-6817 TCGA-D7-6820 
        5.95         6.61         4.14         3.65         4.70         2.93 
TCGA-D7-6822 TCGA-EQ-8122 TCGA-F1-6177 TCGA-F1-6874 TCGA-F1-6875 TCGA-FP-7829 
        4.27         7.79         6.54         2.01        72.23         0.20 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8631 TCGA-HJ-7597 
        3.02         3.58         1.02        59.05         0.56        26.43 
TCGA-IN-7806 TCGA-IP-7968 
        6.87         2.53 

  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
             0.10              0.07 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
            52.96             72.23 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
             1.12              1.27 
[1] "0.1 - 53.0 (1.1)" "0.1 - 72.2 (1.3)"
       TCGA-B7-5816        TCGA-B7-5818        TCGA-BR-6452        TCGA-BR-6455 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-BR-6457        TCGA-BR-6458        TCGA-BR-6563        TCGA-BR-6564 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-BR-6565        TCGA-BR-6566        TCGA-BR-6705        TCGA-BR-6706 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-BR-6707        TCGA-BR-6709        TCGA-BR-6710        TCGA-BR-6801 
  "9Q GAIN MUTATED" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-BR-6802        TCGA-BR-6803        TCGA-BR-6852        TCGA-BR-7196 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-BR-7197        TCGA-BR-7703        TCGA-BR-7704        TCGA-BR-7707 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE"   "9Q GAIN MUTATED"   "9Q GAIN MUTATED" 
       TCGA-BR-7715        TCGA-BR-7716        TCGA-BR-7717        TCGA-BR-7722 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-BR-7723        TCGA-BR-7851        TCGA-BR-7901        TCGA-BR-7957 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-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-BR-8592        TCGA-BR-A4IU        TCGA-BR-A4IV        TCGA-BR-A4IY 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-BR-A4IZ        TCGA-BR-A4J1        TCGA-BR-A4J2        TCGA-BR-A4J4 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE"   "9Q GAIN MUTATED" 
       TCGA-BR-A4J5        TCGA-BR-A4J6        TCGA-BR-A4J8        TCGA-BR-A4J9 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE"   "9Q GAIN MUTATED" 
       TCGA-BR-A4PF        TCGA-CD-5798        TCGA-CD-5799        TCGA-CD-5800 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-CD-5801        TCGA-CD-5802        TCGA-CD-5803        TCGA-CG-4300 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-CG-4301        TCGA-CG-4304        TCGA-CG-4305        TCGA-CG-4306 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-CG-4436        TCGA-CG-4437        TCGA-CG-4438        TCGA-CG-4440 
  "9Q GAIN MUTATED" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-CG-4441        TCGA-CG-4443        TCGA-CG-4444        TCGA-CG-4449 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-CG-4455        TCGA-CG-4460        TCGA-CG-4462        TCGA-CG-4465 
"9Q GAIN WILD-TYPE"   "9Q GAIN MUTATED" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-CG-4466        TCGA-CG-4469        TCGA-CG-4472        TCGA-CG-4474 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-CG-4477        TCGA-CG-5716        TCGA-CG-5717        TCGA-CG-5718 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-CG-5719        TCGA-CG-5720        TCGA-CG-5721        TCGA-CG-5722 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-CG-5723        TCGA-CG-5724        TCGA-CG-5725        TCGA-CG-5726 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-CG-5727        TCGA-CG-5728        TCGA-CG-5730        TCGA-CG-5732 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-CG-5733        TCGA-CG-5734        TCGA-D7-5577        TCGA-D7-5578 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-D7-5579        TCGA-D7-6518        TCGA-D7-6519        TCGA-D7-6520 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-D7-6521        TCGA-D7-6522        TCGA-D7-6524        TCGA-D7-6525 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-D7-6526        TCGA-D7-6527        TCGA-D7-6528        TCGA-D7-6815 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE"   "9Q GAIN MUTATED" "9Q GAIN WILD-TYPE" 
       TCGA-D7-6817        TCGA-D7-6818        TCGA-D7-6820        TCGA-D7-6822 
"9Q GAIN WILD-TYPE"   "9Q GAIN MUTATED" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EQ-5647        TCGA-EQ-8122        TCGA-F1-6177        TCGA-F1-6874 
  "9Q GAIN MUTATED" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-F1-6875        TCGA-FP-7735        TCGA-FP-7829        TCGA-FP-7916 
"9Q GAIN WILD-TYPE"   "9Q GAIN MUTATED" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-FP-7998        TCGA-FP-8099        TCGA-FP-8209        TCGA-FP-8631 
"9Q GAIN WILD-TYPE" "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-BR-8592        TCGA-BR-A4IU        TCGA-BR-A4IV        TCGA-BR-A4IY 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-BR-A4IZ        TCGA-BR-A4J1        TCGA-BR-A4J2        TCGA-BR-A4J4 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE"   "9Q GAIN MUTATED" 
       TCGA-BR-A4J5        TCGA-BR-A4J6        TCGA-BR-A4J8        TCGA-BR-A4J9 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE"   "9Q GAIN MUTATED" 
       TCGA-BR-A4PF        TCGA-CD-5798        TCGA-CD-5799        TCGA-CD-5800 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-CD-5801        TCGA-CD-5802        TCGA-CD-5803        TCGA-CG-4300 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-CG-4301        TCGA-CG-4304        TCGA-CG-4305        TCGA-CG-4306 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-CG-4436        TCGA-CG-4437        TCGA-CG-4438        TCGA-CG-4440 
  "9Q GAIN MUTATED" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-CG-4441        TCGA-CG-4443        TCGA-CG-4444        TCGA-CG-4449 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-CG-4455        TCGA-CG-4460        TCGA-CG-4462        TCGA-CG-4465 
"9Q GAIN WILD-TYPE"   "9Q GAIN MUTATED" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-CG-4466        TCGA-CG-4469        TCGA-CG-4472        TCGA-CG-4474 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-CG-4477        TCGA-CG-5716        TCGA-CG-5717        TCGA-CG-5718 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-CG-5719        TCGA-CG-5720        TCGA-CG-5721        TCGA-CG-5722 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-CG-5723        TCGA-CG-5724        TCGA-CG-5725        TCGA-CG-5726 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-CG-5727        TCGA-CG-5728        TCGA-CG-5730        TCGA-CG-5732 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-CG-5733        TCGA-CG-5734        TCGA-D7-5577        TCGA-D7-5578 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-D7-5579        TCGA-D7-6518        TCGA-D7-6519        TCGA-D7-6520 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-D7-6521        TCGA-D7-6522        TCGA-D7-6524        TCGA-D7-6525 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-D7-6526        TCGA-D7-6527        TCGA-D7-6528        TCGA-D7-6815 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE"   "9Q GAIN MUTATED" "9Q GAIN WILD-TYPE" 
       TCGA-D7-6817        TCGA-D7-6818        TCGA-D7-6820        TCGA-D7-6822 
"9Q GAIN WILD-TYPE"   "9Q GAIN MUTATED" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EQ-5647        TCGA-EQ-8122        TCGA-F1-6177        TCGA-F1-6874 
  "9Q GAIN MUTATED" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-F1-6875        TCGA-FP-7735        TCGA-FP-7829        TCGA-FP-7916 
"9Q GAIN WILD-TYPE"   "9Q GAIN MUTATED" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-FP-7998        TCGA-FP-8099        TCGA-FP-8209        TCGA-FP-8631 
"9Q GAIN WILD-TYPE" "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-BR-8592        TCGA-BR-A4IU        TCGA-BR-A4IV        TCGA-BR-A4IY 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-BR-A4IZ        TCGA-BR-A4J1        TCGA-BR-A4J2        TCGA-BR-A4J4 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE"   "9Q GAIN MUTATED" 
       TCGA-BR-A4J5        TCGA-BR-A4J6        TCGA-BR-A4J8        TCGA-BR-A4J9 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE"   "9Q GAIN MUTATED" 
       TCGA-BR-A4PF        TCGA-CD-5798        TCGA-CD-5799        TCGA-CD-5800 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-CD-5801        TCGA-CD-5802        TCGA-CD-5803        TCGA-CG-4300 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-CG-4301        TCGA-CG-4304        TCGA-CG-4305        TCGA-CG-4306 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-CG-4436        TCGA-CG-4437        TCGA-CG-4438        TCGA-CG-4440 
  "9Q GAIN MUTATED" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-CG-4441        TCGA-CG-4443        TCGA-CG-4444        TCGA-CG-4449 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-CG-4455        TCGA-CG-4460        TCGA-CG-4462        TCGA-CG-4465 
"9Q GAIN WILD-TYPE"   "9Q GAIN MUTATED" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-CG-4466        TCGA-CG-4469        TCGA-CG-4472        TCGA-CG-4474 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-CG-4477        TCGA-CG-5716        TCGA-CG-5717        TCGA-CG-5718 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-CG-5719        TCGA-CG-5720        TCGA-CG-5721        TCGA-CG-5722 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-CG-5723        TCGA-CG-5724        TCGA-CG-5725        TCGA-CG-5726 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-CG-5727        TCGA-CG-5728        TCGA-CG-5730        TCGA-CG-5732 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-CG-5733        TCGA-CG-5734        TCGA-D7-5577        TCGA-D7-5578 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-D7-5579        TCGA-D7-6518        TCGA-D7-6519        TCGA-D7-6520 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-D7-6521        TCGA-D7-6522        TCGA-D7-6524        TCGA-D7-6525 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-D7-6526        TCGA-D7-6527        TCGA-D7-6528        TCGA-D7-6815 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE"   "9Q GAIN MUTATED" "9Q GAIN WILD-TYPE" 
       TCGA-D7-6817        TCGA-D7-6818        TCGA-D7-6820        TCGA-D7-6822 
"9Q GAIN WILD-TYPE"   "9Q GAIN MUTATED" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EQ-5647        TCGA-EQ-8122        TCGA-F1-6177        TCGA-F1-6874 
  "9Q GAIN MUTATED" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-F1-6875        TCGA-FP-7735        TCGA-FP-7829        TCGA-FP-7916 
"9Q GAIN WILD-TYPE"   "9Q GAIN MUTATED" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-FP-7998        TCGA-FP-8099        TCGA-FP-8209        TCGA-FP-8631 
"9Q GAIN WILD-TYPE" "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=" "1.6"
D17V2, continuous
D17V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED      8   10
  9Q GAIN WILD-TYPE   62   97
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  FEMALE               8                62
  MALE                10                97
                   vv
clus                STOMACH ADENOCARCINOMA - DIFFUSE TYPE
  9Q GAIN MUTATED                                       2
  9Q GAIN WILD-TYPE                                    23
                   vv
clus                STOMACH ADENOCARCINOMA - NOT OTHERWISE SPECIFIED (NOS)
  9Q GAIN MUTATED                                                       11
  9Q GAIN WILD-TYPE                                                     76
                   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                                                10
                   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                                                                        4
  9Q GAIN WILD-TYPE                                                                     32
D17V4, multiclass
                   vv
clus                T1 T2 T3 T4
  9Q GAIN MUTATED    2  5  6  3
  9Q GAIN WILD-TYPE  4 49 58 40
D17V5, multiclass
    clus
vv   9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  T1               2                 4
  T2               5                49
  T3               6                58
  T4               3                40
                   vv
clus                N0 N1 N2 N3
  9Q GAIN MUTATED    8  5  1  3
  9Q GAIN WILD-TYPE 48 56 28 17
D17V6, multiclass
    clus
vv   9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  N0               8                48
  N1               5                56
  N2               1                28
  N3               3                17
                   vv
clus                 M0  M1  MX
  9Q GAIN MUTATED    14   3   1
  9Q GAIN WILD-TYPE 132  15  12
D17V7, multiclass
    clus
vv   9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  M0              14               132
  M1               3                15
  MX               1                12
                   vv
clus                 I II III IV
  9Q GAIN MUTATED    5  4   3  3
  9Q GAIN WILD-TYPE 21 44  55 26
D17V8, multiclass
     clus
vv    9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  I                 5                21
  II                4                44
  III               3                55
  IV                3                26
D17V9, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED      1   17
  9Q GAIN WILD-TYPE    4  155
     clus
vv    9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  NO                1                 4
  YES              17               155
                   vv
clus                 R0  R1  R2  RX
  9Q GAIN MUTATED    12   0   2   3
  9Q GAIN WILD-TYPE 111   7  10  22
D17V10, multiclass
    clus
vv   9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  R0              12               111
  R1               0                 7
  R2               2                10
  RX               3                22
D17V11, continuous

Clustering(18) Variable = 10p gain mutation analysis
D18V1, survival
                    sevent
clus2                  0   1
  10P GAIN MUTATED    17   4
  10P GAIN WILD-TYPE 105  14
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                21                119 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                 4                 14 
$`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-BR-A4J8 TCGA-BR-A4PF TCGA-CD-5801 TCGA-CG-4300 TCGA-CG-4440 
        4.54         0.23         0.72         0.49        20.02         4.01 
TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4472 TCGA-CG-5730 TCGA-D7-6518 TCGA-D7-6520 
       47.05        21.99        12.00         4.01         9.80         9.63 
TCGA-EQ-5647 TCGA-F1-6875 TCGA-FP-7735 
        0.62        72.23         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-BR-8592 
        0.26         1.18         1.55         1.48         0.76         0.20 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
        0.59         0.92         0.39         0.79         0.72         0.79 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J9 TCGA-CD-5798 TCGA-CD-5799 
        0.53         0.43         0.13         0.10         0.82         0.69 
TCGA-CD-5800 TCGA-CD-5802 TCGA-CD-5803 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
        0.36         0.30         0.07         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4441 TCGA-CG-4443 
        1.02        52.96         8.05        54.05        14.01        29.98 
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-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-5732 TCGA-CG-5733 TCGA-CG-5734 
       28.96        31.04        65.10        55.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6519 TCGA-D7-6521 TCGA-D7-6522 
        8.65         3.58         4.54        15.65         8.19         6.90 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
        0.69         5.95         6.61         4.14         1.68         3.65 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-EQ-8122 TCGA-F1-6177 
        4.70         4.04         2.93         4.27         7.79         6.54 
TCGA-F1-6874 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        2.01         0.20         3.02         3.58         1.02        59.05 
TCGA-FP-8631 TCGA-HJ-7597 TCGA-IN-7806 TCGA-IN-7808 TCGA-IP-7968 
        0.56        26.43         6.87         3.55         2.53 

  10P GAIN MUTATED 10P GAIN WILD-TYPE 
              0.23               0.07 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
             72.23              70.06 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
              1.48               1.22 
[1] "0.2 - 72.2 (1.5)" "0.1 - 70.1 (1.2)"
        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-BR-8592         TCGA-BR-A4IU         TCGA-BR-A4IV 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BR-A4IY         TCGA-BR-A4IZ         TCGA-BR-A4J1 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BR-A4J2         TCGA-BR-A4J4         TCGA-BR-A4J5 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BR-A4J6         TCGA-BR-A4J8         TCGA-BR-A4J9 
"10P GAIN WILD-TYPE"   "10P GAIN MUTATED" "10P GAIN WILD-TYPE" 
        TCGA-BR-A4PF         TCGA-CD-5798         TCGA-CD-5799 
  "10P GAIN MUTATED" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-CD-5800         TCGA-CD-5801         TCGA-CD-5802 
"10P GAIN WILD-TYPE"   "10P GAIN MUTATED" "10P GAIN WILD-TYPE" 
        TCGA-CD-5803         TCGA-CG-4300         TCGA-CG-4301 
"10P GAIN WILD-TYPE"   "10P GAIN MUTATED" "10P GAIN WILD-TYPE" 
        TCGA-CG-4304         TCGA-CG-4305         TCGA-CG-4306 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-CG-4436         TCGA-CG-4437         TCGA-CG-4438 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-CG-4440         TCGA-CG-4441         TCGA-CG-4443 
  "10P GAIN MUTATED" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-CG-4444         TCGA-CG-4449         TCGA-CG-4455 
  "10P GAIN MUTATED" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-CG-4460         TCGA-CG-4462         TCGA-CG-4465 
  "10P GAIN MUTATED" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-CG-4466         TCGA-CG-4469         TCGA-CG-4472 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE"   "10P GAIN MUTATED" 
        TCGA-CG-4474         TCGA-CG-4477         TCGA-CG-5716 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-CG-5717         TCGA-CG-5718         TCGA-CG-5719 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-CG-5720         TCGA-CG-5721         TCGA-CG-5722 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-CG-5723         TCGA-CG-5724         TCGA-CG-5725 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-CG-5726         TCGA-CG-5727         TCGA-CG-5728 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-CG-5730         TCGA-CG-5732         TCGA-CG-5733 
  "10P GAIN MUTATED" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-CG-5734         TCGA-D7-5577         TCGA-D7-5578 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-D7-5579         TCGA-D7-6518         TCGA-D7-6519 
"10P GAIN WILD-TYPE"   "10P GAIN MUTATED" "10P GAIN WILD-TYPE" 
        TCGA-D7-6520         TCGA-D7-6521         TCGA-D7-6522 
  "10P GAIN MUTATED" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-D7-6524         TCGA-D7-6525         TCGA-D7-6526 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-D7-6527         TCGA-D7-6528         TCGA-D7-6815 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-D7-6817         TCGA-D7-6818         TCGA-D7-6820 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-D7-6822         TCGA-EQ-5647         TCGA-EQ-8122 
"10P GAIN WILD-TYPE"   "10P GAIN MUTATED" "10P GAIN WILD-TYPE" 
        TCGA-F1-6177         TCGA-F1-6874         TCGA-F1-6875 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE"   "10P GAIN MUTATED" 
        TCGA-FP-7735         TCGA-FP-7829         TCGA-FP-7916 
  "10P GAIN MUTATED" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-FP-7998         TCGA-FP-8099         TCGA-FP-8209 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-FP-8631         TCGA-HJ-7597         TCGA-IN-7806 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-IN-7808         TCGA-IP-7968 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE"   "10P GAIN MUTATED" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
  "10P GAIN MUTATED" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE"   "10P GAIN MUTATED" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
  "10P GAIN MUTATED"   "10P GAIN MUTATED"   "10P GAIN MUTATED" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"10P GAIN WILD-TYPE"   "10P GAIN MUTATED" "10P GAIN WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-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-BR-8592         TCGA-BR-A4IU         TCGA-BR-A4IV 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BR-A4IY         TCGA-BR-A4IZ         TCGA-BR-A4J1 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BR-A4J2         TCGA-BR-A4J4         TCGA-BR-A4J5 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BR-A4J6         TCGA-BR-A4J8         TCGA-BR-A4J9 
"10P GAIN WILD-TYPE"   "10P GAIN MUTATED" "10P GAIN WILD-TYPE" 
        TCGA-BR-A4PF         TCGA-CD-5798         TCGA-CD-5799 
  "10P GAIN MUTATED" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-CD-5800         TCGA-CD-5801         TCGA-CD-5802 
"10P GAIN WILD-TYPE"   "10P GAIN MUTATED" "10P GAIN WILD-TYPE" 
        TCGA-CD-5803         TCGA-CG-4300         TCGA-CG-4301 
"10P GAIN WILD-TYPE"   "10P GAIN MUTATED" "10P GAIN WILD-TYPE" 
        TCGA-CG-4304         TCGA-CG-4305         TCGA-CG-4306 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-CG-4436         TCGA-CG-4437         TCGA-CG-4438 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-CG-4440         TCGA-CG-4441         TCGA-CG-4443 
  "10P GAIN MUTATED" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-CG-4444         TCGA-CG-4449         TCGA-CG-4455 
  "10P GAIN MUTATED" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-CG-4460         TCGA-CG-4462         TCGA-CG-4465 
  "10P GAIN MUTATED" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-CG-4466         TCGA-CG-4469         TCGA-CG-4472 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE"   "10P GAIN MUTATED" 
        TCGA-CG-4474         TCGA-CG-4477         TCGA-CG-5716 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-CG-5717         TCGA-CG-5718         TCGA-CG-5719 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-CG-5720         TCGA-CG-5721         TCGA-CG-5722 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-CG-5723         TCGA-CG-5724         TCGA-CG-5725 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-CG-5726         TCGA-CG-5727         TCGA-CG-5728 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-CG-5730         TCGA-CG-5732         TCGA-CG-5733 
  "10P GAIN MUTATED" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-CG-5734         TCGA-D7-5577         TCGA-D7-5578 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-D7-5579         TCGA-D7-6518         TCGA-D7-6519 
"10P GAIN WILD-TYPE"   "10P GAIN MUTATED" "10P GAIN WILD-TYPE" 
        TCGA-D7-6520         TCGA-D7-6521         TCGA-D7-6522 
  "10P GAIN MUTATED" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-D7-6524         TCGA-D7-6525         TCGA-D7-6526 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-D7-6527         TCGA-D7-6528         TCGA-D7-6815 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-D7-6817         TCGA-D7-6818         TCGA-D7-6820 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-D7-6822         TCGA-EQ-5647         TCGA-EQ-8122 
"10P GAIN WILD-TYPE"   "10P GAIN MUTATED" "10P GAIN WILD-TYPE" 
        TCGA-F1-6177         TCGA-F1-6874         TCGA-F1-6875 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE"   "10P GAIN MUTATED" 
        TCGA-FP-7735         TCGA-FP-7829         TCGA-FP-7916 
  "10P GAIN MUTATED" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-FP-7998         TCGA-FP-8099         TCGA-FP-8209 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-FP-8631         TCGA-HJ-7597         TCGA-IN-7806 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-IN-7808         TCGA-IP-7968 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE"   "10P GAIN MUTATED" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
  "10P GAIN MUTATED" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE"   "10P GAIN MUTATED" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
  "10P GAIN MUTATED"   "10P GAIN MUTATED"   "10P GAIN MUTATED" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"10P GAIN WILD-TYPE"   "10P GAIN MUTATED" "10P GAIN WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-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-BR-8592         TCGA-BR-A4IU         TCGA-BR-A4IV 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BR-A4IY         TCGA-BR-A4IZ         TCGA-BR-A4J1 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BR-A4J2         TCGA-BR-A4J4         TCGA-BR-A4J5 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BR-A4J6         TCGA-BR-A4J8         TCGA-BR-A4J9 
"10P GAIN WILD-TYPE"   "10P GAIN MUTATED" "10P GAIN WILD-TYPE" 
        TCGA-BR-A4PF         TCGA-CD-5798         TCGA-CD-5799 
  "10P GAIN MUTATED" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-CD-5800         TCGA-CD-5801         TCGA-CD-5802 
"10P GAIN WILD-TYPE"   "10P GAIN MUTATED" "10P GAIN WILD-TYPE" 
        TCGA-CD-5803         TCGA-CG-4300         TCGA-CG-4301 
"10P GAIN WILD-TYPE"   "10P GAIN MUTATED" "10P GAIN WILD-TYPE" 
        TCGA-CG-4304         TCGA-CG-4305         TCGA-CG-4306 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-CG-4436         TCGA-CG-4437         TCGA-CG-4438 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-CG-4440         TCGA-CG-4441         TCGA-CG-4443 
  "10P GAIN MUTATED" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-CG-4444         TCGA-CG-4449         TCGA-CG-4455 
  "10P GAIN MUTATED" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-CG-4460         TCGA-CG-4462         TCGA-CG-4465 
  "10P GAIN MUTATED" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-CG-4466         TCGA-CG-4469         TCGA-CG-4472 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE"   "10P GAIN MUTATED" 
        TCGA-CG-4474         TCGA-CG-4477         TCGA-CG-5716 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-CG-5717         TCGA-CG-5718         TCGA-CG-5719 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-CG-5720         TCGA-CG-5721         TCGA-CG-5722 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-CG-5723         TCGA-CG-5724         TCGA-CG-5725 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-CG-5726         TCGA-CG-5727         TCGA-CG-5728 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-CG-5730         TCGA-CG-5732         TCGA-CG-5733 
  "10P GAIN MUTATED" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-CG-5734         TCGA-D7-5577         TCGA-D7-5578 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-D7-5579         TCGA-D7-6518         TCGA-D7-6519 
"10P GAIN WILD-TYPE"   "10P GAIN MUTATED" "10P GAIN WILD-TYPE" 
        TCGA-D7-6520         TCGA-D7-6521         TCGA-D7-6522 
  "10P GAIN MUTATED" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-D7-6524         TCGA-D7-6525         TCGA-D7-6526 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-D7-6527         TCGA-D7-6528         TCGA-D7-6815 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-D7-6817         TCGA-D7-6818         TCGA-D7-6820 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-D7-6822         TCGA-EQ-5647         TCGA-EQ-8122 
"10P GAIN WILD-TYPE"   "10P GAIN MUTATED" "10P GAIN WILD-TYPE" 
        TCGA-F1-6177         TCGA-F1-6874         TCGA-F1-6875 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE"   "10P GAIN MUTATED" 
        TCGA-FP-7735         TCGA-FP-7829         TCGA-FP-7916 
  "10P GAIN MUTATED" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-FP-7998         TCGA-FP-8099         TCGA-FP-8209 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-FP-8631         TCGA-HJ-7597         TCGA-IN-7806 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-IN-7808         TCGA-IP-7968 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
[1] "hr=" "1.1"
D18V2, continuous
D18V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED      9   17
  10P GAIN WILD-TYPE   61   90
        clus
vv       10P GAIN MUTATED 10P GAIN WILD-TYPE
  FEMALE                9                 61
  MALE                 17                 90
                    vv
clus                 STOMACH ADENOCARCINOMA - DIFFUSE TYPE
  10P GAIN MUTATED                                       1
  10P GAIN WILD-TYPE                                    24
                    vv
clus                 STOMACH ADENOCARCINOMA - NOT OTHERWISE SPECIFIED (NOS)
  10P GAIN MUTATED                                                       19
  10P GAIN WILD-TYPE                                                     68
                    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                                                10
                    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                                                                     33
D18V4, multiclass
                    vv
clus                 T1 T2 T3 T4
  10P GAIN MUTATED    0  6 11  8
  10P GAIN WILD-TYPE  6 48 53 35
D18V5, multiclass
    clus
vv   10P GAIN MUTATED 10P GAIN WILD-TYPE
  T1                0                  6
  T2                6                 48
  T3               11                 53
  T4                8                 35
                    vv
clus                 N0 N1 N2 N3
  10P GAIN MUTATED    6  9  6  4
  10P GAIN WILD-TYPE 50 52 23 16
D18V6, multiclass
    clus
vv   10P GAIN MUTATED 10P GAIN WILD-TYPE
  N0                6                 50
  N1                9                 52
  N2                6                 23
  N3                4                 16
                    vv
clus                  M0  M1  MX
  10P GAIN MUTATED    20   4   2
  10P GAIN WILD-TYPE 126  14  11
D18V7, multiclass
    clus
vv   10P GAIN MUTATED 10P GAIN WILD-TYPE
  M0               20                126
  M1                4                 14
  MX                2                 11
                    vv
clus                  I II III IV
  10P GAIN MUTATED    2  5   8  9
  10P GAIN WILD-TYPE 24 43  50 20
D18V8, multiclass
     clus
vv    10P GAIN MUTATED 10P GAIN WILD-TYPE
  I                  2                 24
  II                 5                 43
  III                8                 50
  IV                 9                 20
D18V9, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED      0   26
  10P GAIN WILD-TYPE    5  146
     clus
vv    10P GAIN MUTATED 10P GAIN WILD-TYPE
  NO                 0                  5
  YES               26                146
                    vv
clus                  R0  R1  R2  RX
  10P GAIN MUTATED    16   1   4   4
  10P GAIN WILD-TYPE 107   6   8  21
D18V10, multiclass
    clus
vv   10P GAIN MUTATED 10P GAIN WILD-TYPE
  R0               16                107
  R1                1                  6
  R2                4                  8
  RX                4                 21
D18V11, continuous

Clustering(19) Variable = 10q gain mutation analysis
D19V1, survival
                    sevent
clus2                  0   1
  10Q GAIN MUTATED     8   3
  10Q GAIN WILD-TYPE 114  15
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                11                129 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                 3                 15 
$`10Q GAIN MUTATED`
TCGA-BR-7197 TCGA-BR-7715 TCGA-BR-A4PF TCGA-CD-5801 TCGA-CG-4444 TCGA-CG-4460 
        1.48         1.05         0.72         0.49        47.05        21.99 
TCGA-CG-4472 TCGA-D7-6520 TCGA-EQ-5647 TCGA-F1-6875 TCGA-FP-7735 
       12.00         9.63         0.62        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-BR-8592 TCGA-BR-A4IU 
        1.18         1.55         1.48         0.76         0.20         0.59 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
        0.92         0.39         0.79         0.72         0.79         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-CD-5798 TCGA-CD-5799 
        0.43         0.13         0.23         0.10         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-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       14.01        29.98        19.07        12.03         1.02         8.98 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4474 TCGA-CG-4477 TCGA-CG-5716 TCGA-CG-5717 
       18.94         7.07         1.02         1.02         1.02         6.94 
TCGA-CG-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-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
        9.80        15.65         8.19         6.90         0.69         5.95 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 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-8122 TCGA-F1-6177 TCGA-F1-6874 TCGA-FP-7829 
        2.93         4.27         7.79         6.54         2.01         0.20 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8631 TCGA-HJ-7597 
        3.02         3.58         1.02        59.05         0.56        26.43 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IP-7968 
        6.87         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 
              1.48               1.22 
[1] "0.4 - 72.2 (1.5)" "0.1 - 70.1 (1.2)"
        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-BR-8592         TCGA-BR-A4IU         TCGA-BR-A4IV 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BR-A4IY         TCGA-BR-A4IZ         TCGA-BR-A4J1 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BR-A4J2         TCGA-BR-A4J4         TCGA-BR-A4J5 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BR-A4J6         TCGA-BR-A4J8         TCGA-BR-A4J9 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BR-A4PF         TCGA-CD-5798         TCGA-CD-5799 
  "10Q GAIN MUTATED" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CD-5800         TCGA-CD-5801         TCGA-CD-5802 
"10Q GAIN WILD-TYPE"   "10Q GAIN MUTATED" "10Q GAIN WILD-TYPE" 
        TCGA-CD-5803         TCGA-CG-4300         TCGA-CG-4301 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CG-4304         TCGA-CG-4305         TCGA-CG-4306 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CG-4436         TCGA-CG-4437         TCGA-CG-4438 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CG-4440         TCGA-CG-4441         TCGA-CG-4443 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CG-4444         TCGA-CG-4449         TCGA-CG-4455 
  "10Q GAIN MUTATED" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CG-4460         TCGA-CG-4462         TCGA-CG-4465 
  "10Q GAIN MUTATED" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CG-4466         TCGA-CG-4469         TCGA-CG-4472 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE"   "10Q GAIN MUTATED" 
        TCGA-CG-4474         TCGA-CG-4477         TCGA-CG-5716 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CG-5717         TCGA-CG-5718         TCGA-CG-5719 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CG-5720         TCGA-CG-5721         TCGA-CG-5722 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CG-5723         TCGA-CG-5724         TCGA-CG-5725 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CG-5726         TCGA-CG-5727         TCGA-CG-5728 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CG-5730         TCGA-CG-5732         TCGA-CG-5733 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CG-5734         TCGA-D7-5577         TCGA-D7-5578 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-D7-5579         TCGA-D7-6518         TCGA-D7-6519 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-D7-6520         TCGA-D7-6521         TCGA-D7-6522 
  "10Q GAIN MUTATED" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-D7-6524         TCGA-D7-6525         TCGA-D7-6526 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-D7-6527         TCGA-D7-6528         TCGA-D7-6815 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-D7-6817         TCGA-D7-6818         TCGA-D7-6820 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-D7-6822         TCGA-EQ-5647         TCGA-EQ-8122 
"10Q GAIN WILD-TYPE"   "10Q GAIN MUTATED" "10Q GAIN WILD-TYPE" 
        TCGA-F1-6177         TCGA-F1-6874         TCGA-F1-6875 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE"   "10Q GAIN MUTATED" 
        TCGA-FP-7735         TCGA-FP-7829         TCGA-FP-7916 
  "10Q GAIN MUTATED" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-FP-7998         TCGA-FP-8099         TCGA-FP-8209 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-FP-8631         TCGA-HJ-7597         TCGA-IN-7806 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-IN-7808         TCGA-IP-7968 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE"   "10Q GAIN MUTATED" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
  "10Q GAIN MUTATED" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-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-BR-8592         TCGA-BR-A4IU         TCGA-BR-A4IV 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BR-A4IY         TCGA-BR-A4IZ         TCGA-BR-A4J1 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BR-A4J2         TCGA-BR-A4J4         TCGA-BR-A4J5 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BR-A4J6         TCGA-BR-A4J8         TCGA-BR-A4J9 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BR-A4PF         TCGA-CD-5798         TCGA-CD-5799 
  "10Q GAIN MUTATED" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CD-5800         TCGA-CD-5801         TCGA-CD-5802 
"10Q GAIN WILD-TYPE"   "10Q GAIN MUTATED" "10Q GAIN WILD-TYPE" 
        TCGA-CD-5803         TCGA-CG-4300         TCGA-CG-4301 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CG-4304         TCGA-CG-4305         TCGA-CG-4306 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CG-4436         TCGA-CG-4437         TCGA-CG-4438 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CG-4440         TCGA-CG-4441         TCGA-CG-4443 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CG-4444         TCGA-CG-4449         TCGA-CG-4455 
  "10Q GAIN MUTATED" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CG-4460         TCGA-CG-4462         TCGA-CG-4465 
  "10Q GAIN MUTATED" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CG-4466         TCGA-CG-4469         TCGA-CG-4472 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE"   "10Q GAIN MUTATED" 
        TCGA-CG-4474         TCGA-CG-4477         TCGA-CG-5716 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CG-5717         TCGA-CG-5718         TCGA-CG-5719 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CG-5720         TCGA-CG-5721         TCGA-CG-5722 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CG-5723         TCGA-CG-5724         TCGA-CG-5725 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CG-5726         TCGA-CG-5727         TCGA-CG-5728 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CG-5730         TCGA-CG-5732         TCGA-CG-5733 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CG-5734         TCGA-D7-5577         TCGA-D7-5578 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-D7-5579         TCGA-D7-6518         TCGA-D7-6519 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-D7-6520         TCGA-D7-6521         TCGA-D7-6522 
  "10Q GAIN MUTATED" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-D7-6524         TCGA-D7-6525         TCGA-D7-6526 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-D7-6527         TCGA-D7-6528         TCGA-D7-6815 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-D7-6817         TCGA-D7-6818         TCGA-D7-6820 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-D7-6822         TCGA-EQ-5647         TCGA-EQ-8122 
"10Q GAIN WILD-TYPE"   "10Q GAIN MUTATED" "10Q GAIN WILD-TYPE" 
        TCGA-F1-6177         TCGA-F1-6874         TCGA-F1-6875 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE"   "10Q GAIN MUTATED" 
        TCGA-FP-7735         TCGA-FP-7829         TCGA-FP-7916 
  "10Q GAIN MUTATED" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-FP-7998         TCGA-FP-8099         TCGA-FP-8209 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-FP-8631         TCGA-HJ-7597         TCGA-IN-7806 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-IN-7808         TCGA-IP-7968 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE"   "10Q GAIN MUTATED" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
  "10Q GAIN MUTATED" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-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-BR-8592         TCGA-BR-A4IU         TCGA-BR-A4IV 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BR-A4IY         TCGA-BR-A4IZ         TCGA-BR-A4J1 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BR-A4J2         TCGA-BR-A4J4         TCGA-BR-A4J5 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BR-A4J6         TCGA-BR-A4J8         TCGA-BR-A4J9 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BR-A4PF         TCGA-CD-5798         TCGA-CD-5799 
  "10Q GAIN MUTATED" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CD-5800         TCGA-CD-5801         TCGA-CD-5802 
"10Q GAIN WILD-TYPE"   "10Q GAIN MUTATED" "10Q GAIN WILD-TYPE" 
        TCGA-CD-5803         TCGA-CG-4300         TCGA-CG-4301 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CG-4304         TCGA-CG-4305         TCGA-CG-4306 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CG-4436         TCGA-CG-4437         TCGA-CG-4438 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CG-4440         TCGA-CG-4441         TCGA-CG-4443 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CG-4444         TCGA-CG-4449         TCGA-CG-4455 
  "10Q GAIN MUTATED" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CG-4460         TCGA-CG-4462         TCGA-CG-4465 
  "10Q GAIN MUTATED" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CG-4466         TCGA-CG-4469         TCGA-CG-4472 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE"   "10Q GAIN MUTATED" 
        TCGA-CG-4474         TCGA-CG-4477         TCGA-CG-5716 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CG-5717         TCGA-CG-5718         TCGA-CG-5719 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CG-5720         TCGA-CG-5721         TCGA-CG-5722 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CG-5723         TCGA-CG-5724         TCGA-CG-5725 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CG-5726         TCGA-CG-5727         TCGA-CG-5728 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CG-5730         TCGA-CG-5732         TCGA-CG-5733 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CG-5734         TCGA-D7-5577         TCGA-D7-5578 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-D7-5579         TCGA-D7-6518         TCGA-D7-6519 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-D7-6520         TCGA-D7-6521         TCGA-D7-6522 
  "10Q GAIN MUTATED" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-D7-6524         TCGA-D7-6525         TCGA-D7-6526 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-D7-6527         TCGA-D7-6528         TCGA-D7-6815 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-D7-6817         TCGA-D7-6818         TCGA-D7-6820 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-D7-6822         TCGA-EQ-5647         TCGA-EQ-8122 
"10Q GAIN WILD-TYPE"   "10Q GAIN MUTATED" "10Q GAIN WILD-TYPE" 
        TCGA-F1-6177         TCGA-F1-6874         TCGA-F1-6875 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE"   "10Q GAIN MUTATED" 
        TCGA-FP-7735         TCGA-FP-7829         TCGA-FP-7916 
  "10Q GAIN MUTATED" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-FP-7998         TCGA-FP-8099         TCGA-FP-8209 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-FP-8631         TCGA-HJ-7597         TCGA-IN-7806 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-IN-7808         TCGA-IP-7968 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
[1] "hr=" "1.3"
D19V2, continuous
D19V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED      5    9
  10Q GAIN WILD-TYPE   65   98
        clus
vv       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  FEMALE                5                 65
  MALE                  9                 98
                    vv
clus                 STOMACH ADENOCARCINOMA - DIFFUSE TYPE
  10Q GAIN MUTATED                                       0
  10Q GAIN WILD-TYPE                                    25
                    vv
clus                 STOMACH ADENOCARCINOMA - NOT OTHERWISE SPECIFIED (NOS)
  10Q GAIN MUTATED                                                       10
  10Q GAIN WILD-TYPE                                                     77
                    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                                                10
                    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                                                                     35
D19V4, multiclass
                    vv
clus                 T1 T2 T3 T4
  10Q GAIN MUTATED    0  4  5  5
  10Q GAIN WILD-TYPE  6 50 59 38
D19V5, multiclass
    clus
vv   10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  T1                0                  6
  T2                4                 50
  T3                5                 59
  T4                5                 38
                    vv
clus                 N0 N1 N2 N3
  10Q GAIN MUTATED    4  5  4  1
  10Q GAIN WILD-TYPE 52 56 25 19
D19V6, multiclass
    clus
vv   10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  N0                4                 52
  N1                5                 56
  N2                4                 25
  N3                1                 19
                    vv
clus                  M0  M1  MX
  10Q GAIN MUTATED    11   2   1
  10Q GAIN WILD-TYPE 135  16  12
D19V7, multiclass
    clus
vv   10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  M0               11                135
  M1                2                 16
  MX                1                 12
                    vv
clus                  I II III IV
  10Q GAIN MUTATED    2  3   5  4
  10Q GAIN WILD-TYPE 24 45  53 25
D19V8, multiclass
     clus
vv    10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  I                  2                 24
  II                 3                 45
  III                5                 53
  IV                 4                 25
D19V9, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED      0   14
  10Q GAIN WILD-TYPE    5  158
     clus
vv    10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  NO                 0                  5
  YES               14                158
                    vv
clus                  R0  R1  R2  RX
  10Q GAIN MUTATED     9   0   2   2
  10Q GAIN WILD-TYPE 114   7  10  23
D19V10, multiclass
    clus
vv   10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  R0                9                114
  R1                0                  7
  R2                2                 10
  RX                2                 23
D19V11, continuous

Clustering(20) Variable = 11p gain mutation analysis
D20V1, survival
                    sevent
clus2                  0   1
  11P GAIN MUTATED     3   0
  11P GAIN WILD-TYPE 119  18
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 3                137 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 0                 18 
$`11P GAIN MUTATED`
TCGA-BR-6455 TCGA-BR-A4IY TCGA-CG-4300 
        1.41         0.39        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-BR-8592 
        0.26         1.18         1.55         1.48         0.76         0.20 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
        0.59         0.92         0.79         0.72         0.79         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PF TCGA-CD-5798 
        0.43         0.13         0.23         0.10         0.72         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-FP-8099 TCGA-FP-8209 
        0.39         0.20         3.02         3.58         1.02        59.05 
TCGA-FP-8631 TCGA-HJ-7597 TCGA-IN-7806 TCGA-IN-7808 TCGA-IP-7968 
        0.56        26.43         6.87         3.55         2.53 

  11P GAIN MUTATED 11P GAIN WILD-TYPE 
              0.39               0.07 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
             20.02              72.23 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
              1.41               1.22 
[1] "0.4 - 20.0 (1.4)" "0.1 - 72.2 (1.2)"
        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-BR-8592         TCGA-BR-A4IU         TCGA-BR-A4IV 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-BR-A4IY         TCGA-BR-A4IZ         TCGA-BR-A4J1 
  "11P GAIN MUTATED" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-BR-A4J2         TCGA-BR-A4J4         TCGA-BR-A4J5 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-BR-A4J6         TCGA-BR-A4J8         TCGA-BR-A4J9 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-BR-A4PF         TCGA-CD-5798         TCGA-CD-5799 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-CD-5800         TCGA-CD-5801         TCGA-CD-5802 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-CD-5803         TCGA-CG-4300         TCGA-CG-4301 
"11P GAIN WILD-TYPE"   "11P GAIN MUTATED" "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-FP-8099         TCGA-FP-8209 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-FP-8631         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" 
        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-BR-8592         TCGA-BR-A4IU         TCGA-BR-A4IV 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-BR-A4IY         TCGA-BR-A4IZ         TCGA-BR-A4J1 
  "11P GAIN MUTATED" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-BR-A4J2         TCGA-BR-A4J4         TCGA-BR-A4J5 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-BR-A4J6         TCGA-BR-A4J8         TCGA-BR-A4J9 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-BR-A4PF         TCGA-CD-5798         TCGA-CD-5799 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-CD-5800         TCGA-CD-5801         TCGA-CD-5802 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-CD-5803         TCGA-CG-4300         TCGA-CG-4301 
"11P GAIN WILD-TYPE"   "11P GAIN MUTATED" "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-FP-8099         TCGA-FP-8209 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-FP-8631         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" 
        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-BR-8592         TCGA-BR-A4IU         TCGA-BR-A4IV 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-BR-A4IY         TCGA-BR-A4IZ         TCGA-BR-A4J1 
  "11P GAIN MUTATED" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-BR-A4J2         TCGA-BR-A4J4         TCGA-BR-A4J5 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-BR-A4J6         TCGA-BR-A4J8         TCGA-BR-A4J9 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-BR-A4PF         TCGA-CD-5798         TCGA-CD-5799 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-CD-5800         TCGA-CD-5801         TCGA-CD-5802 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-CD-5803         TCGA-CG-4300         TCGA-CG-4301 
"11P GAIN WILD-TYPE"   "11P GAIN MUTATED" "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-FP-8099         TCGA-FP-8209 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-FP-8631         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" 
[1] "hr="     "2.5e+07"
D20V2, continuous
D20V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED      1    4
  11P GAIN WILD-TYPE   69  103
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  FEMALE                1                 69
  MALE                  4                103
                    vv
clus                 STOMACH ADENOCARCINOMA - DIFFUSE TYPE
  11P GAIN MUTATED                                       0
  11P GAIN WILD-TYPE                                    25
                    vv
clus                 STOMACH ADENOCARCINOMA - NOT OTHERWISE SPECIFIED (NOS)
  11P GAIN MUTATED                                                        5
  11P GAIN WILD-TYPE                                                     82
                    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                                                10
                    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                                                                     36
D20V4, multiclass
                    vv
clus                 T1 T2 T3 T4
  11P GAIN MUTATED    0  0  3  2
  11P GAIN WILD-TYPE  6 54 61 41
D20V5, multiclass
    clus
vv   11P GAIN MUTATED 11P GAIN WILD-TYPE
  T1                0                  6
  T2                0                 54
  T3                3                 61
  T4                2                 41
                    vv
clus                 N0 N1 N2 N3
  11P GAIN MUTATED    1  2  2  0
  11P GAIN WILD-TYPE 55 59 27 20
D20V6, multiclass
    clus
vv   11P GAIN MUTATED 11P GAIN WILD-TYPE
  N0                1                 55
  N1                2                 59
  N2                2                 27
  N3                0                 20
                    vv
clus                  M0  M1  MX
  11P GAIN MUTATED     5   0   0
  11P GAIN WILD-TYPE 141  18  13
D20V7, multiclass
    clus
vv   11P GAIN MUTATED 11P GAIN WILD-TYPE
  M0                5                141
  M1                0                 18
  MX                0                 13
                    vv
clus                  I II III IV
  11P GAIN MUTATED    0  1   3  1
  11P GAIN WILD-TYPE 26 47  55 28
D20V8, multiclass
     clus
vv    11P GAIN MUTATED 11P GAIN WILD-TYPE
  I                  0                 26
  II                 1                 47
  III                3                 55
  IV                 1                 28
D20V9, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED      0    5
  11P GAIN WILD-TYPE    5  167
     clus
vv    11P GAIN MUTATED 11P GAIN WILD-TYPE
  NO                 0                  5
  YES                5                167
                    vv
clus                  R0  R1  R2  RX
  11P GAIN MUTATED     3   1   0   1
  11P GAIN WILD-TYPE 120   6  12  24
D20V10, multiclass
    clus
vv   11P GAIN MUTATED 11P GAIN WILD-TYPE
  R0                3                120
  R1                1                  6
  R2                0                 12
  RX                1                 24
D20V11, continuous

Clustering(21) Variable = 11q gain mutation analysis
D21V1, survival
                    sevent
clus2                  0   1
  11Q GAIN MUTATED     6   1
  11Q GAIN WILD-TYPE 116  17
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 7                133 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 1                 17 
$`11Q GAIN MUTATED`
TCGA-BR-6455 TCGA-BR-7704 TCGA-BR-A4IY TCGA-CG-4300 TCGA-CG-4472 TCGA-D7-6528 
        1.41         1.25         0.39        20.02        12.00         1.68 
TCGA-F1-6875 
       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-BR-8592 TCGA-BR-A4IU 
        1.18         1.55         1.48         0.76         0.20         0.59 
TCGA-BR-A4IV TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
        0.92         0.79         0.72         0.79         0.53         0.43 
TCGA-BR-A4J6 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PF TCGA-CD-5798 TCGA-CD-5799 
        0.13         0.23         0.10         0.72         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-FP-8099 TCGA-FP-8209 TCGA-FP-8631 TCGA-HJ-7597 TCGA-IN-7806 TCGA-IN-7808 
        1.02        59.05         0.56        26.43         6.87         3.55 
TCGA-IP-7968 
        2.53 

  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
              0.39               0.07 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
             72.23              70.06 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
              1.68               1.18 
[1] "0.4 - 72.2 (1.7)" "0.1 - 70.1 (1.2)"
        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-BR-8592         TCGA-BR-A4IU         TCGA-BR-A4IV 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-BR-A4IY         TCGA-BR-A4IZ         TCGA-BR-A4J1 
  "11Q GAIN MUTATED" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-BR-A4J2         TCGA-BR-A4J4         TCGA-BR-A4J5 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-BR-A4J6         TCGA-BR-A4J8         TCGA-BR-A4J9 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-BR-A4PF         TCGA-CD-5798         TCGA-CD-5799 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-CD-5800         TCGA-CD-5801         TCGA-CD-5802 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-CD-5803         TCGA-CG-4300         TCGA-CG-4301 
"11Q GAIN WILD-TYPE"   "11Q GAIN MUTATED" "11Q GAIN WILD-TYPE" 
        TCGA-CG-4304         TCGA-CG-4305         TCGA-CG-4306 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-CG-4436         TCGA-CG-4437         TCGA-CG-4438 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-CG-4440         TCGA-CG-4441         TCGA-CG-4443 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-CG-4444         TCGA-CG-4449         TCGA-CG-4455 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-CG-4460         TCGA-CG-4462         TCGA-CG-4465 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-CG-4466         TCGA-CG-4469         TCGA-CG-4472 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE"   "11Q GAIN MUTATED" 
        TCGA-CG-4474         TCGA-CG-4477         TCGA-CG-5716 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-CG-5717         TCGA-CG-5718         TCGA-CG-5719 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-CG-5720         TCGA-CG-5721         TCGA-CG-5722 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-CG-5723         TCGA-CG-5724         TCGA-CG-5725 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-CG-5726         TCGA-CG-5727         TCGA-CG-5728 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-CG-5730         TCGA-CG-5732         TCGA-CG-5733 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-CG-5734         TCGA-D7-5577         TCGA-D7-5578 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-D7-5579         TCGA-D7-6518         TCGA-D7-6519 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-D7-6520         TCGA-D7-6521         TCGA-D7-6522 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-D7-6524         TCGA-D7-6525         TCGA-D7-6526 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-D7-6527         TCGA-D7-6528         TCGA-D7-6815 
"11Q GAIN WILD-TYPE"   "11Q GAIN MUTATED" "11Q GAIN WILD-TYPE" 
        TCGA-D7-6817         TCGA-D7-6818         TCGA-D7-6820 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-D7-6822         TCGA-EQ-5647         TCGA-EQ-8122 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-F1-6177         TCGA-F1-6874         TCGA-F1-6875 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE"   "11Q GAIN MUTATED" 
        TCGA-FP-7735         TCGA-FP-7829         TCGA-FP-7916 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-FP-7998         TCGA-FP-8099         TCGA-FP-8209 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-FP-8631         TCGA-HJ-7597         TCGA-IN-7806 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-IN-7808         TCGA-IP-7968 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
  "11Q GAIN MUTATED" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"11Q GAIN WILD-TYPE"   "11Q GAIN MUTATED" "11Q GAIN WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-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-BR-8592         TCGA-BR-A4IU         TCGA-BR-A4IV 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-BR-A4IY         TCGA-BR-A4IZ         TCGA-BR-A4J1 
  "11Q GAIN MUTATED" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-BR-A4J2         TCGA-BR-A4J4         TCGA-BR-A4J5 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-BR-A4J6         TCGA-BR-A4J8         TCGA-BR-A4J9 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-BR-A4PF         TCGA-CD-5798         TCGA-CD-5799 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-CD-5800         TCGA-CD-5801         TCGA-CD-5802 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-CD-5803         TCGA-CG-4300         TCGA-CG-4301 
"11Q GAIN WILD-TYPE"   "11Q GAIN MUTATED" "11Q GAIN WILD-TYPE" 
        TCGA-CG-4304         TCGA-CG-4305         TCGA-CG-4306 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-CG-4436         TCGA-CG-4437         TCGA-CG-4438 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-CG-4440         TCGA-CG-4441         TCGA-CG-4443 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-CG-4444         TCGA-CG-4449         TCGA-CG-4455 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-CG-4460         TCGA-CG-4462         TCGA-CG-4465 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-CG-4466         TCGA-CG-4469         TCGA-CG-4472 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE"   "11Q GAIN MUTATED" 
        TCGA-CG-4474         TCGA-CG-4477         TCGA-CG-5716 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-CG-5717         TCGA-CG-5718         TCGA-CG-5719 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-CG-5720         TCGA-CG-5721         TCGA-CG-5722 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-CG-5723         TCGA-CG-5724         TCGA-CG-5725 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-CG-5726         TCGA-CG-5727         TCGA-CG-5728 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-CG-5730         TCGA-CG-5732         TCGA-CG-5733 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-CG-5734         TCGA-D7-5577         TCGA-D7-5578 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-D7-5579         TCGA-D7-6518         TCGA-D7-6519 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-D7-6520         TCGA-D7-6521         TCGA-D7-6522 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-D7-6524         TCGA-D7-6525         TCGA-D7-6526 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-D7-6527         TCGA-D7-6528         TCGA-D7-6815 
"11Q GAIN WILD-TYPE"   "11Q GAIN MUTATED" "11Q GAIN WILD-TYPE" 
        TCGA-D7-6817         TCGA-D7-6818         TCGA-D7-6820 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-D7-6822         TCGA-EQ-5647         TCGA-EQ-8122 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-F1-6177         TCGA-F1-6874         TCGA-F1-6875 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE"   "11Q GAIN MUTATED" 
        TCGA-FP-7735         TCGA-FP-7829         TCGA-FP-7916 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-FP-7998         TCGA-FP-8099         TCGA-FP-8209 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-FP-8631         TCGA-HJ-7597         TCGA-IN-7806 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-IN-7808         TCGA-IP-7968 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
  "11Q GAIN MUTATED" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"11Q GAIN WILD-TYPE"   "11Q GAIN MUTATED" "11Q GAIN WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-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-BR-8592         TCGA-BR-A4IU         TCGA-BR-A4IV 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-BR-A4IY         TCGA-BR-A4IZ         TCGA-BR-A4J1 
  "11Q GAIN MUTATED" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-BR-A4J2         TCGA-BR-A4J4         TCGA-BR-A4J5 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-BR-A4J6         TCGA-BR-A4J8         TCGA-BR-A4J9 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-BR-A4PF         TCGA-CD-5798         TCGA-CD-5799 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-CD-5800         TCGA-CD-5801         TCGA-CD-5802 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-CD-5803         TCGA-CG-4300         TCGA-CG-4301 
"11Q GAIN WILD-TYPE"   "11Q GAIN MUTATED" "11Q GAIN WILD-TYPE" 
        TCGA-CG-4304         TCGA-CG-4305         TCGA-CG-4306 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-CG-4436         TCGA-CG-4437         TCGA-CG-4438 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-CG-4440         TCGA-CG-4441         TCGA-CG-4443 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-CG-4444         TCGA-CG-4449         TCGA-CG-4455 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-CG-4460         TCGA-CG-4462         TCGA-CG-4465 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-CG-4466         TCGA-CG-4469         TCGA-CG-4472 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE"   "11Q GAIN MUTATED" 
        TCGA-CG-4474         TCGA-CG-4477         TCGA-CG-5716 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-CG-5717         TCGA-CG-5718         TCGA-CG-5719 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-CG-5720         TCGA-CG-5721         TCGA-CG-5722 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-CG-5723         TCGA-CG-5724         TCGA-CG-5725 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-CG-5726         TCGA-CG-5727         TCGA-CG-5728 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-CG-5730         TCGA-CG-5732         TCGA-CG-5733 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-CG-5734         TCGA-D7-5577         TCGA-D7-5578 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-D7-5579         TCGA-D7-6518         TCGA-D7-6519 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-D7-6520         TCGA-D7-6521         TCGA-D7-6522 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-D7-6524         TCGA-D7-6525         TCGA-D7-6526 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-D7-6527         TCGA-D7-6528         TCGA-D7-6815 
"11Q GAIN WILD-TYPE"   "11Q GAIN MUTATED" "11Q GAIN WILD-TYPE" 
        TCGA-D7-6817         TCGA-D7-6818         TCGA-D7-6820 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-D7-6822         TCGA-EQ-5647         TCGA-EQ-8122 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-F1-6177         TCGA-F1-6874         TCGA-F1-6875 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE"   "11Q GAIN MUTATED" 
        TCGA-FP-7735         TCGA-FP-7829         TCGA-FP-7916 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-FP-7998         TCGA-FP-8099         TCGA-FP-8209 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-FP-8631         TCGA-HJ-7597         TCGA-IN-7806 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-IN-7808         TCGA-IP-7968 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
[1] "hr="     "7.9e+07"
D21V2, continuous
D21V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED      3    6
  11Q GAIN WILD-TYPE   67  101
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  FEMALE                3                 67
  MALE                  6                101
                    vv
clus                 STOMACH ADENOCARCINOMA - DIFFUSE TYPE
  11Q GAIN MUTATED                                       0
  11Q GAIN WILD-TYPE                                    25
                    vv
clus                 STOMACH ADENOCARCINOMA - NOT OTHERWISE SPECIFIED (NOS)
  11Q GAIN MUTATED                                                        6
  11Q GAIN WILD-TYPE                                                     81
                    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                                                10
                    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                                                                     35
D21V4, multiclass
                    vv
clus                 T1 T2 T3 T4
  11Q GAIN MUTATED    0  2  4  3
  11Q GAIN WILD-TYPE  6 52 60 40
D21V5, multiclass
    clus
vv   11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  T1                0                  6
  T2                2                 52
  T3                4                 60
  T4                3                 40
                    vv
clus                 N0 N1 N2 N3
  11Q GAIN MUTATED    4  3  2  0
  11Q GAIN WILD-TYPE 52 58 27 20
D21V6, multiclass
    clus
vv   11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  N0                4                 52
  N1                3                 58
  N2                2                 27
  N3                0                 20
                    vv
clus                  M0  M1  MX
  11Q GAIN MUTATED     9   0   0
  11Q GAIN WILD-TYPE 137  18  13
D21V7, multiclass
    clus
vv   11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  M0                9                137
  M1                0                 18
  MX                0                 13
                    vv
clus                  I II III IV
  11Q GAIN MUTATED    2  2   3  2
  11Q GAIN WILD-TYPE 24 46  55 27
D21V8, multiclass
     clus
vv    11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  I                  2                 24
  II                 2                 46
  III                3                 55
  IV                 2                 27
D21V9, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED      0    9
  11Q GAIN WILD-TYPE    5  163
     clus
vv    11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  NO                 0                  5
  YES                9                163
                    vv
clus                  R0  R1  R2  RX
  11Q GAIN MUTATED     7   1   0   1
  11Q GAIN WILD-TYPE 116   6  12  24
D21V10, multiclass
    clus
vv   11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  R0                7                116
  R1                1                  6
  R2                0                 12
  RX                1                 24
D21V11, continuous

Clustering(22) Variable = 12p gain mutation analysis
D22V1, survival
                    sevent
clus2                  0   1
  12P GAIN MUTATED    11   3
  12P GAIN WILD-TYPE 111  15
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                14                126 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                 3                 15 
$`12P GAIN MUTATED`
TCGA-BR-6709 TCGA-BR-6801 TCGA-BR-7723 TCGA-BR-A4J1 TCGA-BR-A4PF TCGA-CD-5799 
        1.22         1.12         4.54         0.72         0.72         0.69 
TCGA-CG-4460 TCGA-CG-5724 TCGA-CG-5727 TCGA-D7-6820 TCGA-FP-7735 TCGA-FP-7829 
       21.99        12.03        31.04         2.93         0.39         0.20 
TCGA-IN-7808 TCGA-IP-7968 
        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-BR-8592 TCGA-BR-A4IU TCGA-BR-A4IV 
        1.55         1.48         0.76         0.20         0.59         0.92 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
        0.39         0.79         0.79         0.53         0.43         0.13 
TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-CD-5798 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        0.23         0.10         0.82         0.36         0.49         0.30 
TCGA-CD-5803 TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
        0.07        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
       52.96         8.05        54.05         4.01        14.01        29.98 
TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       47.05        19.07        12.03         1.02         8.98        18.94 
TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-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-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       15.02        28.96        65.10         4.01        55.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99         8.65         3.58         4.54         9.80        15.65 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
        9.63         8.19         6.90         0.69         5.95         6.61 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6822 
        4.14         1.68         3.65         4.70         4.04         4.27 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6177 TCGA-F1-6874 TCGA-F1-6875 TCGA-FP-7916 
        0.62         7.79         6.54         2.01        72.23         3.02 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8631 TCGA-HJ-7597 TCGA-IN-7806 
        3.58         1.02        59.05         0.56        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 
             1.875              1.235 
[1] "0.2 - 31.0 (1.9)" "0.1 - 72.2 (1.2)"
        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-BR-8592         TCGA-BR-A4IU         TCGA-BR-A4IV 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-BR-A4IY         TCGA-BR-A4IZ         TCGA-BR-A4J1 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE"   "12P GAIN MUTATED" 
        TCGA-BR-A4J2         TCGA-BR-A4J4         TCGA-BR-A4J5 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-BR-A4J6         TCGA-BR-A4J8         TCGA-BR-A4J9 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-BR-A4PF         TCGA-CD-5798         TCGA-CD-5799 
  "12P GAIN MUTATED" "12P GAIN WILD-TYPE"   "12P GAIN MUTATED" 
        TCGA-CD-5800         TCGA-CD-5801         TCGA-CD-5802 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-CD-5803         TCGA-CG-4300         TCGA-CG-4301 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-CG-4304         TCGA-CG-4305         TCGA-CG-4306 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-CG-4436         TCGA-CG-4437         TCGA-CG-4438 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-CG-4440         TCGA-CG-4441         TCGA-CG-4443 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-CG-4444         TCGA-CG-4449         TCGA-CG-4455 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-CG-4460         TCGA-CG-4462         TCGA-CG-4465 
  "12P GAIN MUTATED" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-CG-4466         TCGA-CG-4469         TCGA-CG-4472 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-CG-4474         TCGA-CG-4477         TCGA-CG-5716 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-CG-5717         TCGA-CG-5718         TCGA-CG-5719 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-CG-5720         TCGA-CG-5721         TCGA-CG-5722 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-CG-5723         TCGA-CG-5724         TCGA-CG-5725 
"12P GAIN WILD-TYPE"   "12P GAIN MUTATED" "12P GAIN WILD-TYPE" 
        TCGA-CG-5726         TCGA-CG-5727         TCGA-CG-5728 
"12P GAIN WILD-TYPE"   "12P GAIN MUTATED" "12P GAIN WILD-TYPE" 
        TCGA-CG-5730         TCGA-CG-5732         TCGA-CG-5733 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-CG-5734         TCGA-D7-5577         TCGA-D7-5578 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-D7-5579         TCGA-D7-6518         TCGA-D7-6519 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-D7-6520         TCGA-D7-6521         TCGA-D7-6522 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-D7-6524         TCGA-D7-6525         TCGA-D7-6526 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-D7-6527         TCGA-D7-6528         TCGA-D7-6815 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-D7-6817         TCGA-D7-6818         TCGA-D7-6820 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE"   "12P GAIN MUTATED" 
        TCGA-D7-6822         TCGA-EQ-5647         TCGA-EQ-8122 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-F1-6177         TCGA-F1-6874         TCGA-F1-6875 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-FP-7735         TCGA-FP-7829         TCGA-FP-7916 
  "12P GAIN MUTATED"   "12P GAIN MUTATED" "12P GAIN WILD-TYPE" 
        TCGA-FP-7998         TCGA-FP-8099         TCGA-FP-8209 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-FP-8631         TCGA-HJ-7597         TCGA-IN-7806 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-IN-7808         TCGA-IP-7968 
  "12P GAIN MUTATED"   "12P GAIN MUTATED" 
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"12P GAIN WILD-TYPE"   "12P GAIN MUTATED" "12P GAIN WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
  "12P GAIN MUTATED" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"12P GAIN WILD-TYPE"   "12P GAIN MUTATED" "12P GAIN WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-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-BR-8592         TCGA-BR-A4IU         TCGA-BR-A4IV 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-BR-A4IY         TCGA-BR-A4IZ         TCGA-BR-A4J1 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE"   "12P GAIN MUTATED" 
        TCGA-BR-A4J2         TCGA-BR-A4J4         TCGA-BR-A4J5 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-BR-A4J6         TCGA-BR-A4J8         TCGA-BR-A4J9 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-BR-A4PF         TCGA-CD-5798         TCGA-CD-5799 
  "12P GAIN MUTATED" "12P GAIN WILD-TYPE"   "12P GAIN MUTATED" 
        TCGA-CD-5800         TCGA-CD-5801         TCGA-CD-5802 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-CD-5803         TCGA-CG-4300         TCGA-CG-4301 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-CG-4304         TCGA-CG-4305         TCGA-CG-4306 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-CG-4436         TCGA-CG-4437         TCGA-CG-4438 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-CG-4440         TCGA-CG-4441         TCGA-CG-4443 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-CG-4444         TCGA-CG-4449         TCGA-CG-4455 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-CG-4460         TCGA-CG-4462         TCGA-CG-4465 
  "12P GAIN MUTATED" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-CG-4466         TCGA-CG-4469         TCGA-CG-4472 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-CG-4474         TCGA-CG-4477         TCGA-CG-5716 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-CG-5717         TCGA-CG-5718         TCGA-CG-5719 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-CG-5720         TCGA-CG-5721         TCGA-CG-5722 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-CG-5723         TCGA-CG-5724         TCGA-CG-5725 
"12P GAIN WILD-TYPE"   "12P GAIN MUTATED" "12P GAIN WILD-TYPE" 
        TCGA-CG-5726         TCGA-CG-5727         TCGA-CG-5728 
"12P GAIN WILD-TYPE"   "12P GAIN MUTATED" "12P GAIN WILD-TYPE" 
        TCGA-CG-5730         TCGA-CG-5732         TCGA-CG-5733 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-CG-5734         TCGA-D7-5577         TCGA-D7-5578 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-D7-5579         TCGA-D7-6518         TCGA-D7-6519 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-D7-6520         TCGA-D7-6521         TCGA-D7-6522 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-D7-6524         TCGA-D7-6525         TCGA-D7-6526 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-D7-6527         TCGA-D7-6528         TCGA-D7-6815 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-D7-6817         TCGA-D7-6818         TCGA-D7-6820 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE"   "12P GAIN MUTATED" 
        TCGA-D7-6822         TCGA-EQ-5647         TCGA-EQ-8122 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-F1-6177         TCGA-F1-6874         TCGA-F1-6875 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-FP-7735         TCGA-FP-7829         TCGA-FP-7916 
  "12P GAIN MUTATED"   "12P GAIN MUTATED" "12P GAIN WILD-TYPE" 
        TCGA-FP-7998         TCGA-FP-8099         TCGA-FP-8209 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-FP-8631         TCGA-HJ-7597         TCGA-IN-7806 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-IN-7808         TCGA-IP-7968 
  "12P GAIN MUTATED"   "12P GAIN MUTATED" 
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"12P GAIN WILD-TYPE"   "12P GAIN MUTATED" "12P GAIN WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
  "12P GAIN MUTATED" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"12P GAIN WILD-TYPE"   "12P GAIN MUTATED" "12P GAIN WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-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-BR-8592         TCGA-BR-A4IU         TCGA-BR-A4IV 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-BR-A4IY         TCGA-BR-A4IZ         TCGA-BR-A4J1 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE"   "12P GAIN MUTATED" 
        TCGA-BR-A4J2         TCGA-BR-A4J4         TCGA-BR-A4J5 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-BR-A4J6         TCGA-BR-A4J8         TCGA-BR-A4J9 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-BR-A4PF         TCGA-CD-5798         TCGA-CD-5799 
  "12P GAIN MUTATED" "12P GAIN WILD-TYPE"   "12P GAIN MUTATED" 
        TCGA-CD-5800         TCGA-CD-5801         TCGA-CD-5802 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-CD-5803         TCGA-CG-4300         TCGA-CG-4301 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-CG-4304         TCGA-CG-4305         TCGA-CG-4306 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-CG-4436         TCGA-CG-4437         TCGA-CG-4438 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-CG-4440         TCGA-CG-4441         TCGA-CG-4443 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-CG-4444         TCGA-CG-4449         TCGA-CG-4455 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-CG-4460         TCGA-CG-4462         TCGA-CG-4465 
  "12P GAIN MUTATED" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-CG-4466         TCGA-CG-4469         TCGA-CG-4472 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-CG-4474         TCGA-CG-4477         TCGA-CG-5716 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-CG-5717         TCGA-CG-5718         TCGA-CG-5719 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-CG-5720         TCGA-CG-5721         TCGA-CG-5722 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-CG-5723         TCGA-CG-5724         TCGA-CG-5725 
"12P GAIN WILD-TYPE"   "12P GAIN MUTATED" "12P GAIN WILD-TYPE" 
        TCGA-CG-5726         TCGA-CG-5727         TCGA-CG-5728 
"12P GAIN WILD-TYPE"   "12P GAIN MUTATED" "12P GAIN WILD-TYPE" 
        TCGA-CG-5730         TCGA-CG-5732         TCGA-CG-5733 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-CG-5734         TCGA-D7-5577         TCGA-D7-5578 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-D7-5579         TCGA-D7-6518         TCGA-D7-6519 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-D7-6520         TCGA-D7-6521         TCGA-D7-6522 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-D7-6524         TCGA-D7-6525         TCGA-D7-6526 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-D7-6527         TCGA-D7-6528         TCGA-D7-6815 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-D7-6817         TCGA-D7-6818         TCGA-D7-6820 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE"   "12P GAIN MUTATED" 
        TCGA-D7-6822         TCGA-EQ-5647         TCGA-EQ-8122 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-F1-6177         TCGA-F1-6874         TCGA-F1-6875 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-FP-7735         TCGA-FP-7829         TCGA-FP-7916 
  "12P GAIN MUTATED"   "12P GAIN MUTATED" "12P GAIN WILD-TYPE" 
        TCGA-FP-7998         TCGA-FP-8099         TCGA-FP-8209 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-FP-8631         TCGA-HJ-7597         TCGA-IN-7806 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-IN-7808         TCGA-IP-7968 
  "12P GAIN MUTATED"   "12P GAIN MUTATED" 
[1] "hr=" "2"  
D22V2, continuous
D22V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED      3   14
  12P GAIN WILD-TYPE   67   93
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  FEMALE                3                 67
  MALE                 14                 93
                    vv
clus                 STOMACH ADENOCARCINOMA - DIFFUSE TYPE
  12P GAIN MUTATED                                       2
  12P GAIN WILD-TYPE                                    23
                    vv
clus                 STOMACH ADENOCARCINOMA - NOT OTHERWISE SPECIFIED (NOS)
  12P GAIN MUTATED                                                        9
  12P GAIN WILD-TYPE                                                     78
                    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                                                 9
                    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                                                                     33
D22V4, multiclass
                    vv
clus                 T1 T2 T3 T4
  12P GAIN MUTATED    0  3  9  5
  12P GAIN WILD-TYPE  6 51 55 38
D22V5, multiclass
    clus
vv   12P GAIN MUTATED 12P GAIN WILD-TYPE
  T1                0                  6
  T2                3                 51
  T3                9                 55
  T4                5                 38
                    vv
clus                 N0 N1 N2 N3
  12P GAIN MUTATED    4  6  5  2
  12P GAIN WILD-TYPE 52 55 24 18
D22V6, multiclass
    clus
vv   12P GAIN MUTATED 12P GAIN WILD-TYPE
  N0                4                 52
  N1                6                 55
  N2                5                 24
  N3                2                 18
                    vv
clus                  M0  M1  MX
  12P GAIN MUTATED    12   3   2
  12P GAIN WILD-TYPE 134  15  11
D22V7, multiclass
    clus
vv   12P GAIN MUTATED 12P GAIN WILD-TYPE
  M0               12                134
  M1                3                 15
  MX                2                 11
                    vv
clus                  I II III IV
  12P GAIN MUTATED    1  6   7  3
  12P GAIN WILD-TYPE 25 42  51 26
D22V8, multiclass
     clus
vv    12P GAIN MUTATED 12P GAIN WILD-TYPE
  I                  1                 25
  II                 6                 42
  III                7                 51
  IV                 3                 26
D22V9, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED      0   17
  12P GAIN WILD-TYPE    5  155
     clus
vv    12P GAIN MUTATED 12P GAIN WILD-TYPE
  NO                 0                  5
  YES               17                155
                    vv
clus                  R0  R1  R2  RX
  12P GAIN MUTATED    10   1   2   1
  12P GAIN WILD-TYPE 113   6  10  24
D22V10, multiclass
    clus
vv   12P GAIN MUTATED 12P GAIN WILD-TYPE
  R0               10                113
  R1                1                  6
  R2                2                 10
  RX                1                 24
D22V11, continuous

Clustering(23) Variable = 12q gain mutation analysis
D23V1, survival
                    sevent
clus2                  0   1
  12Q GAIN MUTATED     8   2
  12Q GAIN WILD-TYPE 114  16
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                10                130 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                 2                 16 
$`12Q GAIN MUTATED`
TCGA-BR-6709 TCGA-BR-7723 TCGA-BR-A4J1 TCGA-BR-A4J4 TCGA-CD-5799 TCGA-CG-4460 
        1.22         4.54         0.72         0.53         0.69        21.99 
TCGA-CG-4472 TCGA-CG-5727 TCGA-D7-6527 TCGA-IP-7968 
       12.00        31.04         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-BR-8592 TCGA-BR-A4IU 
        1.18         1.55         1.48         0.76         0.20         0.59 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J5 TCGA-BR-A4J6 
        0.92         0.39         0.79         0.79         0.43         0.13 
TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PF TCGA-CD-5798 TCGA-CD-5800 TCGA-CD-5801 
        0.23         0.10         0.72         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-4474 TCGA-CG-4477 TCGA-CG-5716 TCGA-CG-5717 
       18.94         7.07         1.02         1.02         1.02         6.94 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
        1.02         1.02         0.99         5.98         0.95        70.06 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        15.02        28.96        65.10         4.01        55.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99         8.65         3.58         4.54         9.80 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       15.65         9.63         8.19         6.90         0.69         5.95 
TCGA-D7-6526 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
        6.61         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-FP-8099 TCGA-FP-8209 
        0.39         0.20         3.02         3.58         1.02        59.05 
TCGA-FP-8631 TCGA-HJ-7597 TCGA-IN-7806 TCGA-IN-7808 
        0.56        26.43         6.87         3.55 

  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
              0.53               0.07 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
             31.04              72.23 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
             3.335              1.200 
[1] "0.5 - 31.0 (3.3)" "0.1 - 72.2 (1.2)"
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-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-BR-8592         TCGA-BR-A4IU         TCGA-BR-A4IV 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-BR-A4IY         TCGA-BR-A4IZ         TCGA-BR-A4J1 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" 
        TCGA-BR-A4J2         TCGA-BR-A4J4         TCGA-BR-A4J5 
"12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" 
        TCGA-BR-A4J6         TCGA-BR-A4J8         TCGA-BR-A4J9 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-BR-A4PF         TCGA-CD-5798         TCGA-CD-5799 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" 
        TCGA-CD-5800         TCGA-CD-5801         TCGA-CD-5802 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-CD-5803         TCGA-CG-4300         TCGA-CG-4301 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-CG-4304         TCGA-CG-4305         TCGA-CG-4306 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-CG-4436         TCGA-CG-4437         TCGA-CG-4438 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-CG-4440         TCGA-CG-4441         TCGA-CG-4443 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-CG-4444         TCGA-CG-4449         TCGA-CG-4455 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-CG-4460         TCGA-CG-4462         TCGA-CG-4465 
  "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-CG-4466         TCGA-CG-4469         TCGA-CG-4472 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" 
        TCGA-CG-4474         TCGA-CG-4477         TCGA-CG-5716 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-CG-5717         TCGA-CG-5718         TCGA-CG-5719 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-CG-5720         TCGA-CG-5721         TCGA-CG-5722 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-CG-5723         TCGA-CG-5724         TCGA-CG-5725 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-CG-5726         TCGA-CG-5727         TCGA-CG-5728 
"12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" 
        TCGA-CG-5730         TCGA-CG-5732         TCGA-CG-5733 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-CG-5734         TCGA-D7-5577         TCGA-D7-5578 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-D7-5579         TCGA-D7-6518         TCGA-D7-6519 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-D7-6520         TCGA-D7-6521         TCGA-D7-6522 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-D7-6524         TCGA-D7-6525         TCGA-D7-6526 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-D7-6527         TCGA-D7-6528         TCGA-D7-6815 
  "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-D7-6817         TCGA-D7-6818         TCGA-D7-6820 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-D7-6822         TCGA-EQ-5647         TCGA-EQ-8122 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-F1-6177         TCGA-F1-6874         TCGA-F1-6875 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-FP-7735         TCGA-FP-7829         TCGA-FP-7916 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-FP-7998         TCGA-FP-8099         TCGA-FP-8209 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-FP-8631         TCGA-HJ-7597         TCGA-IN-7806 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-IN-7808         TCGA-IP-7968 
"12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" 
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-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-BR-8592         TCGA-BR-A4IU         TCGA-BR-A4IV 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-BR-A4IY         TCGA-BR-A4IZ         TCGA-BR-A4J1 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" 
        TCGA-BR-A4J2         TCGA-BR-A4J4         TCGA-BR-A4J5 
"12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" 
        TCGA-BR-A4J6         TCGA-BR-A4J8         TCGA-BR-A4J9 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-BR-A4PF         TCGA-CD-5798         TCGA-CD-5799 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" 
        TCGA-CD-5800         TCGA-CD-5801         TCGA-CD-5802 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-CD-5803         TCGA-CG-4300         TCGA-CG-4301 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-CG-4304         TCGA-CG-4305         TCGA-CG-4306 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-CG-4436         TCGA-CG-4437         TCGA-CG-4438 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-CG-4440         TCGA-CG-4441         TCGA-CG-4443 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-CG-4444         TCGA-CG-4449         TCGA-CG-4455 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-CG-4460         TCGA-CG-4462         TCGA-CG-4465 
  "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-CG-4466         TCGA-CG-4469         TCGA-CG-4472 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" 
        TCGA-CG-4474         TCGA-CG-4477         TCGA-CG-5716 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-CG-5717         TCGA-CG-5718         TCGA-CG-5719 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-CG-5720         TCGA-CG-5721         TCGA-CG-5722 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-CG-5723         TCGA-CG-5724         TCGA-CG-5725 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-CG-5726         TCGA-CG-5727         TCGA-CG-5728 
"12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" 
        TCGA-CG-5730         TCGA-CG-5732         TCGA-CG-5733 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-CG-5734         TCGA-D7-5577         TCGA-D7-5578 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-D7-5579         TCGA-D7-6518         TCGA-D7-6519 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-D7-6520         TCGA-D7-6521         TCGA-D7-6522 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-D7-6524         TCGA-D7-6525         TCGA-D7-6526 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-D7-6527         TCGA-D7-6528         TCGA-D7-6815 
  "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-D7-6817         TCGA-D7-6818         TCGA-D7-6820 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-D7-6822         TCGA-EQ-5647         TCGA-EQ-8122 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-F1-6177         TCGA-F1-6874         TCGA-F1-6875 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-FP-7735         TCGA-FP-7829         TCGA-FP-7916 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-FP-7998         TCGA-FP-8099         TCGA-FP-8209 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-FP-8631         TCGA-HJ-7597         TCGA-IN-7806 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-IN-7808         TCGA-IP-7968 
"12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" 
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-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-BR-8592         TCGA-BR-A4IU         TCGA-BR-A4IV 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-BR-A4IY         TCGA-BR-A4IZ         TCGA-BR-A4J1 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" 
        TCGA-BR-A4J2         TCGA-BR-A4J4         TCGA-BR-A4J5 
"12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" 
        TCGA-BR-A4J6         TCGA-BR-A4J8         TCGA-BR-A4J9 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-BR-A4PF         TCGA-CD-5798         TCGA-CD-5799 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" 
        TCGA-CD-5800         TCGA-CD-5801         TCGA-CD-5802 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-CD-5803         TCGA-CG-4300         TCGA-CG-4301 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-CG-4304         TCGA-CG-4305         TCGA-CG-4306 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-CG-4436         TCGA-CG-4437         TCGA-CG-4438 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-CG-4440         TCGA-CG-4441         TCGA-CG-4443 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-CG-4444         TCGA-CG-4449         TCGA-CG-4455 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-CG-4460         TCGA-CG-4462         TCGA-CG-4465 
  "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-CG-4466         TCGA-CG-4469         TCGA-CG-4472 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" 
        TCGA-CG-4474         TCGA-CG-4477         TCGA-CG-5716 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-CG-5717         TCGA-CG-5718         TCGA-CG-5719 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-CG-5720         TCGA-CG-5721         TCGA-CG-5722 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-CG-5723         TCGA-CG-5724         TCGA-CG-5725 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-CG-5726         TCGA-CG-5727         TCGA-CG-5728 
"12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" 
        TCGA-CG-5730         TCGA-CG-5732         TCGA-CG-5733 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-CG-5734         TCGA-D7-5577         TCGA-D7-5578 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-D7-5579         TCGA-D7-6518         TCGA-D7-6519 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-D7-6520         TCGA-D7-6521         TCGA-D7-6522 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-D7-6524         TCGA-D7-6525         TCGA-D7-6526 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-D7-6527         TCGA-D7-6528         TCGA-D7-6815 
  "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-D7-6817         TCGA-D7-6818         TCGA-D7-6820 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-D7-6822         TCGA-EQ-5647         TCGA-EQ-8122 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-F1-6177         TCGA-F1-6874         TCGA-F1-6875 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-FP-7735         TCGA-FP-7829         TCGA-FP-7916 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-FP-7998         TCGA-FP-8099         TCGA-FP-8209 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-FP-8631         TCGA-HJ-7597         TCGA-IN-7806 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-IN-7808         TCGA-IP-7968 
"12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" 
[1] "hr=" "1.4"
D23V2, continuous
D23V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED      3    9
  12Q GAIN WILD-TYPE   67   98
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  FEMALE                3                 67
  MALE                  9                 98
                    vv
clus                 STOMACH ADENOCARCINOMA - DIFFUSE TYPE
  12Q GAIN MUTATED                                       0
  12Q GAIN WILD-TYPE                                    25
                    vv
clus                 STOMACH ADENOCARCINOMA - NOT OTHERWISE SPECIFIED (NOS)
  12Q GAIN MUTATED                                                        7
  12Q GAIN WILD-TYPE                                                     80
                    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                                                10
                    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                                                                     33
D23V4, multiclass
                    vv
clus                 T1 T2 T3 T4
  12Q GAIN MUTATED    0  3  4  5
  12Q GAIN WILD-TYPE  6 51 60 38
D23V5, multiclass
    clus
vv   12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  T1                0                  6
  T2                3                 51
  T3                4                 60
  T4                5                 38
                    vv
clus                 N0 N1 N2 N3
  12Q GAIN MUTATED    2  5  5  0
  12Q GAIN WILD-TYPE 54 56 24 20
D23V6, multiclass
    clus
vv   12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  N0                2                 54
  N1                5                 56
  N2                5                 24
  N3                0                 20
                    vv
clus                  M0  M1  MX
  12Q GAIN MUTATED    10   1   1
  12Q GAIN WILD-TYPE 136  17  12
D23V7, multiclass
    clus
vv   12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  M0               10                136
  M1                1                 17
  MX                1                 12
                    vv
clus                  I II III IV
  12Q GAIN MUTATED    1  4   4  3
  12Q GAIN WILD-TYPE 25 44  54 26
D23V8, multiclass
     clus
vv    12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  I                  1                 25
  II                 4                 44
  III                4                 54
  IV                 3                 26
D23V9, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED      1   11
  12Q GAIN WILD-TYPE    4  161
     clus
vv    12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  NO                 1                  4
  YES               11                161
                    vv
clus                  R0  R1  R2  RX
  12Q GAIN MUTATED     6   1   1   2
  12Q GAIN WILD-TYPE 117   6  11  23
D23V10, multiclass
    clus
vv   12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  R0                6                117
  R1                1                  6
  R2                1                 11
  RX                2                 23
D23V11, continuous

Clustering(24) Variable = 13q gain mutation analysis
D24V1, survival
                    sevent
clus2                 0  1
  13Q GAIN MUTATED   24  4
  13Q GAIN WILD-TYPE 98 14
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                28                112 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                 4                 14 
$`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-BR-A4J1 TCGA-BR-A4J8 TCGA-BR-A4PF TCGA-CD-5799 
        0.69         4.54         0.72         0.23         0.72         0.69 
TCGA-CD-5800 TCGA-CG-4300 TCGA-CG-4305 TCGA-CG-4436 TCGA-CG-4469 TCGA-CG-4472 
        0.36        20.02        15.95        52.96         7.07        12.00 
TCGA-CG-5730 TCGA-CG-5732 TCGA-D7-5577 TCGA-D7-6518 TCGA-D7-6526 TCGA-D7-6527 
        4.01        55.04         8.65         9.80         6.61         4.14 
TCGA-D7-6820 TCGA-EQ-5647 TCGA-F1-6875 TCGA-FP-7829 
        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-BR-8592 TCGA-BR-A4IU 
        1.18         1.55         1.48         0.76         0.20         0.59 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
        0.92         0.39         0.79         0.79         0.53         0.43 
TCGA-BR-A4J6 TCGA-BR-A4J9 TCGA-CD-5798 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
        0.13         0.10         0.82         0.49         0.30         0.07 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4306 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
        3.02        27.02         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-4474 TCGA-CG-4477 TCGA-CG-5716 
        1.02         8.98        18.94         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-5733 TCGA-CG-5734 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6519 TCGA-D7-6520 
       21.07         7.99         3.58         4.54        15.65         9.63 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6528 TCGA-D7-6815 
        8.19         6.90         0.69         5.95         1.68         3.65 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6822 TCGA-EQ-8122 TCGA-F1-6177 TCGA-F1-6874 
        4.70         4.04         4.27         7.79         6.54         2.01 
TCGA-FP-7735 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8631 
        0.39         3.02         3.58         1.02        59.05         0.56 
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 
              2.32               1.13 
[1] "0.1 - 72.2 (2.3)" "0.1 - 70.1 (1.1)"
        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-BR-8592         TCGA-BR-A4IU         TCGA-BR-A4IV 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-BR-A4IY         TCGA-BR-A4IZ         TCGA-BR-A4J1 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" 
        TCGA-BR-A4J2         TCGA-BR-A4J4         TCGA-BR-A4J5 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-BR-A4J6         TCGA-BR-A4J8         TCGA-BR-A4J9 
"13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" 
        TCGA-BR-A4PF         TCGA-CD-5798         TCGA-CD-5799 
  "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" 
        TCGA-CD-5800         TCGA-CD-5801         TCGA-CD-5802 
  "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-CD-5803         TCGA-CG-4300         TCGA-CG-4301 
"13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" 
        TCGA-CG-4304         TCGA-CG-4305         TCGA-CG-4306 
"13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" 
        TCGA-CG-4436         TCGA-CG-4437         TCGA-CG-4438 
  "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-CG-4440         TCGA-CG-4441         TCGA-CG-4443 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-CG-4444         TCGA-CG-4449         TCGA-CG-4455 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-CG-4460         TCGA-CG-4462         TCGA-CG-4465 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-CG-4466         TCGA-CG-4469         TCGA-CG-4472 
"13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED"   "13Q GAIN MUTATED" 
        TCGA-CG-4474         TCGA-CG-4477         TCGA-CG-5716 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-CG-5717         TCGA-CG-5718         TCGA-CG-5719 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-CG-5720         TCGA-CG-5721         TCGA-CG-5722 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-CG-5723         TCGA-CG-5724         TCGA-CG-5725 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-CG-5726         TCGA-CG-5727         TCGA-CG-5728 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-CG-5730         TCGA-CG-5732         TCGA-CG-5733 
  "13Q GAIN MUTATED"   "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" 
        TCGA-CG-5734         TCGA-D7-5577         TCGA-D7-5578 
"13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" 
        TCGA-D7-5579         TCGA-D7-6518         TCGA-D7-6519 
"13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" 
        TCGA-D7-6520         TCGA-D7-6521         TCGA-D7-6522 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-D7-6524         TCGA-D7-6525         TCGA-D7-6526 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" 
        TCGA-D7-6527         TCGA-D7-6528         TCGA-D7-6815 
  "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-D7-6817         TCGA-D7-6818         TCGA-D7-6820 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" 
        TCGA-D7-6822         TCGA-EQ-5647         TCGA-EQ-8122 
"13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" 
        TCGA-F1-6177         TCGA-F1-6874         TCGA-F1-6875 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" 
        TCGA-FP-7735         TCGA-FP-7829         TCGA-FP-7916 
"13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" 
        TCGA-FP-7998         TCGA-FP-8099         TCGA-FP-8209 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-FP-8631         TCGA-HJ-7597         TCGA-IN-7806 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-IN-7808         TCGA-IP-7968 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"13Q GAIN WILD-TYPE"   "13Q GAIN 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-BR-8592         TCGA-BR-A4IU         TCGA-BR-A4IV 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-BR-A4IY         TCGA-BR-A4IZ         TCGA-BR-A4J1 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" 
        TCGA-BR-A4J2         TCGA-BR-A4J4         TCGA-BR-A4J5 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-BR-A4J6         TCGA-BR-A4J8         TCGA-BR-A4J9 
"13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" 
        TCGA-BR-A4PF         TCGA-CD-5798         TCGA-CD-5799 
  "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" 
        TCGA-CD-5800         TCGA-CD-5801         TCGA-CD-5802 
  "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-CD-5803         TCGA-CG-4300         TCGA-CG-4301 
"13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" 
        TCGA-CG-4304         TCGA-CG-4305         TCGA-CG-4306 
"13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" 
        TCGA-CG-4436         TCGA-CG-4437         TCGA-CG-4438 
  "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-CG-4440         TCGA-CG-4441         TCGA-CG-4443 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-CG-4444         TCGA-CG-4449         TCGA-CG-4455 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-CG-4460         TCGA-CG-4462         TCGA-CG-4465 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-CG-4466         TCGA-CG-4469         TCGA-CG-4472 
"13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED"   "13Q GAIN MUTATED" 
        TCGA-CG-4474         TCGA-CG-4477         TCGA-CG-5716 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-CG-5717         TCGA-CG-5718         TCGA-CG-5719 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-CG-5720         TCGA-CG-5721         TCGA-CG-5722 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-CG-5723         TCGA-CG-5724         TCGA-CG-5725 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-CG-5726         TCGA-CG-5727         TCGA-CG-5728 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-CG-5730         TCGA-CG-5732         TCGA-CG-5733 
  "13Q GAIN MUTATED"   "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" 
        TCGA-CG-5734         TCGA-D7-5577         TCGA-D7-5578 
"13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" 
        TCGA-D7-5579         TCGA-D7-6518         TCGA-D7-6519 
"13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" 
        TCGA-D7-6520         TCGA-D7-6521         TCGA-D7-6522 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-D7-6524         TCGA-D7-6525         TCGA-D7-6526 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" 
        TCGA-D7-6527         TCGA-D7-6528         TCGA-D7-6815 
  "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-D7-6817         TCGA-D7-6818         TCGA-D7-6820 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" 
        TCGA-D7-6822         TCGA-EQ-5647         TCGA-EQ-8122 
"13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" 
        TCGA-F1-6177         TCGA-F1-6874         TCGA-F1-6875 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" 
        TCGA-FP-7735         TCGA-FP-7829         TCGA-FP-7916 
"13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" 
        TCGA-FP-7998         TCGA-FP-8099         TCGA-FP-8209 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-FP-8631         TCGA-HJ-7597         TCGA-IN-7806 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-IN-7808         TCGA-IP-7968 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"13Q GAIN WILD-TYPE"   "13Q GAIN 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-BR-8592         TCGA-BR-A4IU         TCGA-BR-A4IV 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-BR-A4IY         TCGA-BR-A4IZ         TCGA-BR-A4J1 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" 
        TCGA-BR-A4J2         TCGA-BR-A4J4         TCGA-BR-A4J5 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-BR-A4J6         TCGA-BR-A4J8         TCGA-BR-A4J9 
"13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" 
        TCGA-BR-A4PF         TCGA-CD-5798         TCGA-CD-5799 
  "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" 
        TCGA-CD-5800         TCGA-CD-5801         TCGA-CD-5802 
  "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-CD-5803         TCGA-CG-4300         TCGA-CG-4301 
"13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" 
        TCGA-CG-4304         TCGA-CG-4305         TCGA-CG-4306 
"13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" 
        TCGA-CG-4436         TCGA-CG-4437         TCGA-CG-4438 
  "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-CG-4440         TCGA-CG-4441         TCGA-CG-4443 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-CG-4444         TCGA-CG-4449         TCGA-CG-4455 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-CG-4460         TCGA-CG-4462         TCGA-CG-4465 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-CG-4466         TCGA-CG-4469         TCGA-CG-4472 
"13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED"   "13Q GAIN MUTATED" 
        TCGA-CG-4474         TCGA-CG-4477         TCGA-CG-5716 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-CG-5717         TCGA-CG-5718         TCGA-CG-5719 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-CG-5720         TCGA-CG-5721         TCGA-CG-5722 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-CG-5723         TCGA-CG-5724         TCGA-CG-5725 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-CG-5726         TCGA-CG-5727         TCGA-CG-5728 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-CG-5730         TCGA-CG-5732         TCGA-CG-5733 
  "13Q GAIN MUTATED"   "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" 
        TCGA-CG-5734         TCGA-D7-5577         TCGA-D7-5578 
"13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" 
        TCGA-D7-5579         TCGA-D7-6518         TCGA-D7-6519 
"13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" 
        TCGA-D7-6520         TCGA-D7-6521         TCGA-D7-6522 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-D7-6524         TCGA-D7-6525         TCGA-D7-6526 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" 
        TCGA-D7-6527         TCGA-D7-6528         TCGA-D7-6815 
  "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-D7-6817         TCGA-D7-6818         TCGA-D7-6820 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" 
        TCGA-D7-6822         TCGA-EQ-5647         TCGA-EQ-8122 
"13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" 
        TCGA-F1-6177         TCGA-F1-6874         TCGA-F1-6875 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" 
        TCGA-FP-7735         TCGA-FP-7829         TCGA-FP-7916 
"13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" 
        TCGA-FP-7998         TCGA-FP-8099         TCGA-FP-8209 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-FP-8631         TCGA-HJ-7597         TCGA-IN-7806 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-IN-7808         TCGA-IP-7968 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
[1] "hr=" "1.4"
D24V2, continuous
D24V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED     11   23
  13Q GAIN WILD-TYPE   59   84
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  FEMALE               11                 59
  MALE                 23                 84
                    vv
clus                 STOMACH ADENOCARCINOMA - DIFFUSE TYPE
  13Q GAIN MUTATED                                       3
  13Q GAIN WILD-TYPE                                    22
                    vv
clus                 STOMACH ADENOCARCINOMA - NOT OTHERWISE SPECIFIED (NOS)
  13Q GAIN MUTATED                                                       17
  13Q GAIN WILD-TYPE                                                     70
                    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                                                 9
                    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                                                  3
  13Q GAIN WILD-TYPE                                                7
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - TYPE NOT OTHERWISE SPECIFIED (NOS)
  13Q GAIN MUTATED                                                                        7
  13Q GAIN WILD-TYPE                                                                     29
D24V4, multiclass
                    vv
clus                 T1 T2 T3 T4
  13Q GAIN MUTATED    1 13 12  7
  13Q GAIN WILD-TYPE  5 41 52 36
D24V5, multiclass
    clus
vv   13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  T1                1                  5
  T2               13                 41
  T3               12                 52
  T4                7                 36
                    vv
clus                 N0 N1 N2 N3
  13Q GAIN MUTATED    9 11  5  7
  13Q GAIN WILD-TYPE 47 50 24 13
D24V6, multiclass
    clus
vv   13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  N0                9                 47
  N1               11                 50
  N2                5                 24
  N3                7                 13
                    vv
clus                  M0  M1  MX
  13Q GAIN MUTATED    31   2   1
  13Q GAIN WILD-TYPE 115  16  12
D24V7, multiclass
    clus
vv   13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  M0               31                115
  M1                2                 16
  MX                1                 12
                    vv
clus                  I II III IV
  13Q GAIN MUTATED    4  9  11  7
  13Q GAIN WILD-TYPE 22 39  47 22
D24V8, multiclass
     clus
vv    13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  I                  4                 22
  II                 9                 39
  III               11                 47
  IV                 7                 22
D24V9, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED      1   33
  13Q GAIN WILD-TYPE    4  139
     clus
vv    13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  NO                 1                  4
  YES               33                139
                    vv
clus                 R0 R1 R2 RX
  13Q GAIN MUTATED   24  2  2  4
  13Q GAIN WILD-TYPE 99  5 10 21
D24V10, multiclass
    clus
vv   13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  R0               24                 99
  R1                2                  5
  R2                2                 10
  RX                4                 21
D24V11, continuous

Clustering(25) Variable = 15q gain mutation analysis
D25V1, survival
                    sevent
clus2                  0   1
  15Q GAIN MUTATED     6   1
  15Q GAIN WILD-TYPE 116  17
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                 7                133 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                 1                 17 
$`15Q GAIN MUTATED`
TCGA-BR-7197 TCGA-BR-A4J4 TCGA-BR-A4PF TCGA-CG-5727 TCGA-D7-6520 TCGA-F1-6875 
        1.48         0.53         0.72        31.04         9.63        72.23 
TCGA-IN-7808 
        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-BR-8592 
        0.26         1.18         1.55         1.48         0.76         0.20 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
        0.59         0.92         0.39         0.79         0.72         0.79 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-CD-5798 TCGA-CD-5799 
        0.43         0.13         0.23         0.10         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-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-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-D7-6521 
        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-D7-6815 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-FP-8099 TCGA-FP-8209 TCGA-FP-8631 TCGA-HJ-7597 TCGA-IN-7806 
        3.58         1.02        59.05         0.56        26.43         6.87 
TCGA-IP-7968 
        2.53 

  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
              0.53               0.07 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
             72.23              70.06 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
              3.55               1.22 
[1] "0.5 - 72.2 (3.5)" "0.1 - 70.1 (1.2)"
        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-BR-8592         TCGA-BR-A4IU         TCGA-BR-A4IV 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BR-A4IY         TCGA-BR-A4IZ         TCGA-BR-A4J1 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BR-A4J2         TCGA-BR-A4J4         TCGA-BR-A4J5 
"15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" "15Q GAIN WILD-TYPE" 
        TCGA-BR-A4J6         TCGA-BR-A4J8         TCGA-BR-A4J9 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BR-A4PF         TCGA-CD-5798         TCGA-CD-5799 
  "15Q GAIN MUTATED" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-CD-5800         TCGA-CD-5801         TCGA-CD-5802 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-CD-5803         TCGA-CG-4300         TCGA-CG-4301 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-CG-4304         TCGA-CG-4305         TCGA-CG-4306 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-CG-4436         TCGA-CG-4437         TCGA-CG-4438 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-CG-4440         TCGA-CG-4441         TCGA-CG-4443 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-CG-4444         TCGA-CG-4449         TCGA-CG-4455 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-CG-4460         TCGA-CG-4462         TCGA-CG-4465 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-CG-4466         TCGA-CG-4469         TCGA-CG-4472 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-CG-4474         TCGA-CG-4477         TCGA-CG-5716 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-CG-5717         TCGA-CG-5718         TCGA-CG-5719 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-CG-5720         TCGA-CG-5721         TCGA-CG-5722 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-CG-5723         TCGA-CG-5724         TCGA-CG-5725 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-CG-5726         TCGA-CG-5727         TCGA-CG-5728 
"15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" "15Q GAIN WILD-TYPE" 
        TCGA-CG-5730         TCGA-CG-5732         TCGA-CG-5733 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-CG-5734         TCGA-D7-5577         TCGA-D7-5578 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-D7-5579         TCGA-D7-6518         TCGA-D7-6519 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-D7-6520         TCGA-D7-6521         TCGA-D7-6522 
  "15Q GAIN MUTATED" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-D7-6524         TCGA-D7-6525         TCGA-D7-6526 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-D7-6527         TCGA-D7-6528         TCGA-D7-6815 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-D7-6817         TCGA-D7-6818         TCGA-D7-6820 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-D7-6822         TCGA-EQ-5647         TCGA-EQ-8122 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-F1-6177         TCGA-F1-6874         TCGA-F1-6875 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" 
        TCGA-FP-7735         TCGA-FP-7829         TCGA-FP-7916 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-FP-7998         TCGA-FP-8099         TCGA-FP-8209 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-FP-8631         TCGA-HJ-7597         TCGA-IN-7806 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-IN-7808         TCGA-IP-7968 
  "15Q GAIN MUTATED" "15Q GAIN WILD-TYPE" 
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-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-BR-8592         TCGA-BR-A4IU         TCGA-BR-A4IV 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BR-A4IY         TCGA-BR-A4IZ         TCGA-BR-A4J1 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BR-A4J2         TCGA-BR-A4J4         TCGA-BR-A4J5 
"15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" "15Q GAIN WILD-TYPE" 
        TCGA-BR-A4J6         TCGA-BR-A4J8         TCGA-BR-A4J9 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BR-A4PF         TCGA-CD-5798         TCGA-CD-5799 
  "15Q GAIN MUTATED" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-CD-5800         TCGA-CD-5801         TCGA-CD-5802 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-CD-5803         TCGA-CG-4300         TCGA-CG-4301 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-CG-4304         TCGA-CG-4305         TCGA-CG-4306 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-CG-4436         TCGA-CG-4437         TCGA-CG-4438 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-CG-4440         TCGA-CG-4441         TCGA-CG-4443 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-CG-4444         TCGA-CG-4449         TCGA-CG-4455 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-CG-4460         TCGA-CG-4462         TCGA-CG-4465 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-CG-4466         TCGA-CG-4469         TCGA-CG-4472 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-CG-4474         TCGA-CG-4477         TCGA-CG-5716 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-CG-5717         TCGA-CG-5718         TCGA-CG-5719 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-CG-5720         TCGA-CG-5721         TCGA-CG-5722 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-CG-5723         TCGA-CG-5724         TCGA-CG-5725 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-CG-5726         TCGA-CG-5727         TCGA-CG-5728 
"15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" "15Q GAIN WILD-TYPE" 
        TCGA-CG-5730         TCGA-CG-5732         TCGA-CG-5733 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-CG-5734         TCGA-D7-5577         TCGA-D7-5578 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-D7-5579         TCGA-D7-6518         TCGA-D7-6519 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-D7-6520         TCGA-D7-6521         TCGA-D7-6522 
  "15Q GAIN MUTATED" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-D7-6524         TCGA-D7-6525         TCGA-D7-6526 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-D7-6527         TCGA-D7-6528         TCGA-D7-6815 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-D7-6817         TCGA-D7-6818         TCGA-D7-6820 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-D7-6822         TCGA-EQ-5647         TCGA-EQ-8122 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-F1-6177         TCGA-F1-6874         TCGA-F1-6875 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" 
        TCGA-FP-7735         TCGA-FP-7829         TCGA-FP-7916 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-FP-7998         TCGA-FP-8099         TCGA-FP-8209 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-FP-8631         TCGA-HJ-7597         TCGA-IN-7806 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-IN-7808         TCGA-IP-7968 
  "15Q GAIN MUTATED" "15Q GAIN WILD-TYPE" 
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-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-BR-8592         TCGA-BR-A4IU         TCGA-BR-A4IV 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BR-A4IY         TCGA-BR-A4IZ         TCGA-BR-A4J1 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BR-A4J2         TCGA-BR-A4J4         TCGA-BR-A4J5 
"15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" "15Q GAIN WILD-TYPE" 
        TCGA-BR-A4J6         TCGA-BR-A4J8         TCGA-BR-A4J9 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BR-A4PF         TCGA-CD-5798         TCGA-CD-5799 
  "15Q GAIN MUTATED" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-CD-5800         TCGA-CD-5801         TCGA-CD-5802 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-CD-5803         TCGA-CG-4300         TCGA-CG-4301 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-CG-4304         TCGA-CG-4305         TCGA-CG-4306 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-CG-4436         TCGA-CG-4437         TCGA-CG-4438 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-CG-4440         TCGA-CG-4441         TCGA-CG-4443 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-CG-4444         TCGA-CG-4449         TCGA-CG-4455 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-CG-4460         TCGA-CG-4462         TCGA-CG-4465 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-CG-4466         TCGA-CG-4469         TCGA-CG-4472 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-CG-4474         TCGA-CG-4477         TCGA-CG-5716 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-CG-5717         TCGA-CG-5718         TCGA-CG-5719 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-CG-5720         TCGA-CG-5721         TCGA-CG-5722 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-CG-5723         TCGA-CG-5724         TCGA-CG-5725 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-CG-5726         TCGA-CG-5727         TCGA-CG-5728 
"15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" "15Q GAIN WILD-TYPE" 
        TCGA-CG-5730         TCGA-CG-5732         TCGA-CG-5733 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-CG-5734         TCGA-D7-5577         TCGA-D7-5578 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-D7-5579         TCGA-D7-6518         TCGA-D7-6519 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-D7-6520         TCGA-D7-6521         TCGA-D7-6522 
  "15Q GAIN MUTATED" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-D7-6524         TCGA-D7-6525         TCGA-D7-6526 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-D7-6527         TCGA-D7-6528         TCGA-D7-6815 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-D7-6817         TCGA-D7-6818         TCGA-D7-6820 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-D7-6822         TCGA-EQ-5647         TCGA-EQ-8122 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-F1-6177         TCGA-F1-6874         TCGA-F1-6875 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" 
        TCGA-FP-7735         TCGA-FP-7829         TCGA-FP-7916 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-FP-7998         TCGA-FP-8099         TCGA-FP-8209 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-FP-8631         TCGA-HJ-7597         TCGA-IN-7806 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-IN-7808         TCGA-IP-7968 
  "15Q GAIN MUTATED" "15Q GAIN WILD-TYPE" 
[1] "hr="     "8.2e+07"
D25V2, continuous
D25V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED      0    7
  15Q GAIN WILD-TYPE   70  100
        clus
vv       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  FEMALE                0                 70
  MALE                  7                100
                    vv
clus                 STOMACH ADENOCARCINOMA - DIFFUSE TYPE
  15Q GAIN MUTATED                                       1
  15Q GAIN WILD-TYPE                                    24
                    vv
clus                 STOMACH ADENOCARCINOMA - NOT OTHERWISE SPECIFIED (NOS)
  15Q GAIN MUTATED                                                        4
  15Q GAIN WILD-TYPE                                                     83
                    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                                                10
                    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                                                  1
  15Q GAIN WILD-TYPE                                                9
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - TYPE NOT OTHERWISE SPECIFIED (NOS)
  15Q GAIN MUTATED                                                                        1
  15Q GAIN WILD-TYPE                                                                     35
D25V4, multiclass
                    vv
clus                 T1 T2 T3 T4
  15Q GAIN MUTATED    0  2  3  2
  15Q GAIN WILD-TYPE  6 52 61 41
D25V5, multiclass
    clus
vv   15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  T1                0                  6
  T2                2                 52
  T3                3                 61
  T4                2                 41
                    vv
clus                 N0 N1 N2 N3
  15Q GAIN MUTATED    3  0  3  1
  15Q GAIN WILD-TYPE 53 61 26 19
D25V6, multiclass
    clus
vv   15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  N0                3                 53
  N1                0                 61
  N2                3                 26
  N3                1                 19
                    vv
clus                  M0  M1  MX
  15Q GAIN MUTATED     6   1   0
  15Q GAIN WILD-TYPE 140  17  13
D25V7, multiclass
    clus
vv   15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  M0                6                140
  M1                1                 17
  MX                0                 13
                    vv
clus                  I II III IV
  15Q GAIN MUTATED    1  2   4  0
  15Q GAIN WILD-TYPE 25 46  54 29
D25V8, multiclass
     clus
vv    15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  I                  1                 25
  II                 2                 46
  III                4                 54
  IV                 0                 29
D25V9, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED      0    7
  15Q GAIN WILD-TYPE    5  165
     clus
vv    15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  NO                 0                  5
  YES                7                165
                    vv
clus                  R0  R1  R2  RX
  15Q GAIN MUTATED     6   0   0   0
  15Q GAIN WILD-TYPE 117   7  12  25
D25V10, multiclass
    clus
vv   15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  R0                6                117
  R1                0                  7
  R2                0                 12
  RX                0                 25
D25V11, continuous

Clustering(26) Variable = 16p gain mutation analysis
D26V1, survival
                    sevent
clus2                  0   1
  16P GAIN MUTATED     9   1
  16P GAIN WILD-TYPE 113  17
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                10                130 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                 1                 17 
$`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-BR-8592 TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        0.20         0.59         0.92         0.39         0.79         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J8 TCGA-BR-A4J9 
        0.79         0.53         0.43         0.13         0.23         0.10 
TCGA-BR-A4PF TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        0.72         0.82         0.69         0.36         0.49         0.30 
TCGA-CD-5803 TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
        0.07        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 
       52.96         8.05         4.01        14.01        29.98        47.05 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         1.02         8.98        18.94         7.07 
TCGA-CG-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-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-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
        6.90         0.69         5.95         4.14         1.68         3.65 
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-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
       72.23         0.20         3.02         3.58         1.02        59.05 
TCGA-FP-8631 TCGA-HJ-7597 TCGA-IN-7806 TCGA-IN-7808 
        0.56        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              1.150 
[1] "0.4 - 54.0 (5.7)" "0.1 - 72.2 (1.1)"
        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-BR-8592         TCGA-BR-A4IU         TCGA-BR-A4IV 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BR-A4IY         TCGA-BR-A4IZ         TCGA-BR-A4J1 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BR-A4J2         TCGA-BR-A4J4         TCGA-BR-A4J5 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BR-A4J6         TCGA-BR-A4J8         TCGA-BR-A4J9 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BR-A4PF         TCGA-CD-5798         TCGA-CD-5799 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-CD-5800         TCGA-CD-5801         TCGA-CD-5802 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-CD-5803         TCGA-CG-4300         TCGA-CG-4301 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-CG-4304         TCGA-CG-4305         TCGA-CG-4306 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-CG-4436         TCGA-CG-4437         TCGA-CG-4438 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE"   "16P GAIN MUTATED" 
        TCGA-CG-4440         TCGA-CG-4441         TCGA-CG-4443 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-CG-4444         TCGA-CG-4449         TCGA-CG-4455 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-CG-4460         TCGA-CG-4462         TCGA-CG-4465 
  "16P GAIN MUTATED" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-CG-4466         TCGA-CG-4469         TCGA-CG-4472 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE"   "16P GAIN MUTATED" 
        TCGA-CG-4474         TCGA-CG-4477         TCGA-CG-5716 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-CG-5717         TCGA-CG-5718         TCGA-CG-5719 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE"   "16P GAIN MUTATED" 
        TCGA-CG-5720         TCGA-CG-5721         TCGA-CG-5722 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-CG-5723         TCGA-CG-5724         TCGA-CG-5725 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-CG-5726         TCGA-CG-5727         TCGA-CG-5728 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-CG-5730         TCGA-CG-5732         TCGA-CG-5733 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-CG-5734         TCGA-D7-5577         TCGA-D7-5578 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-D7-5579         TCGA-D7-6518         TCGA-D7-6519 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-D7-6520         TCGA-D7-6521         TCGA-D7-6522 
"16P GAIN WILD-TYPE"   "16P GAIN MUTATED" "16P GAIN WILD-TYPE" 
        TCGA-D7-6524         TCGA-D7-6525         TCGA-D7-6526 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE"   "16P GAIN MUTATED" 
        TCGA-D7-6527         TCGA-D7-6528         TCGA-D7-6815 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-D7-6817         TCGA-D7-6818         TCGA-D7-6820 
  "16P GAIN MUTATED"   "16P GAIN MUTATED" "16P GAIN WILD-TYPE" 
        TCGA-D7-6822         TCGA-EQ-5647         TCGA-EQ-8122 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-F1-6177         TCGA-F1-6874         TCGA-F1-6875 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-FP-7735         TCGA-FP-7829         TCGA-FP-7916 
  "16P GAIN MUTATED" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-FP-7998         TCGA-FP-8099         TCGA-FP-8209 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-FP-8631         TCGA-HJ-7597         TCGA-IN-7806 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-IN-7808         TCGA-IP-7968 
"16P GAIN WILD-TYPE"   "16P GAIN MUTATED" 
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-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-BR-8592         TCGA-BR-A4IU         TCGA-BR-A4IV 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BR-A4IY         TCGA-BR-A4IZ         TCGA-BR-A4J1 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BR-A4J2         TCGA-BR-A4J4         TCGA-BR-A4J5 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BR-A4J6         TCGA-BR-A4J8         TCGA-BR-A4J9 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BR-A4PF         TCGA-CD-5798         TCGA-CD-5799 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-CD-5800         TCGA-CD-5801         TCGA-CD-5802 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-CD-5803         TCGA-CG-4300         TCGA-CG-4301 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-CG-4304         TCGA-CG-4305         TCGA-CG-4306 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-CG-4436         TCGA-CG-4437         TCGA-CG-4438 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE"   "16P GAIN MUTATED" 
        TCGA-CG-4440         TCGA-CG-4441         TCGA-CG-4443 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-CG-4444         TCGA-CG-4449         TCGA-CG-4455 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-CG-4460         TCGA-CG-4462         TCGA-CG-4465 
  "16P GAIN MUTATED" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-CG-4466         TCGA-CG-4469         TCGA-CG-4472 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE"   "16P GAIN MUTATED" 
        TCGA-CG-4474         TCGA-CG-4477         TCGA-CG-5716 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-CG-5717         TCGA-CG-5718         TCGA-CG-5719 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE"   "16P GAIN MUTATED" 
        TCGA-CG-5720         TCGA-CG-5721         TCGA-CG-5722 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-CG-5723         TCGA-CG-5724         TCGA-CG-5725 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-CG-5726         TCGA-CG-5727         TCGA-CG-5728 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-CG-5730         TCGA-CG-5732         TCGA-CG-5733 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-CG-5734         TCGA-D7-5577         TCGA-D7-5578 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-D7-5579         TCGA-D7-6518         TCGA-D7-6519 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-D7-6520         TCGA-D7-6521         TCGA-D7-6522 
"16P GAIN WILD-TYPE"   "16P GAIN MUTATED" "16P GAIN WILD-TYPE" 
        TCGA-D7-6524         TCGA-D7-6525         TCGA-D7-6526 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE"   "16P GAIN MUTATED" 
        TCGA-D7-6527         TCGA-D7-6528         TCGA-D7-6815 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-D7-6817         TCGA-D7-6818         TCGA-D7-6820 
  "16P GAIN MUTATED"   "16P GAIN MUTATED" "16P GAIN WILD-TYPE" 
        TCGA-D7-6822         TCGA-EQ-5647         TCGA-EQ-8122 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-F1-6177         TCGA-F1-6874         TCGA-F1-6875 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-FP-7735         TCGA-FP-7829         TCGA-FP-7916 
  "16P GAIN MUTATED" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-FP-7998         TCGA-FP-8099         TCGA-FP-8209 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-FP-8631         TCGA-HJ-7597         TCGA-IN-7806 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-IN-7808         TCGA-IP-7968 
"16P GAIN WILD-TYPE"   "16P GAIN MUTATED" 
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-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-BR-8592         TCGA-BR-A4IU         TCGA-BR-A4IV 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BR-A4IY         TCGA-BR-A4IZ         TCGA-BR-A4J1 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BR-A4J2         TCGA-BR-A4J4         TCGA-BR-A4J5 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BR-A4J6         TCGA-BR-A4J8         TCGA-BR-A4J9 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BR-A4PF         TCGA-CD-5798         TCGA-CD-5799 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-CD-5800         TCGA-CD-5801         TCGA-CD-5802 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-CD-5803         TCGA-CG-4300         TCGA-CG-4301 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-CG-4304         TCGA-CG-4305         TCGA-CG-4306 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-CG-4436         TCGA-CG-4437         TCGA-CG-4438 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE"   "16P GAIN MUTATED" 
        TCGA-CG-4440         TCGA-CG-4441         TCGA-CG-4443 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-CG-4444         TCGA-CG-4449         TCGA-CG-4455 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-CG-4460         TCGA-CG-4462         TCGA-CG-4465 
  "16P GAIN MUTATED" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-CG-4466         TCGA-CG-4469         TCGA-CG-4472 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE"   "16P GAIN MUTATED" 
        TCGA-CG-4474         TCGA-CG-4477         TCGA-CG-5716 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-CG-5717         TCGA-CG-5718         TCGA-CG-5719 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE"   "16P GAIN MUTATED" 
        TCGA-CG-5720         TCGA-CG-5721         TCGA-CG-5722 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-CG-5723         TCGA-CG-5724         TCGA-CG-5725 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-CG-5726         TCGA-CG-5727         TCGA-CG-5728 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-CG-5730         TCGA-CG-5732         TCGA-CG-5733 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-CG-5734         TCGA-D7-5577         TCGA-D7-5578 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-D7-5579         TCGA-D7-6518         TCGA-D7-6519 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-D7-6520         TCGA-D7-6521         TCGA-D7-6522 
"16P GAIN WILD-TYPE"   "16P GAIN MUTATED" "16P GAIN WILD-TYPE" 
        TCGA-D7-6524         TCGA-D7-6525         TCGA-D7-6526 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE"   "16P GAIN MUTATED" 
        TCGA-D7-6527         TCGA-D7-6528         TCGA-D7-6815 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-D7-6817         TCGA-D7-6818         TCGA-D7-6820 
  "16P GAIN MUTATED"   "16P GAIN MUTATED" "16P GAIN WILD-TYPE" 
        TCGA-D7-6822         TCGA-EQ-5647         TCGA-EQ-8122 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-F1-6177         TCGA-F1-6874         TCGA-F1-6875 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-FP-7735         TCGA-FP-7829         TCGA-FP-7916 
  "16P GAIN MUTATED" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-FP-7998         TCGA-FP-8099         TCGA-FP-8209 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-FP-8631         TCGA-HJ-7597         TCGA-IN-7806 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-IN-7808         TCGA-IP-7968 
"16P GAIN WILD-TYPE"   "16P GAIN MUTATED" 
[1] "hr=" "1.8"
D26V2, continuous
D26V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED      4    8
  16P GAIN WILD-TYPE   66   99
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  FEMALE                4                 66
  MALE                  8                 99
                    vv
clus                 STOMACH ADENOCARCINOMA - DIFFUSE TYPE
  16P GAIN MUTATED                                       2
  16P GAIN WILD-TYPE                                    23
                    vv
clus                 STOMACH ADENOCARCINOMA - NOT OTHERWISE SPECIFIED (NOS)
  16P GAIN MUTATED                                                        4
  16P GAIN WILD-TYPE                                                     83
                    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                                                10
                    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                                                                     33
D26V4, multiclass
                    vv
clus                 T1 T2 T3 T4
  16P GAIN MUTATED    0  4  3  5
  16P GAIN WILD-TYPE  6 50 61 38
D26V5, multiclass
    clus
vv   16P GAIN MUTATED 16P GAIN WILD-TYPE
  T1                0                  6
  T2                4                 50
  T3                3                 61
  T4                5                 38
                    vv
clus                 N0 N1 N2 N3
  16P GAIN MUTATED    2  3  5  2
  16P GAIN WILD-TYPE 54 58 24 18
D26V6, multiclass
    clus
vv   16P GAIN MUTATED 16P GAIN WILD-TYPE
  N0                2                 54
  N1                3                 58
  N2                5                 24
  N3                2                 18
                    vv
clus                  M0  M1  MX
  16P GAIN MUTATED     8   2   2
  16P GAIN WILD-TYPE 138  16  11
D26V7, multiclass
    clus
vv   16P GAIN MUTATED 16P GAIN WILD-TYPE
  M0                8                138
  M1                2                 16
  MX                2                 11
                    vv
clus                  I II III IV
  16P GAIN MUTATED    1  0   5  6
  16P GAIN WILD-TYPE 25 48  53 23
D26V8, multiclass
     clus
vv    16P GAIN MUTATED 16P GAIN WILD-TYPE
  I                  1                 25
  II                 0                 48
  III                5                 53
  IV                 6                 23
D26V9, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED      1   11
  16P GAIN WILD-TYPE    4  161
     clus
vv    16P GAIN MUTATED 16P GAIN WILD-TYPE
  NO                 1                  4
  YES               11                161
                    vv
clus                  R0  R1  R2  RX
  16P GAIN MUTATED     9   0   1   1
  16P GAIN WILD-TYPE 114   7  11  24
D26V10, multiclass
    clus
vv   16P GAIN MUTATED 16P GAIN WILD-TYPE
  R0                9                114
  R1                0                  7
  R2                1                 11
  RX                1                 24
D26V11, continuous

Clustering(27) Variable = 16q gain mutation analysis
D27V1, survival
                    sevent
clus2                  0   1
  16Q GAIN MUTATED     5   1
  16Q GAIN WILD-TYPE 117  17
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                 6                134 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                 1                 17 
$`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-BR-8592 TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        0.20         0.59         0.92         0.39         0.79         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J8 TCGA-BR-A4J9 
        0.79         0.53         0.43         0.13         0.23         0.10 
TCGA-BR-A4PF TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        0.72         0.82         0.69         0.36         0.49         0.30 
TCGA-CD-5803 TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
        0.07        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 
       52.96         8.05         4.01        14.01        29.98        47.05 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         1.02         8.98        18.94         7.07 
TCGA-CG-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-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-D7-6526 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-7829 TCGA-FP-7916 
        7.79         6.54         2.01        72.23         0.20         3.02 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8631 TCGA-HJ-7597 TCGA-IN-7806 
        3.58         1.02        59.05         0.56        26.43         6.87 
TCGA-IN-7808 TCGA-IP-7968 
        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              1.220 
[1] "0.4 - 54.0 (10.1)" "0.1 - 72.2 (1.2)" 
        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-BR-8592         TCGA-BR-A4IU         TCGA-BR-A4IV 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BR-A4IY         TCGA-BR-A4IZ         TCGA-BR-A4J1 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BR-A4J2         TCGA-BR-A4J4         TCGA-BR-A4J5 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BR-A4J6         TCGA-BR-A4J8         TCGA-BR-A4J9 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BR-A4PF         TCGA-CD-5798         TCGA-CD-5799 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-CD-5800         TCGA-CD-5801         TCGA-CD-5802 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-CD-5803         TCGA-CG-4300         TCGA-CG-4301 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-CG-4304         TCGA-CG-4305         TCGA-CG-4306 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-CG-4436         TCGA-CG-4437         TCGA-CG-4438 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" 
        TCGA-CG-4440         TCGA-CG-4441         TCGA-CG-4443 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-CG-4444         TCGA-CG-4449         TCGA-CG-4455 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-CG-4460         TCGA-CG-4462         TCGA-CG-4465 
  "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-CG-4466         TCGA-CG-4469         TCGA-CG-4472 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" 
        TCGA-CG-4474         TCGA-CG-4477         TCGA-CG-5716 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-CG-5717         TCGA-CG-5718         TCGA-CG-5719 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" 
        TCGA-CG-5720         TCGA-CG-5721         TCGA-CG-5722 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-CG-5723         TCGA-CG-5724         TCGA-CG-5725 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-CG-5726         TCGA-CG-5727         TCGA-CG-5728 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-CG-5730         TCGA-CG-5732         TCGA-CG-5733 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-CG-5734         TCGA-D7-5577         TCGA-D7-5578 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-D7-5579         TCGA-D7-6518         TCGA-D7-6519 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-D7-6520         TCGA-D7-6521         TCGA-D7-6522 
"16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" 
        TCGA-D7-6524         TCGA-D7-6525         TCGA-D7-6526 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-D7-6527         TCGA-D7-6528         TCGA-D7-6815 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-D7-6817         TCGA-D7-6818         TCGA-D7-6820 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-D7-6822         TCGA-EQ-5647         TCGA-EQ-8122 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-F1-6177         TCGA-F1-6874         TCGA-F1-6875 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-FP-7735         TCGA-FP-7829         TCGA-FP-7916 
  "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-FP-7998         TCGA-FP-8099         TCGA-FP-8209 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-FP-8631         TCGA-HJ-7597         TCGA-IN-7806 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-IN-7808         TCGA-IP-7968 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-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-BR-8592         TCGA-BR-A4IU         TCGA-BR-A4IV 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BR-A4IY         TCGA-BR-A4IZ         TCGA-BR-A4J1 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BR-A4J2         TCGA-BR-A4J4         TCGA-BR-A4J5 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BR-A4J6         TCGA-BR-A4J8         TCGA-BR-A4J9 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BR-A4PF         TCGA-CD-5798         TCGA-CD-5799 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-CD-5800         TCGA-CD-5801         TCGA-CD-5802 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-CD-5803         TCGA-CG-4300         TCGA-CG-4301 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-CG-4304         TCGA-CG-4305         TCGA-CG-4306 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-CG-4436         TCGA-CG-4437         TCGA-CG-4438 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" 
        TCGA-CG-4440         TCGA-CG-4441         TCGA-CG-4443 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-CG-4444         TCGA-CG-4449         TCGA-CG-4455 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-CG-4460         TCGA-CG-4462         TCGA-CG-4465 
  "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-CG-4466         TCGA-CG-4469         TCGA-CG-4472 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" 
        TCGA-CG-4474         TCGA-CG-4477         TCGA-CG-5716 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-CG-5717         TCGA-CG-5718         TCGA-CG-5719 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" 
        TCGA-CG-5720         TCGA-CG-5721         TCGA-CG-5722 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-CG-5723         TCGA-CG-5724         TCGA-CG-5725 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-CG-5726         TCGA-CG-5727         TCGA-CG-5728 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-CG-5730         TCGA-CG-5732         TCGA-CG-5733 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-CG-5734         TCGA-D7-5577         TCGA-D7-5578 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-D7-5579         TCGA-D7-6518         TCGA-D7-6519 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-D7-6520         TCGA-D7-6521         TCGA-D7-6522 
"16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" 
        TCGA-D7-6524         TCGA-D7-6525         TCGA-D7-6526 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-D7-6527         TCGA-D7-6528         TCGA-D7-6815 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-D7-6817         TCGA-D7-6818         TCGA-D7-6820 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-D7-6822         TCGA-EQ-5647         TCGA-EQ-8122 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-F1-6177         TCGA-F1-6874         TCGA-F1-6875 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-FP-7735         TCGA-FP-7829         TCGA-FP-7916 
  "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-FP-7998         TCGA-FP-8099         TCGA-FP-8209 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-FP-8631         TCGA-HJ-7597         TCGA-IN-7806 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-IN-7808         TCGA-IP-7968 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-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-BR-8592         TCGA-BR-A4IU         TCGA-BR-A4IV 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BR-A4IY         TCGA-BR-A4IZ         TCGA-BR-A4J1 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BR-A4J2         TCGA-BR-A4J4         TCGA-BR-A4J5 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BR-A4J6         TCGA-BR-A4J8         TCGA-BR-A4J9 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BR-A4PF         TCGA-CD-5798         TCGA-CD-5799 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-CD-5800         TCGA-CD-5801         TCGA-CD-5802 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-CD-5803         TCGA-CG-4300         TCGA-CG-4301 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-CG-4304         TCGA-CG-4305         TCGA-CG-4306 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-CG-4436         TCGA-CG-4437         TCGA-CG-4438 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" 
        TCGA-CG-4440         TCGA-CG-4441         TCGA-CG-4443 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-CG-4444         TCGA-CG-4449         TCGA-CG-4455 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-CG-4460         TCGA-CG-4462         TCGA-CG-4465 
  "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-CG-4466         TCGA-CG-4469         TCGA-CG-4472 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" 
        TCGA-CG-4474         TCGA-CG-4477         TCGA-CG-5716 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-CG-5717         TCGA-CG-5718         TCGA-CG-5719 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" 
        TCGA-CG-5720         TCGA-CG-5721         TCGA-CG-5722 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-CG-5723         TCGA-CG-5724         TCGA-CG-5725 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-CG-5726         TCGA-CG-5727         TCGA-CG-5728 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-CG-5730         TCGA-CG-5732         TCGA-CG-5733 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-CG-5734         TCGA-D7-5577         TCGA-D7-5578 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-D7-5579         TCGA-D7-6518         TCGA-D7-6519 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-D7-6520         TCGA-D7-6521         TCGA-D7-6522 
"16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" 
        TCGA-D7-6524         TCGA-D7-6525         TCGA-D7-6526 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-D7-6527         TCGA-D7-6528         TCGA-D7-6815 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-D7-6817         TCGA-D7-6818         TCGA-D7-6820 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-D7-6822         TCGA-EQ-5647         TCGA-EQ-8122 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-F1-6177         TCGA-F1-6874         TCGA-F1-6875 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-FP-7735         TCGA-FP-7829         TCGA-FP-7916 
  "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-FP-7998         TCGA-FP-8099         TCGA-FP-8209 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-FP-8631         TCGA-HJ-7597         TCGA-IN-7806 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-IN-7808         TCGA-IP-7968 
"16Q GAIN WILD-TYPE" "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   67  102
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  FEMALE                3                 67
  MALE                  5                102
                    vv
clus                 STOMACH ADENOCARCINOMA - DIFFUSE TYPE
  16Q GAIN MUTATED                                       1
  16Q GAIN WILD-TYPE                                    24
                    vv
clus                 STOMACH ADENOCARCINOMA - NOT OTHERWISE SPECIFIED (NOS)
  16Q GAIN MUTATED                                                        3
  16Q GAIN WILD-TYPE                                                     84
                    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                                                10
                    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                                                                     33
D27V4, multiclass
                    vv
clus                 T1 T2 T3 T4
  16Q GAIN MUTATED    0  2  1  5
  16Q GAIN WILD-TYPE  6 52 63 38
D27V5, multiclass
    clus
vv   16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  T1                0                  6
  T2                2                 52
  T3                1                 63
  T4                5                 38
                    vv
clus                 N0 N1 N2 N3
  16Q GAIN MUTATED    2  3  3  0
  16Q GAIN WILD-TYPE 54 58 26 20
D27V6, multiclass
    clus
vv   16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  N0                2                 54
  N1                3                 58
  N2                3                 26
  N3                0                 20
                    vv
clus                  M0  M1  MX
  16Q GAIN MUTATED     5   2   1
  16Q GAIN WILD-TYPE 141  16  12
D27V7, multiclass
    clus
vv   16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  M0                5                141
  M1                2                 16
  MX                1                 12
                    vv
clus                  I II III IV
  16Q GAIN MUTATED    1  0   2  5
  16Q GAIN WILD-TYPE 25 48  56 24
D27V8, multiclass
     clus
vv    16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  I                  1                 25
  II                 0                 48
  III                2                 56
  IV                 5                 24
D27V9, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED      0    8
  16Q GAIN WILD-TYPE    5  164
     clus
vv    16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  NO                 0                  5
  YES                8                164
                    vv
clus                  R0  R1  R2  RX
  16Q GAIN MUTATED     6   0   1   1
  16Q GAIN WILD-TYPE 117   7  11  24
D27V10, multiclass
    clus
vv   16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  R0                6                117
  R1                0                  7
  R2                1                 11
  RX                1                 24
D27V11, continuous

Clustering(28) Variable = 17p gain mutation analysis
D28V1, survival
                    sevent
clus2                  0   1
  17P GAIN MUTATED     2   3
  17P GAIN WILD-TYPE 120  15
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                 5                135 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                 3                 15 
$`17P GAIN MUTATED`
TCGA-CG-4460 TCGA-CG-5724 TCGA-D7-6817 TCGA-EQ-5647 TCGA-FP-7829 
       21.99        12.03         4.70         0.62         0.20 

$`17P GAIN WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-6452 TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6458 
        5.62         0.10         0.95         1.41         1.35         1.35 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
        0.85         0.82         0.62         0.62         1.71         2.17 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
        0.99         1.22         0.66         1.12         0.76         0.66 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
        0.26         1.22         1.48         0.46         1.25         0.13 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 
        1.05         0.82         0.69         0.16         4.54         0.99 
TCGA-BR-7901 TCGA-BR-7957 TCGA-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-BR-8592 TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        0.20         0.59         0.92         0.39         0.79         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J8 TCGA-BR-A4J9 
        0.79         0.53         0.43         0.13         0.23         0.10 
TCGA-BR-A4PF TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        0.72         0.82         0.69         0.36         0.49         0.30 
TCGA-CD-5803 TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
        0.07        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
       52.96         8.05        54.05         4.01        14.01        29.98 
TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       47.05        19.07        12.03         1.02         8.98        18.94 
TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4474 TCGA-CG-4477 TCGA-CG-5716 TCGA-CG-5717 
        7.07        12.00         1.02         1.02         1.02         6.94 
TCGA-CG-5718 TCGA-CG-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-D7-6818 TCGA-D7-6820 
        6.61         4.14         1.68         3.65         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-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8631 TCGA-HJ-7597 
        3.02         3.58         1.02        59.05         0.56        26.43 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IP-7968 
        6.87         3.55         2.53 

  17P GAIN MUTATED 17P GAIN WILD-TYPE 
              0.20               0.07 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
             21.99              72.23 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
              4.70               1.22 
[1] "0.2 - 22.0 (4.7)" "0.1 - 72.2 (1.2)"
        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-BR-8592         TCGA-BR-A4IU         TCGA-BR-A4IV 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BR-A4IY         TCGA-BR-A4IZ         TCGA-BR-A4J1 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BR-A4J2         TCGA-BR-A4J4         TCGA-BR-A4J5 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BR-A4J6         TCGA-BR-A4J8         TCGA-BR-A4J9 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BR-A4PF         TCGA-CD-5798         TCGA-CD-5799 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-CD-5800         TCGA-CD-5801         TCGA-CD-5802 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-CD-5803         TCGA-CG-4300         TCGA-CG-4301 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-CG-4304         TCGA-CG-4305         TCGA-CG-4306 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-CG-4436         TCGA-CG-4437         TCGA-CG-4438 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-CG-4440         TCGA-CG-4441         TCGA-CG-4443 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-CG-4444         TCGA-CG-4449         TCGA-CG-4455 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-CG-4460         TCGA-CG-4462         TCGA-CG-4465 
  "17P GAIN MUTATED" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-CG-4466         TCGA-CG-4469         TCGA-CG-4472 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-CG-4474         TCGA-CG-4477         TCGA-CG-5716 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-CG-5717         TCGA-CG-5718         TCGA-CG-5719 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-CG-5720         TCGA-CG-5721         TCGA-CG-5722 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-CG-5723         TCGA-CG-5724         TCGA-CG-5725 
"17P GAIN WILD-TYPE"   "17P GAIN MUTATED" "17P GAIN WILD-TYPE" 
        TCGA-CG-5726         TCGA-CG-5727         TCGA-CG-5728 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-CG-5730         TCGA-CG-5732         TCGA-CG-5733 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-CG-5734         TCGA-D7-5577         TCGA-D7-5578 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-D7-5579         TCGA-D7-6518         TCGA-D7-6519 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-D7-6520         TCGA-D7-6521         TCGA-D7-6522 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-D7-6524         TCGA-D7-6525         TCGA-D7-6526 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-D7-6527         TCGA-D7-6528         TCGA-D7-6815 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-D7-6817         TCGA-D7-6818         TCGA-D7-6820 
  "17P GAIN MUTATED" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-D7-6822         TCGA-EQ-5647         TCGA-EQ-8122 
"17P GAIN WILD-TYPE"   "17P GAIN MUTATED" "17P GAIN WILD-TYPE" 
        TCGA-F1-6177         TCGA-F1-6874         TCGA-F1-6875 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-FP-7735         TCGA-FP-7829         TCGA-FP-7916 
"17P GAIN WILD-TYPE"   "17P GAIN MUTATED" "17P GAIN WILD-TYPE" 
        TCGA-FP-7998         TCGA-FP-8099         TCGA-FP-8209 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-FP-8631         TCGA-HJ-7597         TCGA-IN-7806 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-IN-7808         TCGA-IP-7968 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-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-BR-8592         TCGA-BR-A4IU         TCGA-BR-A4IV 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BR-A4IY         TCGA-BR-A4IZ         TCGA-BR-A4J1 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BR-A4J2         TCGA-BR-A4J4         TCGA-BR-A4J5 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BR-A4J6         TCGA-BR-A4J8         TCGA-BR-A4J9 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BR-A4PF         TCGA-CD-5798         TCGA-CD-5799 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-CD-5800         TCGA-CD-5801         TCGA-CD-5802 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-CD-5803         TCGA-CG-4300         TCGA-CG-4301 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-CG-4304         TCGA-CG-4305         TCGA-CG-4306 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-CG-4436         TCGA-CG-4437         TCGA-CG-4438 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-CG-4440         TCGA-CG-4441         TCGA-CG-4443 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-CG-4444         TCGA-CG-4449         TCGA-CG-4455 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-CG-4460         TCGA-CG-4462         TCGA-CG-4465 
  "17P GAIN MUTATED" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-CG-4466         TCGA-CG-4469         TCGA-CG-4472 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-CG-4474         TCGA-CG-4477         TCGA-CG-5716 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-CG-5717         TCGA-CG-5718         TCGA-CG-5719 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-CG-5720         TCGA-CG-5721         TCGA-CG-5722 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-CG-5723         TCGA-CG-5724         TCGA-CG-5725 
"17P GAIN WILD-TYPE"   "17P GAIN MUTATED" "17P GAIN WILD-TYPE" 
        TCGA-CG-5726         TCGA-CG-5727         TCGA-CG-5728 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-CG-5730         TCGA-CG-5732         TCGA-CG-5733 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-CG-5734         TCGA-D7-5577         TCGA-D7-5578 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-D7-5579         TCGA-D7-6518         TCGA-D7-6519 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-D7-6520         TCGA-D7-6521         TCGA-D7-6522 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-D7-6524         TCGA-D7-6525         TCGA-D7-6526 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-D7-6527         TCGA-D7-6528         TCGA-D7-6815 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-D7-6817         TCGA-D7-6818         TCGA-D7-6820 
  "17P GAIN MUTATED" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-D7-6822         TCGA-EQ-5647         TCGA-EQ-8122 
"17P GAIN WILD-TYPE"   "17P GAIN MUTATED" "17P GAIN WILD-TYPE" 
        TCGA-F1-6177         TCGA-F1-6874         TCGA-F1-6875 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-FP-7735         TCGA-FP-7829         TCGA-FP-7916 
"17P GAIN WILD-TYPE"   "17P GAIN MUTATED" "17P GAIN WILD-TYPE" 
        TCGA-FP-7998         TCGA-FP-8099         TCGA-FP-8209 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-FP-8631         TCGA-HJ-7597         TCGA-IN-7806 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-IN-7808         TCGA-IP-7968 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-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-BR-8592         TCGA-BR-A4IU         TCGA-BR-A4IV 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BR-A4IY         TCGA-BR-A4IZ         TCGA-BR-A4J1 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BR-A4J2         TCGA-BR-A4J4         TCGA-BR-A4J5 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BR-A4J6         TCGA-BR-A4J8         TCGA-BR-A4J9 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BR-A4PF         TCGA-CD-5798         TCGA-CD-5799 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-CD-5800         TCGA-CD-5801         TCGA-CD-5802 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-CD-5803         TCGA-CG-4300         TCGA-CG-4301 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-CG-4304         TCGA-CG-4305         TCGA-CG-4306 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-CG-4436         TCGA-CG-4437         TCGA-CG-4438 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-CG-4440         TCGA-CG-4441         TCGA-CG-4443 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-CG-4444         TCGA-CG-4449         TCGA-CG-4455 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-CG-4460         TCGA-CG-4462         TCGA-CG-4465 
  "17P GAIN MUTATED" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-CG-4466         TCGA-CG-4469         TCGA-CG-4472 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-CG-4474         TCGA-CG-4477         TCGA-CG-5716 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-CG-5717         TCGA-CG-5718         TCGA-CG-5719 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-CG-5720         TCGA-CG-5721         TCGA-CG-5722 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-CG-5723         TCGA-CG-5724         TCGA-CG-5725 
"17P GAIN WILD-TYPE"   "17P GAIN MUTATED" "17P GAIN WILD-TYPE" 
        TCGA-CG-5726         TCGA-CG-5727         TCGA-CG-5728 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-CG-5730         TCGA-CG-5732         TCGA-CG-5733 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-CG-5734         TCGA-D7-5577         TCGA-D7-5578 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-D7-5579         TCGA-D7-6518         TCGA-D7-6519 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-D7-6520         TCGA-D7-6521         TCGA-D7-6522 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-D7-6524         TCGA-D7-6525         TCGA-D7-6526 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-D7-6527         TCGA-D7-6528         TCGA-D7-6815 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-D7-6817         TCGA-D7-6818         TCGA-D7-6820 
  "17P GAIN MUTATED" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-D7-6822         TCGA-EQ-5647         TCGA-EQ-8122 
"17P GAIN WILD-TYPE"   "17P GAIN MUTATED" "17P GAIN WILD-TYPE" 
        TCGA-F1-6177         TCGA-F1-6874         TCGA-F1-6875 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-FP-7735         TCGA-FP-7829         TCGA-FP-7916 
"17P GAIN WILD-TYPE"   "17P GAIN MUTATED" "17P GAIN WILD-TYPE" 
        TCGA-FP-7998         TCGA-FP-8099         TCGA-FP-8209 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-FP-8631         TCGA-HJ-7597         TCGA-IN-7806 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-IN-7808         TCGA-IP-7968 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
[1] "hr=" "4.8"
D28V2, continuous
D28V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED      2    3
  17P GAIN WILD-TYPE   68  104
        clus
vv       17P GAIN MUTATED 17P GAIN WILD-TYPE
  FEMALE                2                 68
  MALE                  3                104
                    vv
clus                 STOMACH ADENOCARCINOMA - DIFFUSE TYPE
  17P GAIN MUTATED                                       1
  17P GAIN WILD-TYPE                                    24
                    vv
clus                 STOMACH ADENOCARCINOMA - NOT OTHERWISE SPECIFIED (NOS)
  17P GAIN MUTATED                                                        1
  17P GAIN WILD-TYPE                                                     86
                    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                                                 9
                    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                                                                     35
D28V4, multiclass
                    vv
clus                 T1 T2 T3 T4
  17P GAIN MUTATED    0  1  2  2
  17P GAIN WILD-TYPE  6 53 62 41
D28V5, multiclass
    clus
vv   17P GAIN MUTATED 17P GAIN WILD-TYPE
  T1                0                  6
  T2                1                 53
  T3                2                 62
  T4                2                 41
                    vv
clus                 N0 N1 N2 N3
  17P GAIN MUTATED    0  2  0  3
  17P GAIN WILD-TYPE 56 59 29 17
D28V6, multiclass
    clus
vv   17P GAIN MUTATED 17P GAIN WILD-TYPE
  N0                0                 56
  N1                2                 59
  N2                0                 29
  N3                3                 17
                    vv
clus                  M0  M1  MX
  17P GAIN MUTATED     2   3   0
  17P GAIN WILD-TYPE 144  15  13
D28V7, multiclass
    clus
vv   17P GAIN MUTATED 17P GAIN WILD-TYPE
  M0                2                144
  M1                3                 15
  MX                0                 13
                    vv
clus                  I II III IV
  17P GAIN MUTATED    0  0   2  3
  17P GAIN WILD-TYPE 26 48  56 26
D28V8, multiclass
     clus
vv    17P GAIN MUTATED 17P GAIN WILD-TYPE
  I                  0                 26
  II                 0                 48
  III                2                 56
  IV                 3                 26
D28V9, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED      0    5
  17P GAIN WILD-TYPE    5  167
     clus
vv    17P GAIN MUTATED 17P GAIN WILD-TYPE
  NO                 0                  5
  YES                5                167
                    vv
clus                  R0  R1  R2  RX
  17P GAIN MUTATED     2   0   3   0
  17P GAIN WILD-TYPE 121   7   9  25
D28V10, multiclass
    clus
vv   17P GAIN MUTATED 17P GAIN WILD-TYPE
  R0                2                121
  R1                0                  7
  R2                3                  9
  RX                0                 25
D28V11, continuous

Clustering(29) Variable = 17q gain mutation analysis
D29V1, survival
                    sevent
clus2                  0   1
  17Q GAIN MUTATED     5   4
  17Q GAIN WILD-TYPE 117  14
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                 9                131 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                 4                 14 
$`17Q GAIN MUTATED`
TCGA-B7-5818 TCGA-BR-A4J4 TCGA-CG-4460 TCGA-CG-5719 TCGA-CG-5724 TCGA-D7-6817 
        0.10         0.53        21.99         1.02        12.03         4.70 
TCGA-EQ-5647 TCGA-F1-6875 TCGA-FP-7829 
        0.62        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-BR-8592 
        0.26         1.18         1.55         1.48         0.76         0.20 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
        0.59         0.92         0.39         0.79         0.72         0.79 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PF TCGA-CD-5798 
        0.43         0.13         0.23         0.10         0.72         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-FP-8099 TCGA-FP-8209 
        2.01         0.39         3.02         3.58         1.02        59.05 
TCGA-FP-8631 TCGA-HJ-7597 TCGA-IN-7806 TCGA-IN-7808 TCGA-IP-7968 
        0.56        26.43         6.87         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 
              1.02               1.25 
[1] "0.1 - 72.2 (1.0)" "0.1 - 70.1 (1.2)"
        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-BR-8592         TCGA-BR-A4IU         TCGA-BR-A4IV 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-BR-A4IY         TCGA-BR-A4IZ         TCGA-BR-A4J1 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-BR-A4J2         TCGA-BR-A4J4         TCGA-BR-A4J5 
"17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" 
        TCGA-BR-A4J6         TCGA-BR-A4J8         TCGA-BR-A4J9 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-BR-A4PF         TCGA-CD-5798         TCGA-CD-5799 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-CD-5800         TCGA-CD-5801         TCGA-CD-5802 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-CD-5803         TCGA-CG-4300         TCGA-CG-4301 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-CG-4304         TCGA-CG-4305         TCGA-CG-4306 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-CG-4436         TCGA-CG-4437         TCGA-CG-4438 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-CG-4440         TCGA-CG-4441         TCGA-CG-4443 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-CG-4444         TCGA-CG-4449         TCGA-CG-4455 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-CG-4460         TCGA-CG-4462         TCGA-CG-4465 
  "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-CG-4466         TCGA-CG-4469         TCGA-CG-4472 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-CG-4474         TCGA-CG-4477         TCGA-CG-5716 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-CG-5717         TCGA-CG-5718         TCGA-CG-5719 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
        TCGA-CG-5720         TCGA-CG-5721         TCGA-CG-5722 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-CG-5723         TCGA-CG-5724         TCGA-CG-5725 
"17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" 
        TCGA-CG-5726         TCGA-CG-5727         TCGA-CG-5728 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-CG-5730         TCGA-CG-5732         TCGA-CG-5733 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-CG-5734         TCGA-D7-5577         TCGA-D7-5578 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-D7-5579         TCGA-D7-6518         TCGA-D7-6519 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-D7-6520         TCGA-D7-6521         TCGA-D7-6522 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-D7-6524         TCGA-D7-6525         TCGA-D7-6526 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-D7-6527         TCGA-D7-6528         TCGA-D7-6815 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-D7-6817         TCGA-D7-6818         TCGA-D7-6820 
  "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-D7-6822         TCGA-EQ-5647         TCGA-EQ-8122 
"17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" 
        TCGA-F1-6177         TCGA-F1-6874         TCGA-F1-6875 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
        TCGA-FP-7735         TCGA-FP-7829         TCGA-FP-7916 
"17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" 
        TCGA-FP-7998         TCGA-FP-8099         TCGA-FP-8209 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-FP-8631         TCGA-HJ-7597         TCGA-IN-7806 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-IN-7808         TCGA-IP-7968 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-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-BR-8592         TCGA-BR-A4IU         TCGA-BR-A4IV 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-BR-A4IY         TCGA-BR-A4IZ         TCGA-BR-A4J1 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-BR-A4J2         TCGA-BR-A4J4         TCGA-BR-A4J5 
"17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" 
        TCGA-BR-A4J6         TCGA-BR-A4J8         TCGA-BR-A4J9 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-BR-A4PF         TCGA-CD-5798         TCGA-CD-5799 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-CD-5800         TCGA-CD-5801         TCGA-CD-5802 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-CD-5803         TCGA-CG-4300         TCGA-CG-4301 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-CG-4304         TCGA-CG-4305         TCGA-CG-4306 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-CG-4436         TCGA-CG-4437         TCGA-CG-4438 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-CG-4440         TCGA-CG-4441         TCGA-CG-4443 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-CG-4444         TCGA-CG-4449         TCGA-CG-4455 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-CG-4460         TCGA-CG-4462         TCGA-CG-4465 
  "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-CG-4466         TCGA-CG-4469         TCGA-CG-4472 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-CG-4474         TCGA-CG-4477         TCGA-CG-5716 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-CG-5717         TCGA-CG-5718         TCGA-CG-5719 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
        TCGA-CG-5720         TCGA-CG-5721         TCGA-CG-5722 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-CG-5723         TCGA-CG-5724         TCGA-CG-5725 
"17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" 
        TCGA-CG-5726         TCGA-CG-5727         TCGA-CG-5728 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-CG-5730         TCGA-CG-5732         TCGA-CG-5733 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-CG-5734         TCGA-D7-5577         TCGA-D7-5578 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-D7-5579         TCGA-D7-6518         TCGA-D7-6519 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-D7-6520         TCGA-D7-6521         TCGA-D7-6522 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-D7-6524         TCGA-D7-6525         TCGA-D7-6526 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-D7-6527         TCGA-D7-6528         TCGA-D7-6815 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-D7-6817         TCGA-D7-6818         TCGA-D7-6820 
  "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-D7-6822         TCGA-EQ-5647         TCGA-EQ-8122 
"17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" 
        TCGA-F1-6177         TCGA-F1-6874         TCGA-F1-6875 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
        TCGA-FP-7735         TCGA-FP-7829         TCGA-FP-7916 
"17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" 
        TCGA-FP-7998         TCGA-FP-8099         TCGA-FP-8209 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-FP-8631         TCGA-HJ-7597         TCGA-IN-7806 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-IN-7808         TCGA-IP-7968 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-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-BR-8592         TCGA-BR-A4IU         TCGA-BR-A4IV 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-BR-A4IY         TCGA-BR-A4IZ         TCGA-BR-A4J1 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-BR-A4J2         TCGA-BR-A4J4         TCGA-BR-A4J5 
"17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" 
        TCGA-BR-A4J6         TCGA-BR-A4J8         TCGA-BR-A4J9 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-BR-A4PF         TCGA-CD-5798         TCGA-CD-5799 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-CD-5800         TCGA-CD-5801         TCGA-CD-5802 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-CD-5803         TCGA-CG-4300         TCGA-CG-4301 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-CG-4304         TCGA-CG-4305         TCGA-CG-4306 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-CG-4436         TCGA-CG-4437         TCGA-CG-4438 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-CG-4440         TCGA-CG-4441         TCGA-CG-4443 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-CG-4444         TCGA-CG-4449         TCGA-CG-4455 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-CG-4460         TCGA-CG-4462         TCGA-CG-4465 
  "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-CG-4466         TCGA-CG-4469         TCGA-CG-4472 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-CG-4474         TCGA-CG-4477         TCGA-CG-5716 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-CG-5717         TCGA-CG-5718         TCGA-CG-5719 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
        TCGA-CG-5720         TCGA-CG-5721         TCGA-CG-5722 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-CG-5723         TCGA-CG-5724         TCGA-CG-5725 
"17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" 
        TCGA-CG-5726         TCGA-CG-5727         TCGA-CG-5728 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-CG-5730         TCGA-CG-5732         TCGA-CG-5733 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-CG-5734         TCGA-D7-5577         TCGA-D7-5578 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-D7-5579         TCGA-D7-6518         TCGA-D7-6519 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-D7-6520         TCGA-D7-6521         TCGA-D7-6522 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-D7-6524         TCGA-D7-6525         TCGA-D7-6526 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-D7-6527         TCGA-D7-6528         TCGA-D7-6815 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-D7-6817         TCGA-D7-6818         TCGA-D7-6820 
  "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-D7-6822         TCGA-EQ-5647         TCGA-EQ-8122 
"17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" 
        TCGA-F1-6177         TCGA-F1-6874         TCGA-F1-6875 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
        TCGA-FP-7735         TCGA-FP-7829         TCGA-FP-7916 
"17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" 
        TCGA-FP-7998         TCGA-FP-8099         TCGA-FP-8209 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-FP-8631         TCGA-HJ-7597         TCGA-IN-7806 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-IN-7808         TCGA-IP-7968 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
[1] "hr=" "2"  
D29V2, continuous
D29V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED      3    7
  17Q GAIN WILD-TYPE   67  100
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  FEMALE                3                 67
  MALE                  7                100
                    vv
clus                 STOMACH ADENOCARCINOMA - DIFFUSE TYPE
  17Q GAIN MUTATED                                       2
  17Q GAIN WILD-TYPE                                    23
                    vv
clus                 STOMACH ADENOCARCINOMA - NOT OTHERWISE SPECIFIED (NOS)
  17Q GAIN MUTATED                                                        4
  17Q GAIN WILD-TYPE                                                     83
                    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                                                 9
                    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                                                                     34
D29V4, multiclass
                    vv
clus                 T1 T2 T3 T4
  17Q GAIN MUTATED    0  3  3  4
  17Q GAIN WILD-TYPE  6 51 61 39
D29V5, multiclass
    clus
vv   17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  T1                0                  6
  T2                3                 51
  T3                3                 61
  T4                4                 39
                    vv
clus                 N0 N1 N2 N3
  17Q GAIN MUTATED    4  2  1  3
  17Q GAIN WILD-TYPE 52 59 28 17
D29V6, multiclass
    clus
vv   17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  N0                4                 52
  N1                2                 59
  N2                1                 28
  N3                3                 17
                    vv
clus                  M0  M1  MX
  17Q GAIN MUTATED     6   4   0
  17Q GAIN WILD-TYPE 140  14  13
D29V7, multiclass
    clus
vv   17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  M0                6                140
  M1                4                 14
  MX                0                 13
                    vv
clus                  I II III IV
  17Q GAIN MUTATED    2  1   3  4
  17Q GAIN WILD-TYPE 24 47  55 25
D29V8, multiclass
     clus
vv    17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  I                  2                 24
  II                 1                 47
  III                3                 55
  IV                 4                 25
D29V9, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED      0   10
  17Q GAIN WILD-TYPE    5  162
     clus
vv    17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  NO                 0                  5
  YES               10                162
                    vv
clus                  R0  R1  R2  RX
  17Q GAIN MUTATED     7   0   3   0
  17Q GAIN WILD-TYPE 116   7   9  25
D29V10, multiclass
    clus
vv   17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  R0                7                116
  R1                0                  7
  R2                3                  9
  RX                0                 25
D29V11, continuous

Clustering(30) Variable = 18p gain mutation analysis
D30V1, survival
                    sevent
clus2                  0   1
  18P GAIN MUTATED     9   1
  18P GAIN WILD-TYPE 113  17
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                10                130 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                 1                 17 
$`18P GAIN MUTATED`
TCGA-BR-7722 TCGA-BR-7901 TCGA-BR-A4J8 TCGA-BR-A4PF TCGA-CD-5799 TCGA-CG-4460 
        0.16         0.95         0.23         0.72         0.69        21.99 
TCGA-CG-4474 TCGA-D7-6528 TCGA-D7-6817 TCGA-FP-8631 
        1.02         1.68         4.70         0.56 

$`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-BR-8592 TCGA-BR-A4IU 
        1.18         1.55         1.48         0.76         0.20         0.59 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
        0.92         0.39         0.79         0.72         0.79         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J9 TCGA-CD-5798 TCGA-CD-5800 TCGA-CD-5801 
        0.43         0.13         0.10         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-4477 TCGA-CG-5716 TCGA-CG-5717 
       18.94         7.07        12.00         1.02         1.02         6.94 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-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-D7-6818 TCGA-D7-6820 
        5.95         6.61         4.14         3.65         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-FP-8099 TCGA-FP-8209 
        0.39         0.20         3.02         3.58         1.02        59.05 
TCGA-HJ-7597 TCGA-IN-7806 TCGA-IN-7808 TCGA-IP-7968 
       26.43         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 
             0.835              1.335 
[1] "0.2 - 22.0 (0.8)" "0.1 - 72.2 (1.3)"
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
  "18P GAIN MUTATED" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-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-BR-8592         TCGA-BR-A4IU         TCGA-BR-A4IV 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BR-A4IY         TCGA-BR-A4IZ         TCGA-BR-A4J1 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BR-A4J2         TCGA-BR-A4J4         TCGA-BR-A4J5 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BR-A4J6         TCGA-BR-A4J8         TCGA-BR-A4J9 
"18P GAIN WILD-TYPE"   "18P GAIN MUTATED" "18P GAIN WILD-TYPE" 
        TCGA-BR-A4PF         TCGA-CD-5798         TCGA-CD-5799 
  "18P GAIN MUTATED" "18P GAIN WILD-TYPE"   "18P GAIN MUTATED" 
        TCGA-CD-5800         TCGA-CD-5801         TCGA-CD-5802 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-CD-5803         TCGA-CG-4300         TCGA-CG-4301 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-CG-4304         TCGA-CG-4305         TCGA-CG-4306 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-CG-4436         TCGA-CG-4437         TCGA-CG-4438 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-CG-4440         TCGA-CG-4441         TCGA-CG-4443 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-CG-4444         TCGA-CG-4449         TCGA-CG-4455 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-CG-4460         TCGA-CG-4462         TCGA-CG-4465 
  "18P GAIN MUTATED" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-CG-4466         TCGA-CG-4469         TCGA-CG-4472 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-CG-4474         TCGA-CG-4477         TCGA-CG-5716 
  "18P GAIN MUTATED" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-CG-5717         TCGA-CG-5718         TCGA-CG-5719 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-CG-5720         TCGA-CG-5721         TCGA-CG-5722 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-CG-5723         TCGA-CG-5724         TCGA-CG-5725 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-CG-5726         TCGA-CG-5727         TCGA-CG-5728 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-CG-5730         TCGA-CG-5732         TCGA-CG-5733 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-CG-5734         TCGA-D7-5577         TCGA-D7-5578 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-D7-5579         TCGA-D7-6518         TCGA-D7-6519 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-D7-6520         TCGA-D7-6521         TCGA-D7-6522 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-D7-6524         TCGA-D7-6525         TCGA-D7-6526 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-D7-6527         TCGA-D7-6528         TCGA-D7-6815 
"18P GAIN WILD-TYPE"   "18P GAIN MUTATED" "18P GAIN WILD-TYPE" 
        TCGA-D7-6817         TCGA-D7-6818         TCGA-D7-6820 
  "18P GAIN MUTATED" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-D7-6822         TCGA-EQ-5647         TCGA-EQ-8122 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-F1-6177         TCGA-F1-6874         TCGA-F1-6875 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-FP-7735         TCGA-FP-7829         TCGA-FP-7916 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-FP-7998         TCGA-FP-8099         TCGA-FP-8209 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-FP-8631         TCGA-HJ-7597         TCGA-IN-7806 
  "18P GAIN MUTATED" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-IN-7808         TCGA-IP-7968 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
  "18P GAIN MUTATED" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-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-BR-8592         TCGA-BR-A4IU         TCGA-BR-A4IV 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BR-A4IY         TCGA-BR-A4IZ         TCGA-BR-A4J1 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BR-A4J2         TCGA-BR-A4J4         TCGA-BR-A4J5 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BR-A4J6         TCGA-BR-A4J8         TCGA-BR-A4J9 
"18P GAIN WILD-TYPE"   "18P GAIN MUTATED" "18P GAIN WILD-TYPE" 
        TCGA-BR-A4PF         TCGA-CD-5798         TCGA-CD-5799 
  "18P GAIN MUTATED" "18P GAIN WILD-TYPE"   "18P GAIN MUTATED" 
        TCGA-CD-5800         TCGA-CD-5801         TCGA-CD-5802 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-CD-5803         TCGA-CG-4300         TCGA-CG-4301 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-CG-4304         TCGA-CG-4305         TCGA-CG-4306 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-CG-4436         TCGA-CG-4437         TCGA-CG-4438 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-CG-4440         TCGA-CG-4441         TCGA-CG-4443 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-CG-4444         TCGA-CG-4449         TCGA-CG-4455 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-CG-4460         TCGA-CG-4462         TCGA-CG-4465 
  "18P GAIN MUTATED" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-CG-4466         TCGA-CG-4469         TCGA-CG-4472 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-CG-4474         TCGA-CG-4477         TCGA-CG-5716 
  "18P GAIN MUTATED" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-CG-5717         TCGA-CG-5718         TCGA-CG-5719 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-CG-5720         TCGA-CG-5721         TCGA-CG-5722 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-CG-5723         TCGA-CG-5724         TCGA-CG-5725 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-CG-5726         TCGA-CG-5727         TCGA-CG-5728 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-CG-5730         TCGA-CG-5732         TCGA-CG-5733 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-CG-5734         TCGA-D7-5577         TCGA-D7-5578 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-D7-5579         TCGA-D7-6518         TCGA-D7-6519 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-D7-6520         TCGA-D7-6521         TCGA-D7-6522 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-D7-6524         TCGA-D7-6525         TCGA-D7-6526 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-D7-6527         TCGA-D7-6528         TCGA-D7-6815 
"18P GAIN WILD-TYPE"   "18P GAIN MUTATED" "18P GAIN WILD-TYPE" 
        TCGA-D7-6817         TCGA-D7-6818         TCGA-D7-6820 
  "18P GAIN MUTATED" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-D7-6822         TCGA-EQ-5647         TCGA-EQ-8122 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-F1-6177         TCGA-F1-6874         TCGA-F1-6875 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-FP-7735         TCGA-FP-7829         TCGA-FP-7916 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-FP-7998         TCGA-FP-8099         TCGA-FP-8209 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-FP-8631         TCGA-HJ-7597         TCGA-IN-7806 
  "18P GAIN MUTATED" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-IN-7808         TCGA-IP-7968 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
  "18P GAIN MUTATED" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-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-BR-8592         TCGA-BR-A4IU         TCGA-BR-A4IV 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BR-A4IY         TCGA-BR-A4IZ         TCGA-BR-A4J1 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BR-A4J2         TCGA-BR-A4J4         TCGA-BR-A4J5 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BR-A4J6         TCGA-BR-A4J8         TCGA-BR-A4J9 
"18P GAIN WILD-TYPE"   "18P GAIN MUTATED" "18P GAIN WILD-TYPE" 
        TCGA-BR-A4PF         TCGA-CD-5798         TCGA-CD-5799 
  "18P GAIN MUTATED" "18P GAIN WILD-TYPE"   "18P GAIN MUTATED" 
        TCGA-CD-5800         TCGA-CD-5801         TCGA-CD-5802 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-CD-5803         TCGA-CG-4300         TCGA-CG-4301 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-CG-4304         TCGA-CG-4305         TCGA-CG-4306 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-CG-4436         TCGA-CG-4437         TCGA-CG-4438 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-CG-4440         TCGA-CG-4441         TCGA-CG-4443 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-CG-4444         TCGA-CG-4449         TCGA-CG-4455 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-CG-4460         TCGA-CG-4462         TCGA-CG-4465 
  "18P GAIN MUTATED" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-CG-4466         TCGA-CG-4469         TCGA-CG-4472 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-CG-4474         TCGA-CG-4477         TCGA-CG-5716 
  "18P GAIN MUTATED" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-CG-5717         TCGA-CG-5718         TCGA-CG-5719 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-CG-5720         TCGA-CG-5721         TCGA-CG-5722 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-CG-5723         TCGA-CG-5724         TCGA-CG-5725 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-CG-5726         TCGA-CG-5727         TCGA-CG-5728 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-CG-5730         TCGA-CG-5732         TCGA-CG-5733 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-CG-5734         TCGA-D7-5577         TCGA-D7-5578 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-D7-5579         TCGA-D7-6518         TCGA-D7-6519 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-D7-6520         TCGA-D7-6521         TCGA-D7-6522 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-D7-6524         TCGA-D7-6525         TCGA-D7-6526 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-D7-6527         TCGA-D7-6528         TCGA-D7-6815 
"18P GAIN WILD-TYPE"   "18P GAIN MUTATED" "18P GAIN WILD-TYPE" 
        TCGA-D7-6817         TCGA-D7-6818         TCGA-D7-6820 
  "18P GAIN MUTATED" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-D7-6822         TCGA-EQ-5647         TCGA-EQ-8122 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-F1-6177         TCGA-F1-6874         TCGA-F1-6875 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-FP-7735         TCGA-FP-7829         TCGA-FP-7916 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-FP-7998         TCGA-FP-8099         TCGA-FP-8209 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-FP-8631         TCGA-HJ-7597         TCGA-IN-7806 
  "18P GAIN MUTATED" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-IN-7808         TCGA-IP-7968 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
[1] "hr=" "1.6"
D30V2, continuous
D30V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED      6   10
  18P GAIN WILD-TYPE   64   97
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  FEMALE                6                 64
  MALE                 10                 97
                    vv
clus                 STOMACH ADENOCARCINOMA - DIFFUSE TYPE
  18P GAIN MUTATED                                       1
  18P GAIN WILD-TYPE                                    24
                    vv
clus                 STOMACH ADENOCARCINOMA - NOT OTHERWISE SPECIFIED (NOS)
  18P GAIN MUTATED                                                        8
  18P GAIN WILD-TYPE                                                     79
                    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                                                 9
                    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                                                                        3
  18P GAIN WILD-TYPE                                                                     33
D30V4, multiclass
                    vv
clus                 T1 T2 T3 T4
  18P GAIN MUTATED    0  4  7  3
  18P GAIN WILD-TYPE  6 50 57 40
D30V5, multiclass
    clus
vv   18P GAIN MUTATED 18P GAIN WILD-TYPE
  T1                0                  6
  T2                4                 50
  T3                7                 57
  T4                3                 40
                    vv
clus                 N0 N1 N2 N3
  18P GAIN MUTATED    1  8  3  3
  18P GAIN WILD-TYPE 55 53 26 17
D30V6, multiclass
    clus
vv   18P GAIN MUTATED 18P GAIN WILD-TYPE
  N0                1                 55
  N1                8                 53
  N2                3                 26
  N3                3                 17
                    vv
clus                  M0  M1  MX
  18P GAIN MUTATED    12   2   2
  18P GAIN WILD-TYPE 134  16  11
D30V7, multiclass
    clus
vv   18P GAIN MUTATED 18P GAIN WILD-TYPE
  M0               12                134
  M1                2                 16
  MX                2                 11
                    vv
clus                  I II III IV
  18P GAIN MUTATED    1  2   8  3
  18P GAIN WILD-TYPE 25 46  50 26
D30V8, multiclass
     clus
vv    18P GAIN MUTATED 18P GAIN WILD-TYPE
  I                  1                 25
  II                 2                 46
  III                8                 50
  IV                 3                 26
D30V9, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED      1   15
  18P GAIN WILD-TYPE    4  157
     clus
vv    18P GAIN MUTATED 18P GAIN WILD-TYPE
  NO                 1                  4
  YES               15                157
                    vv
clus                  R0  R1  R2  RX
  18P GAIN MUTATED     9   1   2   3
  18P GAIN WILD-TYPE 114   6  10  22
D30V10, multiclass
    clus
vv   18P GAIN MUTATED 18P GAIN WILD-TYPE
  R0                9                114
  R1                1                  6
  R2                2                 10
  RX                3                 22
D30V11, continuous

Clustering(31) Variable = 18q gain mutation analysis
D31V1, survival
                    sevent
clus2                  0   1
  18Q GAIN MUTATED     6   1
  18Q GAIN WILD-TYPE 116  17
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 7                133 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 1                 17 
$`18Q GAIN MUTATED`
TCGA-BR-A4PF TCGA-CD-5799 TCGA-CG-4460 TCGA-CG-4474 TCGA-D7-6528 TCGA-D7-6817 
        0.72         0.69        21.99         1.02         1.68         4.70 
TCGA-FP-8631 
        0.56 

$`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-BR-8592 TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        0.20         0.59         0.92         0.39         0.79         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J8 TCGA-BR-A4J9 
        0.79         0.53         0.43         0.13         0.23         0.10 
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-FP-8099 TCGA-FP-8209 TCGA-HJ-7597 TCGA-IN-7806 TCGA-IN-7808 
        3.58         1.02        59.05        26.43         6.87         3.55 
TCGA-IP-7968 
        2.53 

  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
              0.56               0.07 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
             21.99              72.23 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
              1.02               1.25 
[1] "0.6 - 22.0 (1.0)" "0.1 - 72.2 (1.2)"
        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-BR-8592         TCGA-BR-A4IU         TCGA-BR-A4IV 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BR-A4IY         TCGA-BR-A4IZ         TCGA-BR-A4J1 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BR-A4J2         TCGA-BR-A4J4         TCGA-BR-A4J5 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BR-A4J6         TCGA-BR-A4J8         TCGA-BR-A4J9 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BR-A4PF         TCGA-CD-5798         TCGA-CD-5799 
  "18Q GAIN MUTATED" "18Q GAIN WILD-TYPE"   "18Q GAIN MUTATED" 
        TCGA-CD-5800         TCGA-CD-5801         TCGA-CD-5802 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-CD-5803         TCGA-CG-4300         TCGA-CG-4301 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-CG-4304         TCGA-CG-4305         TCGA-CG-4306 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-CG-4436         TCGA-CG-4437         TCGA-CG-4438 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-CG-4440         TCGA-CG-4441         TCGA-CG-4443 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-CG-4444         TCGA-CG-4449         TCGA-CG-4455 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-CG-4460         TCGA-CG-4462         TCGA-CG-4465 
  "18Q GAIN MUTATED" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-CG-4466         TCGA-CG-4469         TCGA-CG-4472 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-CG-4474         TCGA-CG-4477         TCGA-CG-5716 
  "18Q GAIN MUTATED" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-CG-5717         TCGA-CG-5718         TCGA-CG-5719 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-CG-5720         TCGA-CG-5721         TCGA-CG-5722 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-CG-5723         TCGA-CG-5724         TCGA-CG-5725 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-CG-5726         TCGA-CG-5727         TCGA-CG-5728 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-CG-5730         TCGA-CG-5732         TCGA-CG-5733 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-CG-5734         TCGA-D7-5577         TCGA-D7-5578 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-D7-5579         TCGA-D7-6518         TCGA-D7-6519 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-D7-6520         TCGA-D7-6521         TCGA-D7-6522 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-D7-6524         TCGA-D7-6525         TCGA-D7-6526 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-D7-6527         TCGA-D7-6528         TCGA-D7-6815 
"18Q GAIN WILD-TYPE"   "18Q GAIN MUTATED" "18Q GAIN WILD-TYPE" 
        TCGA-D7-6817         TCGA-D7-6818         TCGA-D7-6820 
  "18Q GAIN MUTATED" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-D7-6822         TCGA-EQ-5647         TCGA-EQ-8122 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-F1-6177         TCGA-F1-6874         TCGA-F1-6875 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-FP-7735         TCGA-FP-7829         TCGA-FP-7916 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-FP-7998         TCGA-FP-8099         TCGA-FP-8209 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-FP-8631         TCGA-HJ-7597         TCGA-IN-7806 
  "18Q GAIN MUTATED" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-IN-7808         TCGA-IP-7968 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-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-BR-8592         TCGA-BR-A4IU         TCGA-BR-A4IV 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BR-A4IY         TCGA-BR-A4IZ         TCGA-BR-A4J1 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BR-A4J2         TCGA-BR-A4J4         TCGA-BR-A4J5 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BR-A4J6         TCGA-BR-A4J8         TCGA-BR-A4J9 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BR-A4PF         TCGA-CD-5798         TCGA-CD-5799 
  "18Q GAIN MUTATED" "18Q GAIN WILD-TYPE"   "18Q GAIN MUTATED" 
        TCGA-CD-5800         TCGA-CD-5801         TCGA-CD-5802 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-CD-5803         TCGA-CG-4300         TCGA-CG-4301 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-CG-4304         TCGA-CG-4305         TCGA-CG-4306 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-CG-4436         TCGA-CG-4437         TCGA-CG-4438 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-CG-4440         TCGA-CG-4441         TCGA-CG-4443 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-CG-4444         TCGA-CG-4449         TCGA-CG-4455 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-CG-4460         TCGA-CG-4462         TCGA-CG-4465 
  "18Q GAIN MUTATED" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-CG-4466         TCGA-CG-4469         TCGA-CG-4472 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-CG-4474         TCGA-CG-4477         TCGA-CG-5716 
  "18Q GAIN MUTATED" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-CG-5717         TCGA-CG-5718         TCGA-CG-5719 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-CG-5720         TCGA-CG-5721         TCGA-CG-5722 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-CG-5723         TCGA-CG-5724         TCGA-CG-5725 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-CG-5726         TCGA-CG-5727         TCGA-CG-5728 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-CG-5730         TCGA-CG-5732         TCGA-CG-5733 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-CG-5734         TCGA-D7-5577         TCGA-D7-5578 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-D7-5579         TCGA-D7-6518         TCGA-D7-6519 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-D7-6520         TCGA-D7-6521         TCGA-D7-6522 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-D7-6524         TCGA-D7-6525         TCGA-D7-6526 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-D7-6527         TCGA-D7-6528         TCGA-D7-6815 
"18Q GAIN WILD-TYPE"   "18Q GAIN MUTATED" "18Q GAIN WILD-TYPE" 
        TCGA-D7-6817         TCGA-D7-6818         TCGA-D7-6820 
  "18Q GAIN MUTATED" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-D7-6822         TCGA-EQ-5647         TCGA-EQ-8122 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-F1-6177         TCGA-F1-6874         TCGA-F1-6875 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-FP-7735         TCGA-FP-7829         TCGA-FP-7916 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-FP-7998         TCGA-FP-8099         TCGA-FP-8209 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-FP-8631         TCGA-HJ-7597         TCGA-IN-7806 
  "18Q GAIN MUTATED" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-IN-7808         TCGA-IP-7968 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-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-BR-8592         TCGA-BR-A4IU         TCGA-BR-A4IV 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BR-A4IY         TCGA-BR-A4IZ         TCGA-BR-A4J1 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BR-A4J2         TCGA-BR-A4J4         TCGA-BR-A4J5 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BR-A4J6         TCGA-BR-A4J8         TCGA-BR-A4J9 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BR-A4PF         TCGA-CD-5798         TCGA-CD-5799 
  "18Q GAIN MUTATED" "18Q GAIN WILD-TYPE"   "18Q GAIN MUTATED" 
        TCGA-CD-5800         TCGA-CD-5801         TCGA-CD-5802 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-CD-5803         TCGA-CG-4300         TCGA-CG-4301 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-CG-4304         TCGA-CG-4305         TCGA-CG-4306 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-CG-4436         TCGA-CG-4437         TCGA-CG-4438 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-CG-4440         TCGA-CG-4441         TCGA-CG-4443 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-CG-4444         TCGA-CG-4449         TCGA-CG-4455 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-CG-4460         TCGA-CG-4462         TCGA-CG-4465 
  "18Q GAIN MUTATED" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-CG-4466         TCGA-CG-4469         TCGA-CG-4472 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-CG-4474         TCGA-CG-4477         TCGA-CG-5716 
  "18Q GAIN MUTATED" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-CG-5717         TCGA-CG-5718         TCGA-CG-5719 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-CG-5720         TCGA-CG-5721         TCGA-CG-5722 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-CG-5723         TCGA-CG-5724         TCGA-CG-5725 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-CG-5726         TCGA-CG-5727         TCGA-CG-5728 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-CG-5730         TCGA-CG-5732         TCGA-CG-5733 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-CG-5734         TCGA-D7-5577         TCGA-D7-5578 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-D7-5579         TCGA-D7-6518         TCGA-D7-6519 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-D7-6520         TCGA-D7-6521         TCGA-D7-6522 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-D7-6524         TCGA-D7-6525         TCGA-D7-6526 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-D7-6527         TCGA-D7-6528         TCGA-D7-6815 
"18Q GAIN WILD-TYPE"   "18Q GAIN MUTATED" "18Q GAIN WILD-TYPE" 
        TCGA-D7-6817         TCGA-D7-6818         TCGA-D7-6820 
  "18Q GAIN MUTATED" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-D7-6822         TCGA-EQ-5647         TCGA-EQ-8122 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-F1-6177         TCGA-F1-6874         TCGA-F1-6875 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-FP-7735         TCGA-FP-7829         TCGA-FP-7916 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-FP-7998         TCGA-FP-8099         TCGA-FP-8209 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-FP-8631         TCGA-HJ-7597         TCGA-IN-7806 
  "18Q GAIN MUTATED" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-IN-7808         TCGA-IP-7968 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
[1] "hr=" "1.6"
D31V2, continuous
D31V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      4    5
  18Q GAIN WILD-TYPE   66  102
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  FEMALE                4                 66
  MALE                  5                102
                    vv
clus                 STOMACH ADENOCARCINOMA - DIFFUSE TYPE
  18Q GAIN MUTATED                                       1
  18Q GAIN WILD-TYPE                                    24
                    vv
clus                 STOMACH ADENOCARCINOMA - NOT OTHERWISE SPECIFIED (NOS)
  18Q GAIN MUTATED                                                        3
  18Q GAIN WILD-TYPE                                                     84
                    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                                                10
                    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                                                                        3
  18Q GAIN WILD-TYPE                                                                     33
D31V4, multiclass
                    vv
clus                 T1 T2 T3 T4
  18Q GAIN MUTATED    0  3  2  3
  18Q GAIN WILD-TYPE  6 51 62 40
D31V5, multiclass
    clus
vv   18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  T1                0                  6
  T2                3                 51
  T3                2                 62
  T4                3                 40
                    vv
clus                 N0 N1 N2 N3
  18Q GAIN MUTATED    1  3  3  1
  18Q GAIN WILD-TYPE 55 58 26 19
D31V6, multiclass
    clus
vv   18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  N0                1                 55
  N1                3                 58
  N2                3                 26
  N3                1                 19
                    vv
clus                  M0  M1  MX
  18Q GAIN MUTATED     5   2   2
  18Q GAIN WILD-TYPE 141  16  11
D31V7, multiclass
    clus
vv   18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  M0                5                141
  M1                2                 16
  MX                2                 11
                    vv
clus                  I II III IV
  18Q GAIN MUTATED    1  1   4  2
  18Q GAIN WILD-TYPE 25 47  54 27
D31V8, multiclass
     clus
vv    18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  I                  1                 25
  II                 1                 47
  III                4                 54
  IV                 2                 27
D31V9, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      0    9
  18Q GAIN WILD-TYPE    5  163
     clus
vv    18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  NO                 0                  5
  YES                9                163
                    vv
clus                  R0  R1  R2  RX
  18Q GAIN MUTATED     4   0   2   2
  18Q GAIN WILD-TYPE 119   7  10  23
D31V10, multiclass
    clus
vv   18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  R0                4                119
  R1                0                  7
  R2                2                 10
  RX                2                 23
D31V11, continuous

Clustering(32) Variable = 19p gain mutation analysis
D32V1, survival
                    sevent
clus2                  0   1
  19P GAIN MUTATED     6   1
  19P GAIN WILD-TYPE 116  17
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                 7                133 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                 1                 17 
$`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-BR-8592 TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        0.20         0.59         0.92         0.39         0.79         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J8 TCGA-BR-A4J9 
        0.79         0.53         0.43         0.13         0.23         0.10 
TCGA-BR-A4PF TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        0.72         0.82         0.69         0.36         0.49         0.30 
TCGA-CD-5803 TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
        0.07        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
       52.96         8.05        54.05         4.01        14.01        29.98 
TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       47.05        19.07        12.03         1.02         8.98        18.94 
TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4477 TCGA-CG-5716 TCGA-CG-5717 TCGA-CG-5718 
        7.07        12.00         1.02         1.02         6.94         1.02 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 
        1.02         0.99         5.98        70.06        12.03        15.02 
TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       28.96        31.04        65.10        55.04        21.07         7.99 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6522 TCGA-D7-6524 
        3.58         4.54        15.65         9.63         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-FP-8099 TCGA-FP-8209 TCGA-FP-8631 TCGA-HJ-7597 TCGA-IN-7806 TCGA-IN-7808 
        1.02        59.05         0.56        26.43         6.87         3.55 
TCGA-IP-7968 
        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               1.22 
[1] "0.9 - 22.0 (8.2)" "0.1 - 72.2 (1.2)"
        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-BR-8592         TCGA-BR-A4IU         TCGA-BR-A4IV 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-BR-A4IY         TCGA-BR-A4IZ         TCGA-BR-A4J1 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-BR-A4J2         TCGA-BR-A4J4         TCGA-BR-A4J5 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-BR-A4J6         TCGA-BR-A4J8         TCGA-BR-A4J9 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-BR-A4PF         TCGA-CD-5798         TCGA-CD-5799 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-CD-5800         TCGA-CD-5801         TCGA-CD-5802 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-CD-5803         TCGA-CG-4300         TCGA-CG-4301 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-CG-4304         TCGA-CG-4305         TCGA-CG-4306 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-CG-4436         TCGA-CG-4437         TCGA-CG-4438 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-CG-4440         TCGA-CG-4441         TCGA-CG-4443 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-CG-4444         TCGA-CG-4449         TCGA-CG-4455 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-CG-4460         TCGA-CG-4462         TCGA-CG-4465 
  "19P GAIN MUTATED" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-CG-4466         TCGA-CG-4469         TCGA-CG-4472 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-CG-4474         TCGA-CG-4477         TCGA-CG-5716 
  "19P GAIN MUTATED" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-CG-5717         TCGA-CG-5718         TCGA-CG-5719 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-CG-5720         TCGA-CG-5721         TCGA-CG-5722 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE"   "19P GAIN MUTATED" 
        TCGA-CG-5723         TCGA-CG-5724         TCGA-CG-5725 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-CG-5726         TCGA-CG-5727         TCGA-CG-5728 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-CG-5730         TCGA-CG-5732         TCGA-CG-5733 
  "19P GAIN MUTATED" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-CG-5734         TCGA-D7-5577         TCGA-D7-5578 
"19P GAIN WILD-TYPE"   "19P GAIN MUTATED" "19P GAIN WILD-TYPE" 
        TCGA-D7-5579         TCGA-D7-6518         TCGA-D7-6519 
"19P GAIN WILD-TYPE"   "19P GAIN MUTATED" "19P GAIN WILD-TYPE" 
        TCGA-D7-6520         TCGA-D7-6521         TCGA-D7-6522 
"19P GAIN WILD-TYPE"   "19P GAIN MUTATED" "19P GAIN WILD-TYPE" 
        TCGA-D7-6524         TCGA-D7-6525         TCGA-D7-6526 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-D7-6527         TCGA-D7-6528         TCGA-D7-6815 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-D7-6817         TCGA-D7-6818         TCGA-D7-6820 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-D7-6822         TCGA-EQ-5647         TCGA-EQ-8122 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-F1-6177         TCGA-F1-6874         TCGA-F1-6875 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-FP-7735         TCGA-FP-7829         TCGA-FP-7916 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-FP-7998         TCGA-FP-8099         TCGA-FP-8209 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-FP-8631         TCGA-HJ-7597         TCGA-IN-7806 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-IN-7808         TCGA-IP-7968 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-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-BR-8592         TCGA-BR-A4IU         TCGA-BR-A4IV 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-BR-A4IY         TCGA-BR-A4IZ         TCGA-BR-A4J1 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-BR-A4J2         TCGA-BR-A4J4         TCGA-BR-A4J5 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-BR-A4J6         TCGA-BR-A4J8         TCGA-BR-A4J9 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-BR-A4PF         TCGA-CD-5798         TCGA-CD-5799 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-CD-5800         TCGA-CD-5801         TCGA-CD-5802 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-CD-5803         TCGA-CG-4300         TCGA-CG-4301 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-CG-4304         TCGA-CG-4305         TCGA-CG-4306 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-CG-4436         TCGA-CG-4437         TCGA-CG-4438 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-CG-4440         TCGA-CG-4441         TCGA-CG-4443 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-CG-4444         TCGA-CG-4449         TCGA-CG-4455 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-CG-4460         TCGA-CG-4462         TCGA-CG-4465 
  "19P GAIN MUTATED" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-CG-4466         TCGA-CG-4469         TCGA-CG-4472 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-CG-4474         TCGA-CG-4477         TCGA-CG-5716 
  "19P GAIN MUTATED" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-CG-5717         TCGA-CG-5718         TCGA-CG-5719 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-CG-5720         TCGA-CG-5721         TCGA-CG-5722 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE"   "19P GAIN MUTATED" 
        TCGA-CG-5723         TCGA-CG-5724         TCGA-CG-5725 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-CG-5726         TCGA-CG-5727         TCGA-CG-5728 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-CG-5730         TCGA-CG-5732         TCGA-CG-5733 
  "19P GAIN MUTATED" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-CG-5734         TCGA-D7-5577         TCGA-D7-5578 
"19P GAIN WILD-TYPE"   "19P GAIN MUTATED" "19P GAIN WILD-TYPE" 
        TCGA-D7-5579         TCGA-D7-6518         TCGA-D7-6519 
"19P GAIN WILD-TYPE"   "19P GAIN MUTATED" "19P GAIN WILD-TYPE" 
        TCGA-D7-6520         TCGA-D7-6521         TCGA-D7-6522 
"19P GAIN WILD-TYPE"   "19P GAIN MUTATED" "19P GAIN WILD-TYPE" 
        TCGA-D7-6524         TCGA-D7-6525         TCGA-D7-6526 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-D7-6527         TCGA-D7-6528         TCGA-D7-6815 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-D7-6817         TCGA-D7-6818         TCGA-D7-6820 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-D7-6822         TCGA-EQ-5647         TCGA-EQ-8122 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-F1-6177         TCGA-F1-6874         TCGA-F1-6875 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-FP-7735         TCGA-FP-7829         TCGA-FP-7916 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-FP-7998         TCGA-FP-8099         TCGA-FP-8209 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-FP-8631         TCGA-HJ-7597         TCGA-IN-7806 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-IN-7808         TCGA-IP-7968 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-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-BR-8592         TCGA-BR-A4IU         TCGA-BR-A4IV 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-BR-A4IY         TCGA-BR-A4IZ         TCGA-BR-A4J1 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-BR-A4J2         TCGA-BR-A4J4         TCGA-BR-A4J5 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-BR-A4J6         TCGA-BR-A4J8         TCGA-BR-A4J9 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-BR-A4PF         TCGA-CD-5798         TCGA-CD-5799 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-CD-5800         TCGA-CD-5801         TCGA-CD-5802 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-CD-5803         TCGA-CG-4300         TCGA-CG-4301 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-CG-4304         TCGA-CG-4305         TCGA-CG-4306 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-CG-4436         TCGA-CG-4437         TCGA-CG-4438 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-CG-4440         TCGA-CG-4441         TCGA-CG-4443 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-CG-4444         TCGA-CG-4449         TCGA-CG-4455 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-CG-4460         TCGA-CG-4462         TCGA-CG-4465 
  "19P GAIN MUTATED" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-CG-4466         TCGA-CG-4469         TCGA-CG-4472 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-CG-4474         TCGA-CG-4477         TCGA-CG-5716 
  "19P GAIN MUTATED" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-CG-5717         TCGA-CG-5718         TCGA-CG-5719 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-CG-5720         TCGA-CG-5721         TCGA-CG-5722 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE"   "19P GAIN MUTATED" 
        TCGA-CG-5723         TCGA-CG-5724         TCGA-CG-5725 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-CG-5726         TCGA-CG-5727         TCGA-CG-5728 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-CG-5730         TCGA-CG-5732         TCGA-CG-5733 
  "19P GAIN MUTATED" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-CG-5734         TCGA-D7-5577         TCGA-D7-5578 
"19P GAIN WILD-TYPE"   "19P GAIN MUTATED" "19P GAIN WILD-TYPE" 
        TCGA-D7-5579         TCGA-D7-6518         TCGA-D7-6519 
"19P GAIN WILD-TYPE"   "19P GAIN MUTATED" "19P GAIN WILD-TYPE" 
        TCGA-D7-6520         TCGA-D7-6521         TCGA-D7-6522 
"19P GAIN WILD-TYPE"   "19P GAIN MUTATED" "19P GAIN WILD-TYPE" 
        TCGA-D7-6524         TCGA-D7-6525         TCGA-D7-6526 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-D7-6527         TCGA-D7-6528         TCGA-D7-6815 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-D7-6817         TCGA-D7-6818         TCGA-D7-6820 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-D7-6822         TCGA-EQ-5647         TCGA-EQ-8122 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-F1-6177         TCGA-F1-6874         TCGA-F1-6875 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-FP-7735         TCGA-FP-7829         TCGA-FP-7916 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-FP-7998         TCGA-FP-8099         TCGA-FP-8209 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-FP-8631         TCGA-HJ-7597         TCGA-IN-7806 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-IN-7808         TCGA-IP-7968 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
[1] "hr=" "1.1"
D32V2, continuous
D32V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED      8    2
  19P GAIN WILD-TYPE   62  105
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  FEMALE                8                 62
  MALE                  2                105
                    vv
clus                 STOMACH ADENOCARCINOMA - DIFFUSE TYPE
  19P GAIN MUTATED                                       3
  19P GAIN WILD-TYPE                                    22
                    vv
clus                 STOMACH ADENOCARCINOMA - NOT OTHERWISE SPECIFIED (NOS)
  19P GAIN MUTATED                                                        3
  19P GAIN WILD-TYPE                                                     84
                    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                                                10
                    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                                                                     33
D32V4, multiclass
                    vv
clus                 T1 T2 T3 T4
  19P GAIN MUTATED    0  5  3  2
  19P GAIN WILD-TYPE  6 49 61 41
D32V5, multiclass
    clus
vv   19P GAIN MUTATED 19P GAIN WILD-TYPE
  T1                0                  6
  T2                5                 49
  T3                3                 61
  T4                2                 41
                    vv
clus                 N0 N1 N2 N3
  19P GAIN MUTATED    0  4  3  2
  19P GAIN WILD-TYPE 56 57 26 18
D32V6, multiclass
    clus
vv   19P GAIN MUTATED 19P GAIN WILD-TYPE
  N0                0                 56
  N1                4                 57
  N2                3                 26
  N3                2                 18
                    vv
clus                  M0  M1  MX
  19P GAIN MUTATED     6   4   0
  19P GAIN WILD-TYPE 140  14  13
D32V7, multiclass
    clus
vv   19P GAIN MUTATED 19P GAIN WILD-TYPE
  M0                6                140
  M1                4                 14
  MX                0                 13
                    vv
clus                  I II III IV
  19P GAIN MUTATED    0  1   3  5
  19P GAIN WILD-TYPE 26 47  55 24
D32V8, multiclass
     clus
vv    19P GAIN MUTATED 19P GAIN WILD-TYPE
  I                  0                 26
  II                 1                 47
  III                3                 55
  IV                 5                 24
D32V9, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED      0   10
  19P GAIN WILD-TYPE    5  162
     clus
vv    19P GAIN MUTATED 19P GAIN WILD-TYPE
  NO                 0                  5
  YES               10                162
                    vv
clus                  R0  R1  R2  RX
  19P GAIN MUTATED     3   1   4   2
  19P GAIN WILD-TYPE 120   6   8  23
D32V10, multiclass
    clus
vv   19P GAIN MUTATED 19P GAIN WILD-TYPE
  R0                3                120
  R1                1                  6
  R2                4                  8
  RX                2                 23
D32V11, continuous

Clustering(33) Variable = 19q gain mutation analysis
D33V1, survival
                    sevent
clus2                  0   1
  19Q GAIN MUTATED    10   2
  19Q GAIN WILD-TYPE 112  16
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                12                128 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                 2                 16 
$`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-BR-8592 
        0.26         1.18         1.55         1.48         0.76         0.20 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
        0.59         0.92         0.39         0.79         0.72         0.79 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PF 
        0.53         0.43         0.13         0.23         0.10         0.72 
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-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-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5727 
        5.98        70.06        12.03        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-D7-6519 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-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-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8631 TCGA-HJ-7597 TCGA-IN-7806 
        3.58         1.02        59.05         0.56        26.43         6.87 
TCGA-IN-7808 TCGA-IP-7968 
        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               1.15 
[1] "0.8 - 72.2 (6.2)" "0.1 - 70.1 (1.1)"
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
"19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-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-BR-8592         TCGA-BR-A4IU         TCGA-BR-A4IV 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-BR-A4IY         TCGA-BR-A4IZ         TCGA-BR-A4J1 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-BR-A4J2         TCGA-BR-A4J4         TCGA-BR-A4J5 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-BR-A4J6         TCGA-BR-A4J8         TCGA-BR-A4J9 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-BR-A4PF         TCGA-CD-5798         TCGA-CD-5799 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-CD-5800         TCGA-CD-5801         TCGA-CD-5802 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-CD-5803         TCGA-CG-4300         TCGA-CG-4301 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-CG-4304         TCGA-CG-4305         TCGA-CG-4306 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-CG-4436         TCGA-CG-4437         TCGA-CG-4438 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" 
        TCGA-CG-4440         TCGA-CG-4441         TCGA-CG-4443 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-CG-4444         TCGA-CG-4449         TCGA-CG-4455 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-CG-4460         TCGA-CG-4462         TCGA-CG-4465 
  "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-CG-4466         TCGA-CG-4469         TCGA-CG-4472 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-CG-4474         TCGA-CG-4477         TCGA-CG-5716 
  "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-CG-5717         TCGA-CG-5718         TCGA-CG-5719 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-CG-5720         TCGA-CG-5721         TCGA-CG-5722 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" 
        TCGA-CG-5723         TCGA-CG-5724         TCGA-CG-5725 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-CG-5726         TCGA-CG-5727         TCGA-CG-5728 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-CG-5730         TCGA-CG-5732         TCGA-CG-5733 
  "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-CG-5734         TCGA-D7-5577         TCGA-D7-5578 
"19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" 
        TCGA-D7-5579         TCGA-D7-6518         TCGA-D7-6519 
"19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" 
        TCGA-D7-6520         TCGA-D7-6521         TCGA-D7-6522 
"19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" 
        TCGA-D7-6524         TCGA-D7-6525         TCGA-D7-6526 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-D7-6527         TCGA-D7-6528         TCGA-D7-6815 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-D7-6817         TCGA-D7-6818         TCGA-D7-6820 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-D7-6822         TCGA-EQ-5647         TCGA-EQ-8122 
  "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-F1-6177         TCGA-F1-6874         TCGA-F1-6875 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" 
        TCGA-FP-7735         TCGA-FP-7829         TCGA-FP-7916 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" 
        TCGA-FP-7998         TCGA-FP-8099         TCGA-FP-8209 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-FP-8631         TCGA-HJ-7597         TCGA-IN-7806 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-IN-7808         TCGA-IP-7968 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
"19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-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-BR-8592         TCGA-BR-A4IU         TCGA-BR-A4IV 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-BR-A4IY         TCGA-BR-A4IZ         TCGA-BR-A4J1 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-BR-A4J2         TCGA-BR-A4J4         TCGA-BR-A4J5 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-BR-A4J6         TCGA-BR-A4J8         TCGA-BR-A4J9 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-BR-A4PF         TCGA-CD-5798         TCGA-CD-5799 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-CD-5800         TCGA-CD-5801         TCGA-CD-5802 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-CD-5803         TCGA-CG-4300         TCGA-CG-4301 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-CG-4304         TCGA-CG-4305         TCGA-CG-4306 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-CG-4436         TCGA-CG-4437         TCGA-CG-4438 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" 
        TCGA-CG-4440         TCGA-CG-4441         TCGA-CG-4443 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-CG-4444         TCGA-CG-4449         TCGA-CG-4455 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-CG-4460         TCGA-CG-4462         TCGA-CG-4465 
  "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-CG-4466         TCGA-CG-4469         TCGA-CG-4472 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-CG-4474         TCGA-CG-4477         TCGA-CG-5716 
  "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-CG-5717         TCGA-CG-5718         TCGA-CG-5719 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-CG-5720         TCGA-CG-5721         TCGA-CG-5722 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" 
        TCGA-CG-5723         TCGA-CG-5724         TCGA-CG-5725 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-CG-5726         TCGA-CG-5727         TCGA-CG-5728 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-CG-5730         TCGA-CG-5732         TCGA-CG-5733 
  "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-CG-5734         TCGA-D7-5577         TCGA-D7-5578 
"19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" 
        TCGA-D7-5579         TCGA-D7-6518         TCGA-D7-6519 
"19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" 
        TCGA-D7-6520         TCGA-D7-6521         TCGA-D7-6522 
"19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" 
        TCGA-D7-6524         TCGA-D7-6525         TCGA-D7-6526 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-D7-6527         TCGA-D7-6528         TCGA-D7-6815 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-D7-6817         TCGA-D7-6818         TCGA-D7-6820 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-D7-6822         TCGA-EQ-5647         TCGA-EQ-8122 
  "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-F1-6177         TCGA-F1-6874         TCGA-F1-6875 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" 
        TCGA-FP-7735         TCGA-FP-7829         TCGA-FP-7916 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" 
        TCGA-FP-7998         TCGA-FP-8099         TCGA-FP-8209 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-FP-8631         TCGA-HJ-7597         TCGA-IN-7806 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-IN-7808         TCGA-IP-7968 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
"19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-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-BR-8592         TCGA-BR-A4IU         TCGA-BR-A4IV 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-BR-A4IY         TCGA-BR-A4IZ         TCGA-BR-A4J1 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-BR-A4J2         TCGA-BR-A4J4         TCGA-BR-A4J5 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-BR-A4J6         TCGA-BR-A4J8         TCGA-BR-A4J9 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-BR-A4PF         TCGA-CD-5798         TCGA-CD-5799 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-CD-5800         TCGA-CD-5801         TCGA-CD-5802 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-CD-5803         TCGA-CG-4300         TCGA-CG-4301 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-CG-4304         TCGA-CG-4305         TCGA-CG-4306 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-CG-4436         TCGA-CG-4437         TCGA-CG-4438 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" 
        TCGA-CG-4440         TCGA-CG-4441         TCGA-CG-4443 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-CG-4444         TCGA-CG-4449         TCGA-CG-4455 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-CG-4460         TCGA-CG-4462         TCGA-CG-4465 
  "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-CG-4466         TCGA-CG-4469         TCGA-CG-4472 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-CG-4474         TCGA-CG-4477         TCGA-CG-5716 
  "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-CG-5717         TCGA-CG-5718         TCGA-CG-5719 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-CG-5720         TCGA-CG-5721         TCGA-CG-5722 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" 
        TCGA-CG-5723         TCGA-CG-5724         TCGA-CG-5725 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-CG-5726         TCGA-CG-5727         TCGA-CG-5728 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-CG-5730         TCGA-CG-5732         TCGA-CG-5733 
  "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-CG-5734         TCGA-D7-5577         TCGA-D7-5578 
"19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" 
        TCGA-D7-5579         TCGA-D7-6518         TCGA-D7-6519 
"19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" 
        TCGA-D7-6520         TCGA-D7-6521         TCGA-D7-6522 
"19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" 
        TCGA-D7-6524         TCGA-D7-6525         TCGA-D7-6526 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-D7-6527         TCGA-D7-6528         TCGA-D7-6815 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-D7-6817         TCGA-D7-6818         TCGA-D7-6820 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-D7-6822         TCGA-EQ-5647         TCGA-EQ-8122 
  "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-F1-6177         TCGA-F1-6874         TCGA-F1-6875 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" 
        TCGA-FP-7735         TCGA-FP-7829         TCGA-FP-7916 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" 
        TCGA-FP-7998         TCGA-FP-8099         TCGA-FP-8209 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-FP-8631         TCGA-HJ-7597         TCGA-IN-7806 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-IN-7808         TCGA-IP-7968 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
[1] "hr=" "3"  
D33V2, continuous
D33V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED     10    7
  19Q GAIN WILD-TYPE   60  100
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  FEMALE               10                 60
  MALE                  7                100
                    vv
clus                 STOMACH ADENOCARCINOMA - DIFFUSE TYPE
  19Q GAIN MUTATED                                       4
  19Q GAIN WILD-TYPE                                    21
                    vv
clus                 STOMACH ADENOCARCINOMA - NOT OTHERWISE SPECIFIED (NOS)
  19Q GAIN MUTATED                                                        5
  19Q GAIN WILD-TYPE                                                     82
                    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                                                 9
                    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                                                                     32
D33V4, multiclass
                    vv
clus                 T1 T2 T3 T4
  19Q GAIN MUTATED    0  8  4  5
  19Q GAIN WILD-TYPE  6 46 60 38
D33V5, multiclass
    clus
vv   19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  T1                0                  6
  T2                8                 46
  T3                4                 60
  T4                5                 38
                    vv
clus                 N0 N1 N2 N3
  19Q GAIN MUTATED    2  6  4  4
  19Q GAIN WILD-TYPE 54 55 25 16
D33V6, multiclass
    clus
vv   19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  N0                2                 54
  N1                6                 55
  N2                4                 25
  N3                4                 16
                    vv
clus                  M0  M1  MX
  19Q GAIN MUTATED    12   4   1
  19Q GAIN WILD-TYPE 134  14  12
D33V7, multiclass
    clus
vv   19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  M0               12                134
  M1                4                 14
  MX                1                 12
                    vv
clus                  I II III IV
  19Q GAIN MUTATED    2  2   4  8
  19Q GAIN WILD-TYPE 24 46  54 21
D33V8, multiclass
     clus
vv    19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  I                  2                 24
  II                 2                 46
  III                4                 54
  IV                 8                 21
D33V9, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED      1   16
  19Q GAIN WILD-TYPE    4  156
     clus
vv    19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  NO                 1                  4
  YES               16                156
                    vv
clus                  R0  R1  R2  RX
  19Q GAIN MUTATED     8   2   4   2
  19Q GAIN WILD-TYPE 115   5   8  23
D33V10, multiclass
    clus
vv   19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  R0                8                115
  R1                2                  5
  R2                4                  8
  RX                2                 23
D33V11, continuous

Clustering(34) Variable = 20p gain mutation analysis
D34V1, survival
                    sevent
clus2                 0  1
  20P GAIN MUTATED   46  7
  20P GAIN WILD-TYPE 76 11
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                53                 87 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                 7                 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-BR-A4J1 TCGA-BR-A4J4 TCGA-BR-A4J8 TCGA-BR-A4PF TCGA-CD-5799 
        0.95         0.72         0.53         0.23         0.72         0.69 
TCGA-CD-5801 TCGA-CG-4300 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4436 TCGA-CG-4438 
        0.49        20.02        27.02        15.95        52.96        54.05 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4444 TCGA-CG-4455 TCGA-CG-4466 TCGA-CG-4469 
        4.01        14.01        47.05        12.03        18.94         7.07 
TCGA-CG-5718 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5730 TCGA-D7-5577 TCGA-D7-5578 
        1.02        28.96        31.04         4.01         8.65         3.58 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6521 TCGA-D7-6525 TCGA-D7-6528 TCGA-D7-6818 
        4.54         9.80         8.19         5.95         1.68         4.04 
TCGA-D7-6822 TCGA-F1-6874 TCGA-F1-6875 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
        4.27         2.01        72.23         0.20         3.02         3.58 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8631 TCGA-IN-7806 TCGA-IN-7808 
        1.02        59.05         0.56         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-BR-8592 
        0.26         1.18         1.55         1.48         0.76         0.20 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J5 
        0.59         0.92         0.39         0.79         0.79         0.43 
TCGA-BR-A4J6 TCGA-BR-A4J9 TCGA-CD-5798 TCGA-CD-5800 TCGA-CD-5802 TCGA-CD-5803 
        0.13         0.10         0.82         0.36         0.30         0.07 
TCGA-CG-4301 TCGA-CG-4306 TCGA-CG-4437 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4460 
        3.02         1.02         8.05        29.98        19.07        21.99 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4472 TCGA-CG-4474 TCGA-CG-4477 TCGA-CG-5716 
        1.02         8.98        12.00         1.02         1.02         1.02 
TCGA-CG-5717 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
        6.94         1.02         0.99         5.98         0.95        70.06 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5728 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       12.03        15.02        65.10        55.04        21.07         7.99 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6526 TCGA-D7-6527 
       15.65         9.63         6.90         0.69         6.61         4.14 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6820 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6177 
        3.65         4.70         2.93         0.62         7.79         6.54 
TCGA-FP-7735 TCGA-HJ-7597 TCGA-IP-7968 
        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 
              3.58               1.02 
[1] "0.2 - 72.2 (3.6)" "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-BR-8592         TCGA-BR-A4IU         TCGA-BR-A4IV 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-BR-A4IY         TCGA-BR-A4IZ         TCGA-BR-A4J1 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-BR-A4J2         TCGA-BR-A4J4         TCGA-BR-A4J5 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-BR-A4J6         TCGA-BR-A4J8         TCGA-BR-A4J9 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-BR-A4PF         TCGA-CD-5798         TCGA-CD-5799 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-CD-5800         TCGA-CD-5801         TCGA-CD-5802 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-CD-5803         TCGA-CG-4300         TCGA-CG-4301 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-CG-4304         TCGA-CG-4305         TCGA-CG-4306 
  "20P GAIN MUTATED"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-CG-4436         TCGA-CG-4437         TCGA-CG-4438 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-CG-4440         TCGA-CG-4441         TCGA-CG-4443 
  "20P GAIN MUTATED"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-CG-4444         TCGA-CG-4449         TCGA-CG-4455 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-CG-4460         TCGA-CG-4462         TCGA-CG-4465 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-CG-4466         TCGA-CG-4469         TCGA-CG-4472 
  "20P GAIN MUTATED"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-CG-4474         TCGA-CG-4477         TCGA-CG-5716 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-CG-5717         TCGA-CG-5718         TCGA-CG-5719 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-CG-5720         TCGA-CG-5721         TCGA-CG-5722 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-CG-5723         TCGA-CG-5724         TCGA-CG-5725 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-CG-5726         TCGA-CG-5727         TCGA-CG-5728 
  "20P GAIN MUTATED"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-CG-5730         TCGA-CG-5732         TCGA-CG-5733 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-CG-5734         TCGA-D7-5577         TCGA-D7-5578 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED"   "20P GAIN MUTATED" 
        TCGA-D7-5579         TCGA-D7-6518         TCGA-D7-6519 
  "20P GAIN MUTATED"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-D7-6520         TCGA-D7-6521         TCGA-D7-6522 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-D7-6524         TCGA-D7-6525         TCGA-D7-6526 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-D7-6527         TCGA-D7-6528         TCGA-D7-6815 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-D7-6817         TCGA-D7-6818         TCGA-D7-6820 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-D7-6822         TCGA-EQ-5647         TCGA-EQ-8122 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-F1-6177         TCGA-F1-6874         TCGA-F1-6875 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED"   "20P GAIN MUTATED" 
        TCGA-FP-7735         TCGA-FP-7829         TCGA-FP-7916 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED"   "20P GAIN MUTATED" 
        TCGA-FP-7998         TCGA-FP-8099         TCGA-FP-8209 
  "20P GAIN MUTATED"   "20P GAIN MUTATED"   "20P GAIN MUTATED" 
        TCGA-FP-8631         TCGA-HJ-7597         TCGA-IN-7806 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-IN-7808         TCGA-IP-7968 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
  "20P GAIN MUTATED"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-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-BR-8592         TCGA-BR-A4IU         TCGA-BR-A4IV 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-BR-A4IY         TCGA-BR-A4IZ         TCGA-BR-A4J1 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-BR-A4J2         TCGA-BR-A4J4         TCGA-BR-A4J5 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-BR-A4J6         TCGA-BR-A4J8         TCGA-BR-A4J9 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-BR-A4PF         TCGA-CD-5798         TCGA-CD-5799 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-CD-5800         TCGA-CD-5801         TCGA-CD-5802 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-CD-5803         TCGA-CG-4300         TCGA-CG-4301 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-CG-4304         TCGA-CG-4305         TCGA-CG-4306 
  "20P GAIN MUTATED"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-CG-4436         TCGA-CG-4437         TCGA-CG-4438 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-CG-4440         TCGA-CG-4441         TCGA-CG-4443 
  "20P GAIN MUTATED"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-CG-4444         TCGA-CG-4449         TCGA-CG-4455 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-CG-4460         TCGA-CG-4462         TCGA-CG-4465 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-CG-4466         TCGA-CG-4469         TCGA-CG-4472 
  "20P GAIN MUTATED"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-CG-4474         TCGA-CG-4477         TCGA-CG-5716 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-CG-5717         TCGA-CG-5718         TCGA-CG-5719 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-CG-5720         TCGA-CG-5721         TCGA-CG-5722 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-CG-5723         TCGA-CG-5724         TCGA-CG-5725 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-CG-5726         TCGA-CG-5727         TCGA-CG-5728 
  "20P GAIN MUTATED"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-CG-5730         TCGA-CG-5732         TCGA-CG-5733 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-CG-5734         TCGA-D7-5577         TCGA-D7-5578 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED"   "20P GAIN MUTATED" 
        TCGA-D7-5579         TCGA-D7-6518         TCGA-D7-6519 
  "20P GAIN MUTATED"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-D7-6520         TCGA-D7-6521         TCGA-D7-6522 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-D7-6524         TCGA-D7-6525         TCGA-D7-6526 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-D7-6527         TCGA-D7-6528         TCGA-D7-6815 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-D7-6817         TCGA-D7-6818         TCGA-D7-6820 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-D7-6822         TCGA-EQ-5647         TCGA-EQ-8122 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-F1-6177         TCGA-F1-6874         TCGA-F1-6875 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED"   "20P GAIN MUTATED" 
        TCGA-FP-7735         TCGA-FP-7829         TCGA-FP-7916 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED"   "20P GAIN MUTATED" 
        TCGA-FP-7998         TCGA-FP-8099         TCGA-FP-8209 
  "20P GAIN MUTATED"   "20P GAIN MUTATED"   "20P GAIN MUTATED" 
        TCGA-FP-8631         TCGA-HJ-7597         TCGA-IN-7806 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-IN-7808         TCGA-IP-7968 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
  "20P GAIN MUTATED"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-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-BR-8592         TCGA-BR-A4IU         TCGA-BR-A4IV 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-BR-A4IY         TCGA-BR-A4IZ         TCGA-BR-A4J1 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-BR-A4J2         TCGA-BR-A4J4         TCGA-BR-A4J5 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-BR-A4J6         TCGA-BR-A4J8         TCGA-BR-A4J9 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-BR-A4PF         TCGA-CD-5798         TCGA-CD-5799 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-CD-5800         TCGA-CD-5801         TCGA-CD-5802 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-CD-5803         TCGA-CG-4300         TCGA-CG-4301 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-CG-4304         TCGA-CG-4305         TCGA-CG-4306 
  "20P GAIN MUTATED"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-CG-4436         TCGA-CG-4437         TCGA-CG-4438 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-CG-4440         TCGA-CG-4441         TCGA-CG-4443 
  "20P GAIN MUTATED"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-CG-4444         TCGA-CG-4449         TCGA-CG-4455 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-CG-4460         TCGA-CG-4462         TCGA-CG-4465 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-CG-4466         TCGA-CG-4469         TCGA-CG-4472 
  "20P GAIN MUTATED"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-CG-4474         TCGA-CG-4477         TCGA-CG-5716 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-CG-5717         TCGA-CG-5718         TCGA-CG-5719 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-CG-5720         TCGA-CG-5721         TCGA-CG-5722 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-CG-5723         TCGA-CG-5724         TCGA-CG-5725 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-CG-5726         TCGA-CG-5727         TCGA-CG-5728 
  "20P GAIN MUTATED"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-CG-5730         TCGA-CG-5732         TCGA-CG-5733 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-CG-5734         TCGA-D7-5577         TCGA-D7-5578 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED"   "20P GAIN MUTATED" 
        TCGA-D7-5579         TCGA-D7-6518         TCGA-D7-6519 
  "20P GAIN MUTATED"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-D7-6520         TCGA-D7-6521         TCGA-D7-6522 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-D7-6524         TCGA-D7-6525         TCGA-D7-6526 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-D7-6527         TCGA-D7-6528         TCGA-D7-6815 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-D7-6817         TCGA-D7-6818         TCGA-D7-6820 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-D7-6822         TCGA-EQ-5647         TCGA-EQ-8122 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-F1-6177         TCGA-F1-6874         TCGA-F1-6875 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED"   "20P GAIN MUTATED" 
        TCGA-FP-7735         TCGA-FP-7829         TCGA-FP-7916 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED"   "20P GAIN MUTATED" 
        TCGA-FP-7998         TCGA-FP-8099         TCGA-FP-8209 
  "20P GAIN MUTATED"   "20P GAIN MUTATED"   "20P GAIN MUTATED" 
        TCGA-FP-8631         TCGA-HJ-7597         TCGA-IN-7806 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-IN-7808         TCGA-IP-7968 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
[1] "hr=" "2"  
D34V2, continuous
D34V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED     14   53
  20P GAIN WILD-TYPE   56   54
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  FEMALE               14                 56
  MALE                 53                 54
                    vv
clus                 STOMACH ADENOCARCINOMA - DIFFUSE TYPE
  20P GAIN MUTATED                                      10
  20P GAIN WILD-TYPE                                    15
                    vv
clus                 STOMACH ADENOCARCINOMA - NOT OTHERWISE SPECIFIED (NOS)
  20P GAIN MUTATED                                                       34
  20P GAIN WILD-TYPE                                                     53
                    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                                                 7
                    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                                                                     22
D34V4, multiclass
                    vv
clus                 T1 T2 T3 T4
  20P GAIN MUTATED    1 24 29  9
  20P GAIN WILD-TYPE  5 30 35 34
D34V5, multiclass
    clus
vv   20P GAIN MUTATED 20P GAIN WILD-TYPE
  T1                1                  5
  T2               24                 30
  T3               29                 35
  T4                9                 34
                    vv
clus                 N0 N1 N2 N3
  20P GAIN MUTATED   17 22 12 10
  20P GAIN WILD-TYPE 39 39 17 10
D34V6, multiclass
    clus
vv   20P GAIN MUTATED 20P GAIN WILD-TYPE
  N0               17                 39
  N1               22                 39
  N2               12                 17
  N3               10                 10
                    vv
clus                 M0 M1 MX
  20P GAIN MUTATED   58  3  6
  20P GAIN WILD-TYPE 88 15  7
D34V7, multiclass
    clus
vv   20P GAIN MUTATED 20P GAIN WILD-TYPE
  M0               58                 88
  M1                3                 15
  MX                6                  7
                    vv
clus                  I II III IV
  20P GAIN MUTATED    9 15  28  7
  20P GAIN WILD-TYPE 17 33  30 22
D34V8, multiclass
     clus
vv    20P GAIN MUTATED 20P GAIN WILD-TYPE
  I                  9                 17
  II                15                 33
  III               28                 30
  IV                 7                 22
D34V9, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED      1   66
  20P GAIN WILD-TYPE    4  106
     clus
vv    20P GAIN MUTATED 20P GAIN WILD-TYPE
  NO                 1                  4
  YES               66                106
                    vv
clus                 R0 R1 R2 RX
  20P GAIN MUTATED   45  4  2 12
  20P GAIN WILD-TYPE 78  3 10 13
D34V10, multiclass
    clus
vv   20P GAIN MUTATED 20P GAIN WILD-TYPE
  R0               45                 78
  R1                4                  3
  R2                2                 10
  RX               12                 13
D34V11, continuous

Clustering(35) Variable = 20q gain mutation analysis
D35V1, survival
                    sevent
clus2                 0  1
  20Q GAIN MUTATED   53  8
  20Q GAIN WILD-TYPE 69 10
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                61                 79 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                 8                 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-BR-A4J1 TCGA-BR-A4J4 TCGA-BR-A4J8 TCGA-BR-A4PF TCGA-CD-5799 
        0.95         0.72         0.53         0.23         0.72         0.69 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CG-4300 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4436 
        0.36         0.49        20.02        27.02        15.95        52.96 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4444 TCGA-CG-4455 TCGA-CG-4466 
       54.05         4.01        14.01        47.05        12.03        18.94 
TCGA-CG-4469 TCGA-CG-5718 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5730 
        7.07         1.02        12.03        28.96        31.04         4.01 
TCGA-CG-5732 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6520 
       55.04         8.65         3.58         4.54         9.80         9.63 
TCGA-D7-6521 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6818 
        8.19         5.95         6.61         1.68         3.65         4.04 
TCGA-D7-6822 TCGA-F1-6874 TCGA-F1-6875 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
        4.27         2.01        72.23         0.39         0.20         3.02 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8631 TCGA-IN-7806 TCGA-IN-7808 
        3.58         1.02        59.05         0.56         6.87         3.55 
TCGA-IP-7968 
        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-BR-8592 
        0.26         1.18         1.55         1.48         0.76         0.20 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J5 
        0.59         0.92         0.39         0.79         0.79         0.43 
TCGA-BR-A4J6 TCGA-BR-A4J9 TCGA-CD-5798 TCGA-CD-5802 TCGA-CD-5803 TCGA-CG-4301 
        0.13         0.10         0.82         0.30         0.07         3.02 
TCGA-CG-4306 TCGA-CG-4437 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4460 TCGA-CG-4462 
        1.02         8.05        29.98        19.07        21.99         1.02 
TCGA-CG-4465 TCGA-CG-4472 TCGA-CG-4474 TCGA-CG-4477 TCGA-CG-5716 TCGA-CG-5717 
        8.98        12.00         1.02         1.02         1.02         6.94 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5725 
        1.02         0.99         5.98         0.95        70.06        15.02 
TCGA-CG-5728 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-6519 TCGA-D7-6522 TCGA-D7-6524 
       65.10        21.07         7.99        15.65         6.90         0.69 
TCGA-D7-6527 TCGA-D7-6817 TCGA-D7-6820 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6177 
        4.14         4.70         2.93         0.62         7.79         6.54 
TCGA-HJ-7597 
       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 
              3.58               0.99 
[1] "0.2 - 72.2 (3.6)" "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-BR-8592         TCGA-BR-A4IU         TCGA-BR-A4IV 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-BR-A4IY         TCGA-BR-A4IZ         TCGA-BR-A4J1 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-BR-A4J2         TCGA-BR-A4J4         TCGA-BR-A4J5 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-BR-A4J6         TCGA-BR-A4J8         TCGA-BR-A4J9 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-BR-A4PF         TCGA-CD-5798         TCGA-CD-5799 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-CD-5800         TCGA-CD-5801         TCGA-CD-5802 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-CD-5803         TCGA-CG-4300         TCGA-CG-4301 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-CG-4304         TCGA-CG-4305         TCGA-CG-4306 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-CG-4436         TCGA-CG-4437         TCGA-CG-4438 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-CG-4440         TCGA-CG-4441         TCGA-CG-4443 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-CG-4444         TCGA-CG-4449         TCGA-CG-4455 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-CG-4460         TCGA-CG-4462         TCGA-CG-4465 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-CG-4466         TCGA-CG-4469         TCGA-CG-4472 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-CG-4474         TCGA-CG-4477         TCGA-CG-5716 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-CG-5717         TCGA-CG-5718         TCGA-CG-5719 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-CG-5720         TCGA-CG-5721         TCGA-CG-5722 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-CG-5723         TCGA-CG-5724         TCGA-CG-5725 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-CG-5726         TCGA-CG-5727         TCGA-CG-5728 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-CG-5730         TCGA-CG-5732         TCGA-CG-5733 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-CG-5734         TCGA-D7-5577         TCGA-D7-5578 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-D7-5579         TCGA-D7-6518         TCGA-D7-6519 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-D7-6520         TCGA-D7-6521         TCGA-D7-6522 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-D7-6524         TCGA-D7-6525         TCGA-D7-6526 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-D7-6527         TCGA-D7-6528         TCGA-D7-6815 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-D7-6817         TCGA-D7-6818         TCGA-D7-6820 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-D7-6822         TCGA-EQ-5647         TCGA-EQ-8122 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-F1-6177         TCGA-F1-6874         TCGA-F1-6875 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-FP-7735         TCGA-FP-7829         TCGA-FP-7916 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-FP-7998         TCGA-FP-8099         TCGA-FP-8209 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-FP-8631         TCGA-HJ-7597         TCGA-IN-7806 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-IN-7808         TCGA-IP-7968 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-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-BR-8592         TCGA-BR-A4IU         TCGA-BR-A4IV 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-BR-A4IY         TCGA-BR-A4IZ         TCGA-BR-A4J1 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-BR-A4J2         TCGA-BR-A4J4         TCGA-BR-A4J5 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-BR-A4J6         TCGA-BR-A4J8         TCGA-BR-A4J9 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-BR-A4PF         TCGA-CD-5798         TCGA-CD-5799 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-CD-5800         TCGA-CD-5801         TCGA-CD-5802 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-CD-5803         TCGA-CG-4300         TCGA-CG-4301 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-CG-4304         TCGA-CG-4305         TCGA-CG-4306 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-CG-4436         TCGA-CG-4437         TCGA-CG-4438 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-CG-4440         TCGA-CG-4441         TCGA-CG-4443 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-CG-4444         TCGA-CG-4449         TCGA-CG-4455 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-CG-4460         TCGA-CG-4462         TCGA-CG-4465 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-CG-4466         TCGA-CG-4469         TCGA-CG-4472 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-CG-4474         TCGA-CG-4477         TCGA-CG-5716 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-CG-5717         TCGA-CG-5718         TCGA-CG-5719 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-CG-5720         TCGA-CG-5721         TCGA-CG-5722 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-CG-5723         TCGA-CG-5724         TCGA-CG-5725 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-CG-5726         TCGA-CG-5727         TCGA-CG-5728 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-CG-5730         TCGA-CG-5732         TCGA-CG-5733 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-CG-5734         TCGA-D7-5577         TCGA-D7-5578 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-D7-5579         TCGA-D7-6518         TCGA-D7-6519 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-D7-6520         TCGA-D7-6521         TCGA-D7-6522 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-D7-6524         TCGA-D7-6525         TCGA-D7-6526 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-D7-6527         TCGA-D7-6528         TCGA-D7-6815 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-D7-6817         TCGA-D7-6818         TCGA-D7-6820 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-D7-6822         TCGA-EQ-5647         TCGA-EQ-8122 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-F1-6177         TCGA-F1-6874         TCGA-F1-6875 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-FP-7735         TCGA-FP-7829         TCGA-FP-7916 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-FP-7998         TCGA-FP-8099         TCGA-FP-8209 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-FP-8631         TCGA-HJ-7597         TCGA-IN-7806 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-IN-7808         TCGA-IP-7968 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-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-BR-8592         TCGA-BR-A4IU         TCGA-BR-A4IV 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-BR-A4IY         TCGA-BR-A4IZ         TCGA-BR-A4J1 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-BR-A4J2         TCGA-BR-A4J4         TCGA-BR-A4J5 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-BR-A4J6         TCGA-BR-A4J8         TCGA-BR-A4J9 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-BR-A4PF         TCGA-CD-5798         TCGA-CD-5799 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-CD-5800         TCGA-CD-5801         TCGA-CD-5802 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-CD-5803         TCGA-CG-4300         TCGA-CG-4301 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-CG-4304         TCGA-CG-4305         TCGA-CG-4306 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-CG-4436         TCGA-CG-4437         TCGA-CG-4438 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-CG-4440         TCGA-CG-4441         TCGA-CG-4443 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-CG-4444         TCGA-CG-4449         TCGA-CG-4455 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-CG-4460         TCGA-CG-4462         TCGA-CG-4465 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-CG-4466         TCGA-CG-4469         TCGA-CG-4472 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-CG-4474         TCGA-CG-4477         TCGA-CG-5716 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-CG-5717         TCGA-CG-5718         TCGA-CG-5719 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-CG-5720         TCGA-CG-5721         TCGA-CG-5722 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-CG-5723         TCGA-CG-5724         TCGA-CG-5725 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-CG-5726         TCGA-CG-5727         TCGA-CG-5728 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-CG-5730         TCGA-CG-5732         TCGA-CG-5733 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-CG-5734         TCGA-D7-5577         TCGA-D7-5578 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-D7-5579         TCGA-D7-6518         TCGA-D7-6519 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-D7-6520         TCGA-D7-6521         TCGA-D7-6522 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-D7-6524         TCGA-D7-6525         TCGA-D7-6526 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-D7-6527         TCGA-D7-6528         TCGA-D7-6815 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-D7-6817         TCGA-D7-6818         TCGA-D7-6820 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-D7-6822         TCGA-EQ-5647         TCGA-EQ-8122 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-F1-6177         TCGA-F1-6874         TCGA-F1-6875 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-FP-7735         TCGA-FP-7829         TCGA-FP-7916 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-FP-7998         TCGA-FP-8099         TCGA-FP-8209 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-FP-8631         TCGA-HJ-7597         TCGA-IN-7806 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-IN-7808         TCGA-IP-7968 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
[1] "hr=" "2"  
D35V2, continuous
D35V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED     19   62
  20Q GAIN WILD-TYPE   51   45
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  FEMALE               19                 51
  MALE                 62                 45
                    vv
clus                 STOMACH ADENOCARCINOMA - DIFFUSE TYPE
  20Q GAIN MUTATED                                      11
  20Q GAIN WILD-TYPE                                    14
                    vv
clus                 STOMACH ADENOCARCINOMA - NOT OTHERWISE SPECIFIED (NOS)
  20Q GAIN MUTATED                                                       40
  20Q GAIN WILD-TYPE                                                     47
                    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                                                   3
  20Q GAIN WILD-TYPE                                                 7
                    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                                                                       16
  20Q GAIN WILD-TYPE                                                                     20
D35V4, multiclass
                    vv
clus                 T1 T2 T3 T4
  20Q GAIN MUTATED    2 29 37  9
  20Q GAIN WILD-TYPE  4 25 27 34
D35V5, multiclass
    clus
vv   20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  T1                2                  4
  T2               29                 25
  T3               37                 27
  T4                9                 34
                    vv
clus                 N0 N1 N2 N3
  20Q GAIN MUTATED   22 25 16 12
  20Q GAIN WILD-TYPE 34 36 13  8
D35V6, multiclass
    clus
vv   20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  N0               22                 34
  N1               25                 36
  N2               16                 13
  N3               12                  8
                    vv
clus                 M0 M1 MX
  20Q GAIN MUTATED   68  4  9
  20Q GAIN WILD-TYPE 78 14  4
D35V7, multiclass
    clus
vv   20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  M0               68                 78
  M1                4                 14
  MX                9                  4
                    vv
clus                  I II III IV
  20Q GAIN MUTATED   12 19  33  9
  20Q GAIN WILD-TYPE 14 29  25 20
D35V8, multiclass
     clus
vv    20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  I                 12                 14
  II                19                 29
  III               33                 25
  IV                 9                 20
D35V9, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED      2   79
  20Q GAIN WILD-TYPE    3   93
     clus
vv    20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  NO                 2                  3
  YES               79                 93
                    vv
clus                 R0 R1 R2 RX
  20Q GAIN MUTATED   56  4  3 12
  20Q GAIN WILD-TYPE 67  3  9 13
D35V10, multiclass
    clus
vv   20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  R0               56                 67
  R1                4                  3
  R2                3                  9
  RX               12                 13
D35V11, continuous

Clustering(36) Variable = 22q gain mutation analysis
D36V1, survival
                    sevent
clus2                  0   1
  22Q GAIN MUTATED     3   0
  22Q GAIN WILD-TYPE 119  18
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                 3                137 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                 0                 18 
$`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-BR-8592 TCGA-BR-A4IU TCGA-BR-A4IV 
        1.55         1.48         0.76         0.20         0.59         0.92 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
        0.39         0.79         0.72         0.79         0.53         0.43 
TCGA-BR-A4J6 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PF TCGA-CD-5798 TCGA-CD-5799 
        0.13         0.23         0.10         0.72         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-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-FP-8099 TCGA-FP-8209 
        0.39         0.20         3.02         3.58         1.02        59.05 
TCGA-FP-8631 TCGA-HJ-7597 TCGA-IN-7806 TCGA-IN-7808 TCGA-IP-7968 
        0.56        26.43         6.87         3.55         2.53 

  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
              0.10               0.07 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
              4.54              72.23 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
              1.25               1.22 
[1] "0.1 - 4.5 (1.2)"  "0.1 - 72.2 (1.2)"
        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-BR-8592         TCGA-BR-A4IU         TCGA-BR-A4IV 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BR-A4IY         TCGA-BR-A4IZ         TCGA-BR-A4J1 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BR-A4J2         TCGA-BR-A4J4         TCGA-BR-A4J5 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BR-A4J6         TCGA-BR-A4J8         TCGA-BR-A4J9 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BR-A4PF         TCGA-CD-5798         TCGA-CD-5799 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-CD-5800         TCGA-CD-5801         TCGA-CD-5802 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-CD-5803         TCGA-CG-4300         TCGA-CG-4301 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-CG-4304         TCGA-CG-4305         TCGA-CG-4306 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-CG-4436         TCGA-CG-4437         TCGA-CG-4438 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-CG-4440         TCGA-CG-4441         TCGA-CG-4443 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-CG-4444         TCGA-CG-4449         TCGA-CG-4455 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-CG-4460         TCGA-CG-4462         TCGA-CG-4465 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-CG-4466         TCGA-CG-4469         TCGA-CG-4472 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-CG-4474         TCGA-CG-4477         TCGA-CG-5716 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-CG-5717         TCGA-CG-5718         TCGA-CG-5719 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-CG-5720         TCGA-CG-5721         TCGA-CG-5722 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-CG-5723         TCGA-CG-5724         TCGA-CG-5725 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-CG-5726         TCGA-CG-5727         TCGA-CG-5728 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-CG-5730         TCGA-CG-5732         TCGA-CG-5733 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-CG-5734         TCGA-D7-5577         TCGA-D7-5578 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-D7-5579         TCGA-D7-6518         TCGA-D7-6519 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-D7-6520         TCGA-D7-6521         TCGA-D7-6522 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-D7-6524         TCGA-D7-6525         TCGA-D7-6526 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-D7-6527         TCGA-D7-6528         TCGA-D7-6815 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-D7-6817         TCGA-D7-6818         TCGA-D7-6820 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-D7-6822         TCGA-EQ-5647         TCGA-EQ-8122 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-F1-6177         TCGA-F1-6874         TCGA-F1-6875 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-FP-7735         TCGA-FP-7829         TCGA-FP-7916 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-FP-7998         TCGA-FP-8099         TCGA-FP-8209 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-FP-8631         TCGA-HJ-7597         TCGA-IN-7806 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-IN-7808         TCGA-IP-7968 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-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-BR-8592         TCGA-BR-A4IU         TCGA-BR-A4IV 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BR-A4IY         TCGA-BR-A4IZ         TCGA-BR-A4J1 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BR-A4J2         TCGA-BR-A4J4         TCGA-BR-A4J5 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BR-A4J6         TCGA-BR-A4J8         TCGA-BR-A4J9 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BR-A4PF         TCGA-CD-5798         TCGA-CD-5799 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-CD-5800         TCGA-CD-5801         TCGA-CD-5802 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-CD-5803         TCGA-CG-4300         TCGA-CG-4301 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-CG-4304         TCGA-CG-4305         TCGA-CG-4306 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-CG-4436         TCGA-CG-4437         TCGA-CG-4438 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-CG-4440         TCGA-CG-4441         TCGA-CG-4443 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-CG-4444         TCGA-CG-4449         TCGA-CG-4455 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-CG-4460         TCGA-CG-4462         TCGA-CG-4465 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-CG-4466         TCGA-CG-4469         TCGA-CG-4472 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-CG-4474         TCGA-CG-4477         TCGA-CG-5716 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-CG-5717         TCGA-CG-5718         TCGA-CG-5719 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-CG-5720         TCGA-CG-5721         TCGA-CG-5722 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-CG-5723         TCGA-CG-5724         TCGA-CG-5725 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-CG-5726         TCGA-CG-5727         TCGA-CG-5728 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-CG-5730         TCGA-CG-5732         TCGA-CG-5733 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-CG-5734         TCGA-D7-5577         TCGA-D7-5578 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-D7-5579         TCGA-D7-6518         TCGA-D7-6519 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-D7-6520         TCGA-D7-6521         TCGA-D7-6522 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-D7-6524         TCGA-D7-6525         TCGA-D7-6526 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-D7-6527         TCGA-D7-6528         TCGA-D7-6815 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-D7-6817         TCGA-D7-6818         TCGA-D7-6820 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-D7-6822         TCGA-EQ-5647         TCGA-EQ-8122 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-F1-6177         TCGA-F1-6874         TCGA-F1-6875 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-FP-7735         TCGA-FP-7829         TCGA-FP-7916 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-FP-7998         TCGA-FP-8099         TCGA-FP-8209 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-FP-8631         TCGA-HJ-7597         TCGA-IN-7806 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-IN-7808         TCGA-IP-7968 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-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-BR-8592         TCGA-BR-A4IU         TCGA-BR-A4IV 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BR-A4IY         TCGA-BR-A4IZ         TCGA-BR-A4J1 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BR-A4J2         TCGA-BR-A4J4         TCGA-BR-A4J5 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BR-A4J6         TCGA-BR-A4J8         TCGA-BR-A4J9 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BR-A4PF         TCGA-CD-5798         TCGA-CD-5799 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-CD-5800         TCGA-CD-5801         TCGA-CD-5802 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-CD-5803         TCGA-CG-4300         TCGA-CG-4301 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-CG-4304         TCGA-CG-4305         TCGA-CG-4306 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-CG-4436         TCGA-CG-4437         TCGA-CG-4438 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-CG-4440         TCGA-CG-4441         TCGA-CG-4443 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-CG-4444         TCGA-CG-4449         TCGA-CG-4455 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-CG-4460         TCGA-CG-4462         TCGA-CG-4465 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-CG-4466         TCGA-CG-4469         TCGA-CG-4472 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-CG-4474         TCGA-CG-4477         TCGA-CG-5716 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-CG-5717         TCGA-CG-5718         TCGA-CG-5719 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-CG-5720         TCGA-CG-5721         TCGA-CG-5722 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-CG-5723         TCGA-CG-5724         TCGA-CG-5725 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-CG-5726         TCGA-CG-5727         TCGA-CG-5728 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-CG-5730         TCGA-CG-5732         TCGA-CG-5733 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-CG-5734         TCGA-D7-5577         TCGA-D7-5578 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-D7-5579         TCGA-D7-6518         TCGA-D7-6519 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-D7-6520         TCGA-D7-6521         TCGA-D7-6522 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-D7-6524         TCGA-D7-6525         TCGA-D7-6526 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-D7-6527         TCGA-D7-6528         TCGA-D7-6815 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-D7-6817         TCGA-D7-6818         TCGA-D7-6820 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-D7-6822         TCGA-EQ-5647         TCGA-EQ-8122 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-F1-6177         TCGA-F1-6874         TCGA-F1-6875 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-FP-7735         TCGA-FP-7829         TCGA-FP-7916 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-FP-7998         TCGA-FP-8099         TCGA-FP-8209 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-FP-8631         TCGA-HJ-7597         TCGA-IN-7806 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-IN-7808         TCGA-IP-7968 
"22Q GAIN WILD-TYPE" "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   69  105
        clus
vv       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  FEMALE                1                 69
  MALE                  2                105
                    vv
clus                 STOMACH ADENOCARCINOMA - DIFFUSE TYPE
  22Q GAIN MUTATED                                       1
  22Q GAIN WILD-TYPE                                    24
                    vv
clus                 STOMACH ADENOCARCINOMA - NOT OTHERWISE SPECIFIED (NOS)
  22Q GAIN MUTATED                                                        1
  22Q GAIN WILD-TYPE                                                     86
                    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                                                10
                    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                                                                     35
D36V4, multiclass
                    vv
clus                 T1 T2 T3 T4
  22Q GAIN MUTATED    0  1  2  0
  22Q GAIN WILD-TYPE  6 53 62 43
D36V5, multiclass
    clus
vv   22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  T1                0                  6
  T2                1                 53
  T3                2                 62
  T4                0                 43
                    vv
clus                 N0 N1 N2 N3
  22Q GAIN MUTATED    2  0  1  0
  22Q GAIN WILD-TYPE 54 61 28 20
D36V6, multiclass
    clus
vv   22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  N0                2                 54
  N1                0                 61
  N2                1                 28
  N3                0                 20
                    vv
clus                  M0  M1  MX
  22Q GAIN MUTATED     3   0   0
  22Q GAIN WILD-TYPE 143  18  13
D36V7, multiclass
    clus
vv   22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  M0                3                143
  M1                0                 18
  MX                0                 13
                    vv
clus                  I II III IV
  22Q GAIN MUTATED    1  2   0  0
  22Q GAIN WILD-TYPE 25 46  58 29
D36V8, multiclass
     clus
vv    22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  I                  1                 25
  II                 2                 46
  III                0                 58
  IV                 0                 29
D36V9, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED      0    3
  22Q GAIN WILD-TYPE    5  169
     clus
vv    22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  NO                 0                  5
  YES                3                169
                    vv
clus                  R0  R1  R2  RX
  22Q GAIN MUTATED     3   0   0   0
  22Q GAIN WILD-TYPE 120   7  12  25
D36V10, multiclass
    clus
vv   22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  R0                3                120
  R1                0                  7
  R2                0                 12
  RX                0                 25
D36V11, continuous
[1] "Remove cluster labels:" "22Q GAIN MUTATED"      
clus
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                 2                131 
        TCGA-B7-5816         TCGA-BR-4183         TCGA-BR-4184 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BR-4188         TCGA-BR-4191         TCGA-BR-4253 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BR-4255         TCGA-BR-4256         TCGA-BR-4267 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BR-4279         TCGA-BR-4280         TCGA-BR-4361 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BR-4362         TCGA-BR-4367         TCGA-BR-4368 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BR-6452         TCGA-BR-6453         TCGA-BR-6454 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6456         TCGA-BR-6457 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BR-6458         TCGA-BR-6563         TCGA-BR-6564 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BR-6565         TCGA-BR-6566         TCGA-BR-6705 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BR-6706         TCGA-BR-6707         TCGA-BR-6709 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BR-6710         TCGA-BR-6801         TCGA-BR-6802 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BR-6803         TCGA-BR-6852         TCGA-BR-7196 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BR-7197         TCGA-BR-7703         TCGA-BR-7707 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "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-7851         TCGA-BR-7901 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BR-7957         TCGA-BR-7958         TCGA-BR-7959 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BR-8059         TCGA-BR-8060         TCGA-BR-8077 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BR-8078         TCGA-BR-8080         TCGA-BR-8081 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BR-8284         TCGA-BR-8285         TCGA-BR-8286 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BR-8289         TCGA-BR-8291         TCGA-BR-8295 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BR-8296         TCGA-BR-8297         TCGA-BR-8592 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BR-A4IU         TCGA-BR-A4IV         TCGA-BR-A4IY 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BR-A4IZ         TCGA-BR-A4J1         TCGA-BR-A4J2 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BR-A4J4         TCGA-BR-A4J5         TCGA-BR-A4J6 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BR-A4J8         TCGA-BR-A4J9         TCGA-BR-A4PF 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-CD-5804         TCGA-CG-5717         TCGA-CG-5718 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-CG-5719         TCGA-CG-5720         TCGA-CG-5721 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-CG-5722         TCGA-CG-5723         TCGA-CG-5724 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-CG-5725         TCGA-CG-5726         TCGA-CG-5727 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-CG-5728         TCGA-CG-5730         TCGA-CG-5732 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-CG-5733         TCGA-CG-5734         TCGA-D7-5577 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-D7-5578         TCGA-D7-5579         TCGA-D7-6518 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-D7-6519         TCGA-D7-6520         TCGA-D7-6521 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-D7-6522         TCGA-D7-6524         TCGA-D7-6525 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-D7-6526         TCGA-D7-6527         TCGA-D7-6528 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-D7-6815         TCGA-D7-6817         TCGA-D7-6818 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-D7-6820         TCGA-D7-6822         TCGA-EQ-5647 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EQ-8122         TCGA-F1-6177         TCGA-F1-6874 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-F1-6875         TCGA-FP-7735         TCGA-FP-7829 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-FP-7916         TCGA-FP-7998         TCGA-FP-8099 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-FP-8209         TCGA-FP-8631         TCGA-HF-7131 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-HF-7132         TCGA-HF-7133         TCGA-HF-7134 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-HF-7136         TCGA-HJ-7597         TCGA-IN-7806 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-IN-7808         TCGA-IP-7968 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 

Clustering(37) Variable = 1p loss mutation analysis
D37V1, survival
                   sevent
clus2                 0   1
  1P LOSS MUTATED     5   2
  1P LOSS WILD-TYPE 117  16
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
                7               133 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
                2                16 
$`1P LOSS MUTATED`
TCGA-BR-A4PF TCGA-CG-4301 TCGA-CG-5719 TCGA-CG-5724 TCGA-CG-5730 TCGA-D7-6519 
        0.72         3.02         1.02        12.03         4.01        15.65 
TCGA-EQ-5647 
        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-BR-8592 TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        0.20         0.59         0.92         0.39         0.79         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J8 TCGA-BR-A4J9 
        0.79         0.53         0.43         0.13         0.23         0.10 
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-D7-6520 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-D7-6822 TCGA-EQ-8122 TCGA-F1-6177 
        4.70         4.04         2.93         4.27         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-FP-8099 TCGA-FP-8209 TCGA-FP-8631 TCGA-HJ-7597 TCGA-IN-7806 TCGA-IN-7808 
        1.02        59.05         0.56        26.43         6.87         3.55 
TCGA-IP-7968 
        2.53 

  1P LOSS MUTATED 1P LOSS WILD-TYPE 
             0.62              0.07 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
            15.65             72.23 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
             3.02              1.22 
[1] "0.6 - 15.7 (3.0)" "0.1 - 72.2 (1.2)"
       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-BR-8592        TCGA-BR-A4IU        TCGA-BR-A4IV        TCGA-BR-A4IY 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BR-A4IZ        TCGA-BR-A4J1        TCGA-BR-A4J2        TCGA-BR-A4J4 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BR-A4J5        TCGA-BR-A4J6        TCGA-BR-A4J8        TCGA-BR-A4J9 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BR-A4PF        TCGA-CD-5798        TCGA-CD-5799        TCGA-CD-5800 
  "1P LOSS MUTATED" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-CD-5801        TCGA-CD-5802        TCGA-CD-5803        TCGA-CG-4300 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-CG-4301        TCGA-CG-4304        TCGA-CG-4305        TCGA-CG-4306 
  "1P LOSS MUTATED" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-CG-4436        TCGA-CG-4437        TCGA-CG-4438        TCGA-CG-4440 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-CG-4441        TCGA-CG-4443        TCGA-CG-4444        TCGA-CG-4449 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-CG-4455        TCGA-CG-4460        TCGA-CG-4462        TCGA-CG-4465 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-CG-4466        TCGA-CG-4469        TCGA-CG-4472        TCGA-CG-4474 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-CG-4477        TCGA-CG-5716        TCGA-CG-5717        TCGA-CG-5718 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-CG-5719        TCGA-CG-5720        TCGA-CG-5721        TCGA-CG-5722 
  "1P LOSS MUTATED" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-CG-5723        TCGA-CG-5724        TCGA-CG-5725        TCGA-CG-5726 
"1P LOSS WILD-TYPE"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-CG-5727        TCGA-CG-5728        TCGA-CG-5730        TCGA-CG-5732 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE" 
       TCGA-CG-5733        TCGA-CG-5734        TCGA-D7-5577        TCGA-D7-5578 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-D7-5579        TCGA-D7-6518        TCGA-D7-6519        TCGA-D7-6520 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE" 
       TCGA-D7-6521        TCGA-D7-6522        TCGA-D7-6524        TCGA-D7-6525 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-D7-6526        TCGA-D7-6527        TCGA-D7-6528        TCGA-D7-6815 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-D7-6817        TCGA-D7-6818        TCGA-D7-6820        TCGA-D7-6822 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EQ-5647        TCGA-EQ-8122        TCGA-F1-6177        TCGA-F1-6874 
  "1P LOSS MUTATED" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-F1-6875        TCGA-FP-7735        TCGA-FP-7829        TCGA-FP-7916 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-FP-7998        TCGA-FP-8099        TCGA-FP-8209        TCGA-FP-8631 
"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-BR-8592        TCGA-BR-A4IU        TCGA-BR-A4IV        TCGA-BR-A4IY 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BR-A4IZ        TCGA-BR-A4J1        TCGA-BR-A4J2        TCGA-BR-A4J4 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BR-A4J5        TCGA-BR-A4J6        TCGA-BR-A4J8        TCGA-BR-A4J9 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BR-A4PF        TCGA-CD-5798        TCGA-CD-5799        TCGA-CD-5800 
  "1P LOSS MUTATED" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-CD-5801        TCGA-CD-5802        TCGA-CD-5803        TCGA-CG-4300 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-CG-4301        TCGA-CG-4304        TCGA-CG-4305        TCGA-CG-4306 
  "1P LOSS MUTATED" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-CG-4436        TCGA-CG-4437        TCGA-CG-4438        TCGA-CG-4440 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-CG-4441        TCGA-CG-4443        TCGA-CG-4444        TCGA-CG-4449 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-CG-4455        TCGA-CG-4460        TCGA-CG-4462        TCGA-CG-4465 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-CG-4466        TCGA-CG-4469        TCGA-CG-4472        TCGA-CG-4474 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-CG-4477        TCGA-CG-5716        TCGA-CG-5717        TCGA-CG-5718 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-CG-5719        TCGA-CG-5720        TCGA-CG-5721        TCGA-CG-5722 
  "1P LOSS MUTATED" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-CG-5723        TCGA-CG-5724        TCGA-CG-5725        TCGA-CG-5726 
"1P LOSS WILD-TYPE"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-CG-5727        TCGA-CG-5728        TCGA-CG-5730        TCGA-CG-5732 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE" 
       TCGA-CG-5733        TCGA-CG-5734        TCGA-D7-5577        TCGA-D7-5578 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-D7-5579        TCGA-D7-6518        TCGA-D7-6519        TCGA-D7-6520 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE" 
       TCGA-D7-6521        TCGA-D7-6522        TCGA-D7-6524        TCGA-D7-6525 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-D7-6526        TCGA-D7-6527        TCGA-D7-6528        TCGA-D7-6815 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-D7-6817        TCGA-D7-6818        TCGA-D7-6820        TCGA-D7-6822 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EQ-5647        TCGA-EQ-8122        TCGA-F1-6177        TCGA-F1-6874 
  "1P LOSS MUTATED" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-F1-6875        TCGA-FP-7735        TCGA-FP-7829        TCGA-FP-7916 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-FP-7998        TCGA-FP-8099        TCGA-FP-8209        TCGA-FP-8631 
"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-BR-8592        TCGA-BR-A4IU        TCGA-BR-A4IV        TCGA-BR-A4IY 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BR-A4IZ        TCGA-BR-A4J1        TCGA-BR-A4J2        TCGA-BR-A4J4 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BR-A4J5        TCGA-BR-A4J6        TCGA-BR-A4J8        TCGA-BR-A4J9 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BR-A4PF        TCGA-CD-5798        TCGA-CD-5799        TCGA-CD-5800 
  "1P LOSS MUTATED" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-CD-5801        TCGA-CD-5802        TCGA-CD-5803        TCGA-CG-4300 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-CG-4301        TCGA-CG-4304        TCGA-CG-4305        TCGA-CG-4306 
  "1P LOSS MUTATED" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-CG-4436        TCGA-CG-4437        TCGA-CG-4438        TCGA-CG-4440 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-CG-4441        TCGA-CG-4443        TCGA-CG-4444        TCGA-CG-4449 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-CG-4455        TCGA-CG-4460        TCGA-CG-4462        TCGA-CG-4465 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-CG-4466        TCGA-CG-4469        TCGA-CG-4472        TCGA-CG-4474 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-CG-4477        TCGA-CG-5716        TCGA-CG-5717        TCGA-CG-5718 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-CG-5719        TCGA-CG-5720        TCGA-CG-5721        TCGA-CG-5722 
  "1P LOSS MUTATED" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-CG-5723        TCGA-CG-5724        TCGA-CG-5725        TCGA-CG-5726 
"1P LOSS WILD-TYPE"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-CG-5727        TCGA-CG-5728        TCGA-CG-5730        TCGA-CG-5732 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE" 
       TCGA-CG-5733        TCGA-CG-5734        TCGA-D7-5577        TCGA-D7-5578 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-D7-5579        TCGA-D7-6518        TCGA-D7-6519        TCGA-D7-6520 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE" 
       TCGA-D7-6521        TCGA-D7-6522        TCGA-D7-6524        TCGA-D7-6525 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-D7-6526        TCGA-D7-6527        TCGA-D7-6528        TCGA-D7-6815 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-D7-6817        TCGA-D7-6818        TCGA-D7-6820        TCGA-D7-6822 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EQ-5647        TCGA-EQ-8122        TCGA-F1-6177        TCGA-F1-6874 
  "1P LOSS MUTATED" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-F1-6875        TCGA-FP-7735        TCGA-FP-7829        TCGA-FP-7916 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-FP-7998        TCGA-FP-8099        TCGA-FP-8209        TCGA-FP-8631 
"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=" "3.1"
D37V2, continuous
D37V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED      5    3
  1P LOSS WILD-TYPE   65  104
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  FEMALE               5                65
  MALE                 3               104
                   vv
clus                STOMACH ADENOCARCINOMA - DIFFUSE TYPE
  1P LOSS MUTATED                                       2
  1P LOSS WILD-TYPE                                    23
                   vv
clus                STOMACH ADENOCARCINOMA - NOT OTHERWISE SPECIFIED (NOS)
  1P LOSS MUTATED                                                        3
  1P LOSS WILD-TYPE                                                     84
                   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                                                10
                   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                                                                     34
D37V4, multiclass
                   vv
clus                T1 T2 T3 T4
  1P LOSS MUTATED    0  3  1  4
  1P LOSS WILD-TYPE  6 51 63 39
D37V5, multiclass
    clus
vv   1P LOSS MUTATED 1P LOSS WILD-TYPE
  T1               0                 6
  T2               3                51
  T3               1                63
  T4               4                39
                   vv
clus                N0 N1 N2 N3
  1P LOSS MUTATED    1  3  1  2
  1P LOSS WILD-TYPE 55 58 28 18
D37V6, multiclass
    clus
vv   1P LOSS MUTATED 1P LOSS WILD-TYPE
  N0               1                55
  N1               3                58
  N2               1                28
  N3               2                18
                   vv
clus                 M0  M1  MX
  1P LOSS MUTATED     3   5   0
  1P LOSS WILD-TYPE 143  13  13
D37V7, multiclass
    clus
vv   1P LOSS MUTATED 1P LOSS WILD-TYPE
  M0               3               143
  M1               5                13
  MX               0                13
                   vv
clus                 I II III IV
  1P LOSS MUTATED    0  0   2  5
  1P LOSS WILD-TYPE 26 48  56 24
D37V8, multiclass
     clus
vv    1P LOSS MUTATED 1P LOSS WILD-TYPE
  I                 0                26
  II                0                48
  III               2                56
  IV                5                24
D37V9, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED      0    8
  1P LOSS WILD-TYPE    5  164
     clus
vv    1P LOSS MUTATED 1P LOSS WILD-TYPE
  NO                0                 5
  YES               8               164
                   vv
clus                 R0  R1  R2  RX
  1P LOSS MUTATED     3   0   4   1
  1P LOSS WILD-TYPE 120   7   8  24
D37V10, multiclass
    clus
vv   1P LOSS MUTATED 1P LOSS WILD-TYPE
  R0               3               120
  R1               0                 7
  R2               4                 8
  RX               1                24
D37V11, continuous

Clustering(38) Variable = 1q loss mutation analysis
D38V1, survival
                   sevent
clus2                 0   1
  1Q LOSS MUTATED     2   1
  1Q LOSS WILD-TYPE 120  17
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
                3               137 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
                1                17 
$`1Q LOSS MUTATED`
TCGA-CG-5719 TCGA-CG-5724 TCGA-D7-6519 
        1.02        12.03        15.65 

$`1Q LOSS WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-6452 TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6458 
        5.62         0.10         0.95         1.41         1.35         1.35 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
        0.85         0.82         0.62         0.62         1.71         2.17 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
        0.99         1.22         0.66         1.12         0.76         0.66 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
        0.26         1.22         1.48         0.46         1.25         0.13 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 
        1.05         0.82         0.69         0.16         4.54         0.99 
TCGA-BR-7901 TCGA-BR-7957 TCGA-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-BR-8592 TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        0.20         0.59         0.92         0.39         0.79         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J8 TCGA-BR-A4J9 
        0.79         0.53         0.43         0.13         0.23         0.10 
TCGA-BR-A4PF TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        0.72         0.82         0.69         0.36         0.49         0.30 
TCGA-CD-5803 TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
        0.07        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
       52.96         8.05        54.05         4.01        14.01        29.98 
TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4460 TCGA-CG-4462 TCGA-CG-4465 
       47.05        19.07        12.03        21.99         1.02         8.98 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4474 TCGA-CG-4477 TCGA-CG-5716 
       18.94         7.07        12.00         1.02         1.02         1.02 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
        6.94         1.02         0.99         5.98         0.95        70.06 
TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-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-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-FP-8099 TCGA-FP-8209 
        0.39         0.20         3.02         3.58         1.02        59.05 
TCGA-FP-8631 TCGA-HJ-7597 TCGA-IN-7806 TCGA-IN-7808 TCGA-IP-7968 
        0.56        26.43         6.87         3.55         2.53 

  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
             1.02              0.07 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
            15.65             72.23 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
            12.03              1.22 
[1] "1.0 - 15.7 (12.0)" "0.1 - 72.2 (1.2)" 
       TCGA-B7-5816        TCGA-B7-5818        TCGA-BR-6452        TCGA-BR-6455 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BR-6457        TCGA-BR-6458        TCGA-BR-6563        TCGA-BR-6564 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BR-6565        TCGA-BR-6566        TCGA-BR-6705        TCGA-BR-6706 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BR-6707        TCGA-BR-6709        TCGA-BR-6710        TCGA-BR-6801 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BR-6802        TCGA-BR-6803        TCGA-BR-6852        TCGA-BR-7196 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BR-7197        TCGA-BR-7703        TCGA-BR-7704        TCGA-BR-7707 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BR-7715        TCGA-BR-7716        TCGA-BR-7717        TCGA-BR-7722 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BR-7723        TCGA-BR-7851        TCGA-BR-7901        TCGA-BR-7957 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BR-7958        TCGA-BR-7959        TCGA-BR-8059        TCGA-BR-8060 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BR-8077        TCGA-BR-8078        TCGA-BR-8080        TCGA-BR-8081 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BR-8284        TCGA-BR-8285        TCGA-BR-8286        TCGA-BR-8289 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BR-8291        TCGA-BR-8295        TCGA-BR-8296        TCGA-BR-8297 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BR-8592        TCGA-BR-A4IU        TCGA-BR-A4IV        TCGA-BR-A4IY 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BR-A4IZ        TCGA-BR-A4J1        TCGA-BR-A4J2        TCGA-BR-A4J4 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BR-A4J5        TCGA-BR-A4J6        TCGA-BR-A4J8        TCGA-BR-A4J9 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BR-A4PF        TCGA-CD-5798        TCGA-CD-5799        TCGA-CD-5800 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-CD-5801        TCGA-CD-5802        TCGA-CD-5803        TCGA-CG-4300 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-CG-4301        TCGA-CG-4304        TCGA-CG-4305        TCGA-CG-4306 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-CG-4436        TCGA-CG-4437        TCGA-CG-4438        TCGA-CG-4440 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-CG-4441        TCGA-CG-4443        TCGA-CG-4444        TCGA-CG-4449 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-CG-4455        TCGA-CG-4460        TCGA-CG-4462        TCGA-CG-4465 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-CG-4466        TCGA-CG-4469        TCGA-CG-4472        TCGA-CG-4474 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-CG-4477        TCGA-CG-5716        TCGA-CG-5717        TCGA-CG-5718 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-CG-5719        TCGA-CG-5720        TCGA-CG-5721        TCGA-CG-5722 
  "1Q LOSS MUTATED" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-CG-5723        TCGA-CG-5724        TCGA-CG-5725        TCGA-CG-5726 
"1Q LOSS WILD-TYPE"   "1Q LOSS MUTATED" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-CG-5727        TCGA-CG-5728        TCGA-CG-5730        TCGA-CG-5732 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-CG-5733        TCGA-CG-5734        TCGA-D7-5577        TCGA-D7-5578 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-D7-5579        TCGA-D7-6518        TCGA-D7-6519        TCGA-D7-6520 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE"   "1Q LOSS MUTATED" "1Q LOSS WILD-TYPE" 
       TCGA-D7-6521        TCGA-D7-6522        TCGA-D7-6524        TCGA-D7-6525 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-D7-6526        TCGA-D7-6527        TCGA-D7-6528        TCGA-D7-6815 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-D7-6817        TCGA-D7-6818        TCGA-D7-6820        TCGA-D7-6822 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EQ-5647        TCGA-EQ-8122        TCGA-F1-6177        TCGA-F1-6874 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-F1-6875        TCGA-FP-7735        TCGA-FP-7829        TCGA-FP-7916 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-FP-7998        TCGA-FP-8099        TCGA-FP-8209        TCGA-FP-8631 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-HJ-7597        TCGA-IN-7806        TCGA-IN-7808        TCGA-IP-7968 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-B7-5816        TCGA-B7-5818        TCGA-BR-6452        TCGA-BR-6455 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BR-6457        TCGA-BR-6458        TCGA-BR-6563        TCGA-BR-6564 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BR-6565        TCGA-BR-6566        TCGA-BR-6705        TCGA-BR-6706 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BR-6707        TCGA-BR-6709        TCGA-BR-6710        TCGA-BR-6801 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BR-6802        TCGA-BR-6803        TCGA-BR-6852        TCGA-BR-7196 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BR-7197        TCGA-BR-7703        TCGA-BR-7704        TCGA-BR-7707 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BR-7715        TCGA-BR-7716        TCGA-BR-7717        TCGA-BR-7722 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BR-7723        TCGA-BR-7851        TCGA-BR-7901        TCGA-BR-7957 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BR-7958        TCGA-BR-7959        TCGA-BR-8059        TCGA-BR-8060 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BR-8077        TCGA-BR-8078        TCGA-BR-8080        TCGA-BR-8081 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BR-8284        TCGA-BR-8285        TCGA-BR-8286        TCGA-BR-8289 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BR-8291        TCGA-BR-8295        TCGA-BR-8296        TCGA-BR-8297 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BR-8592        TCGA-BR-A4IU        TCGA-BR-A4IV        TCGA-BR-A4IY 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BR-A4IZ        TCGA-BR-A4J1        TCGA-BR-A4J2        TCGA-BR-A4J4 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BR-A4J5        TCGA-BR-A4J6        TCGA-BR-A4J8        TCGA-BR-A4J9 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BR-A4PF        TCGA-CD-5798        TCGA-CD-5799        TCGA-CD-5800 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-CD-5801        TCGA-CD-5802        TCGA-CD-5803        TCGA-CG-4300 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-CG-4301        TCGA-CG-4304        TCGA-CG-4305        TCGA-CG-4306 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-CG-4436        TCGA-CG-4437        TCGA-CG-4438        TCGA-CG-4440 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-CG-4441        TCGA-CG-4443        TCGA-CG-4444        TCGA-CG-4449 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-CG-4455        TCGA-CG-4460        TCGA-CG-4462        TCGA-CG-4465 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-CG-4466        TCGA-CG-4469        TCGA-CG-4472        TCGA-CG-4474 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-CG-4477        TCGA-CG-5716        TCGA-CG-5717        TCGA-CG-5718 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-CG-5719        TCGA-CG-5720        TCGA-CG-5721        TCGA-CG-5722 
  "1Q LOSS MUTATED" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-CG-5723        TCGA-CG-5724        TCGA-CG-5725        TCGA-CG-5726 
"1Q LOSS WILD-TYPE"   "1Q LOSS MUTATED" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-CG-5727        TCGA-CG-5728        TCGA-CG-5730        TCGA-CG-5732 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-CG-5733        TCGA-CG-5734        TCGA-D7-5577        TCGA-D7-5578 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-D7-5579        TCGA-D7-6518        TCGA-D7-6519        TCGA-D7-6520 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE"   "1Q LOSS MUTATED" "1Q LOSS WILD-TYPE" 
       TCGA-D7-6521        TCGA-D7-6522        TCGA-D7-6524        TCGA-D7-6525 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-D7-6526        TCGA-D7-6527        TCGA-D7-6528        TCGA-D7-6815 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-D7-6817        TCGA-D7-6818        TCGA-D7-6820        TCGA-D7-6822 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EQ-5647        TCGA-EQ-8122        TCGA-F1-6177        TCGA-F1-6874 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-F1-6875        TCGA-FP-7735        TCGA-FP-7829        TCGA-FP-7916 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-FP-7998        TCGA-FP-8099        TCGA-FP-8209        TCGA-FP-8631 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-HJ-7597        TCGA-IN-7806        TCGA-IN-7808        TCGA-IP-7968 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-B7-5816        TCGA-B7-5818        TCGA-BR-6452        TCGA-BR-6455 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BR-6457        TCGA-BR-6458        TCGA-BR-6563        TCGA-BR-6564 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BR-6565        TCGA-BR-6566        TCGA-BR-6705        TCGA-BR-6706 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BR-6707        TCGA-BR-6709        TCGA-BR-6710        TCGA-BR-6801 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BR-6802        TCGA-BR-6803        TCGA-BR-6852        TCGA-BR-7196 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BR-7197        TCGA-BR-7703        TCGA-BR-7704        TCGA-BR-7707 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BR-7715        TCGA-BR-7716        TCGA-BR-7717        TCGA-BR-7722 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BR-7723        TCGA-BR-7851        TCGA-BR-7901        TCGA-BR-7957 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BR-7958        TCGA-BR-7959        TCGA-BR-8059        TCGA-BR-8060 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BR-8077        TCGA-BR-8078        TCGA-BR-8080        TCGA-BR-8081 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BR-8284        TCGA-BR-8285        TCGA-BR-8286        TCGA-BR-8289 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BR-8291        TCGA-BR-8295        TCGA-BR-8296        TCGA-BR-8297 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BR-8592        TCGA-BR-A4IU        TCGA-BR-A4IV        TCGA-BR-A4IY 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BR-A4IZ        TCGA-BR-A4J1        TCGA-BR-A4J2        TCGA-BR-A4J4 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BR-A4J5        TCGA-BR-A4J6        TCGA-BR-A4J8        TCGA-BR-A4J9 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BR-A4PF        TCGA-CD-5798        TCGA-CD-5799        TCGA-CD-5800 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-CD-5801        TCGA-CD-5802        TCGA-CD-5803        TCGA-CG-4300 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-CG-4301        TCGA-CG-4304        TCGA-CG-4305        TCGA-CG-4306 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-CG-4436        TCGA-CG-4437        TCGA-CG-4438        TCGA-CG-4440 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-CG-4441        TCGA-CG-4443        TCGA-CG-4444        TCGA-CG-4449 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-CG-4455        TCGA-CG-4460        TCGA-CG-4462        TCGA-CG-4465 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-CG-4466        TCGA-CG-4469        TCGA-CG-4472        TCGA-CG-4474 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-CG-4477        TCGA-CG-5716        TCGA-CG-5717        TCGA-CG-5718 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-CG-5719        TCGA-CG-5720        TCGA-CG-5721        TCGA-CG-5722 
  "1Q LOSS MUTATED" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-CG-5723        TCGA-CG-5724        TCGA-CG-5725        TCGA-CG-5726 
"1Q LOSS WILD-TYPE"   "1Q LOSS MUTATED" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-CG-5727        TCGA-CG-5728        TCGA-CG-5730        TCGA-CG-5732 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-CG-5733        TCGA-CG-5734        TCGA-D7-5577        TCGA-D7-5578 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-D7-5579        TCGA-D7-6518        TCGA-D7-6519        TCGA-D7-6520 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE"   "1Q LOSS MUTATED" "1Q LOSS WILD-TYPE" 
       TCGA-D7-6521        TCGA-D7-6522        TCGA-D7-6524        TCGA-D7-6525 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-D7-6526        TCGA-D7-6527        TCGA-D7-6528        TCGA-D7-6815 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-D7-6817        TCGA-D7-6818        TCGA-D7-6820        TCGA-D7-6822 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EQ-5647        TCGA-EQ-8122        TCGA-F1-6177        TCGA-F1-6874 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-F1-6875        TCGA-FP-7735        TCGA-FP-7829        TCGA-FP-7916 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-FP-7998        TCGA-FP-8099        TCGA-FP-8209        TCGA-FP-8631 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-HJ-7597        TCGA-IN-7806        TCGA-IN-7808        TCGA-IP-7968 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
[1] "hr=" "1.8"
D38V2, continuous
D38V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED      2    1
  1Q LOSS WILD-TYPE   68  106
        clus
vv       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  FEMALE               2                68
  MALE                 1               106
                   vv
clus                STOMACH ADENOCARCINOMA - DIFFUSE TYPE
  1Q LOSS MUTATED                                       2
  1Q LOSS WILD-TYPE                                    23
                   vv
clus                STOMACH ADENOCARCINOMA - NOT OTHERWISE SPECIFIED (NOS)
  1Q LOSS MUTATED                                                        0
  1Q LOSS WILD-TYPE                                                     87
                   vv
clus                STOMACH ADENOCARCINOMA - SIGNET RING TYPE
  1Q LOSS MUTATED                                           0
  1Q LOSS WILD-TYPE                                         1
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - MUCINOUS TYPE
  1Q LOSS MUTATED                                                   0
  1Q LOSS WILD-TYPE                                                10
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - PAPILLARY TYPE
  1Q LOSS MUTATED                                                    0
  1Q LOSS WILD-TYPE                                                  3
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - TUBULAR TYPE
  1Q LOSS MUTATED                                                  0
  1Q LOSS WILD-TYPE                                               10
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - TYPE NOT OTHERWISE SPECIFIED (NOS)
  1Q LOSS MUTATED                                                                        1
  1Q LOSS WILD-TYPE                                                                     35
D38V4, multiclass
                   vv
clus                T1 T2 T3 T4
  1Q LOSS MUTATED    0  1  1  1
  1Q LOSS WILD-TYPE  6 53 63 42
D38V5, multiclass
    clus
vv   1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  T1               0                 6
  T2               1                53
  T3               1                63
  T4               1                42
                   vv
clus                N0 N1 N2 N3
  1Q LOSS MUTATED    1  1  0  1
  1Q LOSS WILD-TYPE 55 60 29 19
D38V6, multiclass
    clus
vv   1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  N0               1                55
  N1               1                60
  N2               0                29
  N3               1                19
                   vv
clus                 M0  M1  MX
  1Q LOSS MUTATED     1   2   0
  1Q LOSS WILD-TYPE 145  16  13
D38V7, multiclass
    clus
vv   1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  M0               1               145
  M1               2                16
  MX               0                13
                   vv
clus                 I II III IV
  1Q LOSS MUTATED    0  0   1  2
  1Q LOSS WILD-TYPE 26 48  57 27
D38V8, multiclass
     clus
vv    1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  I                 0                26
  II                0                48
  III               1                57
  IV                2                27
D38V9, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED      0    3
  1Q LOSS WILD-TYPE    5  169
     clus
vv    1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  NO                0                 5
  YES               3               169
                   vv
clus                 R0  R1  R2  RX
  1Q LOSS MUTATED     2   0   1   0
  1Q LOSS WILD-TYPE 121   7  11  25
D38V10, multiclass
    clus
vv   1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  R0               2               121
  R1               0                 7
  R2               1                11
  RX               0                25
D38V11, continuous

Clustering(39) Variable = 2q loss mutation analysis
D39V1, survival
                   sevent
clus2                 0   1
  2Q LOSS MUTATED     1   0
  2Q LOSS WILD-TYPE 121  18
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
                1               139 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
                0                18 
$`2Q LOSS MUTATED`
TCGA-EQ-8122 
        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-BR-8592 TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        0.20         0.59         0.92         0.39         0.79         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J8 TCGA-BR-A4J9 
        0.79         0.53         0.43         0.13         0.23         0.10 
TCGA-BR-A4PF TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        0.72         0.82         0.69         0.36         0.49         0.30 
TCGA-CD-5803 TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
        0.07        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
       52.96         8.05        54.05         4.01        14.01        29.98 
TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4460 TCGA-CG-4462 TCGA-CG-4465 
       47.05        19.07        12.03        21.99         1.02         8.98 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4474 TCGA-CG-4477 TCGA-CG-5716 
       18.94         7.07        12.00         1.02         1.02         1.02 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.94         1.02         1.02         0.99         5.98         0.95 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 
       70.06        12.03        15.02        28.96        31.04        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        55.04        21.07         7.99         8.65         3.58 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
        4.54         9.80        15.65         9.63         8.19         6.90 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
        0.69         5.95         6.61         4.14         1.68         3.65 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-EQ-5647 TCGA-F1-6177 
        4.70         4.04         2.93         4.27         0.62         6.54 
TCGA-F1-6874 TCGA-F1-6875 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
        2.01        72.23         0.39         0.20         3.02         3.58 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8631 TCGA-HJ-7597 TCGA-IN-7806 TCGA-IN-7808 
        1.02        59.05         0.56        26.43         6.87         3.55 
TCGA-IP-7968 
        2.53 

  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
             7.79              0.07 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
             7.79             72.23 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
             7.79              1.22 
[1] "7.8 - 7.8 (7.8)"  "0.1 - 72.2 (1.2)"
       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-BR-8592        TCGA-BR-A4IU        TCGA-BR-A4IV        TCGA-BR-A4IY 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-BR-A4IZ        TCGA-BR-A4J1        TCGA-BR-A4J2        TCGA-BR-A4J4 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-BR-A4J5        TCGA-BR-A4J6        TCGA-BR-A4J8        TCGA-BR-A4J9 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-BR-A4PF        TCGA-CD-5798        TCGA-CD-5799        TCGA-CD-5800 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-CD-5801        TCGA-CD-5802        TCGA-CD-5803        TCGA-CG-4300 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-CG-4301        TCGA-CG-4304        TCGA-CG-4305        TCGA-CG-4306 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-CG-4436        TCGA-CG-4437        TCGA-CG-4438        TCGA-CG-4440 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-CG-4441        TCGA-CG-4443        TCGA-CG-4444        TCGA-CG-4449 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-CG-4455        TCGA-CG-4460        TCGA-CG-4462        TCGA-CG-4465 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-CG-4466        TCGA-CG-4469        TCGA-CG-4472        TCGA-CG-4474 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-CG-4477        TCGA-CG-5716        TCGA-CG-5717        TCGA-CG-5718 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-CG-5719        TCGA-CG-5720        TCGA-CG-5721        TCGA-CG-5722 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-CG-5723        TCGA-CG-5724        TCGA-CG-5725        TCGA-CG-5726 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-CG-5727        TCGA-CG-5728        TCGA-CG-5730        TCGA-CG-5732 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-CG-5733        TCGA-CG-5734        TCGA-D7-5577        TCGA-D7-5578 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-D7-5579        TCGA-D7-6518        TCGA-D7-6519        TCGA-D7-6520 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-D7-6521        TCGA-D7-6522        TCGA-D7-6524        TCGA-D7-6525 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-D7-6526        TCGA-D7-6527        TCGA-D7-6528        TCGA-D7-6815 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-D7-6817        TCGA-D7-6818        TCGA-D7-6820        TCGA-D7-6822 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-EQ-5647        TCGA-EQ-8122        TCGA-F1-6177        TCGA-F1-6874 
"2Q LOSS WILD-TYPE"   "2Q LOSS MUTATED" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-F1-6875        TCGA-FP-7735        TCGA-FP-7829        TCGA-FP-7916 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-FP-7998        TCGA-FP-8099        TCGA-FP-8209        TCGA-FP-8631 
"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-BR-8592        TCGA-BR-A4IU        TCGA-BR-A4IV        TCGA-BR-A4IY 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-BR-A4IZ        TCGA-BR-A4J1        TCGA-BR-A4J2        TCGA-BR-A4J4 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-BR-A4J5        TCGA-BR-A4J6        TCGA-BR-A4J8        TCGA-BR-A4J9 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-BR-A4PF        TCGA-CD-5798        TCGA-CD-5799        TCGA-CD-5800 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-CD-5801        TCGA-CD-5802        TCGA-CD-5803        TCGA-CG-4300 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-CG-4301        TCGA-CG-4304        TCGA-CG-4305        TCGA-CG-4306 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-CG-4436        TCGA-CG-4437        TCGA-CG-4438        TCGA-CG-4440 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-CG-4441        TCGA-CG-4443        TCGA-CG-4444        TCGA-CG-4449 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-CG-4455        TCGA-CG-4460        TCGA-CG-4462        TCGA-CG-4465 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-CG-4466        TCGA-CG-4469        TCGA-CG-4472        TCGA-CG-4474 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-CG-4477        TCGA-CG-5716        TCGA-CG-5717        TCGA-CG-5718 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-CG-5719        TCGA-CG-5720        TCGA-CG-5721        TCGA-CG-5722 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-CG-5723        TCGA-CG-5724        TCGA-CG-5725        TCGA-CG-5726 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-CG-5727        TCGA-CG-5728        TCGA-CG-5730        TCGA-CG-5732 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-CG-5733        TCGA-CG-5734        TCGA-D7-5577        TCGA-D7-5578 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-D7-5579        TCGA-D7-6518        TCGA-D7-6519        TCGA-D7-6520 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-D7-6521        TCGA-D7-6522        TCGA-D7-6524        TCGA-D7-6525 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-D7-6526        TCGA-D7-6527        TCGA-D7-6528        TCGA-D7-6815 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-D7-6817        TCGA-D7-6818        TCGA-D7-6820        TCGA-D7-6822 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-EQ-5647        TCGA-EQ-8122        TCGA-F1-6177        TCGA-F1-6874 
"2Q LOSS WILD-TYPE"   "2Q LOSS MUTATED" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-F1-6875        TCGA-FP-7735        TCGA-FP-7829        TCGA-FP-7916 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-FP-7998        TCGA-FP-8099        TCGA-FP-8209        TCGA-FP-8631 
"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-BR-8592        TCGA-BR-A4IU        TCGA-BR-A4IV        TCGA-BR-A4IY 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-BR-A4IZ        TCGA-BR-A4J1        TCGA-BR-A4J2        TCGA-BR-A4J4 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-BR-A4J5        TCGA-BR-A4J6        TCGA-BR-A4J8        TCGA-BR-A4J9 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-BR-A4PF        TCGA-CD-5798        TCGA-CD-5799        TCGA-CD-5800 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-CD-5801        TCGA-CD-5802        TCGA-CD-5803        TCGA-CG-4300 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-CG-4301        TCGA-CG-4304        TCGA-CG-4305        TCGA-CG-4306 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-CG-4436        TCGA-CG-4437        TCGA-CG-4438        TCGA-CG-4440 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-CG-4441        TCGA-CG-4443        TCGA-CG-4444        TCGA-CG-4449 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-CG-4455        TCGA-CG-4460        TCGA-CG-4462        TCGA-CG-4465 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-CG-4466        TCGA-CG-4469        TCGA-CG-4472        TCGA-CG-4474 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-CG-4477        TCGA-CG-5716        TCGA-CG-5717        TCGA-CG-5718 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-CG-5719        TCGA-CG-5720        TCGA-CG-5721        TCGA-CG-5722 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-CG-5723        TCGA-CG-5724        TCGA-CG-5725        TCGA-CG-5726 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-CG-5727        TCGA-CG-5728        TCGA-CG-5730        TCGA-CG-5732 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-CG-5733        TCGA-CG-5734        TCGA-D7-5577        TCGA-D7-5578 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-D7-5579        TCGA-D7-6518        TCGA-D7-6519        TCGA-D7-6520 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-D7-6521        TCGA-D7-6522        TCGA-D7-6524        TCGA-D7-6525 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-D7-6526        TCGA-D7-6527        TCGA-D7-6528        TCGA-D7-6815 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-D7-6817        TCGA-D7-6818        TCGA-D7-6820        TCGA-D7-6822 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-EQ-5647        TCGA-EQ-8122        TCGA-F1-6177        TCGA-F1-6874 
"2Q LOSS WILD-TYPE"   "2Q LOSS MUTATED" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-F1-6875        TCGA-FP-7735        TCGA-FP-7829        TCGA-FP-7916 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-FP-7998        TCGA-FP-8099        TCGA-FP-8209        TCGA-FP-8631 
"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 
                1               139 
       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-BR-8592        TCGA-BR-A4IU        TCGA-BR-A4IV        TCGA-BR-A4IY 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-BR-A4IZ        TCGA-BR-A4J1        TCGA-BR-A4J2        TCGA-BR-A4J4 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-BR-A4J5        TCGA-BR-A4J6        TCGA-BR-A4J8        TCGA-BR-A4J9 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-BR-A4PF        TCGA-CD-5798        TCGA-CD-5799        TCGA-CD-5800 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-CD-5801        TCGA-CD-5802        TCGA-CD-5803        TCGA-CG-4300 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-CG-4301        TCGA-CG-4304        TCGA-CG-4305        TCGA-CG-4306 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-CG-4436        TCGA-CG-4437        TCGA-CG-4438        TCGA-CG-4440 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-CG-4441        TCGA-CG-4443        TCGA-CG-4444        TCGA-CG-4449 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-CG-4455        TCGA-CG-4460        TCGA-CG-4462        TCGA-CG-4465 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-CG-4466        TCGA-CG-4469        TCGA-CG-4472        TCGA-CG-4474 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-CG-4477        TCGA-CG-5716        TCGA-CG-5717        TCGA-CG-5718 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-CG-5719        TCGA-CG-5720        TCGA-CG-5721        TCGA-CG-5722 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-CG-5723        TCGA-CG-5724        TCGA-CG-5725        TCGA-CG-5726 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-CG-5727        TCGA-CG-5728        TCGA-CG-5730        TCGA-CG-5732 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-CG-5733        TCGA-CG-5734        TCGA-D7-5577        TCGA-D7-5578 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-D7-5579        TCGA-D7-6518        TCGA-D7-6519        TCGA-D7-6520 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-D7-6521        TCGA-D7-6522        TCGA-D7-6524        TCGA-D7-6525 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-D7-6526        TCGA-D7-6527        TCGA-D7-6528        TCGA-D7-6815 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-D7-6817        TCGA-D7-6818        TCGA-D7-6820        TCGA-D7-6822 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-EQ-5647        TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875 
"2Q LOSS WILD-TYPE" "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-FP-8099        TCGA-FP-8209        TCGA-FP-8631        TCGA-HJ-7597 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-IN-7806        TCGA-IN-7808        TCGA-IP-7968 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
D39V2, continuous
[1] "Remove cluster labels:" "2Q LOSS MUTATED"       
clus
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
                2               168 
       TCGA-B7-5816        TCGA-B7-5818        TCGA-BR-4183        TCGA-BR-4184 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-BR-4187        TCGA-BR-4188        TCGA-BR-4191        TCGA-BR-4201 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-BR-4253        TCGA-BR-4255        TCGA-BR-4256        TCGA-BR-4257 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-BR-4267        TCGA-BR-4279        TCGA-BR-4280        TCGA-BR-4292 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-BR-4294        TCGA-BR-4357        TCGA-BR-4361        TCGA-BR-4362 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-BR-4363        TCGA-BR-4366        TCGA-BR-4367        TCGA-BR-4368 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-BR-4369        TCGA-BR-4370        TCGA-BR-4371        TCGA-BR-6452 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-BR-6453        TCGA-BR-6454        TCGA-BR-6455        TCGA-BR-6456 
"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-BR-8592        TCGA-BR-A4IU        TCGA-BR-A4IV        TCGA-BR-A4IY 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-BR-A4IZ        TCGA-BR-A4J1        TCGA-BR-A4J2        TCGA-BR-A4J4 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-BR-A4J5        TCGA-BR-A4J6        TCGA-BR-A4J8        TCGA-BR-A4J9 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-BR-A4PF        TCGA-CD-5798        TCGA-CD-5799        TCGA-CD-5802 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-CD-5803        TCGA-CD-5804        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-4442        TCGA-CG-4443        TCGA-CG-4444        TCGA-CG-4449 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-CG-4455        TCGA-CG-4460        TCGA-CG-4462        TCGA-CG-4465 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-CG-4466        TCGA-CG-4469        TCGA-CG-4472        TCGA-CG-4474 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-CG-4476        TCGA-CG-4477        TCGA-CG-5716        TCGA-CG-5717 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-CG-5718        TCGA-CG-5719        TCGA-CG-5720        TCGA-CG-5721 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-CG-5722        TCGA-CG-5723        TCGA-CG-5724        TCGA-CG-5725 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-CG-5726        TCGA-CG-5727        TCGA-CG-5728        TCGA-CG-5730 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-CG-5732        TCGA-CG-5733        TCGA-CG-5734        TCGA-D7-5577 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-D7-5578        TCGA-D7-5579        TCGA-D7-6518        TCGA-D7-6519 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-D7-6520        TCGA-D7-6521        TCGA-D7-6522        TCGA-D7-6524 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-D7-6525        TCGA-D7-6526        TCGA-D7-6527        TCGA-D7-6528 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-D7-6815        TCGA-D7-6817        TCGA-D7-6818        TCGA-D7-6820 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-D7-6822        TCGA-EQ-5647        TCGA-F1-6177        TCGA-F1-6874 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-F1-6875        TCGA-FP-7735        TCGA-FP-7829        TCGA-FP-7916 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-FP-7998        TCGA-FP-8099        TCGA-FP-8209        TCGA-FP-8631 
"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" 
D39V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED      2    1
  2Q LOSS WILD-TYPE   68  106
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  FEMALE               2                68
  MALE                 1               106
                   vv
clus                STOMACH ADENOCARCINOMA - DIFFUSE TYPE
  2Q LOSS MUTATED                                       0
  2Q LOSS WILD-TYPE                                    25
                   vv
clus                STOMACH ADENOCARCINOMA - NOT OTHERWISE SPECIFIED (NOS)
  2Q LOSS MUTATED                                                        0
  2Q LOSS WILD-TYPE                                                     87
                   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                                                 9
                   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                                                                     35
D39V4, multiclass
[1] "Remove cluster labels:" "2Q LOSS MUTATED"       
clus
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
                2               170 
       TCGA-B7-5816        TCGA-B7-5818        TCGA-BR-4183        TCGA-BR-4184 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-BR-4187        TCGA-BR-4188        TCGA-BR-4191        TCGA-BR-4201 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-BR-4253        TCGA-BR-4255        TCGA-BR-4256        TCGA-BR-4257 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-BR-4267        TCGA-BR-4279        TCGA-BR-4280        TCGA-BR-4292 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-BR-4294        TCGA-BR-4357        TCGA-BR-4361        TCGA-BR-4362 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-BR-4363        TCGA-BR-4366        TCGA-BR-4367        TCGA-BR-4368 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-BR-4369        TCGA-BR-4370        TCGA-BR-4371        TCGA-BR-6452 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-BR-6453        TCGA-BR-6454        TCGA-BR-6455        TCGA-BR-6456 
"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-BR-8592        TCGA-BR-A4IU        TCGA-BR-A4IV        TCGA-BR-A4IY 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-BR-A4IZ        TCGA-BR-A4J1        TCGA-BR-A4J2        TCGA-BR-A4J4 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-BR-A4J5        TCGA-BR-A4J6        TCGA-BR-A4J8        TCGA-BR-A4J9 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-BR-A4PF        TCGA-CD-5798        TCGA-CD-5799        TCGA-CD-5800 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-CD-5801        TCGA-CD-5802        TCGA-CD-5803        TCGA-CD-5804 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-CG-4300        TCGA-CG-4301        TCGA-CG-4304        TCGA-CG-4305 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-CG-4306        TCGA-CG-4436        TCGA-CG-4437        TCGA-CG-4438 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-CG-4440        TCGA-CG-4441        TCGA-CG-4442        TCGA-CG-4443 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-CG-4449        TCGA-CG-4455        TCGA-CG-4460        TCGA-CG-4466 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-CG-4469        TCGA-CG-4474        TCGA-CG-4476        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 WILD-TYPE" "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-F1-6177        TCGA-F1-6874        TCGA-F1-6875        TCGA-FP-7735 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-FP-7829        TCGA-FP-7916        TCGA-FP-7998        TCGA-FP-8099 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-FP-8209        TCGA-FP-8631        TCGA-HF-7131        TCGA-HF-7132 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-HF-7134        TCGA-HF-7136        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" 
                   vv
clus                T1 T2 T3 T4
  2Q LOSS MUTATED    0  1  2  0
  2Q LOSS WILD-TYPE  6 53 62 43
D39V5, multiclass
    clus
vv   2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  T1               0                 6
  T2               1                53
  T3               2                62
  T4               0                43
                   vv
clus                N0 N1 N2 N3
  2Q LOSS MUTATED    0  2  0  1
  2Q LOSS WILD-TYPE 56 59 29 19
D39V6, multiclass
    clus
vv   2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  N0               0                56
  N1               2                59
  N2               0                29
  N3               1                19
                   vv
clus                 M0  M1  MX
  2Q LOSS MUTATED     2   0   1
  2Q LOSS WILD-TYPE 144  18  12
D39V7, multiclass
    clus
vv   2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  M0               2               144
  M1               0                18
  MX               1                12
                   vv
clus                 I II III IV
  2Q LOSS MUTATED    0  2   0  1
  2Q LOSS WILD-TYPE 26 46  58 28
D39V8, multiclass
     clus
vv    2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  I                 0                26
  II                2                46
  III               0                58
  IV                1                28
D39V9, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED      1    2
  2Q LOSS WILD-TYPE    4  170
     clus
vv    2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  NO                1                 4
  YES               2               170
                   vv
clus                 R0  R1  R2  RX
  2Q LOSS MUTATED     1   1   0   0
  2Q LOSS WILD-TYPE 122   6  12  25
D39V10, multiclass
[1] "Remove cluster labels:" "2Q LOSS MUTATED"       
clus
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
                2               165 
       TCGA-B7-5816        TCGA-B7-5818        TCGA-BR-4183        TCGA-BR-4184 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-BR-4187        TCGA-BR-4188        TCGA-BR-4191        TCGA-BR-4201 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-BR-4253        TCGA-BR-4255        TCGA-BR-4256        TCGA-BR-4257 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-BR-4267        TCGA-BR-4279        TCGA-BR-4280        TCGA-BR-4292 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-BR-4294        TCGA-BR-4357        TCGA-BR-4361        TCGA-BR-4362 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-BR-4363        TCGA-BR-4366        TCGA-BR-4367        TCGA-BR-4368 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-BR-4369        TCGA-BR-4370        TCGA-BR-4371        TCGA-BR-6452 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-BR-6453        TCGA-BR-6454        TCGA-BR-6455        TCGA-BR-6456 
"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-BR-8592        TCGA-BR-A4IU        TCGA-BR-A4IV        TCGA-BR-A4IY 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-BR-A4IZ        TCGA-BR-A4J1        TCGA-BR-A4J2        TCGA-BR-A4J4 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-BR-A4J5        TCGA-BR-A4J6        TCGA-BR-A4J8        TCGA-BR-A4J9 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-BR-A4PF        TCGA-CD-5804        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-4442        TCGA-CG-4443        TCGA-CG-4444        TCGA-CG-4449 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-CG-4455        TCGA-CG-4460        TCGA-CG-4462        TCGA-CG-4465 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-CG-4466        TCGA-CG-4469        TCGA-CG-4472        TCGA-CG-4474 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-CG-4476        TCGA-CG-4477        TCGA-CG-5716        TCGA-CG-5717 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-CG-5718        TCGA-CG-5719        TCGA-CG-5720        TCGA-CG-5721 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-CG-5722        TCGA-CG-5723        TCGA-CG-5724        TCGA-CG-5725 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-CG-5726        TCGA-CG-5727        TCGA-CG-5728        TCGA-CG-5730 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-CG-5732        TCGA-CG-5733        TCGA-CG-5734        TCGA-D7-5577 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-D7-5578        TCGA-D7-5579        TCGA-D7-6518        TCGA-D7-6519 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-D7-6520        TCGA-D7-6521        TCGA-D7-6522        TCGA-D7-6524 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-D7-6525        TCGA-D7-6526        TCGA-D7-6527        TCGA-D7-6528 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-D7-6815        TCGA-D7-6817        TCGA-D7-6818        TCGA-D7-6820 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-D7-6822        TCGA-EQ-5647        TCGA-F1-6177        TCGA-F1-6874 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-F1-6875        TCGA-FP-7735        TCGA-FP-7829        TCGA-FP-7998 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-FP-8099        TCGA-FP-8209        TCGA-FP-8631        TCGA-HF-7131 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-HF-7132        TCGA-HF-7134        TCGA-HF-7136        TCGA-HJ-7597 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-IN-7806 
"2Q LOSS WILD-TYPE" 
D39V11, continuous
[1] "Remove cluster labels:" "2Q LOSS MUTATED"       
clus
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
                2               131 
       TCGA-B7-5816        TCGA-BR-4183        TCGA-BR-4184        TCGA-BR-4188 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-BR-4191        TCGA-BR-4253        TCGA-BR-4255        TCGA-BR-4256 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-BR-4267        TCGA-BR-4279        TCGA-BR-4280        TCGA-BR-4361 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-BR-4362        TCGA-BR-4367        TCGA-BR-4368        TCGA-BR-6452 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-BR-6453        TCGA-BR-6454        TCGA-BR-6455        TCGA-BR-6456 
"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-BR-8592        TCGA-BR-A4IU        TCGA-BR-A4IV        TCGA-BR-A4IY 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-BR-A4IZ        TCGA-BR-A4J1        TCGA-BR-A4J2        TCGA-BR-A4J4 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-BR-A4J5        TCGA-BR-A4J6        TCGA-BR-A4J8        TCGA-BR-A4J9 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-BR-A4PF        TCGA-CD-5804        TCGA-CG-5717        TCGA-CG-5718 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-CG-5719        TCGA-CG-5720        TCGA-CG-5721        TCGA-CG-5722 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-CG-5723        TCGA-CG-5724        TCGA-CG-5725        TCGA-CG-5726 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-CG-5727        TCGA-CG-5728        TCGA-CG-5730        TCGA-CG-5732 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-CG-5733        TCGA-CG-5734        TCGA-D7-5577        TCGA-D7-5578 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-D7-5579        TCGA-D7-6518        TCGA-D7-6519        TCGA-D7-6520 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-D7-6521        TCGA-D7-6522        TCGA-D7-6524        TCGA-D7-6525 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-D7-6526        TCGA-D7-6527        TCGA-D7-6528        TCGA-D7-6815 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-D7-6817        TCGA-D7-6818        TCGA-D7-6820        TCGA-D7-6822 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-EQ-5647        TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875 
"2Q LOSS WILD-TYPE" "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-FP-8099        TCGA-FP-8209        TCGA-FP-8631        TCGA-HF-7131 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-HF-7132        TCGA-HF-7134        TCGA-HF-7136        TCGA-HJ-7597 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-IN-7806        TCGA-IN-7808        TCGA-IP-7968 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 

Clustering(40) Variable = 3p loss mutation analysis
D40V1, survival
                   sevent
clus2                 0   1
  3P LOSS MUTATED    13   2
  3P LOSS WILD-TYPE 109  16
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               15               125 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
                2                16 
$`3P LOSS MUTATED`
TCGA-BR-6458 TCGA-BR-7715 TCGA-BR-A4J1 TCGA-BR-A4J4 TCGA-BR-A4PF TCGA-CG-4438 
        1.35         1.05         0.72         0.53         0.72        54.05 
TCGA-CG-4466 TCGA-CG-5725 TCGA-CG-5730 TCGA-D7-6525 TCGA-D7-6528 TCGA-FP-7829 
       18.94        15.02         4.01         5.95         1.68         0.20 
TCGA-FP-8099 TCGA-FP-8631 TCGA-IN-7806 
        1.02         0.56         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-BR-8592 TCGA-BR-A4IU 
        1.18         1.55         1.48         0.76         0.20         0.59 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J5 TCGA-BR-A4J6 
        0.92         0.39         0.79         0.79         0.43         0.13 
TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
        0.23         0.10         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-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-5732 TCGA-CG-5733 
       12.03        28.96        31.04        65.10        55.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        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-D7-6526 TCGA-D7-6527 
        9.63         8.19         6.90         0.69         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-F1-6875 TCGA-FP-7735 TCGA-FP-7916 
        7.79         6.54         2.01        72.23         0.39         3.02 
TCGA-FP-7998 TCGA-FP-8209 TCGA-HJ-7597 TCGA-IN-7808 TCGA-IP-7968 
        3.58        59.05        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 
             1.35              1.22 
[1] "0.2 - 54.0 (1.4)" "0.1 - 72.2 (1.2)"
       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-BR-8592        TCGA-BR-A4IU        TCGA-BR-A4IV        TCGA-BR-A4IY 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-BR-A4IZ        TCGA-BR-A4J1        TCGA-BR-A4J2        TCGA-BR-A4J4 
"3P LOSS WILD-TYPE"   "3P LOSS MUTATED" "3P LOSS WILD-TYPE"   "3P LOSS MUTATED" 
       TCGA-BR-A4J5        TCGA-BR-A4J6        TCGA-BR-A4J8        TCGA-BR-A4J9 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-BR-A4PF        TCGA-CD-5798        TCGA-CD-5799        TCGA-CD-5800 
  "3P LOSS MUTATED" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-CD-5801        TCGA-CD-5802        TCGA-CD-5803        TCGA-CG-4300 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-CG-4301        TCGA-CG-4304        TCGA-CG-4305        TCGA-CG-4306 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-CG-4436        TCGA-CG-4437        TCGA-CG-4438        TCGA-CG-4440 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE"   "3P LOSS MUTATED" "3P LOSS WILD-TYPE" 
       TCGA-CG-4441        TCGA-CG-4443        TCGA-CG-4444        TCGA-CG-4449 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-CG-4455        TCGA-CG-4460        TCGA-CG-4462        TCGA-CG-4465 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-CG-4466        TCGA-CG-4469        TCGA-CG-4472        TCGA-CG-4474 
  "3P LOSS MUTATED" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-CG-4477        TCGA-CG-5716        TCGA-CG-5717        TCGA-CG-5718 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-CG-5719        TCGA-CG-5720        TCGA-CG-5721        TCGA-CG-5722 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-CG-5723        TCGA-CG-5724        TCGA-CG-5725        TCGA-CG-5726 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE"   "3P LOSS MUTATED" "3P LOSS WILD-TYPE" 
       TCGA-CG-5727        TCGA-CG-5728        TCGA-CG-5730        TCGA-CG-5732 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE"   "3P LOSS MUTATED" "3P LOSS WILD-TYPE" 
       TCGA-CG-5733        TCGA-CG-5734        TCGA-D7-5577        TCGA-D7-5578 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-D7-5579        TCGA-D7-6518        TCGA-D7-6519        TCGA-D7-6520 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-D7-6521        TCGA-D7-6522        TCGA-D7-6524        TCGA-D7-6525 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE"   "3P LOSS MUTATED" 
       TCGA-D7-6526        TCGA-D7-6527        TCGA-D7-6528        TCGA-D7-6815 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE"   "3P LOSS MUTATED" "3P LOSS WILD-TYPE" 
       TCGA-D7-6817        TCGA-D7-6818        TCGA-D7-6820        TCGA-D7-6822 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EQ-5647        TCGA-EQ-8122        TCGA-F1-6177        TCGA-F1-6874 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-F1-6875        TCGA-FP-7735        TCGA-FP-7829        TCGA-FP-7916 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE"   "3P LOSS MUTATED" "3P LOSS WILD-TYPE" 
       TCGA-FP-7998        TCGA-FP-8099        TCGA-FP-8209        TCGA-FP-8631 
"3P LOSS WILD-TYPE"   "3P LOSS MUTATED" "3P LOSS WILD-TYPE"   "3P LOSS MUTATED" 
       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-BR-8592        TCGA-BR-A4IU        TCGA-BR-A4IV        TCGA-BR-A4IY 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-BR-A4IZ        TCGA-BR-A4J1        TCGA-BR-A4J2        TCGA-BR-A4J4 
"3P LOSS WILD-TYPE"   "3P LOSS MUTATED" "3P LOSS WILD-TYPE"   "3P LOSS MUTATED" 
       TCGA-BR-A4J5        TCGA-BR-A4J6        TCGA-BR-A4J8        TCGA-BR-A4J9 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-BR-A4PF        TCGA-CD-5798        TCGA-CD-5799        TCGA-CD-5800 
  "3P LOSS MUTATED" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-CD-5801        TCGA-CD-5802        TCGA-CD-5803        TCGA-CG-4300 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-CG-4301        TCGA-CG-4304        TCGA-CG-4305        TCGA-CG-4306 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-CG-4436        TCGA-CG-4437        TCGA-CG-4438        TCGA-CG-4440 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE"   "3P LOSS MUTATED" "3P LOSS WILD-TYPE" 
       TCGA-CG-4441        TCGA-CG-4443        TCGA-CG-4444        TCGA-CG-4449 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-CG-4455        TCGA-CG-4460        TCGA-CG-4462        TCGA-CG-4465 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-CG-4466        TCGA-CG-4469        TCGA-CG-4472        TCGA-CG-4474 
  "3P LOSS MUTATED" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-CG-4477        TCGA-CG-5716        TCGA-CG-5717        TCGA-CG-5718 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-CG-5719        TCGA-CG-5720        TCGA-CG-5721        TCGA-CG-5722 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-CG-5723        TCGA-CG-5724        TCGA-CG-5725        TCGA-CG-5726 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE"   "3P LOSS MUTATED" "3P LOSS WILD-TYPE" 
       TCGA-CG-5727        TCGA-CG-5728        TCGA-CG-5730        TCGA-CG-5732 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE"   "3P LOSS MUTATED" "3P LOSS WILD-TYPE" 
       TCGA-CG-5733        TCGA-CG-5734        TCGA-D7-5577        TCGA-D7-5578 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-D7-5579        TCGA-D7-6518        TCGA-D7-6519        TCGA-D7-6520 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-D7-6521        TCGA-D7-6522        TCGA-D7-6524        TCGA-D7-6525 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE"   "3P LOSS MUTATED" 
       TCGA-D7-6526        TCGA-D7-6527        TCGA-D7-6528        TCGA-D7-6815 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE"   "3P LOSS MUTATED" "3P LOSS WILD-TYPE" 
       TCGA-D7-6817        TCGA-D7-6818        TCGA-D7-6820        TCGA-D7-6822 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EQ-5647        TCGA-EQ-8122        TCGA-F1-6177        TCGA-F1-6874 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-F1-6875        TCGA-FP-7735        TCGA-FP-7829        TCGA-FP-7916 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE"   "3P LOSS MUTATED" "3P LOSS WILD-TYPE" 
       TCGA-FP-7998        TCGA-FP-8099        TCGA-FP-8209        TCGA-FP-8631 
"3P LOSS WILD-TYPE"   "3P LOSS MUTATED" "3P LOSS WILD-TYPE"   "3P LOSS MUTATED" 
       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-BR-8592        TCGA-BR-A4IU        TCGA-BR-A4IV        TCGA-BR-A4IY 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-BR-A4IZ        TCGA-BR-A4J1        TCGA-BR-A4J2        TCGA-BR-A4J4 
"3P LOSS WILD-TYPE"   "3P LOSS MUTATED" "3P LOSS WILD-TYPE"   "3P LOSS MUTATED" 
       TCGA-BR-A4J5        TCGA-BR-A4J6        TCGA-BR-A4J8        TCGA-BR-A4J9 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-BR-A4PF        TCGA-CD-5798        TCGA-CD-5799        TCGA-CD-5800 
  "3P LOSS MUTATED" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-CD-5801        TCGA-CD-5802        TCGA-CD-5803        TCGA-CG-4300 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-CG-4301        TCGA-CG-4304        TCGA-CG-4305        TCGA-CG-4306 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-CG-4436        TCGA-CG-4437        TCGA-CG-4438        TCGA-CG-4440 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE"   "3P LOSS MUTATED" "3P LOSS WILD-TYPE" 
       TCGA-CG-4441        TCGA-CG-4443        TCGA-CG-4444        TCGA-CG-4449 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-CG-4455        TCGA-CG-4460        TCGA-CG-4462        TCGA-CG-4465 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-CG-4466        TCGA-CG-4469        TCGA-CG-4472        TCGA-CG-4474 
  "3P LOSS MUTATED" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-CG-4477        TCGA-CG-5716        TCGA-CG-5717        TCGA-CG-5718 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-CG-5719        TCGA-CG-5720        TCGA-CG-5721        TCGA-CG-5722 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-CG-5723        TCGA-CG-5724        TCGA-CG-5725        TCGA-CG-5726 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE"   "3P LOSS MUTATED" "3P LOSS WILD-TYPE" 
       TCGA-CG-5727        TCGA-CG-5728        TCGA-CG-5730        TCGA-CG-5732 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE"   "3P LOSS MUTATED" "3P LOSS WILD-TYPE" 
       TCGA-CG-5733        TCGA-CG-5734        TCGA-D7-5577        TCGA-D7-5578 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-D7-5579        TCGA-D7-6518        TCGA-D7-6519        TCGA-D7-6520 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-D7-6521        TCGA-D7-6522        TCGA-D7-6524        TCGA-D7-6525 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE"   "3P LOSS MUTATED" 
       TCGA-D7-6526        TCGA-D7-6527        TCGA-D7-6528        TCGA-D7-6815 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE"   "3P LOSS MUTATED" "3P LOSS WILD-TYPE" 
       TCGA-D7-6817        TCGA-D7-6818        TCGA-D7-6820        TCGA-D7-6822 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EQ-5647        TCGA-EQ-8122        TCGA-F1-6177        TCGA-F1-6874 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-F1-6875        TCGA-FP-7735        TCGA-FP-7829        TCGA-FP-7916 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE"   "3P LOSS MUTATED" "3P LOSS WILD-TYPE" 
       TCGA-FP-7998        TCGA-FP-8099        TCGA-FP-8209        TCGA-FP-8631 
"3P LOSS WILD-TYPE"   "3P LOSS MUTATED" "3P LOSS WILD-TYPE"   "3P LOSS MUTATED" 
       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=" "1.2"
D40V2, continuous
D40V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED      4   11
  3P LOSS WILD-TYPE   66   96
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  FEMALE               4                66
  MALE                11                96
                   vv
clus                STOMACH ADENOCARCINOMA - DIFFUSE TYPE
  3P LOSS MUTATED                                       2
  3P LOSS WILD-TYPE                                    23
                   vv
clus                STOMACH ADENOCARCINOMA - NOT OTHERWISE SPECIFIED (NOS)
  3P LOSS MUTATED                                                        7
  3P LOSS WILD-TYPE                                                     80
                   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                                                 9
                   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                                                                        4
  3P LOSS WILD-TYPE                                                                     32
D40V4, multiclass
                   vv
clus                T1 T2 T3 T4
  3P LOSS MUTATED    0  5  6  4
  3P LOSS WILD-TYPE  6 49 58 39
D40V5, multiclass
    clus
vv   3P LOSS MUTATED 3P LOSS WILD-TYPE
  T1               0                 6
  T2               5                49
  T3               6                58
  T4               4                39
                   vv
clus                N0 N1 N2 N3
  3P LOSS MUTATED    5  5  5  0
  3P LOSS WILD-TYPE 51 56 24 20
D40V6, multiclass
    clus
vv   3P LOSS MUTATED 3P LOSS WILD-TYPE
  N0               5                51
  N1               5                56
  N2               5                24
  N3               0                20
                   vv
clus                 M0  M1  MX
  3P LOSS MUTATED    12   1   2
  3P LOSS WILD-TYPE 134  17  11
D40V7, multiclass
    clus
vv   3P LOSS MUTATED 3P LOSS WILD-TYPE
  M0              12               134
  M1               1                17
  MX               2                11
                   vv
clus                 I II III IV
  3P LOSS MUTATED    3  3   7  2
  3P LOSS WILD-TYPE 23 45  51 27
D40V8, multiclass
     clus
vv    3P LOSS MUTATED 3P LOSS WILD-TYPE
  I                 3                23
  II                3                45
  III               7                51
  IV                2                27
D40V9, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED      0   15
  3P LOSS WILD-TYPE    5  157
     clus
vv    3P LOSS MUTATED 3P LOSS WILD-TYPE
  NO                0                 5
  YES              15               157
                   vv
clus                 R0  R1  R2  RX
  3P LOSS MUTATED    14   0   1   0
  3P LOSS WILD-TYPE 109   7  11  25
D40V10, multiclass
    clus
vv   3P LOSS MUTATED 3P LOSS WILD-TYPE
  R0              14               109
  R1               0                 7
  R2               1                11
  RX               0                25
D40V11, continuous

Clustering(41) Variable = 3q loss mutation analysis
D41V1, survival
                   sevent
clus2                 0   1
  3Q LOSS MUTATED     7   2
  3Q LOSS WILD-TYPE 115  16
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
                9               131 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
                2                16 
$`3Q LOSS MUTATED`
TCGA-BR-7715 TCGA-BR-A4J1 TCGA-BR-A4PF TCGA-CG-4438 TCGA-CG-4466 TCGA-CG-5725 
        1.05         0.72         0.72        54.05        18.94        15.02 
TCGA-FP-7829 TCGA-FP-8099 TCGA-IN-7806 
        0.20         1.02         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-BR-8592 
        0.26         1.18         1.55         1.48         0.76         0.20 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J4 
        0.59         0.92         0.39         0.79         0.79         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-CD-5798 TCGA-CD-5799 
        0.43         0.13         0.23         0.10         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-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-FP-8209 TCGA-FP-8631 TCGA-HJ-7597 TCGA-IN-7808 TCGA-IP-7968 
       59.05         0.56        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 
             1.05              1.25 
[1] "0.2 - 54.0 (1.1)" "0.1 - 72.2 (1.2)"
       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-BR-8592        TCGA-BR-A4IU        TCGA-BR-A4IV        TCGA-BR-A4IY 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-BR-A4IZ        TCGA-BR-A4J1        TCGA-BR-A4J2        TCGA-BR-A4J4 
"3Q LOSS WILD-TYPE"   "3Q LOSS MUTATED" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-BR-A4J5        TCGA-BR-A4J6        TCGA-BR-A4J8        TCGA-BR-A4J9 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-BR-A4PF        TCGA-CD-5798        TCGA-CD-5799        TCGA-CD-5800 
  "3Q LOSS MUTATED" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-CD-5801        TCGA-CD-5802        TCGA-CD-5803        TCGA-CG-4300 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-CG-4301        TCGA-CG-4304        TCGA-CG-4305        TCGA-CG-4306 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-CG-4436        TCGA-CG-4437        TCGA-CG-4438        TCGA-CG-4440 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE"   "3Q LOSS MUTATED" "3Q LOSS WILD-TYPE" 
       TCGA-CG-4441        TCGA-CG-4443        TCGA-CG-4444        TCGA-CG-4449 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-CG-4455        TCGA-CG-4460        TCGA-CG-4462        TCGA-CG-4465 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-CG-4466        TCGA-CG-4469        TCGA-CG-4472        TCGA-CG-4474 
  "3Q LOSS MUTATED" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-CG-4477        TCGA-CG-5716        TCGA-CG-5717        TCGA-CG-5718 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-CG-5719        TCGA-CG-5720        TCGA-CG-5721        TCGA-CG-5722 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-CG-5723        TCGA-CG-5724        TCGA-CG-5725        TCGA-CG-5726 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE"   "3Q LOSS MUTATED" "3Q LOSS WILD-TYPE" 
       TCGA-CG-5727        TCGA-CG-5728        TCGA-CG-5730        TCGA-CG-5732 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-CG-5733        TCGA-CG-5734        TCGA-D7-5577        TCGA-D7-5578 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-D7-5579        TCGA-D7-6518        TCGA-D7-6519        TCGA-D7-6520 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-D7-6521        TCGA-D7-6522        TCGA-D7-6524        TCGA-D7-6525 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-D7-6526        TCGA-D7-6527        TCGA-D7-6528        TCGA-D7-6815 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-D7-6817        TCGA-D7-6818        TCGA-D7-6820        TCGA-D7-6822 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-EQ-5647        TCGA-EQ-8122        TCGA-F1-6177        TCGA-F1-6874 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-F1-6875        TCGA-FP-7735        TCGA-FP-7829        TCGA-FP-7916 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE"   "3Q LOSS MUTATED" "3Q LOSS WILD-TYPE" 
       TCGA-FP-7998        TCGA-FP-8099        TCGA-FP-8209        TCGA-FP-8631 
"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-BR-8592        TCGA-BR-A4IU        TCGA-BR-A4IV        TCGA-BR-A4IY 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-BR-A4IZ        TCGA-BR-A4J1        TCGA-BR-A4J2        TCGA-BR-A4J4 
"3Q LOSS WILD-TYPE"   "3Q LOSS MUTATED" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-BR-A4J5        TCGA-BR-A4J6        TCGA-BR-A4J8        TCGA-BR-A4J9 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-BR-A4PF        TCGA-CD-5798        TCGA-CD-5799        TCGA-CD-5800 
  "3Q LOSS MUTATED" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-CD-5801        TCGA-CD-5802        TCGA-CD-5803        TCGA-CG-4300 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-CG-4301        TCGA-CG-4304        TCGA-CG-4305        TCGA-CG-4306 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-CG-4436        TCGA-CG-4437        TCGA-CG-4438        TCGA-CG-4440 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE"   "3Q LOSS MUTATED" "3Q LOSS WILD-TYPE" 
       TCGA-CG-4441        TCGA-CG-4443        TCGA-CG-4444        TCGA-CG-4449 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-CG-4455        TCGA-CG-4460        TCGA-CG-4462        TCGA-CG-4465 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-CG-4466        TCGA-CG-4469        TCGA-CG-4472        TCGA-CG-4474 
  "3Q LOSS MUTATED" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-CG-4477        TCGA-CG-5716        TCGA-CG-5717        TCGA-CG-5718 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-CG-5719        TCGA-CG-5720        TCGA-CG-5721        TCGA-CG-5722 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-CG-5723        TCGA-CG-5724        TCGA-CG-5725        TCGA-CG-5726 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE"   "3Q LOSS MUTATED" "3Q LOSS WILD-TYPE" 
       TCGA-CG-5727        TCGA-CG-5728        TCGA-CG-5730        TCGA-CG-5732 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-CG-5733        TCGA-CG-5734        TCGA-D7-5577        TCGA-D7-5578 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-D7-5579        TCGA-D7-6518        TCGA-D7-6519        TCGA-D7-6520 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-D7-6521        TCGA-D7-6522        TCGA-D7-6524        TCGA-D7-6525 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-D7-6526        TCGA-D7-6527        TCGA-D7-6528        TCGA-D7-6815 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-D7-6817        TCGA-D7-6818        TCGA-D7-6820        TCGA-D7-6822 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-EQ-5647        TCGA-EQ-8122        TCGA-F1-6177        TCGA-F1-6874 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-F1-6875        TCGA-FP-7735        TCGA-FP-7829        TCGA-FP-7916 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE"   "3Q LOSS MUTATED" "3Q LOSS WILD-TYPE" 
       TCGA-FP-7998        TCGA-FP-8099        TCGA-FP-8209        TCGA-FP-8631 
"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-BR-8592        TCGA-BR-A4IU        TCGA-BR-A4IV        TCGA-BR-A4IY 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-BR-A4IZ        TCGA-BR-A4J1        TCGA-BR-A4J2        TCGA-BR-A4J4 
"3Q LOSS WILD-TYPE"   "3Q LOSS MUTATED" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-BR-A4J5        TCGA-BR-A4J6        TCGA-BR-A4J8        TCGA-BR-A4J9 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-BR-A4PF        TCGA-CD-5798        TCGA-CD-5799        TCGA-CD-5800 
  "3Q LOSS MUTATED" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-CD-5801        TCGA-CD-5802        TCGA-CD-5803        TCGA-CG-4300 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-CG-4301        TCGA-CG-4304        TCGA-CG-4305        TCGA-CG-4306 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-CG-4436        TCGA-CG-4437        TCGA-CG-4438        TCGA-CG-4440 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE"   "3Q LOSS MUTATED" "3Q LOSS WILD-TYPE" 
       TCGA-CG-4441        TCGA-CG-4443        TCGA-CG-4444        TCGA-CG-4449 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-CG-4455        TCGA-CG-4460        TCGA-CG-4462        TCGA-CG-4465 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-CG-4466        TCGA-CG-4469        TCGA-CG-4472        TCGA-CG-4474 
  "3Q LOSS MUTATED" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-CG-4477        TCGA-CG-5716        TCGA-CG-5717        TCGA-CG-5718 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-CG-5719        TCGA-CG-5720        TCGA-CG-5721        TCGA-CG-5722 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-CG-5723        TCGA-CG-5724        TCGA-CG-5725        TCGA-CG-5726 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE"   "3Q LOSS MUTATED" "3Q LOSS WILD-TYPE" 
       TCGA-CG-5727        TCGA-CG-5728        TCGA-CG-5730        TCGA-CG-5732 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-CG-5733        TCGA-CG-5734        TCGA-D7-5577        TCGA-D7-5578 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-D7-5579        TCGA-D7-6518        TCGA-D7-6519        TCGA-D7-6520 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-D7-6521        TCGA-D7-6522        TCGA-D7-6524        TCGA-D7-6525 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-D7-6526        TCGA-D7-6527        TCGA-D7-6528        TCGA-D7-6815 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-D7-6817        TCGA-D7-6818        TCGA-D7-6820        TCGA-D7-6822 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-EQ-5647        TCGA-EQ-8122        TCGA-F1-6177        TCGA-F1-6874 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-F1-6875        TCGA-FP-7735        TCGA-FP-7829        TCGA-FP-7916 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE"   "3Q LOSS MUTATED" "3Q LOSS WILD-TYPE" 
       TCGA-FP-7998        TCGA-FP-8099        TCGA-FP-8209        TCGA-FP-8631 
"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    8
  3Q LOSS WILD-TYPE   69   99
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  FEMALE               1                69
  MALE                 8                99
                   vv
clus                STOMACH ADENOCARCINOMA - DIFFUSE TYPE
  3Q LOSS MUTATED                                       1
  3Q LOSS WILD-TYPE                                    24
                   vv
clus                STOMACH ADENOCARCINOMA - NOT OTHERWISE SPECIFIED (NOS)
  3Q LOSS MUTATED                                                        5
  3Q LOSS WILD-TYPE                                                     82
                   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                                                 9
                   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                                                                     34
D41V4, multiclass
                   vv
clus                T1 T2 T3 T4
  3Q LOSS MUTATED    0  2  4  3
  3Q LOSS WILD-TYPE  6 52 60 40
D41V5, multiclass
    clus
vv   3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  T1               0                 6
  T2               2                52
  T3               4                60
  T4               3                40
                   vv
clus                N0 N1 N2 N3
  3Q LOSS MUTATED    4  3  2  0
  3Q LOSS WILD-TYPE 52 58 27 20
D41V6, multiclass
    clus
vv   3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  N0               4                52
  N1               3                58
  N2               2                27
  N3               0                20
                   vv
clus                 M0  M1  MX
  3Q LOSS MUTATED     8   0   1
  3Q LOSS WILD-TYPE 138  18  12
D41V7, multiclass
    clus
vv   3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  M0               8               138
  M1               0                18
  MX               1                12
                   vv
clus                 I II III IV
  3Q LOSS MUTATED    2  2   4  1
  3Q LOSS WILD-TYPE 24 46  54 28
D41V8, multiclass
     clus
vv    3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  I                 2                24
  II                2                46
  III               4                54
  IV                1                28
D41V9, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED      0    9
  3Q LOSS WILD-TYPE    5  163
     clus
vv    3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  NO                0                 5
  YES               9               163
                   vv
clus                 R0  R1  R2  RX
  3Q LOSS MUTATED     9   0   0   0
  3Q LOSS WILD-TYPE 114   7  12  25
D41V10, multiclass
    clus
vv   3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  R0               9               114
  R1               0                 7
  R2               0                12
  RX               0                25
D41V11, continuous

Clustering(42) Variable = 4p loss mutation analysis
D42V1, survival
                   sevent
clus2                 0   1
  4P LOSS MUTATED    16   6
  4P LOSS WILD-TYPE 106  12
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               22               118 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
                6                12 
$`4P LOSS MUTATED`
TCGA-BR-7197 TCGA-BR-7723 TCGA-BR-A4J1 TCGA-BR-A4J6 TCGA-CD-5799 TCGA-CD-5802 
        1.48         4.54         0.72         0.13         0.69         0.30 
TCGA-CG-4300 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4449 TCGA-CG-4466 TCGA-CG-4469 
       20.02        54.05         4.01        19.07        18.94         7.07 
TCGA-CG-4477 TCGA-CG-5725 TCGA-D7-6519 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6820 
        1.02        15.02        15.65         4.14         1.68         2.93 
TCGA-EQ-8122 TCGA-FP-8099 TCGA-FP-8209 TCGA-HJ-7597 
        7.79         1.02        59.05        26.43 

$`4P LOSS WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-6452 TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6458 
        5.62         0.10         0.95         1.41         1.35         1.35 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
        0.85         0.82         0.62         0.62         1.71         2.17 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
        0.99         1.22         0.66         1.12         0.76         0.66 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
        0.26         1.22         0.46         1.25         0.13         1.05 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 
        0.82         0.69         0.16         0.99         0.95         0.69 
TCGA-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-BR-8592 TCGA-BR-A4IU 
        1.18         1.55         1.48         0.76         0.20         0.59 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
        0.92         0.39         0.79         0.79         0.53         0.43 
TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PF TCGA-CD-5798 TCGA-CD-5800 TCGA-CD-5801 
        0.23         0.10         0.72         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-FP-8631 TCGA-IN-7806 TCGA-IN-7808 TCGA-IP-7968 
        0.56         6.87         3.55         2.53 

  4P LOSS MUTATED 4P LOSS WILD-TYPE 
             0.13              0.07 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
            59.05             72.23 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
            4.340             1.065 
[1] "0.1 - 59.0 (4.3)" "0.1 - 72.2 (1.1)"
       TCGA-B7-5816        TCGA-B7-5818        TCGA-BR-6452        TCGA-BR-6455 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-BR-6457        TCGA-BR-6458        TCGA-BR-6563        TCGA-BR-6564 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-BR-6565        TCGA-BR-6566        TCGA-BR-6705        TCGA-BR-6706 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-BR-6707        TCGA-BR-6709        TCGA-BR-6710        TCGA-BR-6801 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-BR-6802        TCGA-BR-6803        TCGA-BR-6852        TCGA-BR-7196 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-BR-7197        TCGA-BR-7703        TCGA-BR-7704        TCGA-BR-7707 
  "4P LOSS MUTATED" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-BR-7715        TCGA-BR-7716        TCGA-BR-7717        TCGA-BR-7722 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-BR-7723        TCGA-BR-7851        TCGA-BR-7901        TCGA-BR-7957 
  "4P LOSS MUTATED" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-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-BR-8592        TCGA-BR-A4IU        TCGA-BR-A4IV        TCGA-BR-A4IY 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-BR-A4IZ        TCGA-BR-A4J1        TCGA-BR-A4J2        TCGA-BR-A4J4 
"4P LOSS WILD-TYPE"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-BR-A4J5        TCGA-BR-A4J6        TCGA-BR-A4J8        TCGA-BR-A4J9 
"4P LOSS WILD-TYPE"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-BR-A4PF        TCGA-CD-5798        TCGA-CD-5799        TCGA-CD-5800 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" 
       TCGA-CD-5801        TCGA-CD-5802        TCGA-CD-5803        TCGA-CG-4300 
"4P LOSS WILD-TYPE"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" 
       TCGA-CG-4301        TCGA-CG-4304        TCGA-CG-4305        TCGA-CG-4306 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-CG-4436        TCGA-CG-4437        TCGA-CG-4438        TCGA-CG-4440 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED"   "4P LOSS MUTATED" 
       TCGA-CG-4441        TCGA-CG-4443        TCGA-CG-4444        TCGA-CG-4449 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" 
       TCGA-CG-4455        TCGA-CG-4460        TCGA-CG-4462        TCGA-CG-4465 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-CG-4466        TCGA-CG-4469        TCGA-CG-4472        TCGA-CG-4474 
  "4P LOSS MUTATED"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-CG-4477        TCGA-CG-5716        TCGA-CG-5717        TCGA-CG-5718 
  "4P LOSS MUTATED" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-CG-5719        TCGA-CG-5720        TCGA-CG-5721        TCGA-CG-5722 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-CG-5723        TCGA-CG-5724        TCGA-CG-5725        TCGA-CG-5726 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" 
       TCGA-CG-5727        TCGA-CG-5728        TCGA-CG-5730        TCGA-CG-5732 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-CG-5733        TCGA-CG-5734        TCGA-D7-5577        TCGA-D7-5578 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-D7-5579        TCGA-D7-6518        TCGA-D7-6519        TCGA-D7-6520 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" 
       TCGA-D7-6521        TCGA-D7-6522        TCGA-D7-6524        TCGA-D7-6525 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-D7-6526        TCGA-D7-6527        TCGA-D7-6528        TCGA-D7-6815 
"4P LOSS WILD-TYPE"   "4P LOSS MUTATED"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" 
       TCGA-D7-6817        TCGA-D7-6818        TCGA-D7-6820        TCGA-D7-6822 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" 
       TCGA-EQ-5647        TCGA-EQ-8122        TCGA-F1-6177        TCGA-F1-6874 
"4P LOSS WILD-TYPE"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-F1-6875        TCGA-FP-7735        TCGA-FP-7829        TCGA-FP-7916 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-FP-7998        TCGA-FP-8099        TCGA-FP-8209        TCGA-FP-8631 
"4P LOSS WILD-TYPE"   "4P LOSS MUTATED"   "4P LOSS MUTATED" "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 WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-BR-6565        TCGA-BR-6566        TCGA-BR-6705        TCGA-BR-6706 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-BR-6707        TCGA-BR-6709        TCGA-BR-6710        TCGA-BR-6801 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-BR-6802        TCGA-BR-6803        TCGA-BR-6852        TCGA-BR-7196 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-BR-7197        TCGA-BR-7703        TCGA-BR-7704        TCGA-BR-7707 
  "4P LOSS MUTATED" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-BR-7715        TCGA-BR-7716        TCGA-BR-7717        TCGA-BR-7722 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-BR-7723        TCGA-BR-7851        TCGA-BR-7901        TCGA-BR-7957 
  "4P LOSS MUTATED" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-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-BR-8592        TCGA-BR-A4IU        TCGA-BR-A4IV        TCGA-BR-A4IY 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-BR-A4IZ        TCGA-BR-A4J1        TCGA-BR-A4J2        TCGA-BR-A4J4 
"4P LOSS WILD-TYPE"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-BR-A4J5        TCGA-BR-A4J6        TCGA-BR-A4J8        TCGA-BR-A4J9 
"4P LOSS WILD-TYPE"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-BR-A4PF        TCGA-CD-5798        TCGA-CD-5799        TCGA-CD-5800 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" 
       TCGA-CD-5801        TCGA-CD-5802        TCGA-CD-5803        TCGA-CG-4300 
"4P LOSS WILD-TYPE"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" 
       TCGA-CG-4301        TCGA-CG-4304        TCGA-CG-4305        TCGA-CG-4306 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-CG-4436        TCGA-CG-4437        TCGA-CG-4438        TCGA-CG-4440 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED"   "4P LOSS MUTATED" 
       TCGA-CG-4441        TCGA-CG-4443        TCGA-CG-4444        TCGA-CG-4449 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" 
       TCGA-CG-4455        TCGA-CG-4460        TCGA-CG-4462        TCGA-CG-4465 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-CG-4466        TCGA-CG-4469        TCGA-CG-4472        TCGA-CG-4474 
  "4P LOSS MUTATED"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-CG-4477        TCGA-CG-5716        TCGA-CG-5717        TCGA-CG-5718 
  "4P LOSS MUTATED" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-CG-5719        TCGA-CG-5720        TCGA-CG-5721        TCGA-CG-5722 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-CG-5723        TCGA-CG-5724        TCGA-CG-5725        TCGA-CG-5726 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" 
       TCGA-CG-5727        TCGA-CG-5728        TCGA-CG-5730        TCGA-CG-5732 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-CG-5733        TCGA-CG-5734        TCGA-D7-5577        TCGA-D7-5578 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-D7-5579        TCGA-D7-6518        TCGA-D7-6519        TCGA-D7-6520 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" 
       TCGA-D7-6521        TCGA-D7-6522        TCGA-D7-6524        TCGA-D7-6525 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-D7-6526        TCGA-D7-6527        TCGA-D7-6528        TCGA-D7-6815 
"4P LOSS WILD-TYPE"   "4P LOSS MUTATED"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" 
       TCGA-D7-6817        TCGA-D7-6818        TCGA-D7-6820        TCGA-D7-6822 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" 
       TCGA-EQ-5647        TCGA-EQ-8122        TCGA-F1-6177        TCGA-F1-6874 
"4P LOSS WILD-TYPE"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-F1-6875        TCGA-FP-7735        TCGA-FP-7829        TCGA-FP-7916 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-FP-7998        TCGA-FP-8099        TCGA-FP-8209        TCGA-FP-8631 
"4P LOSS WILD-TYPE"   "4P LOSS MUTATED"   "4P LOSS MUTATED" "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 WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-BR-6565        TCGA-BR-6566        TCGA-BR-6705        TCGA-BR-6706 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-BR-6707        TCGA-BR-6709        TCGA-BR-6710        TCGA-BR-6801 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-BR-6802        TCGA-BR-6803        TCGA-BR-6852        TCGA-BR-7196 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-BR-7197        TCGA-BR-7703        TCGA-BR-7704        TCGA-BR-7707 
  "4P LOSS MUTATED" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-BR-7715        TCGA-BR-7716        TCGA-BR-7717        TCGA-BR-7722 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-BR-7723        TCGA-BR-7851        TCGA-BR-7901        TCGA-BR-7957 
  "4P LOSS MUTATED" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-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-BR-8592        TCGA-BR-A4IU        TCGA-BR-A4IV        TCGA-BR-A4IY 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-BR-A4IZ        TCGA-BR-A4J1        TCGA-BR-A4J2        TCGA-BR-A4J4 
"4P LOSS WILD-TYPE"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-BR-A4J5        TCGA-BR-A4J6        TCGA-BR-A4J8        TCGA-BR-A4J9 
"4P LOSS WILD-TYPE"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-BR-A4PF        TCGA-CD-5798        TCGA-CD-5799        TCGA-CD-5800 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" 
       TCGA-CD-5801        TCGA-CD-5802        TCGA-CD-5803        TCGA-CG-4300 
"4P LOSS WILD-TYPE"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" 
       TCGA-CG-4301        TCGA-CG-4304        TCGA-CG-4305        TCGA-CG-4306 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-CG-4436        TCGA-CG-4437        TCGA-CG-4438        TCGA-CG-4440 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED"   "4P LOSS MUTATED" 
       TCGA-CG-4441        TCGA-CG-4443        TCGA-CG-4444        TCGA-CG-4449 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" 
       TCGA-CG-4455        TCGA-CG-4460        TCGA-CG-4462        TCGA-CG-4465 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-CG-4466        TCGA-CG-4469        TCGA-CG-4472        TCGA-CG-4474 
  "4P LOSS MUTATED"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-CG-4477        TCGA-CG-5716        TCGA-CG-5717        TCGA-CG-5718 
  "4P LOSS MUTATED" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-CG-5719        TCGA-CG-5720        TCGA-CG-5721        TCGA-CG-5722 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-CG-5723        TCGA-CG-5724        TCGA-CG-5725        TCGA-CG-5726 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" 
       TCGA-CG-5727        TCGA-CG-5728        TCGA-CG-5730        TCGA-CG-5732 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-CG-5733        TCGA-CG-5734        TCGA-D7-5577        TCGA-D7-5578 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-D7-5579        TCGA-D7-6518        TCGA-D7-6519        TCGA-D7-6520 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" 
       TCGA-D7-6521        TCGA-D7-6522        TCGA-D7-6524        TCGA-D7-6525 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-D7-6526        TCGA-D7-6527        TCGA-D7-6528        TCGA-D7-6815 
"4P LOSS WILD-TYPE"   "4P LOSS MUTATED"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" 
       TCGA-D7-6817        TCGA-D7-6818        TCGA-D7-6820        TCGA-D7-6822 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" 
       TCGA-EQ-5647        TCGA-EQ-8122        TCGA-F1-6177        TCGA-F1-6874 
"4P LOSS WILD-TYPE"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-F1-6875        TCGA-FP-7735        TCGA-FP-7829        TCGA-FP-7916 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-FP-7998        TCGA-FP-8099        TCGA-FP-8209        TCGA-FP-8631 
"4P LOSS WILD-TYPE"   "4P LOSS MUTATED"   "4P LOSS MUTATED" "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=" "1.6"
D42V2, continuous
D42V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED      9   18
  4P LOSS WILD-TYPE   61   89
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  FEMALE               9                61
  MALE                18                89
                   vv
clus                STOMACH ADENOCARCINOMA - DIFFUSE TYPE
  4P LOSS MUTATED                                       2
  4P LOSS WILD-TYPE                                    23
                   vv
clus                STOMACH ADENOCARCINOMA - NOT OTHERWISE SPECIFIED (NOS)
  4P LOSS MUTATED                                                       11
  4P LOSS WILD-TYPE                                                     76
                   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                                                 8
                   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                                                                     29
D42V4, multiclass
                   vv
clus                T1 T2 T3 T4
  4P LOSS MUTATED    0 14 11  2
  4P LOSS WILD-TYPE  6 40 53 41
D42V5, multiclass
    clus
vv   4P LOSS MUTATED 4P LOSS WILD-TYPE
  T1               0                 6
  T2              14                40
  T3              11                53
  T4               2                41
                   vv
clus                N0 N1 N2 N3
  4P LOSS MUTATED   11  9  3  3
  4P LOSS WILD-TYPE 45 52 26 17
D42V6, multiclass
    clus
vv   4P LOSS MUTATED 4P LOSS WILD-TYPE
  N0              11                45
  N1               9                52
  N2               3                26
  N3               3                17
                   vv
clus                 M0  M1  MX
  4P LOSS MUTATED    23   1   3
  4P LOSS WILD-TYPE 123  17  10
D42V7, multiclass
    clus
vv   4P LOSS MUTATED 4P LOSS WILD-TYPE
  M0              23               123
  M1               1                17
  MX               3                10
                   vv
clus                 I II III IV
  4P LOSS MUTATED    6 12   4  4
  4P LOSS WILD-TYPE 20 36  54 25
D42V8, multiclass
     clus
vv    4P LOSS MUTATED 4P LOSS WILD-TYPE
  I                 6                20
  II               12                36
  III               4                54
  IV                4                25
D42V9, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED      2   25
  4P LOSS WILD-TYPE    3  147
     clus
vv    4P LOSS MUTATED 4P LOSS WILD-TYPE
  NO                2                 3
  YES              25               147
                   vv
clus                 R0  R1  R2  RX
  4P LOSS MUTATED    18   3   1   2
  4P LOSS WILD-TYPE 105   4  11  23
D42V10, multiclass
    clus
vv   4P LOSS MUTATED 4P LOSS WILD-TYPE
  R0              18               105
  R1               3                 4
  R2               1                11
  RX               2                23
D42V11, continuous

Clustering(43) Variable = 4q loss mutation analysis
D43V1, survival
                   sevent
clus2                 0   1
  4Q LOSS MUTATED    18   4
  4Q LOSS WILD-TYPE 104  14
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               22               118 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
                4                14 
$`4Q LOSS MUTATED`
TCGA-BR-6458 TCGA-BR-7723 TCGA-BR-A4J1 TCGA-BR-A4J6 TCGA-BR-A4PF TCGA-CD-5799 
        1.35         4.54         0.72         0.13         0.72         0.69 
TCGA-CD-5802 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4449 TCGA-CG-4466 TCGA-CG-5725 
        0.30        54.05         4.01        19.07        18.94        15.02 
TCGA-CG-5730 TCGA-D7-5578 TCGA-D7-6519 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
        4.01         3.58        15.65         4.14         1.68         3.65 
TCGA-D7-6820 TCGA-EQ-8122 TCGA-FP-8099 TCGA-FP-8209 
        2.93         7.79         1.02        59.05 

$`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-BR-8592 TCGA-BR-A4IU 
        1.18         1.55         1.48         0.76         0.20         0.59 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
        0.92         0.39         0.79         0.79         0.53         0.43 
TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-CD-5798 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5803 
        0.23         0.10         0.82         0.36         0.49         0.07 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02        52.96 
TCGA-CG-4437 TCGA-CG-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-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-D7-5579 TCGA-D7-6518 
       55.04        21.07         7.99         8.65         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-D7-6817 TCGA-D7-6818 TCGA-D7-6822 TCGA-EQ-5647 TCGA-F1-6177 TCGA-F1-6874 
        4.70         4.04         4.27         0.62         6.54         2.01 
TCGA-F1-6875 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8631 
       72.23         0.39         0.20         3.02         3.58         0.56 
TCGA-HJ-7597 TCGA-IN-7806 TCGA-IN-7808 TCGA-IP-7968 
       26.43         6.87         3.55         2.53 

  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
             0.13              0.07 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
            59.05             72.23 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
            3.830             1.065 
[1] "0.1 - 59.0 (3.8)" "0.1 - 72.2 (1.1)"
       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-BR-8592        TCGA-BR-A4IU        TCGA-BR-A4IV        TCGA-BR-A4IY 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-BR-A4IZ        TCGA-BR-A4J1        TCGA-BR-A4J2        TCGA-BR-A4J4 
"4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-BR-A4J5        TCGA-BR-A4J6        TCGA-BR-A4J8        TCGA-BR-A4J9 
"4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-BR-A4PF        TCGA-CD-5798        TCGA-CD-5799        TCGA-CD-5800 
  "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" 
       TCGA-CD-5801        TCGA-CD-5802        TCGA-CD-5803        TCGA-CG-4300 
"4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-CG-4301        TCGA-CG-4304        TCGA-CG-4305        TCGA-CG-4306 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-CG-4436        TCGA-CG-4437        TCGA-CG-4438        TCGA-CG-4440 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED"   "4Q LOSS MUTATED" 
       TCGA-CG-4441        TCGA-CG-4443        TCGA-CG-4444        TCGA-CG-4449 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" 
       TCGA-CG-4455        TCGA-CG-4460        TCGA-CG-4462        TCGA-CG-4465 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-CG-4466        TCGA-CG-4469        TCGA-CG-4472        TCGA-CG-4474 
  "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-CG-4477        TCGA-CG-5716        TCGA-CG-5717        TCGA-CG-5718 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-CG-5719        TCGA-CG-5720        TCGA-CG-5721        TCGA-CG-5722 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-CG-5723        TCGA-CG-5724        TCGA-CG-5725        TCGA-CG-5726 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" 
       TCGA-CG-5727        TCGA-CG-5728        TCGA-CG-5730        TCGA-CG-5732 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" 
       TCGA-CG-5733        TCGA-CG-5734        TCGA-D7-5577        TCGA-D7-5578 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" 
       TCGA-D7-5579        TCGA-D7-6518        TCGA-D7-6519        TCGA-D7-6520 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" 
       TCGA-D7-6521        TCGA-D7-6522        TCGA-D7-6524        TCGA-D7-6525 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-D7-6526        TCGA-D7-6527        TCGA-D7-6528        TCGA-D7-6815 
"4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED"   "4Q LOSS MUTATED"   "4Q LOSS MUTATED" 
       TCGA-D7-6817        TCGA-D7-6818        TCGA-D7-6820        TCGA-D7-6822 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" 
       TCGA-EQ-5647        TCGA-EQ-8122        TCGA-F1-6177        TCGA-F1-6874 
"4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-F1-6875        TCGA-FP-7735        TCGA-FP-7829        TCGA-FP-7916 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-FP-7998        TCGA-FP-8099        TCGA-FP-8209        TCGA-FP-8631 
"4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED"   "4Q LOSS MUTATED" "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-BR-8592        TCGA-BR-A4IU        TCGA-BR-A4IV        TCGA-BR-A4IY 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-BR-A4IZ        TCGA-BR-A4J1        TCGA-BR-A4J2        TCGA-BR-A4J4 
"4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-BR-A4J5        TCGA-BR-A4J6        TCGA-BR-A4J8        TCGA-BR-A4J9 
"4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-BR-A4PF        TCGA-CD-5798        TCGA-CD-5799        TCGA-CD-5800 
  "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" 
       TCGA-CD-5801        TCGA-CD-5802        TCGA-CD-5803        TCGA-CG-4300 
"4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-CG-4301        TCGA-CG-4304        TCGA-CG-4305        TCGA-CG-4306 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-CG-4436        TCGA-CG-4437        TCGA-CG-4438        TCGA-CG-4440 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED"   "4Q LOSS MUTATED" 
       TCGA-CG-4441        TCGA-CG-4443        TCGA-CG-4444        TCGA-CG-4449 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" 
       TCGA-CG-4455        TCGA-CG-4460        TCGA-CG-4462        TCGA-CG-4465 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-CG-4466        TCGA-CG-4469        TCGA-CG-4472        TCGA-CG-4474 
  "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-CG-4477        TCGA-CG-5716        TCGA-CG-5717        TCGA-CG-5718 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-CG-5719        TCGA-CG-5720        TCGA-CG-5721        TCGA-CG-5722 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-CG-5723        TCGA-CG-5724        TCGA-CG-5725        TCGA-CG-5726 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" 
       TCGA-CG-5727        TCGA-CG-5728        TCGA-CG-5730        TCGA-CG-5732 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" 
       TCGA-CG-5733        TCGA-CG-5734        TCGA-D7-5577        TCGA-D7-5578 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" 
       TCGA-D7-5579        TCGA-D7-6518        TCGA-D7-6519        TCGA-D7-6520 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" 
       TCGA-D7-6521        TCGA-D7-6522        TCGA-D7-6524        TCGA-D7-6525 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-D7-6526        TCGA-D7-6527        TCGA-D7-6528        TCGA-D7-6815 
"4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED"   "4Q LOSS MUTATED"   "4Q LOSS MUTATED" 
       TCGA-D7-6817        TCGA-D7-6818        TCGA-D7-6820        TCGA-D7-6822 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" 
       TCGA-EQ-5647        TCGA-EQ-8122        TCGA-F1-6177        TCGA-F1-6874 
"4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-F1-6875        TCGA-FP-7735        TCGA-FP-7829        TCGA-FP-7916 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-FP-7998        TCGA-FP-8099        TCGA-FP-8209        TCGA-FP-8631 
"4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED"   "4Q LOSS MUTATED" "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-BR-8592        TCGA-BR-A4IU        TCGA-BR-A4IV        TCGA-BR-A4IY 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-BR-A4IZ        TCGA-BR-A4J1        TCGA-BR-A4J2        TCGA-BR-A4J4 
"4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-BR-A4J5        TCGA-BR-A4J6        TCGA-BR-A4J8        TCGA-BR-A4J9 
"4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-BR-A4PF        TCGA-CD-5798        TCGA-CD-5799        TCGA-CD-5800 
  "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" 
       TCGA-CD-5801        TCGA-CD-5802        TCGA-CD-5803        TCGA-CG-4300 
"4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-CG-4301        TCGA-CG-4304        TCGA-CG-4305        TCGA-CG-4306 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-CG-4436        TCGA-CG-4437        TCGA-CG-4438        TCGA-CG-4440 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED"   "4Q LOSS MUTATED" 
       TCGA-CG-4441        TCGA-CG-4443        TCGA-CG-4444        TCGA-CG-4449 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" 
       TCGA-CG-4455        TCGA-CG-4460        TCGA-CG-4462        TCGA-CG-4465 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-CG-4466        TCGA-CG-4469        TCGA-CG-4472        TCGA-CG-4474 
  "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-CG-4477        TCGA-CG-5716        TCGA-CG-5717        TCGA-CG-5718 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-CG-5719        TCGA-CG-5720        TCGA-CG-5721        TCGA-CG-5722 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-CG-5723        TCGA-CG-5724        TCGA-CG-5725        TCGA-CG-5726 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" 
       TCGA-CG-5727        TCGA-CG-5728        TCGA-CG-5730        TCGA-CG-5732 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" 
       TCGA-CG-5733        TCGA-CG-5734        TCGA-D7-5577        TCGA-D7-5578 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" 
       TCGA-D7-5579        TCGA-D7-6518        TCGA-D7-6519        TCGA-D7-6520 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" 
       TCGA-D7-6521        TCGA-D7-6522        TCGA-D7-6524        TCGA-D7-6525 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-D7-6526        TCGA-D7-6527        TCGA-D7-6528        TCGA-D7-6815 
"4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED"   "4Q LOSS MUTATED"   "4Q LOSS MUTATED" 
       TCGA-D7-6817        TCGA-D7-6818        TCGA-D7-6820        TCGA-D7-6822 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" 
       TCGA-EQ-5647        TCGA-EQ-8122        TCGA-F1-6177        TCGA-F1-6874 
"4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-F1-6875        TCGA-FP-7735        TCGA-FP-7829        TCGA-FP-7916 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-FP-7998        TCGA-FP-8099        TCGA-FP-8209        TCGA-FP-8631 
"4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED"   "4Q LOSS MUTATED" "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=" "1.2"
D43V2, continuous
D43V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED     10   15
  4Q LOSS WILD-TYPE   60   92
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  FEMALE              10                60
  MALE                15                92
                   vv
clus                STOMACH ADENOCARCINOMA - DIFFUSE TYPE
  4Q LOSS MUTATED                                       2
  4Q LOSS WILD-TYPE                                    23
                   vv
clus                STOMACH ADENOCARCINOMA - NOT OTHERWISE SPECIFIED (NOS)
  4Q LOSS MUTATED                                                        9
  4Q LOSS WILD-TYPE                                                     78
                   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                                                 8
                   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                                                  5
  4Q LOSS WILD-TYPE                                                5
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - TYPE NOT OTHERWISE SPECIFIED (NOS)
  4Q LOSS MUTATED                                                                        6
  4Q LOSS WILD-TYPE                                                                     30
D43V4, multiclass
                   vv
clus                T1 T2 T3 T4
  4Q LOSS MUTATED    0 13  9  3
  4Q LOSS WILD-TYPE  6 41 55 40
D43V5, multiclass
    clus
vv   4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  T1               0                 6
  T2              13                41
  T3               9                55
  T4               3                40
                   vv
clus                N0 N1 N2 N3
  4Q LOSS MUTATED    7 10  5  2
  4Q LOSS WILD-TYPE 49 51 24 18
D43V6, multiclass
    clus
vv   4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  N0               7                49
  N1              10                51
  N2               5                24
  N3               2                18
                   vv
clus                 M0  M1  MX
  4Q LOSS MUTATED    21   2   2
  4Q LOSS WILD-TYPE 125  16  11
D43V7, multiclass
    clus
vv   4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  M0              21               125
  M1               2                16
  MX               2                11
                   vv
clus                 I II III IV
  4Q LOSS MUTATED    4 11   5  4
  4Q LOSS WILD-TYPE 22 37  53 25
D43V8, multiclass
     clus
vv    4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  I                 4                22
  II               11                37
  III               5                53
  IV                4                25
D43V9, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED      2   23
  4Q LOSS WILD-TYPE    3  149
     clus
vv    4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  NO                2                 3
  YES              23               149
                   vv
clus                 R0  R1  R2  RX
  4Q LOSS MUTATED    17   2   2   1
  4Q LOSS WILD-TYPE 106   5  10  24
D43V10, multiclass
    clus
vv   4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  R0              17               106
  R1               2                 5
  R2               2                10
  RX               1                24
D43V11, continuous

Clustering(44) Variable = 5p loss mutation analysis
D44V1, survival
                   sevent
clus2                 0   1
  5P LOSS MUTATED     6   1
  5P LOSS WILD-TYPE 116  17
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
                7               133 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
                1                17 
$`5P LOSS MUTATED`
TCGA-BR-6458 TCGA-BR-A4J1 TCGA-CG-4449 TCGA-D7-6520 TCGA-D7-6815 TCGA-FP-8631 
        1.35         0.72        19.07         9.63         3.65         0.56 
TCGA-IN-7806 
        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-BR-8592 
        0.26         1.18         1.55         1.48         0.76         0.20 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J4 
        0.59         0.92         0.39         0.79         0.79         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PF TCGA-CD-5798 
        0.43         0.13         0.23         0.10         0.72         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-4455 
       54.05         4.01        14.01        29.98        47.05        12.03 
TCGA-CG-4460 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 
       21.99         1.02         8.98        18.94         7.07        12.00 
TCGA-CG-4474 TCGA-CG-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-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
        8.19         6.90         0.69         5.95         6.61         4.14 
TCGA-D7-6528 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-EQ-5647 
        1.68         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-FP-8099 TCGA-FP-8209 TCGA-HJ-7597 TCGA-IN-7808 
        3.02         3.58         1.02        59.05        26.43         3.55 
TCGA-IP-7968 
        2.53 

  5P LOSS MUTATED 5P LOSS WILD-TYPE 
             0.56              0.07 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
            19.07             72.23 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
             3.65              1.22 
[1] "0.6 - 19.1 (3.6)" "0.1 - 72.2 (1.2)"
       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-BR-8592        TCGA-BR-A4IU        TCGA-BR-A4IV        TCGA-BR-A4IY 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-BR-A4IZ        TCGA-BR-A4J1        TCGA-BR-A4J2        TCGA-BR-A4J4 
"5P LOSS WILD-TYPE"   "5P LOSS MUTATED" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-BR-A4J5        TCGA-BR-A4J6        TCGA-BR-A4J8        TCGA-BR-A4J9 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-BR-A4PF        TCGA-CD-5798        TCGA-CD-5799        TCGA-CD-5800 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-CD-5801        TCGA-CD-5802        TCGA-CD-5803        TCGA-CG-4300 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-CG-4301        TCGA-CG-4304        TCGA-CG-4305        TCGA-CG-4306 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-CG-4436        TCGA-CG-4437        TCGA-CG-4438        TCGA-CG-4440 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-CG-4441        TCGA-CG-4443        TCGA-CG-4444        TCGA-CG-4449 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE"   "5P LOSS MUTATED" 
       TCGA-CG-4455        TCGA-CG-4460        TCGA-CG-4462        TCGA-CG-4465 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-CG-4466        TCGA-CG-4469        TCGA-CG-4472        TCGA-CG-4474 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-CG-4477        TCGA-CG-5716        TCGA-CG-5717        TCGA-CG-5718 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-CG-5719        TCGA-CG-5720        TCGA-CG-5721        TCGA-CG-5722 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-CG-5723        TCGA-CG-5724        TCGA-CG-5725        TCGA-CG-5726 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-CG-5727        TCGA-CG-5728        TCGA-CG-5730        TCGA-CG-5732 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-CG-5733        TCGA-CG-5734        TCGA-D7-5577        TCGA-D7-5578 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-D7-5579        TCGA-D7-6518        TCGA-D7-6519        TCGA-D7-6520 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE"   "5P LOSS MUTATED" 
       TCGA-D7-6521        TCGA-D7-6522        TCGA-D7-6524        TCGA-D7-6525 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-D7-6526        TCGA-D7-6527        TCGA-D7-6528        TCGA-D7-6815 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE"   "5P LOSS MUTATED" 
       TCGA-D7-6817        TCGA-D7-6818        TCGA-D7-6820        TCGA-D7-6822 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-EQ-5647        TCGA-EQ-8122        TCGA-F1-6177        TCGA-F1-6874 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-F1-6875        TCGA-FP-7735        TCGA-FP-7829        TCGA-FP-7916 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-FP-7998        TCGA-FP-8099        TCGA-FP-8209        TCGA-FP-8631 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE"   "5P LOSS MUTATED" 
       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-BR-8592        TCGA-BR-A4IU        TCGA-BR-A4IV        TCGA-BR-A4IY 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-BR-A4IZ        TCGA-BR-A4J1        TCGA-BR-A4J2        TCGA-BR-A4J4 
"5P LOSS WILD-TYPE"   "5P LOSS MUTATED" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-BR-A4J5        TCGA-BR-A4J6        TCGA-BR-A4J8        TCGA-BR-A4J9 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-BR-A4PF        TCGA-CD-5798        TCGA-CD-5799        TCGA-CD-5800 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-CD-5801        TCGA-CD-5802        TCGA-CD-5803        TCGA-CG-4300 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-CG-4301        TCGA-CG-4304        TCGA-CG-4305        TCGA-CG-4306 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-CG-4436        TCGA-CG-4437        TCGA-CG-4438        TCGA-CG-4440 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-CG-4441        TCGA-CG-4443        TCGA-CG-4444        TCGA-CG-4449 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE"   "5P LOSS MUTATED" 
       TCGA-CG-4455        TCGA-CG-4460        TCGA-CG-4462        TCGA-CG-4465 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-CG-4466        TCGA-CG-4469        TCGA-CG-4472        TCGA-CG-4474 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-CG-4477        TCGA-CG-5716        TCGA-CG-5717        TCGA-CG-5718 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-CG-5719        TCGA-CG-5720        TCGA-CG-5721        TCGA-CG-5722 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-CG-5723        TCGA-CG-5724        TCGA-CG-5725        TCGA-CG-5726 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-CG-5727        TCGA-CG-5728        TCGA-CG-5730        TCGA-CG-5732 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-CG-5733        TCGA-CG-5734        TCGA-D7-5577        TCGA-D7-5578 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-D7-5579        TCGA-D7-6518        TCGA-D7-6519        TCGA-D7-6520 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE"   "5P LOSS MUTATED" 
       TCGA-D7-6521        TCGA-D7-6522        TCGA-D7-6524        TCGA-D7-6525 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-D7-6526        TCGA-D7-6527        TCGA-D7-6528        TCGA-D7-6815 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE"   "5P LOSS MUTATED" 
       TCGA-D7-6817        TCGA-D7-6818        TCGA-D7-6820        TCGA-D7-6822 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-EQ-5647        TCGA-EQ-8122        TCGA-F1-6177        TCGA-F1-6874 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-F1-6875        TCGA-FP-7735        TCGA-FP-7829        TCGA-FP-7916 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-FP-7998        TCGA-FP-8099        TCGA-FP-8209        TCGA-FP-8631 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE"   "5P LOSS MUTATED" 
       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-BR-8592        TCGA-BR-A4IU        TCGA-BR-A4IV        TCGA-BR-A4IY 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-BR-A4IZ        TCGA-BR-A4J1        TCGA-BR-A4J2        TCGA-BR-A4J4 
"5P LOSS WILD-TYPE"   "5P LOSS MUTATED" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-BR-A4J5        TCGA-BR-A4J6        TCGA-BR-A4J8        TCGA-BR-A4J9 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-BR-A4PF        TCGA-CD-5798        TCGA-CD-5799        TCGA-CD-5800 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-CD-5801        TCGA-CD-5802        TCGA-CD-5803        TCGA-CG-4300 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-CG-4301        TCGA-CG-4304        TCGA-CG-4305        TCGA-CG-4306 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-CG-4436        TCGA-CG-4437        TCGA-CG-4438        TCGA-CG-4440 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-CG-4441        TCGA-CG-4443        TCGA-CG-4444        TCGA-CG-4449 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE"   "5P LOSS MUTATED" 
       TCGA-CG-4455        TCGA-CG-4460        TCGA-CG-4462        TCGA-CG-4465 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-CG-4466        TCGA-CG-4469        TCGA-CG-4472        TCGA-CG-4474 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-CG-4477        TCGA-CG-5716        TCGA-CG-5717        TCGA-CG-5718 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-CG-5719        TCGA-CG-5720        TCGA-CG-5721        TCGA-CG-5722 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-CG-5723        TCGA-CG-5724        TCGA-CG-5725        TCGA-CG-5726 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-CG-5727        TCGA-CG-5728        TCGA-CG-5730        TCGA-CG-5732 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-CG-5733        TCGA-CG-5734        TCGA-D7-5577        TCGA-D7-5578 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-D7-5579        TCGA-D7-6518        TCGA-D7-6519        TCGA-D7-6520 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE"   "5P LOSS MUTATED" 
       TCGA-D7-6521        TCGA-D7-6522        TCGA-D7-6524        TCGA-D7-6525 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-D7-6526        TCGA-D7-6527        TCGA-D7-6528        TCGA-D7-6815 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE"   "5P LOSS MUTATED" 
       TCGA-D7-6817        TCGA-D7-6818        TCGA-D7-6820        TCGA-D7-6822 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-EQ-5647        TCGA-EQ-8122        TCGA-F1-6177        TCGA-F1-6874 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-F1-6875        TCGA-FP-7735        TCGA-FP-7829        TCGA-FP-7916 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-FP-7998        TCGA-FP-8099        TCGA-FP-8209        TCGA-FP-8631 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE"   "5P LOSS MUTATED" 
       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=" "1.5"
D44V2, continuous
D44V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED      2    6
  5P LOSS WILD-TYPE   68  101
        clus
vv       5P LOSS MUTATED 5P LOSS WILD-TYPE
  FEMALE               2                68
  MALE                 6               101
                   vv
clus                STOMACH ADENOCARCINOMA - DIFFUSE TYPE
  5P LOSS MUTATED                                       1
  5P LOSS WILD-TYPE                                    24
                   vv
clus                STOMACH ADENOCARCINOMA - NOT OTHERWISE SPECIFIED (NOS)
  5P LOSS MUTATED                                                        3
  5P LOSS WILD-TYPE                                                     84
                   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                                                 9
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - PAPILLARY TYPE
  5P LOSS MUTATED                                                    0
  5P LOSS WILD-TYPE                                                  3
                   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                                                                        1
  5P LOSS WILD-TYPE                                                                     35
D44V4, multiclass
                   vv
clus                T1 T2 T3 T4
  5P LOSS MUTATED    0  3  3  1
  5P LOSS WILD-TYPE  6 51 61 42
D44V5, multiclass
    clus
vv   5P LOSS MUTATED 5P LOSS WILD-TYPE
  T1               0                 6
  T2               3                51
  T3               3                61
  T4               1                42
                   vv
clus                N0 N1 N2 N3
  5P LOSS MUTATED    0  5  3  0
  5P LOSS WILD-TYPE 56 56 26 20
D44V6, multiclass
    clus
vv   5P LOSS MUTATED 5P LOSS WILD-TYPE
  N0               0                56
  N1               5                56
  N2               3                26
  N3               0                20
                   vv
clus                 M0  M1  MX
  5P LOSS MUTATED     7   0   1
  5P LOSS WILD-TYPE 139  18  12
D44V7, multiclass
    clus
vv   5P LOSS MUTATED 5P LOSS WILD-TYPE
  M0               7               139
  M1               0                18
  MX               1                12
                   vv
clus                 I II III IV
  5P LOSS MUTATED    0  2   5  0
  5P LOSS WILD-TYPE 26 46  53 29
D44V8, multiclass
     clus
vv    5P LOSS MUTATED 5P LOSS WILD-TYPE
  I                 0                26
  II                2                46
  III               5                53
  IV                0                29
D44V9, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED      0    8
  5P LOSS WILD-TYPE    5  164
     clus
vv    5P LOSS MUTATED 5P LOSS WILD-TYPE
  NO                0                 5
  YES               8               164
                   vv
clus                 R0  R1  R2  RX
  5P LOSS MUTATED     7   0   0   1
  5P LOSS WILD-TYPE 116   7  12  24
D44V10, multiclass
    clus
vv   5P LOSS MUTATED 5P LOSS WILD-TYPE
  R0               7               116
  R1               0                 7
  R2               0                12
  RX               1                24
D44V11, continuous

Clustering(45) Variable = 5q loss mutation analysis
D45V1, survival
                   sevent
clus2                 0   1
  5Q LOSS MUTATED    14   2
  5Q LOSS WILD-TYPE 108  16
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               16               124 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
                2                16 
$`5Q LOSS MUTATED`
TCGA-BR-6458 TCGA-BR-7197 TCGA-BR-7901 TCGA-BR-A4J1 TCGA-CG-4304 TCGA-CG-4449 
        1.35         1.48         0.95         0.72        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-FP-8099 TCGA-FP-8631 TCGA-IN-7806 
       72.23         1.02         0.56         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-BR-8592 TCGA-BR-A4IU TCGA-BR-A4IV 
        1.55         1.48         0.76         0.20         0.59         0.92 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
        0.39         0.79         0.79         0.53         0.43         0.13 
TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PF TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
        0.23         0.10         0.72         0.82         0.69         0.36 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4305 
        0.49         0.30         0.07        20.02         3.02        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-4455 TCGA-CG-4460 TCGA-CG-4462 TCGA-CG-4465 
       29.98        47.05        12.03        21.99         1.02         8.98 
TCGA-CG-4466 TCGA-CG-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-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
        6.94         1.02         0.99         5.98         0.95        70.06 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-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-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
        9.80        15.65         8.19         6.90         0.69         5.95 
TCGA-D7-6526 TCGA-D7-6528 TCGA-D7-6818 TCGA-D7-6820 TCGA-EQ-5647 TCGA-EQ-8122 
        6.61         1.68         4.04         2.93         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-FP-8209 TCGA-HJ-7597 TCGA-IN-7808 TCGA-IP-7968 
       59.05        26.43         3.55         2.53 

  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
             0.56              0.07 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
            72.23             70.06 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
            3.895             1.150 
[1] "0.6 - 72.2 (3.9)" "0.1 - 70.1 (1.1)"
       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-BR-8592        TCGA-BR-A4IU        TCGA-BR-A4IV        TCGA-BR-A4IY 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-BR-A4IZ        TCGA-BR-A4J1        TCGA-BR-A4J2        TCGA-BR-A4J4 
"5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-BR-A4J5        TCGA-BR-A4J6        TCGA-BR-A4J8        TCGA-BR-A4J9 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-BR-A4PF        TCGA-CD-5798        TCGA-CD-5799        TCGA-CD-5800 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-CD-5801        TCGA-CD-5802        TCGA-CD-5803        TCGA-CG-4300 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-CG-4301        TCGA-CG-4304        TCGA-CG-4305        TCGA-CG-4306 
"5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-CG-4436        TCGA-CG-4437        TCGA-CG-4438        TCGA-CG-4440 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-CG-4441        TCGA-CG-4443        TCGA-CG-4444        TCGA-CG-4449 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" 
       TCGA-CG-4455        TCGA-CG-4460        TCGA-CG-4462        TCGA-CG-4465 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-CG-4466        TCGA-CG-4469        TCGA-CG-4472        TCGA-CG-4474 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-CG-4477        TCGA-CG-5716        TCGA-CG-5717        TCGA-CG-5718 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" 
       TCGA-CG-5719        TCGA-CG-5720        TCGA-CG-5721        TCGA-CG-5722 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-CG-5723        TCGA-CG-5724        TCGA-CG-5725        TCGA-CG-5726 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-CG-5727        TCGA-CG-5728        TCGA-CG-5730        TCGA-CG-5732 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-CG-5733        TCGA-CG-5734        TCGA-D7-5577        TCGA-D7-5578 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-D7-5579        TCGA-D7-6518        TCGA-D7-6519        TCGA-D7-6520 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" 
       TCGA-D7-6521        TCGA-D7-6522        TCGA-D7-6524        TCGA-D7-6525 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-D7-6526        TCGA-D7-6527        TCGA-D7-6528        TCGA-D7-6815 
"5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" 
       TCGA-D7-6817        TCGA-D7-6818        TCGA-D7-6820        TCGA-D7-6822 
  "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" 
       TCGA-EQ-5647        TCGA-EQ-8122        TCGA-F1-6177        TCGA-F1-6874 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-F1-6875        TCGA-FP-7735        TCGA-FP-7829        TCGA-FP-7916 
  "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-FP-7998        TCGA-FP-8099        TCGA-FP-8209        TCGA-FP-8631 
"5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" 
       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-BR-8592        TCGA-BR-A4IU        TCGA-BR-A4IV        TCGA-BR-A4IY 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-BR-A4IZ        TCGA-BR-A4J1        TCGA-BR-A4J2        TCGA-BR-A4J4 
"5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-BR-A4J5        TCGA-BR-A4J6        TCGA-BR-A4J8        TCGA-BR-A4J9 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-BR-A4PF        TCGA-CD-5798        TCGA-CD-5799        TCGA-CD-5800 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-CD-5801        TCGA-CD-5802        TCGA-CD-5803        TCGA-CG-4300 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-CG-4301        TCGA-CG-4304        TCGA-CG-4305        TCGA-CG-4306 
"5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-CG-4436        TCGA-CG-4437        TCGA-CG-4438        TCGA-CG-4440 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-CG-4441        TCGA-CG-4443        TCGA-CG-4444        TCGA-CG-4449 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" 
       TCGA-CG-4455        TCGA-CG-4460        TCGA-CG-4462        TCGA-CG-4465 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-CG-4466        TCGA-CG-4469        TCGA-CG-4472        TCGA-CG-4474 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-CG-4477        TCGA-CG-5716        TCGA-CG-5717        TCGA-CG-5718 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" 
       TCGA-CG-5719        TCGA-CG-5720        TCGA-CG-5721        TCGA-CG-5722 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-CG-5723        TCGA-CG-5724        TCGA-CG-5725        TCGA-CG-5726 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-CG-5727        TCGA-CG-5728        TCGA-CG-5730        TCGA-CG-5732 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-CG-5733        TCGA-CG-5734        TCGA-D7-5577        TCGA-D7-5578 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-D7-5579        TCGA-D7-6518        TCGA-D7-6519        TCGA-D7-6520 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" 
       TCGA-D7-6521        TCGA-D7-6522        TCGA-D7-6524        TCGA-D7-6525 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-D7-6526        TCGA-D7-6527        TCGA-D7-6528        TCGA-D7-6815 
"5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" 
       TCGA-D7-6817        TCGA-D7-6818        TCGA-D7-6820        TCGA-D7-6822 
  "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" 
       TCGA-EQ-5647        TCGA-EQ-8122        TCGA-F1-6177        TCGA-F1-6874 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-F1-6875        TCGA-FP-7735        TCGA-FP-7829        TCGA-FP-7916 
  "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-FP-7998        TCGA-FP-8099        TCGA-FP-8209        TCGA-FP-8631 
"5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" 
       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-BR-8592        TCGA-BR-A4IU        TCGA-BR-A4IV        TCGA-BR-A4IY 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-BR-A4IZ        TCGA-BR-A4J1        TCGA-BR-A4J2        TCGA-BR-A4J4 
"5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-BR-A4J5        TCGA-BR-A4J6        TCGA-BR-A4J8        TCGA-BR-A4J9 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-BR-A4PF        TCGA-CD-5798        TCGA-CD-5799        TCGA-CD-5800 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-CD-5801        TCGA-CD-5802        TCGA-CD-5803        TCGA-CG-4300 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-CG-4301        TCGA-CG-4304        TCGA-CG-4305        TCGA-CG-4306 
"5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-CG-4436        TCGA-CG-4437        TCGA-CG-4438        TCGA-CG-4440 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-CG-4441        TCGA-CG-4443        TCGA-CG-4444        TCGA-CG-4449 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" 
       TCGA-CG-4455        TCGA-CG-4460        TCGA-CG-4462        TCGA-CG-4465 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-CG-4466        TCGA-CG-4469        TCGA-CG-4472        TCGA-CG-4474 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-CG-4477        TCGA-CG-5716        TCGA-CG-5717        TCGA-CG-5718 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" 
       TCGA-CG-5719        TCGA-CG-5720        TCGA-CG-5721        TCGA-CG-5722 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-CG-5723        TCGA-CG-5724        TCGA-CG-5725        TCGA-CG-5726 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-CG-5727        TCGA-CG-5728        TCGA-CG-5730        TCGA-CG-5732 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-CG-5733        TCGA-CG-5734        TCGA-D7-5577        TCGA-D7-5578 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-D7-5579        TCGA-D7-6518        TCGA-D7-6519        TCGA-D7-6520 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" 
       TCGA-D7-6521        TCGA-D7-6522        TCGA-D7-6524        TCGA-D7-6525 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-D7-6526        TCGA-D7-6527        TCGA-D7-6528        TCGA-D7-6815 
"5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" 
       TCGA-D7-6817        TCGA-D7-6818        TCGA-D7-6820        TCGA-D7-6822 
  "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" 
       TCGA-EQ-5647        TCGA-EQ-8122        TCGA-F1-6177        TCGA-F1-6874 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-F1-6875        TCGA-FP-7735        TCGA-FP-7829        TCGA-FP-7916 
  "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-FP-7998        TCGA-FP-8099        TCGA-FP-8209        TCGA-FP-8631 
"5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" 
       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=" "2.7"
D45V2, continuous
D45V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED      3   14
  5Q LOSS WILD-TYPE   67   93
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  FEMALE               3                67
  MALE                14                93
                   vv
clus                STOMACH ADENOCARCINOMA - DIFFUSE TYPE
  5Q LOSS MUTATED                                       1
  5Q LOSS WILD-TYPE                                    24
                   vv
clus                STOMACH ADENOCARCINOMA - NOT OTHERWISE SPECIFIED (NOS)
  5Q LOSS MUTATED                                                        8
  5Q LOSS WILD-TYPE                                                     79
                   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                                                 9
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - PAPILLARY TYPE
  5Q LOSS MUTATED                                                    1
  5Q LOSS WILD-TYPE                                                  2
                   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                                                                        2
  5Q LOSS WILD-TYPE                                                                     34
D45V4, multiclass
                   vv
clus                T1 T2 T3 T4
  5Q LOSS MUTATED    0  9  6  1
  5Q LOSS WILD-TYPE  6 45 58 42
D45V5, multiclass
    clus
vv   5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  T1               0                 6
  T2               9                45
  T3               6                58
  T4               1                42
                   vv
clus                N0 N1 N2 N3
  5Q LOSS MUTATED    5  8  3  1
  5Q LOSS WILD-TYPE 51 53 26 19
D45V6, multiclass
    clus
vv   5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  N0               5                51
  N1               8                53
  N2               3                26
  N3               1                19
                   vv
clus                 M0  M1  MX
  5Q LOSS MUTATED    15   0   2
  5Q LOSS WILD-TYPE 131  18  11
D45V7, multiclass
    clus
vv   5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  M0              15               131
  M1               0                18
  MX               2                11
                   vv
clus                 I II III IV
  5Q LOSS MUTATED    3  6   7  0
  5Q LOSS WILD-TYPE 23 42  51 29
D45V8, multiclass
     clus
vv    5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  I                 3                23
  II                6                42
  III               7                51
  IV                0                29
D45V9, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED      1   16
  5Q LOSS WILD-TYPE    4  156
     clus
vv    5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  NO                1                 4
  YES              16               156
                   vv
clus                 R0  R1  R2  RX
  5Q LOSS MUTATED    16   0   0   1
  5Q LOSS WILD-TYPE 107   7  12  24
D45V10, multiclass
    clus
vv   5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  R0              16               107
  R1               0                 7
  R2               0                12
  RX               1                24
D45V11, continuous

Clustering(46) Variable = 6p loss mutation analysis
D46V1, survival
                   sevent
clus2                 0   1
  6P LOSS MUTATED     6   2
  6P LOSS WILD-TYPE 116  16
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
                8               132 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
                2                16 
$`6P LOSS MUTATED`
TCGA-BR-A4J8 TCGA-BR-A4PF TCGA-CG-5719 TCGA-CG-5725 TCGA-D7-6520 TCGA-D7-6525 
        0.23         0.72         1.02        15.02         9.63         5.95 
TCGA-D7-6815 TCGA-FP-8209 
        3.65        59.05 

$`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-BR-8592 TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        0.20         0.59         0.92         0.39         0.79         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J9 TCGA-CD-5798 
        0.79         0.53         0.43         0.13         0.10         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-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-D7-6519 TCGA-D7-6521 
        8.65         3.58         4.54         9.80        15.65         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-FP-8099 TCGA-FP-8631 TCGA-HJ-7597 TCGA-IN-7806 TCGA-IN-7808 TCGA-IP-7968 
        1.02         0.56        26.43         6.87         3.55         2.53 

  6P LOSS MUTATED 6P LOSS WILD-TYPE 
             0.23              0.07 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
            59.05             72.23 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
             4.80              1.22 
[1] "0.2 - 59.0 (4.8)" "0.1 - 72.2 (1.2)"
       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-BR-8592        TCGA-BR-A4IU        TCGA-BR-A4IV        TCGA-BR-A4IY 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-BR-A4IZ        TCGA-BR-A4J1        TCGA-BR-A4J2        TCGA-BR-A4J4 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-BR-A4J5        TCGA-BR-A4J6        TCGA-BR-A4J8        TCGA-BR-A4J9 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE"   "6P LOSS MUTATED" "6P LOSS WILD-TYPE" 
       TCGA-BR-A4PF        TCGA-CD-5798        TCGA-CD-5799        TCGA-CD-5800 
  "6P LOSS MUTATED" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-CD-5801        TCGA-CD-5802        TCGA-CD-5803        TCGA-CG-4300 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-CG-4301        TCGA-CG-4304        TCGA-CG-4305        TCGA-CG-4306 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-CG-4436        TCGA-CG-4437        TCGA-CG-4438        TCGA-CG-4440 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-CG-4441        TCGA-CG-4443        TCGA-CG-4444        TCGA-CG-4449 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-CG-4455        TCGA-CG-4460        TCGA-CG-4462        TCGA-CG-4465 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-CG-4466        TCGA-CG-4469        TCGA-CG-4472        TCGA-CG-4474 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-CG-4477        TCGA-CG-5716        TCGA-CG-5717        TCGA-CG-5718 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-CG-5719        TCGA-CG-5720        TCGA-CG-5721        TCGA-CG-5722 
  "6P LOSS MUTATED" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-CG-5723        TCGA-CG-5724        TCGA-CG-5725        TCGA-CG-5726 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE"   "6P LOSS MUTATED" "6P LOSS WILD-TYPE" 
       TCGA-CG-5727        TCGA-CG-5728        TCGA-CG-5730        TCGA-CG-5732 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-CG-5733        TCGA-CG-5734        TCGA-D7-5577        TCGA-D7-5578 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-D7-5579        TCGA-D7-6518        TCGA-D7-6519        TCGA-D7-6520 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE"   "6P LOSS MUTATED" 
       TCGA-D7-6521        TCGA-D7-6522        TCGA-D7-6524        TCGA-D7-6525 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE"   "6P LOSS MUTATED" 
       TCGA-D7-6526        TCGA-D7-6527        TCGA-D7-6528        TCGA-D7-6815 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE"   "6P LOSS MUTATED" 
       TCGA-D7-6817        TCGA-D7-6818        TCGA-D7-6820        TCGA-D7-6822 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EQ-5647        TCGA-EQ-8122        TCGA-F1-6177        TCGA-F1-6874 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-F1-6875        TCGA-FP-7735        TCGA-FP-7829        TCGA-FP-7916 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-FP-7998        TCGA-FP-8099        TCGA-FP-8209        TCGA-FP-8631 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE"   "6P LOSS MUTATED" "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-BR-8592        TCGA-BR-A4IU        TCGA-BR-A4IV        TCGA-BR-A4IY 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-BR-A4IZ        TCGA-BR-A4J1        TCGA-BR-A4J2        TCGA-BR-A4J4 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-BR-A4J5        TCGA-BR-A4J6        TCGA-BR-A4J8        TCGA-BR-A4J9 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE"   "6P LOSS MUTATED" "6P LOSS WILD-TYPE" 
       TCGA-BR-A4PF        TCGA-CD-5798        TCGA-CD-5799        TCGA-CD-5800 
  "6P LOSS MUTATED" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-CD-5801        TCGA-CD-5802        TCGA-CD-5803        TCGA-CG-4300 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-CG-4301        TCGA-CG-4304        TCGA-CG-4305        TCGA-CG-4306 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-CG-4436        TCGA-CG-4437        TCGA-CG-4438        TCGA-CG-4440 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-CG-4441        TCGA-CG-4443        TCGA-CG-4444        TCGA-CG-4449 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-CG-4455        TCGA-CG-4460        TCGA-CG-4462        TCGA-CG-4465 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-CG-4466        TCGA-CG-4469        TCGA-CG-4472        TCGA-CG-4474 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-CG-4477        TCGA-CG-5716        TCGA-CG-5717        TCGA-CG-5718 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-CG-5719        TCGA-CG-5720        TCGA-CG-5721        TCGA-CG-5722 
  "6P LOSS MUTATED" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-CG-5723        TCGA-CG-5724        TCGA-CG-5725        TCGA-CG-5726 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE"   "6P LOSS MUTATED" "6P LOSS WILD-TYPE" 
       TCGA-CG-5727        TCGA-CG-5728        TCGA-CG-5730        TCGA-CG-5732 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-CG-5733        TCGA-CG-5734        TCGA-D7-5577        TCGA-D7-5578 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-D7-5579        TCGA-D7-6518        TCGA-D7-6519        TCGA-D7-6520 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE"   "6P LOSS MUTATED" 
       TCGA-D7-6521        TCGA-D7-6522        TCGA-D7-6524        TCGA-D7-6525 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE"   "6P LOSS MUTATED" 
       TCGA-D7-6526        TCGA-D7-6527        TCGA-D7-6528        TCGA-D7-6815 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE"   "6P LOSS MUTATED" 
       TCGA-D7-6817        TCGA-D7-6818        TCGA-D7-6820        TCGA-D7-6822 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EQ-5647        TCGA-EQ-8122        TCGA-F1-6177        TCGA-F1-6874 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-F1-6875        TCGA-FP-7735        TCGA-FP-7829        TCGA-FP-7916 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-FP-7998        TCGA-FP-8099        TCGA-FP-8209        TCGA-FP-8631 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE"   "6P LOSS MUTATED" "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-BR-8592        TCGA-BR-A4IU        TCGA-BR-A4IV        TCGA-BR-A4IY 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-BR-A4IZ        TCGA-BR-A4J1        TCGA-BR-A4J2        TCGA-BR-A4J4 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-BR-A4J5        TCGA-BR-A4J6        TCGA-BR-A4J8        TCGA-BR-A4J9 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE"   "6P LOSS MUTATED" "6P LOSS WILD-TYPE" 
       TCGA-BR-A4PF        TCGA-CD-5798        TCGA-CD-5799        TCGA-CD-5800 
  "6P LOSS MUTATED" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-CD-5801        TCGA-CD-5802        TCGA-CD-5803        TCGA-CG-4300 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-CG-4301        TCGA-CG-4304        TCGA-CG-4305        TCGA-CG-4306 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-CG-4436        TCGA-CG-4437        TCGA-CG-4438        TCGA-CG-4440 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-CG-4441        TCGA-CG-4443        TCGA-CG-4444        TCGA-CG-4449 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-CG-4455        TCGA-CG-4460        TCGA-CG-4462        TCGA-CG-4465 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-CG-4466        TCGA-CG-4469        TCGA-CG-4472        TCGA-CG-4474 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-CG-4477        TCGA-CG-5716        TCGA-CG-5717        TCGA-CG-5718 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-CG-5719        TCGA-CG-5720        TCGA-CG-5721        TCGA-CG-5722 
  "6P LOSS MUTATED" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-CG-5723        TCGA-CG-5724        TCGA-CG-5725        TCGA-CG-5726 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE"   "6P LOSS MUTATED" "6P LOSS WILD-TYPE" 
       TCGA-CG-5727        TCGA-CG-5728        TCGA-CG-5730        TCGA-CG-5732 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-CG-5733        TCGA-CG-5734        TCGA-D7-5577        TCGA-D7-5578 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-D7-5579        TCGA-D7-6518        TCGA-D7-6519        TCGA-D7-6520 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE"   "6P LOSS MUTATED" 
       TCGA-D7-6521        TCGA-D7-6522        TCGA-D7-6524        TCGA-D7-6525 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE"   "6P LOSS MUTATED" 
       TCGA-D7-6526        TCGA-D7-6527        TCGA-D7-6528        TCGA-D7-6815 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE"   "6P LOSS MUTATED" 
       TCGA-D7-6817        TCGA-D7-6818        TCGA-D7-6820        TCGA-D7-6822 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EQ-5647        TCGA-EQ-8122        TCGA-F1-6177        TCGA-F1-6874 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-F1-6875        TCGA-FP-7735        TCGA-FP-7829        TCGA-FP-7916 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-FP-7998        TCGA-FP-8099        TCGA-FP-8209        TCGA-FP-8631 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE"   "6P LOSS MUTATED" "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=" "1.3"
D46V2, continuous
D46V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED      4    6
  6P LOSS WILD-TYPE   66  101
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  FEMALE               4                66
  MALE                 6               101
                   vv
clus                STOMACH ADENOCARCINOMA - DIFFUSE TYPE
  6P LOSS MUTATED                                       2
  6P LOSS WILD-TYPE                                    23
                   vv
clus                STOMACH ADENOCARCINOMA - NOT OTHERWISE SPECIFIED (NOS)
  6P LOSS MUTATED                                                        4
  6P LOSS WILD-TYPE                                                     83
                   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                                                10
                   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                                                                     35
D46V4, multiclass
                   vv
clus                T1 T2 T3 T4
  6P LOSS MUTATED    0  6  2  2
  6P LOSS WILD-TYPE  6 48 62 41
D46V5, multiclass
    clus
vv   6P LOSS MUTATED 6P LOSS WILD-TYPE
  T1               0                 6
  T2               6                48
  T3               2                62
  T4               2                41
                   vv
clus                N0 N1 N2 N3
  6P LOSS MUTATED    3  0  4  1
  6P LOSS WILD-TYPE 53 61 25 19
D46V6, multiclass
    clus
vv   6P LOSS MUTATED 6P LOSS WILD-TYPE
  N0               3                53
  N1               0                61
  N2               4                25
  N3               1                19
                   vv
clus                 M0  M1  MX
  6P LOSS MUTATED     8   1   1
  6P LOSS WILD-TYPE 138  17  12
D46V7, multiclass
    clus
vv   6P LOSS MUTATED 6P LOSS WILD-TYPE
  M0               8               138
  M1               1                17
  MX               1                12
                   vv
clus                 I II III IV
  6P LOSS MUTATED    2  0   5  1
  6P LOSS WILD-TYPE 24 48  53 28
D46V8, multiclass
     clus
vv    6P LOSS MUTATED 6P LOSS WILD-TYPE
  I                 2                24
  II                0                48
  III               5                53
  IV                1                28
D46V9, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED      0   10
  6P LOSS WILD-TYPE    5  162
     clus
vv    6P LOSS MUTATED 6P LOSS WILD-TYPE
  NO                0                 5
  YES              10               162
                   vv
clus                 R0  R1  R2  RX
  6P LOSS MUTATED     8   0   0   2
  6P LOSS WILD-TYPE 115   7  12  23
D46V10, multiclass
    clus
vv   6P LOSS MUTATED 6P LOSS WILD-TYPE
  R0               8               115
  R1               0                 7
  R2               0                12
  RX               2                23
D46V11, continuous

Clustering(47) Variable = 6q loss mutation analysis
D47V1, survival
                   sevent
clus2                 0   1
  6Q LOSS MUTATED     9   2
  6Q LOSS WILD-TYPE 113  16
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               11               129 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
                2                16 
$`6Q LOSS MUTATED`
TCGA-BR-7722 TCGA-BR-A4J8 TCGA-BR-A4PF TCGA-CG-4443 TCGA-CG-5719 TCGA-CG-5725 
        0.16         0.23         0.72        29.98         1.02        15.02 
TCGA-D7-6520 TCGA-D7-6525 TCGA-D7-6815 TCGA-FP-8209 TCGA-FP-8631 
        9.63         5.95         3.65        59.05         0.56 

$`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-BR-8592 
        0.26         1.18         1.55         1.48         0.76         0.20 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
        0.59         0.92         0.39         0.79         0.72         0.79 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J9 TCGA-CD-5798 TCGA-CD-5799 
        0.53         0.43         0.13         0.10         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-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-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-5726 TCGA-CG-5727 TCGA-CG-5728 
        0.95        70.06        12.03        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-D7-6526 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-FP-8099 TCGA-HJ-7597 
        0.39         0.20         3.02         3.58         1.02        26.43 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IP-7968 
        6.87         3.55         2.53 

  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
             0.16              0.07 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
            59.05             72.23 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
             3.65              1.22 
[1] "0.2 - 59.0 (3.6)" "0.1 - 72.2 (1.2)"
       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-BR-8592        TCGA-BR-A4IU        TCGA-BR-A4IV        TCGA-BR-A4IY 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-BR-A4IZ        TCGA-BR-A4J1        TCGA-BR-A4J2        TCGA-BR-A4J4 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-BR-A4J5        TCGA-BR-A4J6        TCGA-BR-A4J8        TCGA-BR-A4J9 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" 
       TCGA-BR-A4PF        TCGA-CD-5798        TCGA-CD-5799        TCGA-CD-5800 
  "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-CD-5801        TCGA-CD-5802        TCGA-CD-5803        TCGA-CG-4300 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-CG-4301        TCGA-CG-4304        TCGA-CG-4305        TCGA-CG-4306 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-CG-4436        TCGA-CG-4437        TCGA-CG-4438        TCGA-CG-4440 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-CG-4441        TCGA-CG-4443        TCGA-CG-4444        TCGA-CG-4449 
"6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-CG-4455        TCGA-CG-4460        TCGA-CG-4462        TCGA-CG-4465 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-CG-4466        TCGA-CG-4469        TCGA-CG-4472        TCGA-CG-4474 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-CG-4477        TCGA-CG-5716        TCGA-CG-5717        TCGA-CG-5718 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-CG-5719        TCGA-CG-5720        TCGA-CG-5721        TCGA-CG-5722 
  "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-CG-5723        TCGA-CG-5724        TCGA-CG-5725        TCGA-CG-5726 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" 
       TCGA-CG-5727        TCGA-CG-5728        TCGA-CG-5730        TCGA-CG-5732 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-CG-5733        TCGA-CG-5734        TCGA-D7-5577        TCGA-D7-5578 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-D7-5579        TCGA-D7-6518        TCGA-D7-6519        TCGA-D7-6520 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" 
       TCGA-D7-6521        TCGA-D7-6522        TCGA-D7-6524        TCGA-D7-6525 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" 
       TCGA-D7-6526        TCGA-D7-6527        TCGA-D7-6528        TCGA-D7-6815 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" 
       TCGA-D7-6817        TCGA-D7-6818        TCGA-D7-6820        TCGA-D7-6822 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-EQ-5647        TCGA-EQ-8122        TCGA-F1-6177        TCGA-F1-6874 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-F1-6875        TCGA-FP-7735        TCGA-FP-7829        TCGA-FP-7916 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-FP-7998        TCGA-FP-8099        TCGA-FP-8209        TCGA-FP-8631 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED"   "6Q LOSS MUTATED" 
       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-BR-8592        TCGA-BR-A4IU        TCGA-BR-A4IV        TCGA-BR-A4IY 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-BR-A4IZ        TCGA-BR-A4J1        TCGA-BR-A4J2        TCGA-BR-A4J4 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-BR-A4J5        TCGA-BR-A4J6        TCGA-BR-A4J8        TCGA-BR-A4J9 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" 
       TCGA-BR-A4PF        TCGA-CD-5798        TCGA-CD-5799        TCGA-CD-5800 
  "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-CD-5801        TCGA-CD-5802        TCGA-CD-5803        TCGA-CG-4300 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-CG-4301        TCGA-CG-4304        TCGA-CG-4305        TCGA-CG-4306 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-CG-4436        TCGA-CG-4437        TCGA-CG-4438        TCGA-CG-4440 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-CG-4441        TCGA-CG-4443        TCGA-CG-4444        TCGA-CG-4449 
"6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-CG-4455        TCGA-CG-4460        TCGA-CG-4462        TCGA-CG-4465 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-CG-4466        TCGA-CG-4469        TCGA-CG-4472        TCGA-CG-4474 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-CG-4477        TCGA-CG-5716        TCGA-CG-5717        TCGA-CG-5718 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-CG-5719        TCGA-CG-5720        TCGA-CG-5721        TCGA-CG-5722 
  "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-CG-5723        TCGA-CG-5724        TCGA-CG-5725        TCGA-CG-5726 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" 
       TCGA-CG-5727        TCGA-CG-5728        TCGA-CG-5730        TCGA-CG-5732 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-CG-5733        TCGA-CG-5734        TCGA-D7-5577        TCGA-D7-5578 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-D7-5579        TCGA-D7-6518        TCGA-D7-6519        TCGA-D7-6520 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" 
       TCGA-D7-6521        TCGA-D7-6522        TCGA-D7-6524        TCGA-D7-6525 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" 
       TCGA-D7-6526        TCGA-D7-6527        TCGA-D7-6528        TCGA-D7-6815 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" 
       TCGA-D7-6817        TCGA-D7-6818        TCGA-D7-6820        TCGA-D7-6822 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-EQ-5647        TCGA-EQ-8122        TCGA-F1-6177        TCGA-F1-6874 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-F1-6875        TCGA-FP-7735        TCGA-FP-7829        TCGA-FP-7916 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-FP-7998        TCGA-FP-8099        TCGA-FP-8209        TCGA-FP-8631 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED"   "6Q LOSS MUTATED" 
       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-BR-8592        TCGA-BR-A4IU        TCGA-BR-A4IV        TCGA-BR-A4IY 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-BR-A4IZ        TCGA-BR-A4J1        TCGA-BR-A4J2        TCGA-BR-A4J4 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-BR-A4J5        TCGA-BR-A4J6        TCGA-BR-A4J8        TCGA-BR-A4J9 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" 
       TCGA-BR-A4PF        TCGA-CD-5798        TCGA-CD-5799        TCGA-CD-5800 
  "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-CD-5801        TCGA-CD-5802        TCGA-CD-5803        TCGA-CG-4300 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-CG-4301        TCGA-CG-4304        TCGA-CG-4305        TCGA-CG-4306 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-CG-4436        TCGA-CG-4437        TCGA-CG-4438        TCGA-CG-4440 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-CG-4441        TCGA-CG-4443        TCGA-CG-4444        TCGA-CG-4449 
"6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-CG-4455        TCGA-CG-4460        TCGA-CG-4462        TCGA-CG-4465 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-CG-4466        TCGA-CG-4469        TCGA-CG-4472        TCGA-CG-4474 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-CG-4477        TCGA-CG-5716        TCGA-CG-5717        TCGA-CG-5718 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-CG-5719        TCGA-CG-5720        TCGA-CG-5721        TCGA-CG-5722 
  "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-CG-5723        TCGA-CG-5724        TCGA-CG-5725        TCGA-CG-5726 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" 
       TCGA-CG-5727        TCGA-CG-5728        TCGA-CG-5730        TCGA-CG-5732 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-CG-5733        TCGA-CG-5734        TCGA-D7-5577        TCGA-D7-5578 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-D7-5579        TCGA-D7-6518        TCGA-D7-6519        TCGA-D7-6520 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" 
       TCGA-D7-6521        TCGA-D7-6522        TCGA-D7-6524        TCGA-D7-6525 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" 
       TCGA-D7-6526        TCGA-D7-6527        TCGA-D7-6528        TCGA-D7-6815 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" 
       TCGA-D7-6817        TCGA-D7-6818        TCGA-D7-6820        TCGA-D7-6822 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-EQ-5647        TCGA-EQ-8122        TCGA-F1-6177        TCGA-F1-6874 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-F1-6875        TCGA-FP-7735        TCGA-FP-7829        TCGA-FP-7916 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-FP-7998        TCGA-FP-8099        TCGA-FP-8209        TCGA-FP-8631 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED"   "6Q LOSS MUTATED" 
       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=" "1.1"
D47V2, continuous
D47V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED      4   11
  6Q LOSS WILD-TYPE   66   96
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  FEMALE               4                66
  MALE                11                96
                   vv
clus                STOMACH ADENOCARCINOMA - DIFFUSE TYPE
  6Q LOSS MUTATED                                       2
  6Q LOSS WILD-TYPE                                    23
                   vv
clus                STOMACH ADENOCARCINOMA - NOT OTHERWISE SPECIFIED (NOS)
  6Q LOSS MUTATED                                                        7
  6Q LOSS WILD-TYPE                                                     80
                   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                                                10
                   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                                                                        3
  6Q LOSS WILD-TYPE                                                                     33
D47V4, multiclass
                   vv
clus                T1 T2 T3 T4
  6Q LOSS MUTATED    1  7  5  2
  6Q LOSS WILD-TYPE  5 47 59 41
D47V5, multiclass
    clus
vv   6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  T1               1                 5
  T2               7                47
  T3               5                59
  T4               2                41
                   vv
clus                N0 N1 N2 N3
  6Q LOSS MUTATED    5  2  5  1
  6Q LOSS WILD-TYPE 51 59 24 19
D47V6, multiclass
    clus
vv   6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  N0               5                51
  N1               2                59
  N2               5                24
  N3               1                19
                   vv
clus                 M0  M1  MX
  6Q LOSS MUTATED    12   1   2
  6Q LOSS WILD-TYPE 134  17  11
D47V7, multiclass
    clus
vv   6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  M0              12               134
  M1               1                17
  MX               2                11
                   vv
clus                 I II III IV
  6Q LOSS MUTATED    4  0   8  1
  6Q LOSS WILD-TYPE 22 48  50 28
D47V8, multiclass
     clus
vv    6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  I                 4                22
  II                0                48
  III               8                50
  IV                1                28
D47V9, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED      0   15
  6Q LOSS WILD-TYPE    5  157
     clus
vv    6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  NO                0                 5
  YES              15               157
                   vv
clus                 R0  R1  R2  RX
  6Q LOSS MUTATED    12   0   0   3
  6Q LOSS WILD-TYPE 111   7  12  22
D47V10, multiclass
    clus
vv   6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  R0              12               111
  R1               0                 7
  R2               0                12
  RX               3                22
D47V11, continuous

Clustering(48) Variable = 7p loss mutation analysis
D48V1, survival
                   sevent
clus2                 0   1
  7P LOSS MUTATED     3   0
  7P LOSS WILD-TYPE 119  18
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
                3               137 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
                0                18 
$`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-BR-8592 
        0.26         1.18         1.55         1.48         0.76         0.20 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
        0.59         0.92         0.39         0.79         0.72         0.79 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PF 
        0.53         0.43         0.13         0.23         0.10         0.72 
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-4444 TCGA-CG-4449 TCGA-CG-4455 
        8.05         4.01        14.01        47.05        19.07        12.03 
TCGA-CG-4460 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 
       21.99         1.02         8.98        18.94         7.07        12.00 
TCGA-CG-4474 TCGA-CG-4477 TCGA-CG-5716 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
        1.02         1.02         1.02         6.94         1.02         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-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-FP-8099 TCGA-FP-8209 
        0.39         0.20         3.02         3.58         1.02        59.05 
TCGA-FP-8631 TCGA-HJ-7597 TCGA-IN-7806 TCGA-IN-7808 TCGA-IP-7968 
        0.56        26.43         6.87         3.55         2.53 

  7P LOSS MUTATED 7P LOSS WILD-TYPE 
             4.54              0.07 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
            54.05             72.23 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
            29.98              1.22 
[1] "4.5 - 54.0 (30.0)" "0.1 - 72.2 (1.2)" 
       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-BR-8592        TCGA-BR-A4IU        TCGA-BR-A4IV        TCGA-BR-A4IY 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-BR-A4IZ        TCGA-BR-A4J1        TCGA-BR-A4J2        TCGA-BR-A4J4 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-BR-A4J5        TCGA-BR-A4J6        TCGA-BR-A4J8        TCGA-BR-A4J9 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-BR-A4PF        TCGA-CD-5798        TCGA-CD-5799        TCGA-CD-5800 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-CD-5801        TCGA-CD-5802        TCGA-CD-5803        TCGA-CG-4300 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-CG-4301        TCGA-CG-4304        TCGA-CG-4305        TCGA-CG-4306 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-CG-4436        TCGA-CG-4437        TCGA-CG-4438        TCGA-CG-4440 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE"   "7P LOSS MUTATED" "7P LOSS WILD-TYPE" 
       TCGA-CG-4441        TCGA-CG-4443        TCGA-CG-4444        TCGA-CG-4449 
"7P LOSS WILD-TYPE"   "7P LOSS MUTATED" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-CG-4455        TCGA-CG-4460        TCGA-CG-4462        TCGA-CG-4465 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-CG-4466        TCGA-CG-4469        TCGA-CG-4472        TCGA-CG-4474 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-CG-4477        TCGA-CG-5716        TCGA-CG-5717        TCGA-CG-5718 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-CG-5719        TCGA-CG-5720        TCGA-CG-5721        TCGA-CG-5722 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-CG-5723        TCGA-CG-5724        TCGA-CG-5725        TCGA-CG-5726 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-CG-5727        TCGA-CG-5728        TCGA-CG-5730        TCGA-CG-5732 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-CG-5733        TCGA-CG-5734        TCGA-D7-5577        TCGA-D7-5578 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-D7-5579        TCGA-D7-6518        TCGA-D7-6519        TCGA-D7-6520 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-D7-6521        TCGA-D7-6522        TCGA-D7-6524        TCGA-D7-6525 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-D7-6526        TCGA-D7-6527        TCGA-D7-6528        TCGA-D7-6815 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-D7-6817        TCGA-D7-6818        TCGA-D7-6820        TCGA-D7-6822 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-EQ-5647        TCGA-EQ-8122        TCGA-F1-6177        TCGA-F1-6874 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-F1-6875        TCGA-FP-7735        TCGA-FP-7829        TCGA-FP-7916 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-FP-7998        TCGA-FP-8099        TCGA-FP-8209        TCGA-FP-8631 
"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-BR-8592        TCGA-BR-A4IU        TCGA-BR-A4IV        TCGA-BR-A4IY 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-BR-A4IZ        TCGA-BR-A4J1        TCGA-BR-A4J2        TCGA-BR-A4J4 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-BR-A4J5        TCGA-BR-A4J6        TCGA-BR-A4J8        TCGA-BR-A4J9 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-BR-A4PF        TCGA-CD-5798        TCGA-CD-5799        TCGA-CD-5800 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-CD-5801        TCGA-CD-5802        TCGA-CD-5803        TCGA-CG-4300 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-CG-4301        TCGA-CG-4304        TCGA-CG-4305        TCGA-CG-4306 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-CG-4436        TCGA-CG-4437        TCGA-CG-4438        TCGA-CG-4440 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE"   "7P LOSS MUTATED" "7P LOSS WILD-TYPE" 
       TCGA-CG-4441        TCGA-CG-4443        TCGA-CG-4444        TCGA-CG-4449 
"7P LOSS WILD-TYPE"   "7P LOSS MUTATED" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-CG-4455        TCGA-CG-4460        TCGA-CG-4462        TCGA-CG-4465 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-CG-4466        TCGA-CG-4469        TCGA-CG-4472        TCGA-CG-4474 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-CG-4477        TCGA-CG-5716        TCGA-CG-5717        TCGA-CG-5718 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-CG-5719        TCGA-CG-5720        TCGA-CG-5721        TCGA-CG-5722 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-CG-5723        TCGA-CG-5724        TCGA-CG-5725        TCGA-CG-5726 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-CG-5727        TCGA-CG-5728        TCGA-CG-5730        TCGA-CG-5732 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-CG-5733        TCGA-CG-5734        TCGA-D7-5577        TCGA-D7-5578 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-D7-5579        TCGA-D7-6518        TCGA-D7-6519        TCGA-D7-6520 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-D7-6521        TCGA-D7-6522        TCGA-D7-6524        TCGA-D7-6525 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-D7-6526        TCGA-D7-6527        TCGA-D7-6528        TCGA-D7-6815 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-D7-6817        TCGA-D7-6818        TCGA-D7-6820        TCGA-D7-6822 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-EQ-5647        TCGA-EQ-8122        TCGA-F1-6177        TCGA-F1-6874 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-F1-6875        TCGA-FP-7735        TCGA-FP-7829        TCGA-FP-7916 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-FP-7998        TCGA-FP-8099        TCGA-FP-8209        TCGA-FP-8631 
"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-BR-8592        TCGA-BR-A4IU        TCGA-BR-A4IV        TCGA-BR-A4IY 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-BR-A4IZ        TCGA-BR-A4J1        TCGA-BR-A4J2        TCGA-BR-A4J4 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-BR-A4J5        TCGA-BR-A4J6        TCGA-BR-A4J8        TCGA-BR-A4J9 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-BR-A4PF        TCGA-CD-5798        TCGA-CD-5799        TCGA-CD-5800 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-CD-5801        TCGA-CD-5802        TCGA-CD-5803        TCGA-CG-4300 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-CG-4301        TCGA-CG-4304        TCGA-CG-4305        TCGA-CG-4306 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-CG-4436        TCGA-CG-4437        TCGA-CG-4438        TCGA-CG-4440 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE"   "7P LOSS MUTATED" "7P LOSS WILD-TYPE" 
       TCGA-CG-4441        TCGA-CG-4443        TCGA-CG-4444        TCGA-CG-4449 
"7P LOSS WILD-TYPE"   "7P LOSS MUTATED" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-CG-4455        TCGA-CG-4460        TCGA-CG-4462        TCGA-CG-4465 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-CG-4466        TCGA-CG-4469        TCGA-CG-4472        TCGA-CG-4474 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-CG-4477        TCGA-CG-5716        TCGA-CG-5717        TCGA-CG-5718 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-CG-5719        TCGA-CG-5720        TCGA-CG-5721        TCGA-CG-5722 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-CG-5723        TCGA-CG-5724        TCGA-CG-5725        TCGA-CG-5726 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-CG-5727        TCGA-CG-5728        TCGA-CG-5730        TCGA-CG-5732 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-CG-5733        TCGA-CG-5734        TCGA-D7-5577        TCGA-D7-5578 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-D7-5579        TCGA-D7-6518        TCGA-D7-6519        TCGA-D7-6520 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-D7-6521        TCGA-D7-6522        TCGA-D7-6524        TCGA-D7-6525 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-D7-6526        TCGA-D7-6527        TCGA-D7-6528        TCGA-D7-6815 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-D7-6817        TCGA-D7-6818        TCGA-D7-6820        TCGA-D7-6822 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-EQ-5647        TCGA-EQ-8122        TCGA-F1-6177        TCGA-F1-6874 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-F1-6875        TCGA-FP-7735        TCGA-FP-7829        TCGA-FP-7916 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-FP-7998        TCGA-FP-8099        TCGA-FP-8209        TCGA-FP-8631 
"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="     "7.9e+07"
D48V2, continuous
D48V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED      0    3
  7P LOSS WILD-TYPE   70  104
        clus
vv       7P LOSS MUTATED 7P LOSS WILD-TYPE
  FEMALE               0                70
  MALE                 3               104
                   vv
clus                STOMACH ADENOCARCINOMA - DIFFUSE TYPE
  7P LOSS MUTATED                                       0
  7P LOSS WILD-TYPE                                    25
                   vv
clus                STOMACH ADENOCARCINOMA - NOT OTHERWISE SPECIFIED (NOS)
  7P LOSS MUTATED                                                        1
  7P LOSS WILD-TYPE                                                     86
                   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                                                10
                   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                                                                     34
D48V4, multiclass
                   vv
clus                T1 T2 T3 T4
  7P LOSS MUTATED    1  0  1  1
  7P LOSS WILD-TYPE  5 54 63 42
D48V5, multiclass
    clus
vv   7P LOSS MUTATED 7P LOSS WILD-TYPE
  T1               1                 5
  T2               0                54
  T3               1                63
  T4               1                42
                   vv
clus                N0 N1 N2 N3
  7P LOSS MUTATED    1  0  2  0
  7P LOSS WILD-TYPE 55 61 27 20
D48V6, multiclass
    clus
vv   7P LOSS MUTATED 7P LOSS WILD-TYPE
  N0               1                55
  N1               0                61
  N2               2                27
  N3               0                20
                   vv
clus                 M0  M1  MX
  7P LOSS MUTATED     3   0   0
  7P LOSS WILD-TYPE 143  18  13
D48V7, multiclass
    clus
vv   7P LOSS MUTATED 7P LOSS WILD-TYPE
  M0               3               143
  M1               0                18
  MX               0                13
                   vv
clus                 I II III IV
  7P LOSS MUTATED    1  1   0  1
  7P LOSS WILD-TYPE 25 47  58 28
D48V8, multiclass
     clus
vv    7P LOSS MUTATED 7P LOSS WILD-TYPE
  I                 1                25
  II                1                47
  III               0                58
  IV                1                28
D48V9, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED      0    3
  7P LOSS WILD-TYPE    5  169
     clus
vv    7P LOSS MUTATED 7P LOSS WILD-TYPE
  NO                0                 5
  YES               3               169
                   vv
clus                 R0  R1  R2  RX
  7P LOSS MUTATED     3   0   0   0
  7P LOSS WILD-TYPE 120   7  12  25
D48V10, multiclass
    clus
vv   7P LOSS MUTATED 7P LOSS WILD-TYPE
  R0               3               120
  R1               0                 7
  R2               0                12
  RX               0                25
D48V11, continuous
[1] "Remove cluster labels:" "7P LOSS MUTATED"       
clus
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
                1               132 
       TCGA-B7-5816        TCGA-BR-4183        TCGA-BR-4184        TCGA-BR-4188 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-BR-4191        TCGA-BR-4253        TCGA-BR-4255        TCGA-BR-4256 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-BR-4267        TCGA-BR-4279        TCGA-BR-4280        TCGA-BR-4361 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-BR-4362        TCGA-BR-4367        TCGA-BR-4368        TCGA-BR-6452 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-BR-6453        TCGA-BR-6454        TCGA-BR-6455        TCGA-BR-6456 
"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-7851        TCGA-BR-7901        TCGA-BR-7957        TCGA-BR-7958 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-BR-7959        TCGA-BR-8059        TCGA-BR-8060        TCGA-BR-8077 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-BR-8078        TCGA-BR-8080        TCGA-BR-8081        TCGA-BR-8284 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-BR-8285        TCGA-BR-8286        TCGA-BR-8289        TCGA-BR-8291 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-BR-8295        TCGA-BR-8296        TCGA-BR-8297        TCGA-BR-8592 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-BR-A4IU        TCGA-BR-A4IV        TCGA-BR-A4IY        TCGA-BR-A4IZ 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-BR-A4J1        TCGA-BR-A4J2        TCGA-BR-A4J4        TCGA-BR-A4J5 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-BR-A4J6        TCGA-BR-A4J8        TCGA-BR-A4J9        TCGA-BR-A4PF 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-CD-5804        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-FP-8099        TCGA-FP-8209        TCGA-FP-8631        TCGA-HF-7131 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-HF-7132        TCGA-HF-7133        TCGA-HF-7134        TCGA-HF-7136 
"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" 

Clustering(49) Variable = 7q loss mutation analysis
D49V1, survival
                   sevent
clus2                 0   1
  7Q LOSS MUTATED     6   0
  7Q LOSS WILD-TYPE 116  18
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
                6               134 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
                0                18 
$`7Q LOSS MUTATED`
TCGA-BR-7723 TCGA-CG-4438 TCGA-CG-4443 TCGA-D7-6820 TCGA-FP-7829 TCGA-FP-8631 
        4.54        54.05        29.98         2.93         0.20         0.56 

$`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-BR-8592 
        0.26         1.18         1.55         1.48         0.76         0.20 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
        0.59         0.92         0.39         0.79         0.72         0.79 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PF 
        0.53         0.43         0.13         0.23         0.10         0.72 
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-4444 TCGA-CG-4449 TCGA-CG-4455 
        8.05         4.01        14.01        47.05        19.07        12.03 
TCGA-CG-4460 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 
       21.99         1.02         8.98        18.94         7.07        12.00 
TCGA-CG-4474 TCGA-CG-4477 TCGA-CG-5716 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
        1.02         1.02         1.02         6.94         1.02         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-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-D7-6822 
        4.14         1.68         3.65         4.70         4.04         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-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-HJ-7597 TCGA-IN-7806 
        3.02         3.58         1.02        59.05        26.43         6.87 
TCGA-IN-7808 TCGA-IP-7968 
        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 
            3.735             1.220 
[1] "0.2 - 54.0 (3.7)" "0.1 - 72.2 (1.2)"
       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-BR-8592        TCGA-BR-A4IU        TCGA-BR-A4IV        TCGA-BR-A4IY 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-BR-A4IZ        TCGA-BR-A4J1        TCGA-BR-A4J2        TCGA-BR-A4J4 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-BR-A4J5        TCGA-BR-A4J6        TCGA-BR-A4J8        TCGA-BR-A4J9 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-BR-A4PF        TCGA-CD-5798        TCGA-CD-5799        TCGA-CD-5800 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-CD-5801        TCGA-CD-5802        TCGA-CD-5803        TCGA-CG-4300 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-CG-4301        TCGA-CG-4304        TCGA-CG-4305        TCGA-CG-4306 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-CG-4436        TCGA-CG-4437        TCGA-CG-4438        TCGA-CG-4440 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE"   "7Q LOSS MUTATED" "7Q LOSS WILD-TYPE" 
       TCGA-CG-4441        TCGA-CG-4443        TCGA-CG-4444        TCGA-CG-4449 
"7Q LOSS WILD-TYPE"   "7Q LOSS MUTATED" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-CG-4455        TCGA-CG-4460        TCGA-CG-4462        TCGA-CG-4465 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-CG-4466        TCGA-CG-4469        TCGA-CG-4472        TCGA-CG-4474 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-CG-4477        TCGA-CG-5716        TCGA-CG-5717        TCGA-CG-5718 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-CG-5719        TCGA-CG-5720        TCGA-CG-5721        TCGA-CG-5722 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-CG-5723        TCGA-CG-5724        TCGA-CG-5725        TCGA-CG-5726 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-CG-5727        TCGA-CG-5728        TCGA-CG-5730        TCGA-CG-5732 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-CG-5733        TCGA-CG-5734        TCGA-D7-5577        TCGA-D7-5578 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-D7-5579        TCGA-D7-6518        TCGA-D7-6519        TCGA-D7-6520 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-D7-6521        TCGA-D7-6522        TCGA-D7-6524        TCGA-D7-6525 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-D7-6526        TCGA-D7-6527        TCGA-D7-6528        TCGA-D7-6815 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-D7-6817        TCGA-D7-6818        TCGA-D7-6820        TCGA-D7-6822 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE"   "7Q LOSS MUTATED" "7Q LOSS WILD-TYPE" 
       TCGA-EQ-5647        TCGA-EQ-8122        TCGA-F1-6177        TCGA-F1-6874 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-F1-6875        TCGA-FP-7735        TCGA-FP-7829        TCGA-FP-7916 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE"   "7Q LOSS MUTATED" "7Q LOSS WILD-TYPE" 
       TCGA-FP-7998        TCGA-FP-8099        TCGA-FP-8209        TCGA-FP-8631 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE"   "7Q LOSS MUTATED" 
       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-BR-8592        TCGA-BR-A4IU        TCGA-BR-A4IV        TCGA-BR-A4IY 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-BR-A4IZ        TCGA-BR-A4J1        TCGA-BR-A4J2        TCGA-BR-A4J4 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-BR-A4J5        TCGA-BR-A4J6        TCGA-BR-A4J8        TCGA-BR-A4J9 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-BR-A4PF        TCGA-CD-5798        TCGA-CD-5799        TCGA-CD-5800 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-CD-5801        TCGA-CD-5802        TCGA-CD-5803        TCGA-CG-4300 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-CG-4301        TCGA-CG-4304        TCGA-CG-4305        TCGA-CG-4306 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-CG-4436        TCGA-CG-4437        TCGA-CG-4438        TCGA-CG-4440 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE"   "7Q LOSS MUTATED" "7Q LOSS WILD-TYPE" 
       TCGA-CG-4441        TCGA-CG-4443        TCGA-CG-4444        TCGA-CG-4449 
"7Q LOSS WILD-TYPE"   "7Q LOSS MUTATED" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-CG-4455        TCGA-CG-4460        TCGA-CG-4462        TCGA-CG-4465 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-CG-4466        TCGA-CG-4469        TCGA-CG-4472        TCGA-CG-4474 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-CG-4477        TCGA-CG-5716        TCGA-CG-5717        TCGA-CG-5718 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-CG-5719        TCGA-CG-5720        TCGA-CG-5721        TCGA-CG-5722 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-CG-5723        TCGA-CG-5724        TCGA-CG-5725        TCGA-CG-5726 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-CG-5727        TCGA-CG-5728        TCGA-CG-5730        TCGA-CG-5732 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-CG-5733        TCGA-CG-5734        TCGA-D7-5577        TCGA-D7-5578 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-D7-5579        TCGA-D7-6518        TCGA-D7-6519        TCGA-D7-6520 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-D7-6521        TCGA-D7-6522        TCGA-D7-6524        TCGA-D7-6525 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-D7-6526        TCGA-D7-6527        TCGA-D7-6528        TCGA-D7-6815 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-D7-6817        TCGA-D7-6818        TCGA-D7-6820        TCGA-D7-6822 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE"   "7Q LOSS MUTATED" "7Q LOSS WILD-TYPE" 
       TCGA-EQ-5647        TCGA-EQ-8122        TCGA-F1-6177        TCGA-F1-6874 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-F1-6875        TCGA-FP-7735        TCGA-FP-7829        TCGA-FP-7916 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE"   "7Q LOSS MUTATED" "7Q LOSS WILD-TYPE" 
       TCGA-FP-7998        TCGA-FP-8099        TCGA-FP-8209        TCGA-FP-8631 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE"   "7Q LOSS MUTATED" 
       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-BR-8592        TCGA-BR-A4IU        TCGA-BR-A4IV        TCGA-BR-A4IY 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-BR-A4IZ        TCGA-BR-A4J1        TCGA-BR-A4J2        TCGA-BR-A4J4 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-BR-A4J5        TCGA-BR-A4J6        TCGA-BR-A4J8        TCGA-BR-A4J9 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-BR-A4PF        TCGA-CD-5798        TCGA-CD-5799        TCGA-CD-5800 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-CD-5801        TCGA-CD-5802        TCGA-CD-5803        TCGA-CG-4300 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-CG-4301        TCGA-CG-4304        TCGA-CG-4305        TCGA-CG-4306 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-CG-4436        TCGA-CG-4437        TCGA-CG-4438        TCGA-CG-4440 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE"   "7Q LOSS MUTATED" "7Q LOSS WILD-TYPE" 
       TCGA-CG-4441        TCGA-CG-4443        TCGA-CG-4444        TCGA-CG-4449 
"7Q LOSS WILD-TYPE"   "7Q LOSS MUTATED" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-CG-4455        TCGA-CG-4460        TCGA-CG-4462        TCGA-CG-4465 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-CG-4466        TCGA-CG-4469        TCGA-CG-4472        TCGA-CG-4474 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-CG-4477        TCGA-CG-5716        TCGA-CG-5717        TCGA-CG-5718 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-CG-5719        TCGA-CG-5720        TCGA-CG-5721        TCGA-CG-5722 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-CG-5723        TCGA-CG-5724        TCGA-CG-5725        TCGA-CG-5726 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-CG-5727        TCGA-CG-5728        TCGA-CG-5730        TCGA-CG-5732 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-CG-5733        TCGA-CG-5734        TCGA-D7-5577        TCGA-D7-5578 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-D7-5579        TCGA-D7-6518        TCGA-D7-6519        TCGA-D7-6520 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-D7-6521        TCGA-D7-6522        TCGA-D7-6524        TCGA-D7-6525 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-D7-6526        TCGA-D7-6527        TCGA-D7-6528        TCGA-D7-6815 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-D7-6817        TCGA-D7-6818        TCGA-D7-6820        TCGA-D7-6822 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE"   "7Q LOSS MUTATED" "7Q LOSS WILD-TYPE" 
       TCGA-EQ-5647        TCGA-EQ-8122        TCGA-F1-6177        TCGA-F1-6874 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-F1-6875        TCGA-FP-7735        TCGA-FP-7829        TCGA-FP-7916 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE"   "7Q LOSS MUTATED" "7Q LOSS WILD-TYPE" 
       TCGA-FP-7998        TCGA-FP-8099        TCGA-FP-8209        TCGA-FP-8631 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE"   "7Q LOSS MUTATED" 
       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="     "7.9e+07"
D49V2, continuous
D49V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED      0    6
  7Q LOSS WILD-TYPE   70  101
        clus
vv       7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  FEMALE               0                70
  MALE                 6               101
                   vv
clus                STOMACH ADENOCARCINOMA - DIFFUSE TYPE
  7Q LOSS MUTATED                                       0
  7Q LOSS WILD-TYPE                                    25
                   vv
clus                STOMACH ADENOCARCINOMA - NOT OTHERWISE SPECIFIED (NOS)
  7Q LOSS MUTATED                                                        1
  7Q LOSS WILD-TYPE                                                     86
                   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                                                 9
                   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                                                                        3
  7Q LOSS WILD-TYPE                                                                     33
D49V4, multiclass
                   vv
clus                T1 T2 T3 T4
  7Q LOSS MUTATED    1  1  3  1
  7Q LOSS WILD-TYPE  5 53 61 42
D49V5, multiclass
    clus
vv   7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  T1               1                 5
  T2               1                53
  T3               3                61
  T4               1                42
                   vv
clus                N0 N1 N2 N3
  7Q LOSS MUTATED    1  2  3  0
  7Q LOSS WILD-TYPE 55 59 26 20
D49V6, multiclass
    clus
vv   7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  N0               1                55
  N1               2                59
  N2               3                26
  N3               0                20
                   vv
clus                 M0  M1  MX
  7Q LOSS MUTATED     5   0   1
  7Q LOSS WILD-TYPE 141  18  12
D49V7, multiclass
    clus
vv   7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  M0               5               141
  M1               0                18
  MX               1                12
                   vv
clus                 I II III IV
  7Q LOSS MUTATED    1  2   2  1
  7Q LOSS WILD-TYPE 25 46  56 28
D49V8, multiclass
     clus
vv    7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  I                 1                25
  II                2                46
  III               2                56
  IV                1                28
D49V9, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED      0    6
  7Q LOSS WILD-TYPE    5  166
     clus
vv    7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  NO                0                 5
  YES               6               166
                   vv
clus                 R0  R1  R2  RX
  7Q LOSS MUTATED     6   0   0   0
  7Q LOSS WILD-TYPE 117   7  12  25
D49V10, multiclass
    clus
vv   7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  R0               6               117
  R1               0                 7
  R2               0                12
  RX               0                25
D49V11, continuous

Clustering(50) Variable = 8p loss mutation analysis
D50V1, survival
                   sevent
clus2                 0   1
  8P LOSS MUTATED    11   1
  8P LOSS WILD-TYPE 111  17
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               12               128 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
                1                17 
$`8P LOSS MUTATED`
TCGA-BR-7716 TCGA-BR-A4IY TCGA-BR-A4J1 TCGA-BR-A4PF TCGA-CG-4301 TCGA-CG-4436 
        0.82         0.39         0.72         0.72         3.02        52.96 
TCGA-CG-4449 TCGA-D7-6528 TCGA-D7-6820 TCGA-F1-6177 TCGA-FP-8099 TCGA-IP-7968 
       19.07         1.68         2.93         6.54         1.02         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-BR-8592 
        0.26         1.18         1.55         1.48         0.76         0.20 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
        0.59         0.92         0.79         0.79         0.53         0.43 
TCGA-BR-A4J6 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
        0.13         0.23         0.10         0.82         0.69         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-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        1.02         8.05        54.05         4.01        14.01        29.98 
TCGA-CG-4444 TCGA-CG-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-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-D7-6822 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-FP-7735 
        4.27         0.62         7.79         2.01        72.23         0.39 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8209 TCGA-FP-8631 TCGA-HJ-7597 
        0.20         3.02         3.58        59.05         0.56        26.43 
TCGA-IN-7806 TCGA-IN-7808 
        6.87         3.55 

  8P LOSS MUTATED 8P LOSS WILD-TYPE 
             0.39              0.07 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
            52.96             72.23 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
            2.105             1.220 
[1] "0.4 - 53.0 (2.1)" "0.1 - 72.2 (1.2)"
       TCGA-B7-5816        TCGA-B7-5818        TCGA-BR-6452        TCGA-BR-6455 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-BR-6457        TCGA-BR-6458        TCGA-BR-6563        TCGA-BR-6564 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-BR-6565        TCGA-BR-6566        TCGA-BR-6705        TCGA-BR-6706 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-BR-6707        TCGA-BR-6709        TCGA-BR-6710        TCGA-BR-6801 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-BR-6802        TCGA-BR-6803        TCGA-BR-6852        TCGA-BR-7196 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-BR-7197        TCGA-BR-7703        TCGA-BR-7704        TCGA-BR-7707 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-BR-7715        TCGA-BR-7716        TCGA-BR-7717        TCGA-BR-7722 
"8P LOSS WILD-TYPE"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-BR-7723        TCGA-BR-7851        TCGA-BR-7901        TCGA-BR-7957 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-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-BR-8592        TCGA-BR-A4IU        TCGA-BR-A4IV        TCGA-BR-A4IY 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" 
       TCGA-BR-A4IZ        TCGA-BR-A4J1        TCGA-BR-A4J2        TCGA-BR-A4J4 
"8P LOSS WILD-TYPE"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-BR-A4J5        TCGA-BR-A4J6        TCGA-BR-A4J8        TCGA-BR-A4J9 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-BR-A4PF        TCGA-CD-5798        TCGA-CD-5799        TCGA-CD-5800 
  "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-CD-5801        TCGA-CD-5802        TCGA-CD-5803        TCGA-CG-4300 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-CG-4301        TCGA-CG-4304        TCGA-CG-4305        TCGA-CG-4306 
  "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-CG-4436        TCGA-CG-4437        TCGA-CG-4438        TCGA-CG-4440 
  "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-CG-4441        TCGA-CG-4443        TCGA-CG-4444        TCGA-CG-4449 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" 
       TCGA-CG-4455        TCGA-CG-4460        TCGA-CG-4462        TCGA-CG-4465 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-CG-4466        TCGA-CG-4469        TCGA-CG-4472        TCGA-CG-4474 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-CG-4477        TCGA-CG-5716        TCGA-CG-5717        TCGA-CG-5718 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-CG-5719        TCGA-CG-5720        TCGA-CG-5721        TCGA-CG-5722 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-CG-5723        TCGA-CG-5724        TCGA-CG-5725        TCGA-CG-5726 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-CG-5727        TCGA-CG-5728        TCGA-CG-5730        TCGA-CG-5732 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-CG-5733        TCGA-CG-5734        TCGA-D7-5577        TCGA-D7-5578 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-D7-5579        TCGA-D7-6518        TCGA-D7-6519        TCGA-D7-6520 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-D7-6521        TCGA-D7-6522        TCGA-D7-6524        TCGA-D7-6525 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-D7-6526        TCGA-D7-6527        TCGA-D7-6528        TCGA-D7-6815 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" 
       TCGA-D7-6817        TCGA-D7-6818        TCGA-D7-6820        TCGA-D7-6822 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" 
       TCGA-EQ-5647        TCGA-EQ-8122        TCGA-F1-6177        TCGA-F1-6874 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" 
       TCGA-F1-6875        TCGA-FP-7735        TCGA-FP-7829        TCGA-FP-7916 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-FP-7998        TCGA-FP-8099        TCGA-FP-8209        TCGA-FP-8631 
"8P LOSS WILD-TYPE"   "8P LOSS MUTATED" "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-BR-8592        TCGA-BR-A4IU        TCGA-BR-A4IV        TCGA-BR-A4IY 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" 
       TCGA-BR-A4IZ        TCGA-BR-A4J1        TCGA-BR-A4J2        TCGA-BR-A4J4 
"8P LOSS WILD-TYPE"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-BR-A4J5        TCGA-BR-A4J6        TCGA-BR-A4J8        TCGA-BR-A4J9 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-BR-A4PF        TCGA-CD-5798        TCGA-CD-5799        TCGA-CD-5800 
  "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-CD-5801        TCGA-CD-5802        TCGA-CD-5803        TCGA-CG-4300 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-CG-4301        TCGA-CG-4304        TCGA-CG-4305        TCGA-CG-4306 
  "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-CG-4436        TCGA-CG-4437        TCGA-CG-4438        TCGA-CG-4440 
  "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-CG-4441        TCGA-CG-4443        TCGA-CG-4444        TCGA-CG-4449 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" 
       TCGA-CG-4455        TCGA-CG-4460        TCGA-CG-4462        TCGA-CG-4465 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-CG-4466        TCGA-CG-4469        TCGA-CG-4472        TCGA-CG-4474 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-CG-4477        TCGA-CG-5716        TCGA-CG-5717        TCGA-CG-5718 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-CG-5719        TCGA-CG-5720        TCGA-CG-5721        TCGA-CG-5722 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-CG-5723        TCGA-CG-5724        TCGA-CG-5725        TCGA-CG-5726 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-CG-5727        TCGA-CG-5728        TCGA-CG-5730        TCGA-CG-5732 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-CG-5733        TCGA-CG-5734        TCGA-D7-5577        TCGA-D7-5578 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-D7-5579        TCGA-D7-6518        TCGA-D7-6519        TCGA-D7-6520 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-D7-6521        TCGA-D7-6522        TCGA-D7-6524        TCGA-D7-6525 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-D7-6526        TCGA-D7-6527        TCGA-D7-6528        TCGA-D7-6815 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" 
       TCGA-D7-6817        TCGA-D7-6818        TCGA-D7-6820        TCGA-D7-6822 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" 
       TCGA-EQ-5647        TCGA-EQ-8122        TCGA-F1-6177        TCGA-F1-6874 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" 
       TCGA-F1-6875        TCGA-FP-7735        TCGA-FP-7829        TCGA-FP-7916 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-FP-7998        TCGA-FP-8099        TCGA-FP-8209        TCGA-FP-8631 
"8P LOSS WILD-TYPE"   "8P LOSS MUTATED" "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-BR-8592        TCGA-BR-A4IU        TCGA-BR-A4IV        TCGA-BR-A4IY 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" 
       TCGA-BR-A4IZ        TCGA-BR-A4J1        TCGA-BR-A4J2        TCGA-BR-A4J4 
"8P LOSS WILD-TYPE"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-BR-A4J5        TCGA-BR-A4J6        TCGA-BR-A4J8        TCGA-BR-A4J9 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-BR-A4PF        TCGA-CD-5798        TCGA-CD-5799        TCGA-CD-5800 
  "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-CD-5801        TCGA-CD-5802        TCGA-CD-5803        TCGA-CG-4300 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-CG-4301        TCGA-CG-4304        TCGA-CG-4305        TCGA-CG-4306 
  "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-CG-4436        TCGA-CG-4437        TCGA-CG-4438        TCGA-CG-4440 
  "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-CG-4441        TCGA-CG-4443        TCGA-CG-4444        TCGA-CG-4449 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" 
       TCGA-CG-4455        TCGA-CG-4460        TCGA-CG-4462        TCGA-CG-4465 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-CG-4466        TCGA-CG-4469        TCGA-CG-4472        TCGA-CG-4474 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-CG-4477        TCGA-CG-5716        TCGA-CG-5717        TCGA-CG-5718 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-CG-5719        TCGA-CG-5720        TCGA-CG-5721        TCGA-CG-5722 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-CG-5723        TCGA-CG-5724        TCGA-CG-5725        TCGA-CG-5726 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-CG-5727        TCGA-CG-5728        TCGA-CG-5730        TCGA-CG-5732 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-CG-5733        TCGA-CG-5734        TCGA-D7-5577        TCGA-D7-5578 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-D7-5579        TCGA-D7-6518        TCGA-D7-6519        TCGA-D7-6520 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-D7-6521        TCGA-D7-6522        TCGA-D7-6524        TCGA-D7-6525 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-D7-6526        TCGA-D7-6527        TCGA-D7-6528        TCGA-D7-6815 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" 
       TCGA-D7-6817        TCGA-D7-6818        TCGA-D7-6820        TCGA-D7-6822 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" 
       TCGA-EQ-5647        TCGA-EQ-8122        TCGA-F1-6177        TCGA-F1-6874 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" 
       TCGA-F1-6875        TCGA-FP-7735        TCGA-FP-7829        TCGA-FP-7916 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-FP-7998        TCGA-FP-8099        TCGA-FP-8209        TCGA-FP-8631 
"8P LOSS WILD-TYPE"   "8P LOSS MUTATED" "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=" "1.3"
D50V2, continuous
D50V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED      3   12
  8P LOSS WILD-TYPE   67   95
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  FEMALE               3                67
  MALE                12                95
                   vv
clus                STOMACH ADENOCARCINOMA - DIFFUSE TYPE
  8P LOSS MUTATED                                       0
  8P LOSS WILD-TYPE                                    25
                   vv
clus                STOMACH ADENOCARCINOMA - NOT OTHERWISE SPECIFIED (NOS)
  8P LOSS MUTATED                                                        9
  8P LOSS WILD-TYPE                                                     78
                   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                                                 9
                   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                                                                     35
D50V4, multiclass
                   vv
clus                T1 T2 T3 T4
  8P LOSS MUTATED    1  5  3  5
  8P LOSS WILD-TYPE  5 49 61 38
D50V5, multiclass
    clus
vv   8P LOSS MUTATED 8P LOSS WILD-TYPE
  T1               1                 5
  T2               5                49
  T3               3                61
  T4               5                38
                   vv
clus                N0 N1 N2 N3
  8P LOSS MUTATED    4  8  2  0
  8P LOSS WILD-TYPE 52 53 27 20
D50V6, multiclass
    clus
vv   8P LOSS MUTATED 8P LOSS WILD-TYPE
  N0               4                52
  N1               8                53
  N2               2                27
  N3               0                20
                   vv
clus                 M0  M1  MX
  8P LOSS MUTATED    11   1   3
  8P LOSS WILD-TYPE 135  17  10
D50V7, multiclass
    clus
vv   8P LOSS MUTATED 8P LOSS WILD-TYPE
  M0              11               135
  M1               1                17
  MX               3                10
                   vv
clus                 I II III IV
  8P LOSS MUTATED    3  5   3  2
  8P LOSS WILD-TYPE 23 43  55 27
D50V8, multiclass
     clus
vv    8P LOSS MUTATED 8P LOSS WILD-TYPE
  I                 3                23
  II                5                43
  III               3                55
  IV                2                27
D50V9, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED      0   15
  8P LOSS WILD-TYPE    5  157
     clus
vv    8P LOSS MUTATED 8P LOSS WILD-TYPE
  NO                0                 5
  YES              15               157
                   vv
clus                 R0  R1  R2  RX
  8P LOSS MUTATED    11   0   1   2
  8P LOSS WILD-TYPE 112   7  11  23
D50V10, multiclass
    clus
vv   8P LOSS MUTATED 8P LOSS WILD-TYPE
  R0              11               112
  R1               0                 7
  R2               1                11
  RX               2                23
D50V11, continuous

Clustering(51) Variable = 8q loss mutation analysis
D51V1, survival
                   sevent
clus2                 0   1
  8Q LOSS MUTATED     1   0
  8Q LOSS WILD-TYPE 121  18
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                1               139 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                0                18 
$`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-BR-8592 TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        0.20         0.59         0.92         0.39         0.79         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J8 TCGA-BR-A4J9 
        0.79         0.53         0.43         0.13         0.23         0.10 
TCGA-BR-A4PF TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        0.72         0.82         0.69         0.36         0.49         0.30 
TCGA-CD-5803 TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
        0.07        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
       52.96         8.05        54.05         4.01        14.01        29.98 
TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4460 TCGA-CG-4462 TCGA-CG-4465 
       47.05        19.07        12.03        21.99         1.02         8.98 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4474 TCGA-CG-4477 TCGA-CG-5716 
       18.94         7.07        12.00         1.02         1.02         1.02 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.94         1.02         1.02         0.99         5.98         0.95 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 
       70.06        12.03        15.02        28.96        31.04        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        55.04        21.07         7.99         8.65         3.58 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
        4.54         9.80        15.65         9.63         8.19         6.90 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6815 TCGA-D7-6817 
        0.69         5.95         6.61         4.14         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-FP-8099 TCGA-FP-8209 TCGA-FP-8631 TCGA-HJ-7597 TCGA-IN-7806 TCGA-IN-7808 
        1.02        59.05         0.56        26.43         6.87         3.55 
TCGA-IP-7968 
        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              1.22 
[1] "1.7 - 1.7 (1.7)"  "0.1 - 72.2 (1.2)"
       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-BR-8592        TCGA-BR-A4IU        TCGA-BR-A4IV        TCGA-BR-A4IY 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BR-A4IZ        TCGA-BR-A4J1        TCGA-BR-A4J2        TCGA-BR-A4J4 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BR-A4J5        TCGA-BR-A4J6        TCGA-BR-A4J8        TCGA-BR-A4J9 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BR-A4PF        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-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-4443        TCGA-CG-4444        TCGA-CG-4449 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-CG-4455        TCGA-CG-4460        TCGA-CG-4462        TCGA-CG-4465 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-CG-4466        TCGA-CG-4469        TCGA-CG-4472        TCGA-CG-4474 
"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-D7-6528        TCGA-D7-6815 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE"   "8Q LOSS MUTATED" "8Q LOSS WILD-TYPE" 
       TCGA-D7-6817        TCGA-D7-6818        TCGA-D7-6820        TCGA-D7-6822 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EQ-5647        TCGA-EQ-8122        TCGA-F1-6177        TCGA-F1-6874 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-F1-6875        TCGA-FP-7735        TCGA-FP-7829        TCGA-FP-7916 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-FP-7998        TCGA-FP-8099        TCGA-FP-8209        TCGA-FP-8631 
"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-BR-8592        TCGA-BR-A4IU        TCGA-BR-A4IV        TCGA-BR-A4IY 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BR-A4IZ        TCGA-BR-A4J1        TCGA-BR-A4J2        TCGA-BR-A4J4 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BR-A4J5        TCGA-BR-A4J6        TCGA-BR-A4J8        TCGA-BR-A4J9 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BR-A4PF        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-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-4443        TCGA-CG-4444        TCGA-CG-4449 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-CG-4455        TCGA-CG-4460        TCGA-CG-4462        TCGA-CG-4465 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-CG-4466        TCGA-CG-4469        TCGA-CG-4472        TCGA-CG-4474 
"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-D7-6528        TCGA-D7-6815 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE"   "8Q LOSS MUTATED" "8Q LOSS WILD-TYPE" 
       TCGA-D7-6817        TCGA-D7-6818        TCGA-D7-6820        TCGA-D7-6822 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EQ-5647        TCGA-EQ-8122        TCGA-F1-6177        TCGA-F1-6874 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-F1-6875        TCGA-FP-7735        TCGA-FP-7829        TCGA-FP-7916 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-FP-7998        TCGA-FP-8099        TCGA-FP-8209        TCGA-FP-8631 
"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-BR-8592        TCGA-BR-A4IU        TCGA-BR-A4IV        TCGA-BR-A4IY 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BR-A4IZ        TCGA-BR-A4J1        TCGA-BR-A4J2        TCGA-BR-A4J4 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BR-A4J5        TCGA-BR-A4J6        TCGA-BR-A4J8        TCGA-BR-A4J9 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BR-A4PF        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-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-4443        TCGA-CG-4444        TCGA-CG-4449 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-CG-4455        TCGA-CG-4460        TCGA-CG-4462        TCGA-CG-4465 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-CG-4466        TCGA-CG-4469        TCGA-CG-4472        TCGA-CG-4474 
"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-D7-6528        TCGA-D7-6815 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE"   "8Q LOSS MUTATED" "8Q LOSS WILD-TYPE" 
       TCGA-D7-6817        TCGA-D7-6818        TCGA-D7-6820        TCGA-D7-6822 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EQ-5647        TCGA-EQ-8122        TCGA-F1-6177        TCGA-F1-6874 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-F1-6875        TCGA-FP-7735        TCGA-FP-7829        TCGA-FP-7916 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-FP-7998        TCGA-FP-8099        TCGA-FP-8209        TCGA-FP-8631 
"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               139 
       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-BR-8592        TCGA-BR-A4IU        TCGA-BR-A4IV        TCGA-BR-A4IY 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BR-A4IZ        TCGA-BR-A4J1        TCGA-BR-A4J2        TCGA-BR-A4J4 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BR-A4J5        TCGA-BR-A4J6        TCGA-BR-A4J8        TCGA-BR-A4J9 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BR-A4PF        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-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-4443        TCGA-CG-4444        TCGA-CG-4449 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-CG-4455        TCGA-CG-4460        TCGA-CG-4462        TCGA-CG-4465 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-CG-4466        TCGA-CG-4469        TCGA-CG-4472        TCGA-CG-4474 
"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-FP-8099        TCGA-FP-8209        TCGA-FP-8631        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   69  105
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  FEMALE               1                69
  MALE                 2               105
                   vv
clus                STOMACH ADENOCARCINOMA - DIFFUSE TYPE
  8Q LOSS MUTATED                                       0
  8Q LOSS WILD-TYPE                                    25
                   vv
clus                STOMACH ADENOCARCINOMA - NOT OTHERWISE SPECIFIED (NOS)
  8Q LOSS MUTATED                                                        1
  8Q LOSS WILD-TYPE                                                     86
                   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                                                10
                   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                                                                     36
D51V4, multiclass
                   vv
clus                T1 T2 T3 T4
  8Q LOSS MUTATED    0  2  0  0
  8Q LOSS WILD-TYPE  6 52 64 43
D51V5, multiclass
[1] "Remove cluster labels:" "8Q LOSS MUTATED"       
clus
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                2               165 
       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-BR-8592        TCGA-BR-A4IU        TCGA-BR-A4IV 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BR-A4IY        TCGA-BR-A4IZ        TCGA-BR-A4J1        TCGA-BR-A4J2 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BR-A4J4        TCGA-BR-A4J5        TCGA-BR-A4J6        TCGA-BR-A4J8 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BR-A4J9        TCGA-BR-A4PF        TCGA-CD-5798        TCGA-CD-5799 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-CD-5800        TCGA-CD-5801        TCGA-CD-5802        TCGA-CD-5803 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-CD-5804        TCGA-CG-4300        TCGA-CG-4301        TCGA-CG-4304 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-CG-4305        TCGA-CG-4306        TCGA-CG-4436        TCGA-CG-4437 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-CG-4438        TCGA-CG-4440        TCGA-CG-4441        TCGA-CG-4442 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-CG-4443        TCGA-CG-4444        TCGA-CG-4449        TCGA-CG-4455 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-CG-4460        TCGA-CG-4462        TCGA-CG-4465        TCGA-CG-4466 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-CG-4469        TCGA-CG-4472        TCGA-CG-4474        TCGA-CG-4475 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-CG-4476        TCGA-CG-4477        TCGA-CG-5716        TCGA-CG-5717 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-CG-5718        TCGA-CG-5719        TCGA-CG-5720        TCGA-CG-5721 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-CG-5722        TCGA-CG-5723        TCGA-CG-5724        TCGA-CG-5725 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-CG-5726        TCGA-CG-5727        TCGA-CG-5728        TCGA-CG-5730 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-CG-5732        TCGA-CG-5733        TCGA-CG-5734        TCGA-D7-5577 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-D7-5578        TCGA-D7-5579        TCGA-D7-6518        TCGA-D7-6519 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-D7-6520        TCGA-D7-6521        TCGA-D7-6522        TCGA-D7-6524 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-D7-6525        TCGA-D7-6526        TCGA-D7-6527        TCGA-D7-6815 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-D7-6817        TCGA-D7-6818        TCGA-D7-6820        TCGA-D7-6822 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EQ-5647        TCGA-EQ-8122        TCGA-F1-6177        TCGA-F1-6874 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-F1-6875        TCGA-FP-7735        TCGA-FP-7829        TCGA-FP-7916 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-FP-7998        TCGA-FP-8099        TCGA-FP-8209        TCGA-FP-8631 
"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 55 60 29 20
D51V6, multiclass
[1] "Remove cluster labels:" "8Q LOSS MUTATED"       
clus
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                2               164 
       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-BR-8592        TCGA-BR-A4IU        TCGA-BR-A4IV        TCGA-BR-A4IY 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BR-A4IZ        TCGA-BR-A4J1        TCGA-BR-A4J2        TCGA-BR-A4J4 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BR-A4J5        TCGA-BR-A4J6        TCGA-BR-A4J8        TCGA-BR-A4J9 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BR-A4PF        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-FP-8099        TCGA-FP-8209        TCGA-FP-8631        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 143  18  13
D51V7, multiclass
    clus
vv   8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  M0               3               143
  M1               0                18
  MX               0                13
                   vv
clus                 I II III IV
  8Q LOSS MUTATED    1  0   0  0
  8Q LOSS WILD-TYPE 25 48  58 29
D51V8, multiclass
[1] "Remove cluster labels:" "8Q LOSS MUTATED"       
clus
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                1               160 
       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-BR-8592        TCGA-BR-A4IU        TCGA-BR-A4IV        TCGA-BR-A4IY 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BR-A4IZ        TCGA-BR-A4J1        TCGA-BR-A4J2        TCGA-BR-A4J4 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BR-A4J5        TCGA-BR-A4J6        TCGA-BR-A4J8        TCGA-BR-A4J9 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BR-A4PF        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-FP-8099        TCGA-FP-8209        TCGA-FP-8631        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  169
     clus
vv    8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  NO                0                 5
  YES               3               169
                   vv
clus                 R0  R1  R2  RX
  8Q LOSS MUTATED     1   0   0   2
  8Q LOSS WILD-TYPE 122   7  12  23
D51V10, multiclass
    clus
vv   8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  R0               1               122
  R1               0                 7
  R2               0                12
  RX               2                23
D51V11, continuous
[1] "Remove cluster labels:" "8Q LOSS MUTATED"       
clus
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                2               131 
       TCGA-B7-5816        TCGA-BR-4183        TCGA-BR-4184        TCGA-BR-4188 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BR-4253        TCGA-BR-4255        TCGA-BR-4256        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-4361        TCGA-BR-4362 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BR-4367        TCGA-BR-4368        TCGA-BR-6452        TCGA-BR-6453 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BR-6454        TCGA-BR-6455        TCGA-BR-6456        TCGA-BR-6457 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BR-6458        TCGA-BR-6563        TCGA-BR-6564        TCGA-BR-6565 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BR-6566        TCGA-BR-6705        TCGA-BR-6706        TCGA-BR-6707 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BR-6709        TCGA-BR-6710        TCGA-BR-6801        TCGA-BR-6802 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BR-6803        TCGA-BR-6852        TCGA-BR-7196        TCGA-BR-7197 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BR-7703        TCGA-BR-7704        TCGA-BR-7707        TCGA-BR-7715 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BR-7716        TCGA-BR-7717        TCGA-BR-7722        TCGA-BR-7723 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BR-7851        TCGA-BR-7901        TCGA-BR-7957        TCGA-BR-7958 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BR-7959        TCGA-BR-8059        TCGA-BR-8060        TCGA-BR-8077 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BR-8078        TCGA-BR-8080        TCGA-BR-8081        TCGA-BR-8284 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BR-8285        TCGA-BR-8286        TCGA-BR-8289        TCGA-BR-8291 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BR-8295        TCGA-BR-8296        TCGA-BR-8297        TCGA-BR-8592 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BR-A4IU        TCGA-BR-A4IV        TCGA-BR-A4IY        TCGA-BR-A4IZ 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BR-A4J1        TCGA-BR-A4J2        TCGA-BR-A4J4        TCGA-BR-A4J5 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BR-A4J6        TCGA-BR-A4J8        TCGA-BR-A4J9        TCGA-BR-A4PF 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-CD-5804        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-FP-8099 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-FP-8209        TCGA-FP-8631        TCGA-HF-7131        TCGA-HF-7132 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-HF-7133        TCGA-HF-7134        TCGA-HF-7136        TCGA-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" 

Clustering(52) Variable = 9p loss mutation analysis
D52V1, survival
                   sevent
clus2                 0   1
  9P LOSS MUTATED    22   4
  9P LOSS WILD-TYPE 100  14
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               26               114 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
                4                14 
$`9P LOSS MUTATED`
TCGA-BR-7197 TCGA-BR-7723 TCGA-BR-A4J1 TCGA-BR-A4J6 TCGA-CD-5799 TCGA-CG-4438 
        1.48         4.54         0.72         0.13         0.69        54.05 
TCGA-CG-4449 TCGA-CG-4466 TCGA-CG-4472 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5725 
       19.07        18.94        12.00         1.02         1.02        15.02 
TCGA-CG-5730 TCGA-CG-5732 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6525 
        4.01        55.04        15.65         9.63         8.19         5.95 
TCGA-D7-6526 TCGA-D7-6817 TCGA-EQ-8122 TCGA-F1-6875 TCGA-FP-8099 TCGA-FP-8209 
        6.61         4.70         7.79        72.23         1.02        59.05 
TCGA-FP-8631 TCGA-IN-7806 
        0.56         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-BR-8592 TCGA-BR-A4IU 
        1.18         1.55         1.48         0.76         0.20         0.59 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
        0.92         0.39         0.79         0.79         0.53         0.43 
TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PF TCGA-CD-5798 TCGA-CD-5800 TCGA-CD-5801 
        0.23         0.10         0.72         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-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 
             0.13              0.07 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
            72.23             70.06 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
            6.740             1.035 
[1] "0.1 - 72.2 (6.7)" "0.1 - 70.1 (1.0)"
       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-BR-8592        TCGA-BR-A4IU        TCGA-BR-A4IV        TCGA-BR-A4IY 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-BR-A4IZ        TCGA-BR-A4J1        TCGA-BR-A4J2        TCGA-BR-A4J4 
"9P LOSS WILD-TYPE"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-BR-A4J5        TCGA-BR-A4J6        TCGA-BR-A4J8        TCGA-BR-A4J9 
"9P LOSS WILD-TYPE"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-BR-A4PF        TCGA-CD-5798        TCGA-CD-5799        TCGA-CD-5800 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" 
       TCGA-CD-5801        TCGA-CD-5802        TCGA-CD-5803        TCGA-CG-4300 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-CG-4301        TCGA-CG-4304        TCGA-CG-4305        TCGA-CG-4306 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-CG-4436        TCGA-CG-4437        TCGA-CG-4438        TCGA-CG-4440 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" 
       TCGA-CG-4441        TCGA-CG-4443        TCGA-CG-4444        TCGA-CG-4449 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" 
       TCGA-CG-4455        TCGA-CG-4460        TCGA-CG-4462        TCGA-CG-4465 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-CG-4466        TCGA-CG-4469        TCGA-CG-4472        TCGA-CG-4474 
  "9P LOSS MUTATED" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" 
       TCGA-CG-4477        TCGA-CG-5716        TCGA-CG-5717        TCGA-CG-5718 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" 
       TCGA-CG-5719        TCGA-CG-5720        TCGA-CG-5721        TCGA-CG-5722 
  "9P LOSS MUTATED" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-CG-5723        TCGA-CG-5724        TCGA-CG-5725        TCGA-CG-5726 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" 
       TCGA-CG-5727        TCGA-CG-5728        TCGA-CG-5730        TCGA-CG-5732 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED"   "9P LOSS MUTATED" 
       TCGA-CG-5733        TCGA-CG-5734        TCGA-D7-5577        TCGA-D7-5578 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-D7-5579        TCGA-D7-6518        TCGA-D7-6519        TCGA-D7-6520 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED"   "9P LOSS MUTATED" 
       TCGA-D7-6521        TCGA-D7-6522        TCGA-D7-6524        TCGA-D7-6525 
  "9P LOSS MUTATED" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" 
       TCGA-D7-6526        TCGA-D7-6527        TCGA-D7-6528        TCGA-D7-6815 
  "9P LOSS MUTATED" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-D7-6817        TCGA-D7-6818        TCGA-D7-6820        TCGA-D7-6822 
  "9P LOSS MUTATED" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-EQ-5647        TCGA-EQ-8122        TCGA-F1-6177        TCGA-F1-6874 
"9P LOSS WILD-TYPE"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-F1-6875        TCGA-FP-7735        TCGA-FP-7829        TCGA-FP-7916 
  "9P LOSS MUTATED" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-FP-7998        TCGA-FP-8099        TCGA-FP-8209        TCGA-FP-8631 
"9P LOSS WILD-TYPE"   "9P LOSS MUTATED"   "9P LOSS MUTATED"   "9P LOSS MUTATED" 
       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-BR-8592        TCGA-BR-A4IU        TCGA-BR-A4IV        TCGA-BR-A4IY 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-BR-A4IZ        TCGA-BR-A4J1        TCGA-BR-A4J2        TCGA-BR-A4J4 
"9P LOSS WILD-TYPE"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-BR-A4J5        TCGA-BR-A4J6        TCGA-BR-A4J8        TCGA-BR-A4J9 
"9P LOSS WILD-TYPE"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-BR-A4PF        TCGA-CD-5798        TCGA-CD-5799        TCGA-CD-5800 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" 
       TCGA-CD-5801        TCGA-CD-5802        TCGA-CD-5803        TCGA-CG-4300 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-CG-4301        TCGA-CG-4304        TCGA-CG-4305        TCGA-CG-4306 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-CG-4436        TCGA-CG-4437        TCGA-CG-4438        TCGA-CG-4440 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" 
       TCGA-CG-4441        TCGA-CG-4443        TCGA-CG-4444        TCGA-CG-4449 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" 
       TCGA-CG-4455        TCGA-CG-4460        TCGA-CG-4462        TCGA-CG-4465 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-CG-4466        TCGA-CG-4469        TCGA-CG-4472        TCGA-CG-4474 
  "9P LOSS MUTATED" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" 
       TCGA-CG-4477        TCGA-CG-5716        TCGA-CG-5717        TCGA-CG-5718 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" 
       TCGA-CG-5719        TCGA-CG-5720        TCGA-CG-5721        TCGA-CG-5722 
  "9P LOSS MUTATED" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-CG-5723        TCGA-CG-5724        TCGA-CG-5725        TCGA-CG-5726 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" 
       TCGA-CG-5727        TCGA-CG-5728        TCGA-CG-5730        TCGA-CG-5732 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED"   "9P LOSS MUTATED" 
       TCGA-CG-5733        TCGA-CG-5734        TCGA-D7-5577        TCGA-D7-5578 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-D7-5579        TCGA-D7-6518        TCGA-D7-6519        TCGA-D7-6520 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED"   "9P LOSS MUTATED" 
       TCGA-D7-6521        TCGA-D7-6522        TCGA-D7-6524        TCGA-D7-6525 
  "9P LOSS MUTATED" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" 
       TCGA-D7-6526        TCGA-D7-6527        TCGA-D7-6528        TCGA-D7-6815 
  "9P LOSS MUTATED" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-D7-6817        TCGA-D7-6818        TCGA-D7-6820        TCGA-D7-6822 
  "9P LOSS MUTATED" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-EQ-5647        TCGA-EQ-8122        TCGA-F1-6177        TCGA-F1-6874 
"9P LOSS WILD-TYPE"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-F1-6875        TCGA-FP-7735        TCGA-FP-7829        TCGA-FP-7916 
  "9P LOSS MUTATED" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-FP-7998        TCGA-FP-8099        TCGA-FP-8209        TCGA-FP-8631 
"9P LOSS WILD-TYPE"   "9P LOSS MUTATED"   "9P LOSS MUTATED"   "9P LOSS MUTATED" 
       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-BR-8592        TCGA-BR-A4IU        TCGA-BR-A4IV        TCGA-BR-A4IY 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-BR-A4IZ        TCGA-BR-A4J1        TCGA-BR-A4J2        TCGA-BR-A4J4 
"9P LOSS WILD-TYPE"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-BR-A4J5        TCGA-BR-A4J6        TCGA-BR-A4J8        TCGA-BR-A4J9 
"9P LOSS WILD-TYPE"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-BR-A4PF        TCGA-CD-5798        TCGA-CD-5799        TCGA-CD-5800 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" 
       TCGA-CD-5801        TCGA-CD-5802        TCGA-CD-5803        TCGA-CG-4300 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-CG-4301        TCGA-CG-4304        TCGA-CG-4305        TCGA-CG-4306 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-CG-4436        TCGA-CG-4437        TCGA-CG-4438        TCGA-CG-4440 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" 
       TCGA-CG-4441        TCGA-CG-4443        TCGA-CG-4444        TCGA-CG-4449 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" 
       TCGA-CG-4455        TCGA-CG-4460        TCGA-CG-4462        TCGA-CG-4465 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-CG-4466        TCGA-CG-4469        TCGA-CG-4472        TCGA-CG-4474 
  "9P LOSS MUTATED" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" 
       TCGA-CG-4477        TCGA-CG-5716        TCGA-CG-5717        TCGA-CG-5718 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" 
       TCGA-CG-5719        TCGA-CG-5720        TCGA-CG-5721        TCGA-CG-5722 
  "9P LOSS MUTATED" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-CG-5723        TCGA-CG-5724        TCGA-CG-5725        TCGA-CG-5726 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" 
       TCGA-CG-5727        TCGA-CG-5728        TCGA-CG-5730        TCGA-CG-5732 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED"   "9P LOSS MUTATED" 
       TCGA-CG-5733        TCGA-CG-5734        TCGA-D7-5577        TCGA-D7-5578 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-D7-5579        TCGA-D7-6518        TCGA-D7-6519        TCGA-D7-6520 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED"   "9P LOSS MUTATED" 
       TCGA-D7-6521        TCGA-D7-6522        TCGA-D7-6524        TCGA-D7-6525 
  "9P LOSS MUTATED" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" 
       TCGA-D7-6526        TCGA-D7-6527        TCGA-D7-6528        TCGA-D7-6815 
  "9P LOSS MUTATED" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-D7-6817        TCGA-D7-6818        TCGA-D7-6820        TCGA-D7-6822 
  "9P LOSS MUTATED" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-EQ-5647        TCGA-EQ-8122        TCGA-F1-6177        TCGA-F1-6874 
"9P LOSS WILD-TYPE"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-F1-6875        TCGA-FP-7735        TCGA-FP-7829        TCGA-FP-7916 
  "9P LOSS MUTATED" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-FP-7998        TCGA-FP-8099        TCGA-FP-8209        TCGA-FP-8631 
"9P LOSS WILD-TYPE"   "9P LOSS MUTATED"   "9P LOSS MUTATED"   "9P LOSS MUTATED" 
       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=" "2.3"
D52V2, continuous
D52V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED      9   21
  9P LOSS WILD-TYPE   61   86
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  FEMALE               9                61
  MALE                21                86
                   vv
clus                STOMACH ADENOCARCINOMA - DIFFUSE TYPE
  9P LOSS MUTATED                                       5
  9P LOSS WILD-TYPE                                    20
                   vv
clus                STOMACH ADENOCARCINOMA - NOT OTHERWISE SPECIFIED (NOS)
  9P LOSS MUTATED                                                       10
  9P LOSS WILD-TYPE                                                     77
                   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                                                 8
                   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                                                                        9
  9P LOSS WILD-TYPE                                                                     27
D52V4, multiclass
                   vv
clus                T1 T2 T3 T4
  9P LOSS MUTATED    0 15  8  4
  9P LOSS WILD-TYPE  6 39 56 39
D52V5, multiclass
    clus
vv   9P LOSS MUTATED 9P LOSS WILD-TYPE
  T1               0                 6
  T2              15                39
  T3               8                56
  T4               4                39
                   vv
clus                N0 N1 N2 N3
  9P LOSS MUTATED    8 11  7  3
  9P LOSS WILD-TYPE 48 50 22 17
D52V6, multiclass
    clus
vv   9P LOSS MUTATED 9P LOSS WILD-TYPE
  N0               8                48
  N1              11                50
  N2               7                22
  N3               3                17
                   vv
clus                 M0  M1  MX
  9P LOSS MUTATED    25   2   3
  9P LOSS WILD-TYPE 121  16  10
D52V7, multiclass
    clus
vv   9P LOSS MUTATED 9P LOSS WILD-TYPE
  M0              25               121
  M1               2                16
  MX               3                10
                   vv
clus                 I II III IV
  9P LOSS MUTATED    4  8   9  6
  9P LOSS WILD-TYPE 22 40  49 23
D52V8, multiclass
     clus
vv    9P LOSS MUTATED 9P LOSS WILD-TYPE
  I                 4                22
  II                8                40
  III               9                49
  IV                6                23
D52V9, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED      1   29
  9P LOSS WILD-TYPE    4  143
     clus
vv    9P LOSS MUTATED 9P LOSS WILD-TYPE
  NO                1                 4
  YES              29               143
                   vv
clus                 R0  R1  R2  RX
  9P LOSS MUTATED    23   1   1   3
  9P LOSS WILD-TYPE 100   6  11  22
D52V10, multiclass
    clus
vv   9P LOSS MUTATED 9P LOSS WILD-TYPE
  R0              23               100
  R1               1                 6
  R2               1                11
  RX               3                22
D52V11, continuous

Clustering(53) Variable = 9q loss mutation analysis
D53V1, survival
                   sevent
clus2                 0   1
  9Q LOSS MUTATED     9   2
  9Q LOSS WILD-TYPE 113  16
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               11               129 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
                2                16 
$`9Q LOSS MUTATED`
TCGA-BR-7723 TCGA-BR-A4J1 TCGA-CD-5799 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6525 
        4.54         0.72         0.69        15.65         9.63         5.95 
TCGA-D7-6817 TCGA-EQ-8122 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8631 
        4.70         7.79         1.02        59.05         0.56 

$`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-BR-8592 
        0.26         1.18         1.55         1.48         0.76         0.20 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J4 
        0.59         0.92         0.39         0.79         0.79         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PF TCGA-CD-5798 
        0.43         0.13         0.23         0.10         0.72         0.82 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CG-4300 TCGA-CG-4301 
        0.36         0.49         0.30         0.07        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02        52.96         8.05        54.05 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 
        4.01        14.01        29.98        47.05        19.07        12.03 
TCGA-CG-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-D7-6521 
        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-D7-6815 
        6.90         0.69         6.61         4.14         1.68         3.65 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-EQ-5647 TCGA-F1-6177 TCGA-F1-6874 
        4.04         2.93         4.27         0.62         6.54         2.01 
TCGA-F1-6875 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-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 

  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
             0.56              0.07 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
            59.05             72.23 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
             4.70              1.22 
[1] "0.6 - 59.0 (4.7)" "0.1 - 72.2 (1.2)"
       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-BR-8592        TCGA-BR-A4IU        TCGA-BR-A4IV        TCGA-BR-A4IY 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-BR-A4IZ        TCGA-BR-A4J1        TCGA-BR-A4J2        TCGA-BR-A4J4 
"9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-BR-A4J5        TCGA-BR-A4J6        TCGA-BR-A4J8        TCGA-BR-A4J9 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-BR-A4PF        TCGA-CD-5798        TCGA-CD-5799        TCGA-CD-5800 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" 
       TCGA-CD-5801        TCGA-CD-5802        TCGA-CD-5803        TCGA-CG-4300 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-CG-4301        TCGA-CG-4304        TCGA-CG-4305        TCGA-CG-4306 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-CG-4436        TCGA-CG-4437        TCGA-CG-4438        TCGA-CG-4440 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-CG-4441        TCGA-CG-4443        TCGA-CG-4444        TCGA-CG-4449 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-CG-4455        TCGA-CG-4460        TCGA-CG-4462        TCGA-CG-4465 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-CG-4466        TCGA-CG-4469        TCGA-CG-4472        TCGA-CG-4474 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-CG-4477        TCGA-CG-5716        TCGA-CG-5717        TCGA-CG-5718 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-CG-5719        TCGA-CG-5720        TCGA-CG-5721        TCGA-CG-5722 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-CG-5723        TCGA-CG-5724        TCGA-CG-5725        TCGA-CG-5726 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-CG-5727        TCGA-CG-5728        TCGA-CG-5730        TCGA-CG-5732 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-CG-5733        TCGA-CG-5734        TCGA-D7-5577        TCGA-D7-5578 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-D7-5579        TCGA-D7-6518        TCGA-D7-6519        TCGA-D7-6520 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED"   "9Q LOSS MUTATED" 
       TCGA-D7-6521        TCGA-D7-6522        TCGA-D7-6524        TCGA-D7-6525 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" 
       TCGA-D7-6526        TCGA-D7-6527        TCGA-D7-6528        TCGA-D7-6815 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-D7-6817        TCGA-D7-6818        TCGA-D7-6820        TCGA-D7-6822 
  "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-EQ-5647        TCGA-EQ-8122        TCGA-F1-6177        TCGA-F1-6874 
"9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-F1-6875        TCGA-FP-7735        TCGA-FP-7829        TCGA-FP-7916 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-FP-7998        TCGA-FP-8099        TCGA-FP-8209        TCGA-FP-8631 
"9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED"   "9Q LOSS MUTATED"   "9Q LOSS MUTATED" 
       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-BR-8592        TCGA-BR-A4IU        TCGA-BR-A4IV        TCGA-BR-A4IY 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-BR-A4IZ        TCGA-BR-A4J1        TCGA-BR-A4J2        TCGA-BR-A4J4 
"9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-BR-A4J5        TCGA-BR-A4J6        TCGA-BR-A4J8        TCGA-BR-A4J9 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-BR-A4PF        TCGA-CD-5798        TCGA-CD-5799        TCGA-CD-5800 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" 
       TCGA-CD-5801        TCGA-CD-5802        TCGA-CD-5803        TCGA-CG-4300 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-CG-4301        TCGA-CG-4304        TCGA-CG-4305        TCGA-CG-4306 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-CG-4436        TCGA-CG-4437        TCGA-CG-4438        TCGA-CG-4440 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-CG-4441        TCGA-CG-4443        TCGA-CG-4444        TCGA-CG-4449 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-CG-4455        TCGA-CG-4460        TCGA-CG-4462        TCGA-CG-4465 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-CG-4466        TCGA-CG-4469        TCGA-CG-4472        TCGA-CG-4474 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-CG-4477        TCGA-CG-5716        TCGA-CG-5717        TCGA-CG-5718 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-CG-5719        TCGA-CG-5720        TCGA-CG-5721        TCGA-CG-5722 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-CG-5723        TCGA-CG-5724        TCGA-CG-5725        TCGA-CG-5726 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-CG-5727        TCGA-CG-5728        TCGA-CG-5730        TCGA-CG-5732 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-CG-5733        TCGA-CG-5734        TCGA-D7-5577        TCGA-D7-5578 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-D7-5579        TCGA-D7-6518        TCGA-D7-6519        TCGA-D7-6520 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED"   "9Q LOSS MUTATED" 
       TCGA-D7-6521        TCGA-D7-6522        TCGA-D7-6524        TCGA-D7-6525 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" 
       TCGA-D7-6526        TCGA-D7-6527        TCGA-D7-6528        TCGA-D7-6815 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-D7-6817        TCGA-D7-6818        TCGA-D7-6820        TCGA-D7-6822 
  "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-EQ-5647        TCGA-EQ-8122        TCGA-F1-6177        TCGA-F1-6874 
"9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-F1-6875        TCGA-FP-7735        TCGA-FP-7829        TCGA-FP-7916 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-FP-7998        TCGA-FP-8099        TCGA-FP-8209        TCGA-FP-8631 
"9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED"   "9Q LOSS MUTATED"   "9Q LOSS MUTATED" 
       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-BR-8592        TCGA-BR-A4IU        TCGA-BR-A4IV        TCGA-BR-A4IY 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-BR-A4IZ        TCGA-BR-A4J1        TCGA-BR-A4J2        TCGA-BR-A4J4 
"9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-BR-A4J5        TCGA-BR-A4J6        TCGA-BR-A4J8        TCGA-BR-A4J9 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-BR-A4PF        TCGA-CD-5798        TCGA-CD-5799        TCGA-CD-5800 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" 
       TCGA-CD-5801        TCGA-CD-5802        TCGA-CD-5803        TCGA-CG-4300 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-CG-4301        TCGA-CG-4304        TCGA-CG-4305        TCGA-CG-4306 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-CG-4436        TCGA-CG-4437        TCGA-CG-4438        TCGA-CG-4440 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-CG-4441        TCGA-CG-4443        TCGA-CG-4444        TCGA-CG-4449 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-CG-4455        TCGA-CG-4460        TCGA-CG-4462        TCGA-CG-4465 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-CG-4466        TCGA-CG-4469        TCGA-CG-4472        TCGA-CG-4474 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-CG-4477        TCGA-CG-5716        TCGA-CG-5717        TCGA-CG-5718 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-CG-5719        TCGA-CG-5720        TCGA-CG-5721        TCGA-CG-5722 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-CG-5723        TCGA-CG-5724        TCGA-CG-5725        TCGA-CG-5726 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-CG-5727        TCGA-CG-5728        TCGA-CG-5730        TCGA-CG-5732 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-CG-5733        TCGA-CG-5734        TCGA-D7-5577        TCGA-D7-5578 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-D7-5579        TCGA-D7-6518        TCGA-D7-6519        TCGA-D7-6520 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED"   "9Q LOSS MUTATED" 
       TCGA-D7-6521        TCGA-D7-6522        TCGA-D7-6524        TCGA-D7-6525 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" 
       TCGA-D7-6526        TCGA-D7-6527        TCGA-D7-6528        TCGA-D7-6815 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-D7-6817        TCGA-D7-6818        TCGA-D7-6820        TCGA-D7-6822 
  "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-EQ-5647        TCGA-EQ-8122        TCGA-F1-6177        TCGA-F1-6874 
"9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-F1-6875        TCGA-FP-7735        TCGA-FP-7829        TCGA-FP-7916 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-FP-7998        TCGA-FP-8099        TCGA-FP-8209        TCGA-FP-8631 
"9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED"   "9Q LOSS MUTATED"   "9Q LOSS MUTATED" 
       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=" "1.2"
D53V2, continuous
D53V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED      3   10
  9Q LOSS WILD-TYPE   67   97
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  FEMALE               3                67
  MALE                10                97
                   vv
clus                STOMACH ADENOCARCINOMA - DIFFUSE TYPE
  9Q LOSS MUTATED                                       3
  9Q LOSS WILD-TYPE                                    22
                   vv
clus                STOMACH ADENOCARCINOMA - NOT OTHERWISE SPECIFIED (NOS)
  9Q LOSS MUTATED                                                        4
  9Q LOSS WILD-TYPE                                                     83
                   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                                                 9
                   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                                                                        3
  9Q LOSS WILD-TYPE                                                                     33
D53V4, multiclass
                   vv
clus                T1 T2 T3 T4
  9Q LOSS MUTATED    0  7  4  1
  9Q LOSS WILD-TYPE  6 47 60 42
D53V5, multiclass
    clus
vv   9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  T1               0                 6
  T2               7                47
  T3               4                60
  T4               1                42
                   vv
clus                N0 N1 N2 N3
  9Q LOSS MUTATED    2  5  4  2
  9Q LOSS WILD-TYPE 54 56 25 18
D53V6, multiclass
    clus
vv   9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  N0               2                54
  N1               5                56
  N2               4                25
  N3               2                18
                   vv
clus                 M0  M1  MX
  9Q LOSS MUTATED    10   0   3
  9Q LOSS WILD-TYPE 136  18  10
D53V7, multiclass
    clus
vv   9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  M0              10               136
  M1               0                18
  MX               3                10
                   vv
clus                 I II III IV
  9Q LOSS MUTATED    1  4   6  1
  9Q LOSS WILD-TYPE 25 44  52 28
D53V8, multiclass
     clus
vv    9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  I                 1                25
  II                4                44
  III               6                52
  IV                1                28
D53V9, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED      1   12
  9Q LOSS WILD-TYPE    4  160
     clus
vv    9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  NO                1                 4
  YES              12               160
                   vv
clus                 R0  R1  R2  RX
  9Q LOSS MUTATED     9   1   0   1
  9Q LOSS WILD-TYPE 114   6  12  24
D53V10, multiclass
    clus
vv   9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  R0               9               114
  R1               1                 6
  R2               0                12
  RX               1                24
D53V11, continuous

Clustering(54) Variable = 10p loss mutation analysis
D54V1, survival
                    sevent
clus2                  0   1
  10P LOSS MUTATED     8   0
  10P LOSS WILD-TYPE 114  18
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                 8                132 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                 0                 18 
$`10P LOSS MUTATED`
TCGA-BR-A4IY TCGA-CG-4436 TCGA-CG-5732 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6820 
        0.39        52.96        55.04         4.14         1.68         2.93 
TCGA-FP-7829 TCGA-FP-8631 
        0.20         0.56 

$`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-BR-8592 TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
        0.20         0.59         0.92         0.79         0.72         0.79 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PF 
        0.53         0.43         0.13         0.23         0.10         0.72 
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-FP-8099 TCGA-FP-8209 TCGA-HJ-7597 TCGA-IN-7806 TCGA-IN-7808 TCGA-IP-7968 
        1.02        59.05        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 
             2.305              1.220 
[1] "0.2 - 55.0 (2.3)" "0.1 - 72.2 (1.2)"
        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-BR-8592         TCGA-BR-A4IU         TCGA-BR-A4IV 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-BR-A4IY         TCGA-BR-A4IZ         TCGA-BR-A4J1 
  "10P LOSS MUTATED" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-BR-A4J2         TCGA-BR-A4J4         TCGA-BR-A4J5 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-BR-A4J6         TCGA-BR-A4J8         TCGA-BR-A4J9 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-BR-A4PF         TCGA-CD-5798         TCGA-CD-5799 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-CD-5800         TCGA-CD-5801         TCGA-CD-5802 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-CD-5803         TCGA-CG-4300         TCGA-CG-4301 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-CG-4304         TCGA-CG-4305         TCGA-CG-4306 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-CG-4436         TCGA-CG-4437         TCGA-CG-4438 
  "10P LOSS MUTATED" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-CG-4440         TCGA-CG-4441         TCGA-CG-4443 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-CG-4444         TCGA-CG-4449         TCGA-CG-4455 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-CG-4460         TCGA-CG-4462         TCGA-CG-4465 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-CG-4466         TCGA-CG-4469         TCGA-CG-4472 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-CG-4474         TCGA-CG-4477         TCGA-CG-5716 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-CG-5717         TCGA-CG-5718         TCGA-CG-5719 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-CG-5720         TCGA-CG-5721         TCGA-CG-5722 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-CG-5723         TCGA-CG-5724         TCGA-CG-5725 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-CG-5726         TCGA-CG-5727         TCGA-CG-5728 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-CG-5730         TCGA-CG-5732         TCGA-CG-5733 
"10P LOSS WILD-TYPE"   "10P LOSS MUTATED" "10P LOSS WILD-TYPE" 
        TCGA-CG-5734         TCGA-D7-5577         TCGA-D7-5578 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-D7-5579         TCGA-D7-6518         TCGA-D7-6519 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-D7-6520         TCGA-D7-6521         TCGA-D7-6522 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-D7-6524         TCGA-D7-6525         TCGA-D7-6526 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-D7-6527         TCGA-D7-6528         TCGA-D7-6815 
  "10P LOSS MUTATED"   "10P LOSS MUTATED" "10P LOSS WILD-TYPE" 
        TCGA-D7-6817         TCGA-D7-6818         TCGA-D7-6820 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE"   "10P LOSS MUTATED" 
        TCGA-D7-6822         TCGA-EQ-5647         TCGA-EQ-8122 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-F1-6177         TCGA-F1-6874         TCGA-F1-6875 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-FP-7735         TCGA-FP-7829         TCGA-FP-7916 
"10P LOSS WILD-TYPE"   "10P LOSS MUTATED" "10P LOSS WILD-TYPE" 
        TCGA-FP-7998         TCGA-FP-8099         TCGA-FP-8209 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-FP-8631         TCGA-HJ-7597         TCGA-IN-7806 
  "10P LOSS MUTATED" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-IN-7808         TCGA-IP-7968 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-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-BR-8592         TCGA-BR-A4IU         TCGA-BR-A4IV 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-BR-A4IY         TCGA-BR-A4IZ         TCGA-BR-A4J1 
  "10P LOSS MUTATED" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-BR-A4J2         TCGA-BR-A4J4         TCGA-BR-A4J5 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-BR-A4J6         TCGA-BR-A4J8         TCGA-BR-A4J9 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-BR-A4PF         TCGA-CD-5798         TCGA-CD-5799 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-CD-5800         TCGA-CD-5801         TCGA-CD-5802 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-CD-5803         TCGA-CG-4300         TCGA-CG-4301 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-CG-4304         TCGA-CG-4305         TCGA-CG-4306 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-CG-4436         TCGA-CG-4437         TCGA-CG-4438 
  "10P LOSS MUTATED" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-CG-4440         TCGA-CG-4441         TCGA-CG-4443 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-CG-4444         TCGA-CG-4449         TCGA-CG-4455 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-CG-4460         TCGA-CG-4462         TCGA-CG-4465 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-CG-4466         TCGA-CG-4469         TCGA-CG-4472 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-CG-4474         TCGA-CG-4477         TCGA-CG-5716 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-CG-5717         TCGA-CG-5718         TCGA-CG-5719 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-CG-5720         TCGA-CG-5721         TCGA-CG-5722 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-CG-5723         TCGA-CG-5724         TCGA-CG-5725 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-CG-5726         TCGA-CG-5727         TCGA-CG-5728 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-CG-5730         TCGA-CG-5732         TCGA-CG-5733 
"10P LOSS WILD-TYPE"   "10P LOSS MUTATED" "10P LOSS WILD-TYPE" 
        TCGA-CG-5734         TCGA-D7-5577         TCGA-D7-5578 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-D7-5579         TCGA-D7-6518         TCGA-D7-6519 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-D7-6520         TCGA-D7-6521         TCGA-D7-6522 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-D7-6524         TCGA-D7-6525         TCGA-D7-6526 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-D7-6527         TCGA-D7-6528         TCGA-D7-6815 
  "10P LOSS MUTATED"   "10P LOSS MUTATED" "10P LOSS WILD-TYPE" 
        TCGA-D7-6817         TCGA-D7-6818         TCGA-D7-6820 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE"   "10P LOSS MUTATED" 
        TCGA-D7-6822         TCGA-EQ-5647         TCGA-EQ-8122 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-F1-6177         TCGA-F1-6874         TCGA-F1-6875 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-FP-7735         TCGA-FP-7829         TCGA-FP-7916 
"10P LOSS WILD-TYPE"   "10P LOSS MUTATED" "10P LOSS WILD-TYPE" 
        TCGA-FP-7998         TCGA-FP-8099         TCGA-FP-8209 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-FP-8631         TCGA-HJ-7597         TCGA-IN-7806 
  "10P LOSS MUTATED" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-IN-7808         TCGA-IP-7968 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-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-BR-8592         TCGA-BR-A4IU         TCGA-BR-A4IV 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-BR-A4IY         TCGA-BR-A4IZ         TCGA-BR-A4J1 
  "10P LOSS MUTATED" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-BR-A4J2         TCGA-BR-A4J4         TCGA-BR-A4J5 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-BR-A4J6         TCGA-BR-A4J8         TCGA-BR-A4J9 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-BR-A4PF         TCGA-CD-5798         TCGA-CD-5799 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-CD-5800         TCGA-CD-5801         TCGA-CD-5802 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-CD-5803         TCGA-CG-4300         TCGA-CG-4301 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-CG-4304         TCGA-CG-4305         TCGA-CG-4306 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-CG-4436         TCGA-CG-4437         TCGA-CG-4438 
  "10P LOSS MUTATED" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-CG-4440         TCGA-CG-4441         TCGA-CG-4443 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-CG-4444         TCGA-CG-4449         TCGA-CG-4455 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-CG-4460         TCGA-CG-4462         TCGA-CG-4465 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-CG-4466         TCGA-CG-4469         TCGA-CG-4472 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-CG-4474         TCGA-CG-4477         TCGA-CG-5716 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-CG-5717         TCGA-CG-5718         TCGA-CG-5719 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-CG-5720         TCGA-CG-5721         TCGA-CG-5722 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-CG-5723         TCGA-CG-5724         TCGA-CG-5725 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-CG-5726         TCGA-CG-5727         TCGA-CG-5728 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-CG-5730         TCGA-CG-5732         TCGA-CG-5733 
"10P LOSS WILD-TYPE"   "10P LOSS MUTATED" "10P LOSS WILD-TYPE" 
        TCGA-CG-5734         TCGA-D7-5577         TCGA-D7-5578 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-D7-5579         TCGA-D7-6518         TCGA-D7-6519 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-D7-6520         TCGA-D7-6521         TCGA-D7-6522 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-D7-6524         TCGA-D7-6525         TCGA-D7-6526 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-D7-6527         TCGA-D7-6528         TCGA-D7-6815 
  "10P LOSS MUTATED"   "10P LOSS MUTATED" "10P LOSS WILD-TYPE" 
        TCGA-D7-6817         TCGA-D7-6818         TCGA-D7-6820 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE"   "10P LOSS MUTATED" 
        TCGA-D7-6822         TCGA-EQ-5647         TCGA-EQ-8122 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-F1-6177         TCGA-F1-6874         TCGA-F1-6875 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-FP-7735         TCGA-FP-7829         TCGA-FP-7916 
"10P LOSS WILD-TYPE"   "10P LOSS MUTATED" "10P LOSS WILD-TYPE" 
        TCGA-FP-7998         TCGA-FP-8099         TCGA-FP-8209 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-FP-8631         TCGA-HJ-7597         TCGA-IN-7806 
  "10P LOSS MUTATED" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-IN-7808         TCGA-IP-7968 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
[1] "hr="     "7.9e+07"
D54V2, continuous
D54V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED      2   10
  10P LOSS WILD-TYPE   68   97
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  FEMALE                2                 68
  MALE                 10                 97
                    vv
clus                 STOMACH ADENOCARCINOMA - DIFFUSE TYPE
  10P LOSS MUTATED                                       0
  10P LOSS WILD-TYPE                                    25
                    vv
clus                 STOMACH ADENOCARCINOMA - NOT OTHERWISE SPECIFIED (NOS)
  10P LOSS MUTATED                                                        3
  10P LOSS WILD-TYPE                                                     84
                    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                                                 8
                    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                                                                        3
  10P LOSS WILD-TYPE                                                                     33
D54V4, multiclass
                    vv
clus                 T1 T2 T3 T4
  10P LOSS MUTATED    0  7  3  1
  10P LOSS WILD-TYPE  6 47 61 42
D54V5, multiclass
    clus
vv   10P LOSS MUTATED 10P LOSS WILD-TYPE
  T1                0                  6
  T2                7                 47
  T3                3                 61
  T4                1                 42
                    vv
clus                 N0 N1 N2 N3
  10P LOSS MUTATED    4  5  1  2
  10P LOSS WILD-TYPE 52 56 28 18
D54V6, multiclass
    clus
vv   10P LOSS MUTATED 10P LOSS WILD-TYPE
  N0                4                 52
  N1                5                 56
  N2                1                 28
  N3                2                 18
                    vv
clus                  M0  M1  MX
  10P LOSS MUTATED    11   0   1
  10P LOSS WILD-TYPE 135  18  12
D54V7, multiclass
    clus
vv   10P LOSS MUTATED 10P LOSS WILD-TYPE
  M0               11                135
  M1                0                 18
  MX                1                 12
                    vv
clus                  I II III IV
  10P LOSS MUTATED    3  4   2  2
  10P LOSS WILD-TYPE 23 44  56 27
D54V8, multiclass
     clus
vv    10P LOSS MUTATED 10P LOSS WILD-TYPE
  I                  3                 23
  II                 4                 44
  III                2                 56
  IV                 2                 27
D54V9, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED      2   10
  10P LOSS WILD-TYPE    3  162
     clus
vv    10P LOSS MUTATED 10P LOSS WILD-TYPE
  NO                 2                  3
  YES               10                162
                    vv
clus                  R0  R1  R2  RX
  10P LOSS MUTATED     9   1   0   2
  10P LOSS WILD-TYPE 114   6  12  23
D54V10, multiclass
    clus
vv   10P LOSS MUTATED 10P LOSS WILD-TYPE
  R0                9                114
  R1                1                  6
  R2                0                 12
  RX                2                 23
D54V11, continuous

Clustering(55) Variable = 10q loss mutation analysis
D55V1, survival
                    sevent
clus2                  0   1
  10Q LOSS MUTATED     8   0
  10Q LOSS WILD-TYPE 114  18
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                 8                132 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                 0                 18 
$`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 TCGA-FP-8631 
        0.20         0.56 

$`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-BR-8592 
        0.26         1.18         1.55         1.48         0.76         0.20 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
        0.59         0.92         0.39         0.79         0.72         0.79 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PF 
        0.53         0.43         0.13         0.23         0.10         0.72 
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-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-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-D7-6815 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-7916 TCGA-FP-7998 
        6.54         2.01        72.23         0.39         3.02         3.58 
TCGA-FP-8099 TCGA-FP-8209 TCGA-HJ-7597 TCGA-IN-7806 TCGA-IN-7808 TCGA-IP-7968 
        1.02        59.05        26.43         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 
              2.91               1.20 
[1] "0.2 - 53.0 (2.9)" "0.1 - 72.2 (1.2)"
        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-BR-8592         TCGA-BR-A4IU         TCGA-BR-A4IV 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BR-A4IY         TCGA-BR-A4IZ         TCGA-BR-A4J1 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BR-A4J2         TCGA-BR-A4J4         TCGA-BR-A4J5 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BR-A4J6         TCGA-BR-A4J8         TCGA-BR-A4J9 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BR-A4PF         TCGA-CD-5798         TCGA-CD-5799 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-CD-5800         TCGA-CD-5801         TCGA-CD-5802 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-CD-5803         TCGA-CG-4300         TCGA-CG-4301 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-CG-4304         TCGA-CG-4305         TCGA-CG-4306 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-CG-4436         TCGA-CG-4437         TCGA-CG-4438 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-CG-4440         TCGA-CG-4441         TCGA-CG-4443 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-CG-4444         TCGA-CG-4449         TCGA-CG-4455 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-CG-4460         TCGA-CG-4462         TCGA-CG-4465 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-CG-4466         TCGA-CG-4469         TCGA-CG-4472 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-CG-4474         TCGA-CG-4477         TCGA-CG-5716 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-CG-5717         TCGA-CG-5718         TCGA-CG-5719 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-CG-5720         TCGA-CG-5721         TCGA-CG-5722 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-CG-5723         TCGA-CG-5724         TCGA-CG-5725 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-CG-5726         TCGA-CG-5727         TCGA-CG-5728 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-CG-5730         TCGA-CG-5732         TCGA-CG-5733 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-CG-5734         TCGA-D7-5577         TCGA-D7-5578 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-D7-5579         TCGA-D7-6518         TCGA-D7-6519 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-D7-6520         TCGA-D7-6521         TCGA-D7-6522 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-D7-6524         TCGA-D7-6525         TCGA-D7-6526 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-D7-6527         TCGA-D7-6528         TCGA-D7-6815 
  "10Q LOSS MUTATED"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-D7-6817         TCGA-D7-6818         TCGA-D7-6820 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-D7-6822         TCGA-EQ-5647         TCGA-EQ-8122 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-F1-6177         TCGA-F1-6874         TCGA-F1-6875 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-FP-7735         TCGA-FP-7829         TCGA-FP-7916 
"10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-FP-7998         TCGA-FP-8099         TCGA-FP-8209 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-FP-8631         TCGA-HJ-7597         TCGA-IN-7806 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-IN-7808         TCGA-IP-7968 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-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-BR-8592         TCGA-BR-A4IU         TCGA-BR-A4IV 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BR-A4IY         TCGA-BR-A4IZ         TCGA-BR-A4J1 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BR-A4J2         TCGA-BR-A4J4         TCGA-BR-A4J5 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BR-A4J6         TCGA-BR-A4J8         TCGA-BR-A4J9 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BR-A4PF         TCGA-CD-5798         TCGA-CD-5799 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-CD-5800         TCGA-CD-5801         TCGA-CD-5802 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-CD-5803         TCGA-CG-4300         TCGA-CG-4301 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-CG-4304         TCGA-CG-4305         TCGA-CG-4306 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-CG-4436         TCGA-CG-4437         TCGA-CG-4438 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-CG-4440         TCGA-CG-4441         TCGA-CG-4443 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-CG-4444         TCGA-CG-4449         TCGA-CG-4455 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-CG-4460         TCGA-CG-4462         TCGA-CG-4465 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-CG-4466         TCGA-CG-4469         TCGA-CG-4472 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-CG-4474         TCGA-CG-4477         TCGA-CG-5716 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-CG-5717         TCGA-CG-5718         TCGA-CG-5719 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-CG-5720         TCGA-CG-5721         TCGA-CG-5722 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-CG-5723         TCGA-CG-5724         TCGA-CG-5725 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-CG-5726         TCGA-CG-5727         TCGA-CG-5728 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-CG-5730         TCGA-CG-5732         TCGA-CG-5733 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-CG-5734         TCGA-D7-5577         TCGA-D7-5578 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-D7-5579         TCGA-D7-6518         TCGA-D7-6519 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-D7-6520         TCGA-D7-6521         TCGA-D7-6522 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-D7-6524         TCGA-D7-6525         TCGA-D7-6526 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-D7-6527         TCGA-D7-6528         TCGA-D7-6815 
  "10Q LOSS MUTATED"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-D7-6817         TCGA-D7-6818         TCGA-D7-6820 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-D7-6822         TCGA-EQ-5647         TCGA-EQ-8122 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-F1-6177         TCGA-F1-6874         TCGA-F1-6875 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-FP-7735         TCGA-FP-7829         TCGA-FP-7916 
"10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-FP-7998         TCGA-FP-8099         TCGA-FP-8209 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-FP-8631         TCGA-HJ-7597         TCGA-IN-7806 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-IN-7808         TCGA-IP-7968 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-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-BR-8592         TCGA-BR-A4IU         TCGA-BR-A4IV 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BR-A4IY         TCGA-BR-A4IZ         TCGA-BR-A4J1 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BR-A4J2         TCGA-BR-A4J4         TCGA-BR-A4J5 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BR-A4J6         TCGA-BR-A4J8         TCGA-BR-A4J9 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BR-A4PF         TCGA-CD-5798         TCGA-CD-5799 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-CD-5800         TCGA-CD-5801         TCGA-CD-5802 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-CD-5803         TCGA-CG-4300         TCGA-CG-4301 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-CG-4304         TCGA-CG-4305         TCGA-CG-4306 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-CG-4436         TCGA-CG-4437         TCGA-CG-4438 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-CG-4440         TCGA-CG-4441         TCGA-CG-4443 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-CG-4444         TCGA-CG-4449         TCGA-CG-4455 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-CG-4460         TCGA-CG-4462         TCGA-CG-4465 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-CG-4466         TCGA-CG-4469         TCGA-CG-4472 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-CG-4474         TCGA-CG-4477         TCGA-CG-5716 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-CG-5717         TCGA-CG-5718         TCGA-CG-5719 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-CG-5720         TCGA-CG-5721         TCGA-CG-5722 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-CG-5723         TCGA-CG-5724         TCGA-CG-5725 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-CG-5726         TCGA-CG-5727         TCGA-CG-5728 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-CG-5730         TCGA-CG-5732         TCGA-CG-5733 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-CG-5734         TCGA-D7-5577         TCGA-D7-5578 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-D7-5579         TCGA-D7-6518         TCGA-D7-6519 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-D7-6520         TCGA-D7-6521         TCGA-D7-6522 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-D7-6524         TCGA-D7-6525         TCGA-D7-6526 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-D7-6527         TCGA-D7-6528         TCGA-D7-6815 
  "10Q LOSS MUTATED"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-D7-6817         TCGA-D7-6818         TCGA-D7-6820 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-D7-6822         TCGA-EQ-5647         TCGA-EQ-8122 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-F1-6177         TCGA-F1-6874         TCGA-F1-6875 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-FP-7735         TCGA-FP-7829         TCGA-FP-7916 
"10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-FP-7998         TCGA-FP-8099         TCGA-FP-8209 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-FP-8631         TCGA-HJ-7597         TCGA-IN-7806 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-IN-7808         TCGA-IP-7968 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
[1] "hr="     "7.4e+07"
D55V2, continuous
D55V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED      3    7
  10Q LOSS WILD-TYPE   67  100
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  FEMALE                3                 67
  MALE                  7                100
                    vv
clus                 STOMACH ADENOCARCINOMA - DIFFUSE TYPE
  10Q LOSS MUTATED                                       0
  10Q LOSS WILD-TYPE                                    25
                    vv
clus                 STOMACH ADENOCARCINOMA - NOT OTHERWISE SPECIFIED (NOS)
  10Q LOSS MUTATED                                                        1
  10Q LOSS WILD-TYPE                                                     86
                    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                                                 9
                    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                                                                        4
  10Q LOSS WILD-TYPE                                                                     32
D55V4, multiclass
                    vv
clus                 T1 T2 T3 T4
  10Q LOSS MUTATED    0  5  4  0
  10Q LOSS WILD-TYPE  6 49 60 43
D55V5, multiclass
    clus
vv   10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  T1                0                  6
  T2                5                 49
  T3                4                 60
  T4                0                 43
                    vv
clus                 N0 N1 N2 N3
  10Q LOSS MUTATED    4  4  1  1
  10Q LOSS WILD-TYPE 52 57 28 19
D55V6, multiclass
    clus
vv   10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  N0                4                 52
  N1                4                 57
  N2                1                 28
  N3                1                 19
                    vv
clus                  M0  M1  MX
  10Q LOSS MUTATED     9   0   1
  10Q LOSS WILD-TYPE 137  18  12
D55V7, multiclass
    clus
vv   10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  M0                9                137
  M1                0                 18
  MX                1                 12
                    vv
clus                  I II III IV
  10Q LOSS MUTATED    3  3   3  0
  10Q LOSS WILD-TYPE 23 45  55 29
D55V8, multiclass
     clus
vv    10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  I                  3                 23
  II                 3                 45
  III                3                 55
  IV                 0                 29
D55V9, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED      1    9
  10Q LOSS WILD-TYPE    4  163
     clus
vv    10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  NO                 1                  4
  YES                9                163
                    vv
clus                  R0  R1  R2  RX
  10Q LOSS MUTATED     9   0   0   1
  10Q LOSS WILD-TYPE 114   7  12  24
D55V10, multiclass
    clus
vv   10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  R0                9                114
  R1                0                  7
  R2                0                 12
  RX                1                 24
D55V11, continuous

Clustering(56) Variable = 11p loss mutation analysis
D56V1, survival
                    sevent
clus2                  0   1
  11P LOSS MUTATED     7   4
  11P LOSS WILD-TYPE 115  14
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                11                129 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                 4                 14 
$`11P LOSS MUTATED`
TCGA-BR-A4J1 TCGA-CD-5799 TCGA-CD-5802 TCGA-CG-4443 TCGA-CG-4460 TCGA-CG-4477 
        0.72         0.69         0.30        29.98        21.99         1.02 
TCGA-CG-5724 TCGA-CG-5730 TCGA-D7-6519 TCGA-D7-6815 TCGA-EQ-5647 
       12.03         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-BR-8592 TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J2 
        0.20         0.59         0.92         0.39         0.79         0.79 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PF 
        0.53         0.43         0.13         0.23         0.10         0.72 
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-FP-8099 TCGA-FP-8209 TCGA-FP-8631 TCGA-HJ-7597 
        3.02         3.58         1.02        59.05         0.56        26.43 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IP-7968 
        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 
              3.65               1.22 
[1] "0.3 - 30.0 (3.6)" "0.1 - 72.2 (1.2)"
        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-BR-8592         TCGA-BR-A4IU         TCGA-BR-A4IV 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BR-A4IY         TCGA-BR-A4IZ         TCGA-BR-A4J1 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE"   "11P LOSS MUTATED" 
        TCGA-BR-A4J2         TCGA-BR-A4J4         TCGA-BR-A4J5 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BR-A4J6         TCGA-BR-A4J8         TCGA-BR-A4J9 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BR-A4PF         TCGA-CD-5798         TCGA-CD-5799 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE"   "11P LOSS MUTATED" 
        TCGA-CD-5800         TCGA-CD-5801         TCGA-CD-5802 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE"   "11P LOSS MUTATED" 
        TCGA-CD-5803         TCGA-CG-4300         TCGA-CG-4301 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-CG-4304         TCGA-CG-4305         TCGA-CG-4306 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-CG-4436         TCGA-CG-4437         TCGA-CG-4438 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-CG-4440         TCGA-CG-4441         TCGA-CG-4443 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE"   "11P LOSS MUTATED" 
        TCGA-CG-4444         TCGA-CG-4449         TCGA-CG-4455 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-CG-4460         TCGA-CG-4462         TCGA-CG-4465 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-CG-4466         TCGA-CG-4469         TCGA-CG-4472 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-CG-4474         TCGA-CG-4477         TCGA-CG-5716 
"11P LOSS WILD-TYPE"   "11P LOSS MUTATED" "11P LOSS WILD-TYPE" 
        TCGA-CG-5717         TCGA-CG-5718         TCGA-CG-5719 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-CG-5720         TCGA-CG-5721         TCGA-CG-5722 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-CG-5723         TCGA-CG-5724         TCGA-CG-5725 
"11P LOSS WILD-TYPE"   "11P LOSS MUTATED" "11P LOSS WILD-TYPE" 
        TCGA-CG-5726         TCGA-CG-5727         TCGA-CG-5728 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-CG-5730         TCGA-CG-5732         TCGA-CG-5733 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-CG-5734         TCGA-D7-5577         TCGA-D7-5578 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-D7-5579         TCGA-D7-6518         TCGA-D7-6519 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE"   "11P LOSS MUTATED" 
        TCGA-D7-6520         TCGA-D7-6521         TCGA-D7-6522 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-D7-6524         TCGA-D7-6525         TCGA-D7-6526 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-D7-6527         TCGA-D7-6528         TCGA-D7-6815 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE"   "11P LOSS MUTATED" 
        TCGA-D7-6817         TCGA-D7-6818         TCGA-D7-6820 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-D7-6822         TCGA-EQ-5647         TCGA-EQ-8122 
"11P LOSS WILD-TYPE"   "11P LOSS MUTATED" "11P LOSS WILD-TYPE" 
        TCGA-F1-6177         TCGA-F1-6874         TCGA-F1-6875 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-FP-7735         TCGA-FP-7829         TCGA-FP-7916 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-FP-7998         TCGA-FP-8099         TCGA-FP-8209 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-FP-8631         TCGA-HJ-7597         TCGA-IN-7806 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-IN-7808         TCGA-IP-7968 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-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-BR-8592         TCGA-BR-A4IU         TCGA-BR-A4IV 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BR-A4IY         TCGA-BR-A4IZ         TCGA-BR-A4J1 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE"   "11P LOSS MUTATED" 
        TCGA-BR-A4J2         TCGA-BR-A4J4         TCGA-BR-A4J5 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BR-A4J6         TCGA-BR-A4J8         TCGA-BR-A4J9 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BR-A4PF         TCGA-CD-5798         TCGA-CD-5799 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE"   "11P LOSS MUTATED" 
        TCGA-CD-5800         TCGA-CD-5801         TCGA-CD-5802 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE"   "11P LOSS MUTATED" 
        TCGA-CD-5803         TCGA-CG-4300         TCGA-CG-4301 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-CG-4304         TCGA-CG-4305         TCGA-CG-4306 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-CG-4436         TCGA-CG-4437         TCGA-CG-4438 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-CG-4440         TCGA-CG-4441         TCGA-CG-4443 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE"   "11P LOSS MUTATED" 
        TCGA-CG-4444         TCGA-CG-4449         TCGA-CG-4455 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-CG-4460         TCGA-CG-4462         TCGA-CG-4465 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-CG-4466         TCGA-CG-4469         TCGA-CG-4472 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-CG-4474         TCGA-CG-4477         TCGA-CG-5716 
"11P LOSS WILD-TYPE"   "11P LOSS MUTATED" "11P LOSS WILD-TYPE" 
        TCGA-CG-5717         TCGA-CG-5718         TCGA-CG-5719 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-CG-5720         TCGA-CG-5721         TCGA-CG-5722 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-CG-5723         TCGA-CG-5724         TCGA-CG-5725 
"11P LOSS WILD-TYPE"   "11P LOSS MUTATED" "11P LOSS WILD-TYPE" 
        TCGA-CG-5726         TCGA-CG-5727         TCGA-CG-5728 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-CG-5730         TCGA-CG-5732         TCGA-CG-5733 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-CG-5734         TCGA-D7-5577         TCGA-D7-5578 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-D7-5579         TCGA-D7-6518         TCGA-D7-6519 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE"   "11P LOSS MUTATED" 
        TCGA-D7-6520         TCGA-D7-6521         TCGA-D7-6522 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-D7-6524         TCGA-D7-6525         TCGA-D7-6526 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-D7-6527         TCGA-D7-6528         TCGA-D7-6815 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE"   "11P LOSS MUTATED" 
        TCGA-D7-6817         TCGA-D7-6818         TCGA-D7-6820 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-D7-6822         TCGA-EQ-5647         TCGA-EQ-8122 
"11P LOSS WILD-TYPE"   "11P LOSS MUTATED" "11P LOSS WILD-TYPE" 
        TCGA-F1-6177         TCGA-F1-6874         TCGA-F1-6875 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-FP-7735         TCGA-FP-7829         TCGA-FP-7916 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-FP-7998         TCGA-FP-8099         TCGA-FP-8209 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-FP-8631         TCGA-HJ-7597         TCGA-IN-7806 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-IN-7808         TCGA-IP-7968 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-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-BR-8592         TCGA-BR-A4IU         TCGA-BR-A4IV 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BR-A4IY         TCGA-BR-A4IZ         TCGA-BR-A4J1 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE"   "11P LOSS MUTATED" 
        TCGA-BR-A4J2         TCGA-BR-A4J4         TCGA-BR-A4J5 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BR-A4J6         TCGA-BR-A4J8         TCGA-BR-A4J9 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BR-A4PF         TCGA-CD-5798         TCGA-CD-5799 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE"   "11P LOSS MUTATED" 
        TCGA-CD-5800         TCGA-CD-5801         TCGA-CD-5802 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE"   "11P LOSS MUTATED" 
        TCGA-CD-5803         TCGA-CG-4300         TCGA-CG-4301 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-CG-4304         TCGA-CG-4305         TCGA-CG-4306 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-CG-4436         TCGA-CG-4437         TCGA-CG-4438 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-CG-4440         TCGA-CG-4441         TCGA-CG-4443 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE"   "11P LOSS MUTATED" 
        TCGA-CG-4444         TCGA-CG-4449         TCGA-CG-4455 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-CG-4460         TCGA-CG-4462         TCGA-CG-4465 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-CG-4466         TCGA-CG-4469         TCGA-CG-4472 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-CG-4474         TCGA-CG-4477         TCGA-CG-5716 
"11P LOSS WILD-TYPE"   "11P LOSS MUTATED" "11P LOSS WILD-TYPE" 
        TCGA-CG-5717         TCGA-CG-5718         TCGA-CG-5719 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-CG-5720         TCGA-CG-5721         TCGA-CG-5722 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-CG-5723         TCGA-CG-5724         TCGA-CG-5725 
"11P LOSS WILD-TYPE"   "11P LOSS MUTATED" "11P LOSS WILD-TYPE" 
        TCGA-CG-5726         TCGA-CG-5727         TCGA-CG-5728 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-CG-5730         TCGA-CG-5732         TCGA-CG-5733 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-CG-5734         TCGA-D7-5577         TCGA-D7-5578 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-D7-5579         TCGA-D7-6518         TCGA-D7-6519 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE"   "11P LOSS MUTATED" 
        TCGA-D7-6520         TCGA-D7-6521         TCGA-D7-6522 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-D7-6524         TCGA-D7-6525         TCGA-D7-6526 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-D7-6527         TCGA-D7-6528         TCGA-D7-6815 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE"   "11P LOSS MUTATED" 
        TCGA-D7-6817         TCGA-D7-6818         TCGA-D7-6820 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-D7-6822         TCGA-EQ-5647         TCGA-EQ-8122 
"11P LOSS WILD-TYPE"   "11P LOSS MUTATED" "11P LOSS WILD-TYPE" 
        TCGA-F1-6177         TCGA-F1-6874         TCGA-F1-6875 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-FP-7735         TCGA-FP-7829         TCGA-FP-7916 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-FP-7998         TCGA-FP-8099         TCGA-FP-8209 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-FP-8631         TCGA-HJ-7597         TCGA-IN-7806 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-IN-7808         TCGA-IP-7968 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
[1] "hr=" "2.6"
D56V2, continuous
D56V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED      6    7
  11P LOSS WILD-TYPE   64  100
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  FEMALE                6                 64
  MALE                  7                100
                    vv
clus                 STOMACH ADENOCARCINOMA - DIFFUSE TYPE
  11P LOSS MUTATED                                       2
  11P LOSS WILD-TYPE                                    23
                    vv
clus                 STOMACH ADENOCARCINOMA - NOT OTHERWISE SPECIFIED (NOS)
  11P LOSS MUTATED                                                        4
  11P LOSS WILD-TYPE                                                     83
                    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                                                10
                    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                                                                     31
D56V4, multiclass
                    vv
clus                 T1 T2 T3 T4
  11P LOSS MUTATED    1  7  2  3
  11P LOSS WILD-TYPE  5 47 62 40
D56V5, multiclass
    clus
vv   11P LOSS MUTATED 11P LOSS WILD-TYPE
  T1                1                  5
  T2                7                 47
  T3                2                 62
  T4                3                 40
                    vv
clus                 N0 N1 N2 N3
  11P LOSS MUTATED    3  6  1  2
  11P LOSS WILD-TYPE 53 55 28 18
D56V6, multiclass
    clus
vv   11P LOSS MUTATED 11P LOSS WILD-TYPE
  N0                3                 53
  N1                6                 55
  N2                1                 28
  N3                2                 18
                    vv
clus                  M0  M1  MX
  11P LOSS MUTATED     9   4   0
  11P LOSS WILD-TYPE 137  14  13
D56V7, multiclass
    clus
vv   11P LOSS MUTATED 11P LOSS WILD-TYPE
  M0                9                137
  M1                4                 14
  MX                0                 13
                    vv
clus                  I II III IV
  11P LOSS MUTATED    2  3   3  4
  11P LOSS WILD-TYPE 24 45  55 25
D56V8, multiclass
     clus
vv    11P LOSS MUTATED 11P LOSS WILD-TYPE
  I                  2                 24
  II                 3                 45
  III                3                 55
  IV                 4                 25
D56V9, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED      0   13
  11P LOSS WILD-TYPE    5  159
     clus
vv    11P LOSS MUTATED 11P LOSS WILD-TYPE
  NO                 0                  5
  YES               13                159
                    vv
clus                  R0  R1  R2  RX
  11P LOSS MUTATED     5   0   4   2
  11P LOSS WILD-TYPE 118   7   8  23
D56V10, multiclass
    clus
vv   11P LOSS MUTATED 11P LOSS WILD-TYPE
  R0                5                118
  R1                0                  7
  R2                4                  8
  RX                2                 23
D56V11, continuous

Clustering(57) Variable = 11q loss mutation analysis
D57V1, survival
                    sevent
clus2                  0   1
  11Q LOSS MUTATED     6   3
  11Q LOSS WILD-TYPE 116  15
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                 9                131 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                 3                 15 
$`11Q LOSS MUTATED`
TCGA-BR-A4J1 TCGA-BR-A4PF TCGA-CD-5799 TCGA-CD-5802 TCGA-CG-4437 TCGA-CG-4443 
        0.72         0.72         0.69         0.30         8.05        29.98 
TCGA-CG-5724 TCGA-D7-6815 TCGA-EQ-5647 
       12.03         3.65         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-BR-8592 TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J2 
        0.20         0.59         0.92         0.39         0.79         0.79 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-CD-5798 
        0.53         0.43         0.13         0.23         0.10         0.82 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5803 TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
        0.36         0.49         0.07        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
       15.95         1.02        52.96        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-4477 TCGA-CG-5716 
       18.94         7.07        12.00         1.02         1.02         1.02 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.94         1.02         1.02         0.99         5.98         0.95 
TCGA-CG-5723 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 
       70.06        15.02        28.96        31.04        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       55.04        21.07         7.99         8.65         3.58         4.54 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
        9.80        15.65         9.63         8.19         6.90         0.69 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6817 TCGA-D7-6818 
        5.95         6.61         4.14         1.68         4.70         4.04 
TCGA-D7-6820 TCGA-D7-6822 TCGA-EQ-8122 TCGA-F1-6177 TCGA-F1-6874 TCGA-F1-6875 
        2.93         4.27         7.79         6.54         2.01        72.23 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        0.39         0.20         3.02         3.58         1.02        59.05 
TCGA-FP-8631 TCGA-HJ-7597 TCGA-IN-7806 TCGA-IN-7808 TCGA-IP-7968 
        0.56        26.43         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 
              0.72               1.25 
[1] "0.3 - 30.0 (0.7)" "0.1 - 72.2 (1.2)"
        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-BR-8592         TCGA-BR-A4IU         TCGA-BR-A4IV 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-BR-A4IY         TCGA-BR-A4IZ         TCGA-BR-A4J1 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" 
        TCGA-BR-A4J2         TCGA-BR-A4J4         TCGA-BR-A4J5 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-BR-A4J6         TCGA-BR-A4J8         TCGA-BR-A4J9 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-BR-A4PF         TCGA-CD-5798         TCGA-CD-5799 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" 
        TCGA-CD-5800         TCGA-CD-5801         TCGA-CD-5802 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" 
        TCGA-CD-5803         TCGA-CG-4300         TCGA-CG-4301 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-CG-4304         TCGA-CG-4305         TCGA-CG-4306 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-CG-4436         TCGA-CG-4437         TCGA-CG-4438 
"11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" 
        TCGA-CG-4440         TCGA-CG-4441         TCGA-CG-4443 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" 
        TCGA-CG-4444         TCGA-CG-4449         TCGA-CG-4455 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-CG-4460         TCGA-CG-4462         TCGA-CG-4465 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-CG-4466         TCGA-CG-4469         TCGA-CG-4472 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-CG-4474         TCGA-CG-4477         TCGA-CG-5716 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-CG-5717         TCGA-CG-5718         TCGA-CG-5719 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-CG-5720         TCGA-CG-5721         TCGA-CG-5722 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-CG-5723         TCGA-CG-5724         TCGA-CG-5725 
"11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" 
        TCGA-CG-5726         TCGA-CG-5727         TCGA-CG-5728 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-CG-5730         TCGA-CG-5732         TCGA-CG-5733 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-CG-5734         TCGA-D7-5577         TCGA-D7-5578 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-D7-5579         TCGA-D7-6518         TCGA-D7-6519 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-D7-6520         TCGA-D7-6521         TCGA-D7-6522 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-D7-6524         TCGA-D7-6525         TCGA-D7-6526 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-D7-6527         TCGA-D7-6528         TCGA-D7-6815 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" 
        TCGA-D7-6817         TCGA-D7-6818         TCGA-D7-6820 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-D7-6822         TCGA-EQ-5647         TCGA-EQ-8122 
"11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" 
        TCGA-F1-6177         TCGA-F1-6874         TCGA-F1-6875 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-FP-7735         TCGA-FP-7829         TCGA-FP-7916 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-FP-7998         TCGA-FP-8099         TCGA-FP-8209 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-FP-8631         TCGA-HJ-7597         TCGA-IN-7806 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-IN-7808         TCGA-IP-7968 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-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-BR-8592         TCGA-BR-A4IU         TCGA-BR-A4IV 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-BR-A4IY         TCGA-BR-A4IZ         TCGA-BR-A4J1 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" 
        TCGA-BR-A4J2         TCGA-BR-A4J4         TCGA-BR-A4J5 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-BR-A4J6         TCGA-BR-A4J8         TCGA-BR-A4J9 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-BR-A4PF         TCGA-CD-5798         TCGA-CD-5799 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" 
        TCGA-CD-5800         TCGA-CD-5801         TCGA-CD-5802 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" 
        TCGA-CD-5803         TCGA-CG-4300         TCGA-CG-4301 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-CG-4304         TCGA-CG-4305         TCGA-CG-4306 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-CG-4436         TCGA-CG-4437         TCGA-CG-4438 
"11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" 
        TCGA-CG-4440         TCGA-CG-4441         TCGA-CG-4443 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" 
        TCGA-CG-4444         TCGA-CG-4449         TCGA-CG-4455 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-CG-4460         TCGA-CG-4462         TCGA-CG-4465 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-CG-4466         TCGA-CG-4469         TCGA-CG-4472 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-CG-4474         TCGA-CG-4477         TCGA-CG-5716 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-CG-5717         TCGA-CG-5718         TCGA-CG-5719 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-CG-5720         TCGA-CG-5721         TCGA-CG-5722 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-CG-5723         TCGA-CG-5724         TCGA-CG-5725 
"11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" 
        TCGA-CG-5726         TCGA-CG-5727         TCGA-CG-5728 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-CG-5730         TCGA-CG-5732         TCGA-CG-5733 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-CG-5734         TCGA-D7-5577         TCGA-D7-5578 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-D7-5579         TCGA-D7-6518         TCGA-D7-6519 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-D7-6520         TCGA-D7-6521         TCGA-D7-6522 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-D7-6524         TCGA-D7-6525         TCGA-D7-6526 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-D7-6527         TCGA-D7-6528         TCGA-D7-6815 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" 
        TCGA-D7-6817         TCGA-D7-6818         TCGA-D7-6820 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-D7-6822         TCGA-EQ-5647         TCGA-EQ-8122 
"11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" 
        TCGA-F1-6177         TCGA-F1-6874         TCGA-F1-6875 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-FP-7735         TCGA-FP-7829         TCGA-FP-7916 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-FP-7998         TCGA-FP-8099         TCGA-FP-8209 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-FP-8631         TCGA-HJ-7597         TCGA-IN-7806 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-IN-7808         TCGA-IP-7968 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-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-BR-8592         TCGA-BR-A4IU         TCGA-BR-A4IV 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-BR-A4IY         TCGA-BR-A4IZ         TCGA-BR-A4J1 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" 
        TCGA-BR-A4J2         TCGA-BR-A4J4         TCGA-BR-A4J5 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-BR-A4J6         TCGA-BR-A4J8         TCGA-BR-A4J9 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-BR-A4PF         TCGA-CD-5798         TCGA-CD-5799 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" 
        TCGA-CD-5800         TCGA-CD-5801         TCGA-CD-5802 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" 
        TCGA-CD-5803         TCGA-CG-4300         TCGA-CG-4301 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-CG-4304         TCGA-CG-4305         TCGA-CG-4306 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-CG-4436         TCGA-CG-4437         TCGA-CG-4438 
"11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" 
        TCGA-CG-4440         TCGA-CG-4441         TCGA-CG-4443 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" 
        TCGA-CG-4444         TCGA-CG-4449         TCGA-CG-4455 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-CG-4460         TCGA-CG-4462         TCGA-CG-4465 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-CG-4466         TCGA-CG-4469         TCGA-CG-4472 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-CG-4474         TCGA-CG-4477         TCGA-CG-5716 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-CG-5717         TCGA-CG-5718         TCGA-CG-5719 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-CG-5720         TCGA-CG-5721         TCGA-CG-5722 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-CG-5723         TCGA-CG-5724         TCGA-CG-5725 
"11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" 
        TCGA-CG-5726         TCGA-CG-5727         TCGA-CG-5728 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-CG-5730         TCGA-CG-5732         TCGA-CG-5733 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-CG-5734         TCGA-D7-5577         TCGA-D7-5578 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-D7-5579         TCGA-D7-6518         TCGA-D7-6519 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-D7-6520         TCGA-D7-6521         TCGA-D7-6522 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-D7-6524         TCGA-D7-6525         TCGA-D7-6526 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-D7-6527         TCGA-D7-6528         TCGA-D7-6815 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" 
        TCGA-D7-6817         TCGA-D7-6818         TCGA-D7-6820 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-D7-6822         TCGA-EQ-5647         TCGA-EQ-8122 
"11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" 
        TCGA-F1-6177         TCGA-F1-6874         TCGA-F1-6875 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-FP-7735         TCGA-FP-7829         TCGA-FP-7916 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-FP-7998         TCGA-FP-8099         TCGA-FP-8209 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-FP-8631         TCGA-HJ-7597         TCGA-IN-7806 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-IN-7808         TCGA-IP-7968 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
[1] "hr=" "3.1"
D57V2, continuous
D57V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED      2    9
  11Q LOSS WILD-TYPE   68   98
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  FEMALE                2                 68
  MALE                  9                 98
                    vv
clus                 STOMACH ADENOCARCINOMA - DIFFUSE TYPE
  11Q LOSS MUTATED                                       1
  11Q LOSS WILD-TYPE                                    24
                    vv
clus                 STOMACH ADENOCARCINOMA - NOT OTHERWISE SPECIFIED (NOS)
  11Q LOSS MUTATED                                                        5
  11Q LOSS WILD-TYPE                                                     82
                    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                                                10
                    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                                                                     33
D57V4, multiclass
                    vv
clus                 T1 T2 T3 T4
  11Q LOSS MUTATED    1  5  2  3
  11Q LOSS WILD-TYPE  5 49 62 40
D57V5, multiclass
    clus
vv   11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  T1                1                  5
  T2                5                 49
  T3                2                 62
  T4                3                 40
                    vv
clus                 N0 N1 N2 N3
  11Q LOSS MUTATED    2  4  2  2
  11Q LOSS WILD-TYPE 54 57 27 18
D57V6, multiclass
    clus
vv   11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  N0                2                 54
  N1                4                 57
  N2                2                 27
  N3                2                 18
                    vv
clus                  M0  M1  MX
  11Q LOSS MUTATED     9   2   0
  11Q LOSS WILD-TYPE 137  16  13
D57V7, multiclass
    clus
vv   11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  M0                9                137
  M1                2                 16
  MX                0                 13
                    vv
clus                  I II III IV
  11Q LOSS MUTATED    1  4   3  2
  11Q LOSS WILD-TYPE 25 44  55 27
D57V8, multiclass
     clus
vv    11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  I                  1                 25
  II                 4                 44
  III                3                 55
  IV                 2                 27
D57V9, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED      0   11
  11Q LOSS WILD-TYPE    5  161
     clus
vv    11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  NO                 0                  5
  YES               11                161
                    vv
clus                  R0  R1  R2  RX
  11Q LOSS MUTATED     5   0   2   2
  11Q LOSS WILD-TYPE 118   7  10  23
D57V10, multiclass
    clus
vv   11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  R0                5                118
  R1                0                  7
  R2                2                 10
  RX                2                 23
D57V11, continuous

Clustering(58) Variable = 12p loss mutation analysis
D58V1, survival
                    sevent
clus2                  0   1
  12P LOSS MUTATED    10   2
  12P LOSS WILD-TYPE 112  16
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                12                128 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                 2                 16 
$`12P LOSS MUTATED`
TCGA-BR-7715 TCGA-BR-A4J6 TCGA-CD-5800 TCGA-CD-5802 TCGA-CG-4436 TCGA-CG-4443 
        1.05         0.13         0.36         0.30        52.96        29.98 
TCGA-CG-4477 TCGA-CG-5725 TCGA-CG-5732 TCGA-D7-6822 TCGA-F1-6875 TCGA-FP-8631 
        1.02        15.02        55.04         4.27        72.23         0.56 

$`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-BR-8592 
        0.26         1.18         1.55         1.48         0.76         0.20 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
        0.59         0.92         0.39         0.79         0.72         0.79 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PF TCGA-CD-5798 
        0.53         0.43         0.23         0.10         0.72         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-FP-8099 TCGA-FP-8209 TCGA-HJ-7597 TCGA-IN-7806 
        3.02         3.58         1.02        59.05        26.43         6.87 
TCGA-IN-7808 TCGA-IP-7968 
        3.55         2.53 

  12P LOSS MUTATED 12P LOSS WILD-TYPE 
              0.13               0.07 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
             72.23              70.06 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
             2.660              1.235 
[1] "0.1 - 72.2 (2.7)" "0.1 - 70.1 (1.2)"
        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-BR-8592         TCGA-BR-A4IU         TCGA-BR-A4IV 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-BR-A4IY         TCGA-BR-A4IZ         TCGA-BR-A4J1 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-BR-A4J2         TCGA-BR-A4J4         TCGA-BR-A4J5 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-BR-A4J6         TCGA-BR-A4J8         TCGA-BR-A4J9 
  "12P LOSS MUTATED" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-BR-A4PF         TCGA-CD-5798         TCGA-CD-5799 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-CD-5800         TCGA-CD-5801         TCGA-CD-5802 
  "12P LOSS MUTATED" "12P LOSS WILD-TYPE"   "12P LOSS MUTATED" 
        TCGA-CD-5803         TCGA-CG-4300         TCGA-CG-4301 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-CG-4304         TCGA-CG-4305         TCGA-CG-4306 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-CG-4436         TCGA-CG-4437         TCGA-CG-4438 
  "12P LOSS MUTATED" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-CG-4440         TCGA-CG-4441         TCGA-CG-4443 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE"   "12P LOSS MUTATED" 
        TCGA-CG-4444         TCGA-CG-4449         TCGA-CG-4455 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-CG-4460         TCGA-CG-4462         TCGA-CG-4465 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-CG-4466         TCGA-CG-4469         TCGA-CG-4472 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-CG-4474         TCGA-CG-4477         TCGA-CG-5716 
"12P LOSS WILD-TYPE"   "12P LOSS MUTATED" "12P LOSS WILD-TYPE" 
        TCGA-CG-5717         TCGA-CG-5718         TCGA-CG-5719 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-CG-5720         TCGA-CG-5721         TCGA-CG-5722 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-CG-5723         TCGA-CG-5724         TCGA-CG-5725 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE"   "12P LOSS MUTATED" 
        TCGA-CG-5726         TCGA-CG-5727         TCGA-CG-5728 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-CG-5730         TCGA-CG-5732         TCGA-CG-5733 
"12P LOSS WILD-TYPE"   "12P LOSS MUTATED" "12P LOSS WILD-TYPE" 
        TCGA-CG-5734         TCGA-D7-5577         TCGA-D7-5578 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-D7-5579         TCGA-D7-6518         TCGA-D7-6519 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-D7-6520         TCGA-D7-6521         TCGA-D7-6522 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-D7-6524         TCGA-D7-6525         TCGA-D7-6526 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-D7-6527         TCGA-D7-6528         TCGA-D7-6815 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-D7-6817         TCGA-D7-6818         TCGA-D7-6820 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-D7-6822         TCGA-EQ-5647         TCGA-EQ-8122 
  "12P LOSS MUTATED" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-F1-6177         TCGA-F1-6874         TCGA-F1-6875 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE"   "12P LOSS MUTATED" 
        TCGA-FP-7735         TCGA-FP-7829         TCGA-FP-7916 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-FP-7998         TCGA-FP-8099         TCGA-FP-8209 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-FP-8631         TCGA-HJ-7597         TCGA-IN-7806 
  "12P LOSS MUTATED" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-IN-7808         TCGA-IP-7968 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
  "12P LOSS MUTATED" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-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-BR-8592         TCGA-BR-A4IU         TCGA-BR-A4IV 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-BR-A4IY         TCGA-BR-A4IZ         TCGA-BR-A4J1 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-BR-A4J2         TCGA-BR-A4J4         TCGA-BR-A4J5 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-BR-A4J6         TCGA-BR-A4J8         TCGA-BR-A4J9 
  "12P LOSS MUTATED" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-BR-A4PF         TCGA-CD-5798         TCGA-CD-5799 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-CD-5800         TCGA-CD-5801         TCGA-CD-5802 
  "12P LOSS MUTATED" "12P LOSS WILD-TYPE"   "12P LOSS MUTATED" 
        TCGA-CD-5803         TCGA-CG-4300         TCGA-CG-4301 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-CG-4304         TCGA-CG-4305         TCGA-CG-4306 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-CG-4436         TCGA-CG-4437         TCGA-CG-4438 
  "12P LOSS MUTATED" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-CG-4440         TCGA-CG-4441         TCGA-CG-4443 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE"   "12P LOSS MUTATED" 
        TCGA-CG-4444         TCGA-CG-4449         TCGA-CG-4455 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-CG-4460         TCGA-CG-4462         TCGA-CG-4465 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-CG-4466         TCGA-CG-4469         TCGA-CG-4472 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-CG-4474         TCGA-CG-4477         TCGA-CG-5716 
"12P LOSS WILD-TYPE"   "12P LOSS MUTATED" "12P LOSS WILD-TYPE" 
        TCGA-CG-5717         TCGA-CG-5718         TCGA-CG-5719 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-CG-5720         TCGA-CG-5721         TCGA-CG-5722 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-CG-5723         TCGA-CG-5724         TCGA-CG-5725 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE"   "12P LOSS MUTATED" 
        TCGA-CG-5726         TCGA-CG-5727         TCGA-CG-5728 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-CG-5730         TCGA-CG-5732         TCGA-CG-5733 
"12P LOSS WILD-TYPE"   "12P LOSS MUTATED" "12P LOSS WILD-TYPE" 
        TCGA-CG-5734         TCGA-D7-5577         TCGA-D7-5578 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-D7-5579         TCGA-D7-6518         TCGA-D7-6519 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-D7-6520         TCGA-D7-6521         TCGA-D7-6522 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-D7-6524         TCGA-D7-6525         TCGA-D7-6526 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-D7-6527         TCGA-D7-6528         TCGA-D7-6815 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-D7-6817         TCGA-D7-6818         TCGA-D7-6820 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-D7-6822         TCGA-EQ-5647         TCGA-EQ-8122 
  "12P LOSS MUTATED" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-F1-6177         TCGA-F1-6874         TCGA-F1-6875 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE"   "12P LOSS MUTATED" 
        TCGA-FP-7735         TCGA-FP-7829         TCGA-FP-7916 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-FP-7998         TCGA-FP-8099         TCGA-FP-8209 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-FP-8631         TCGA-HJ-7597         TCGA-IN-7806 
  "12P LOSS MUTATED" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-IN-7808         TCGA-IP-7968 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
  "12P LOSS MUTATED" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-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-BR-8592         TCGA-BR-A4IU         TCGA-BR-A4IV 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-BR-A4IY         TCGA-BR-A4IZ         TCGA-BR-A4J1 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-BR-A4J2         TCGA-BR-A4J4         TCGA-BR-A4J5 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-BR-A4J6         TCGA-BR-A4J8         TCGA-BR-A4J9 
  "12P LOSS MUTATED" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-BR-A4PF         TCGA-CD-5798         TCGA-CD-5799 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-CD-5800         TCGA-CD-5801         TCGA-CD-5802 
  "12P LOSS MUTATED" "12P LOSS WILD-TYPE"   "12P LOSS MUTATED" 
        TCGA-CD-5803         TCGA-CG-4300         TCGA-CG-4301 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-CG-4304         TCGA-CG-4305         TCGA-CG-4306 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-CG-4436         TCGA-CG-4437         TCGA-CG-4438 
  "12P LOSS MUTATED" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-CG-4440         TCGA-CG-4441         TCGA-CG-4443 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE"   "12P LOSS MUTATED" 
        TCGA-CG-4444         TCGA-CG-4449         TCGA-CG-4455 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-CG-4460         TCGA-CG-4462         TCGA-CG-4465 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-CG-4466         TCGA-CG-4469         TCGA-CG-4472 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-CG-4474         TCGA-CG-4477         TCGA-CG-5716 
"12P LOSS WILD-TYPE"   "12P LOSS MUTATED" "12P LOSS WILD-TYPE" 
        TCGA-CG-5717         TCGA-CG-5718         TCGA-CG-5719 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-CG-5720         TCGA-CG-5721         TCGA-CG-5722 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-CG-5723         TCGA-CG-5724         TCGA-CG-5725 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE"   "12P LOSS MUTATED" 
        TCGA-CG-5726         TCGA-CG-5727         TCGA-CG-5728 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-CG-5730         TCGA-CG-5732         TCGA-CG-5733 
"12P LOSS WILD-TYPE"   "12P LOSS MUTATED" "12P LOSS WILD-TYPE" 
        TCGA-CG-5734         TCGA-D7-5577         TCGA-D7-5578 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-D7-5579         TCGA-D7-6518         TCGA-D7-6519 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-D7-6520         TCGA-D7-6521         TCGA-D7-6522 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-D7-6524         TCGA-D7-6525         TCGA-D7-6526 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-D7-6527         TCGA-D7-6528         TCGA-D7-6815 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-D7-6817         TCGA-D7-6818         TCGA-D7-6820 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-D7-6822         TCGA-EQ-5647         TCGA-EQ-8122 
  "12P LOSS MUTATED" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-F1-6177         TCGA-F1-6874         TCGA-F1-6875 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE"   "12P LOSS MUTATED" 
        TCGA-FP-7735         TCGA-FP-7829         TCGA-FP-7916 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-FP-7998         TCGA-FP-8099         TCGA-FP-8209 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-FP-8631         TCGA-HJ-7597         TCGA-IN-7806 
  "12P LOSS MUTATED" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-IN-7808         TCGA-IP-7968 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
[1] "hr=" "3.9"
D58V2, continuous
D58V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED      3    9
  12P LOSS WILD-TYPE   67   98
        clus
vv       12P LOSS MUTATED 12P LOSS WILD-TYPE
  FEMALE                3                 67
  MALE                  9                 98
                    vv
clus                 STOMACH ADENOCARCINOMA - DIFFUSE TYPE
  12P LOSS MUTATED                                       0
  12P LOSS WILD-TYPE                                    25
                    vv
clus                 STOMACH ADENOCARCINOMA - NOT OTHERWISE SPECIFIED (NOS)
  12P LOSS MUTATED                                                        5
  12P LOSS WILD-TYPE                                                     82
                    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                                                10
                    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                                                                        5
  12P LOSS WILD-TYPE                                                                     31
D58V4, multiclass
                    vv
clus                 T1 T2 T3 T4
  12P LOSS MUTATED    1  6  5  0
  12P LOSS WILD-TYPE  5 48 59 43
D58V5, multiclass
    clus
vv   12P LOSS MUTATED 12P LOSS WILD-TYPE
  T1                1                  5
  T2                6                 48
  T3                5                 59
  T4                0                 43
                    vv
clus                 N0 N1 N2 N3
  12P LOSS MUTATED   10  0  1  1
  12P LOSS WILD-TYPE 46 61 28 19
D58V6, multiclass
    clus
vv   12P LOSS MUTATED 12P LOSS WILD-TYPE
  N0               10                 46
  N1                0                 61
  N2                1                 28
  N3                1                 19
                    vv
clus                  M0  M1  MX
  12P LOSS MUTATED    11   0   1
  12P LOSS WILD-TYPE 135  18  12
D58V7, multiclass
    clus
vv   12P LOSS MUTATED 12P LOSS WILD-TYPE
  M0               11                135
  M1                0                 18
  MX                1                 12
                    vv
clus                  I II III IV
  12P LOSS MUTATED    6  4   1  1
  12P LOSS WILD-TYPE 20 44  57 28
D58V8, multiclass
     clus
vv    12P LOSS MUTATED 12P LOSS WILD-TYPE
  I                  6                 20
  II                 4                 44
  III                1                 57
  IV                 1                 28
D58V9, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED      0   12
  12P LOSS WILD-TYPE    5  160
     clus
vv    12P LOSS MUTATED 12P LOSS WILD-TYPE
  NO                 0                  5
  YES               12                160
                    vv
clus                  R0  R1  R2  RX
  12P LOSS MUTATED    10   0   0   0
  12P LOSS WILD-TYPE 113   7  12  25
D58V10, multiclass
    clus
vv   12P LOSS MUTATED 12P LOSS WILD-TYPE
  R0               10                113
  R1                0                  7
  R2                0                 12
  RX                0                 25
D58V11, continuous

Clustering(59) Variable = 12q loss mutation analysis
D59V1, survival
                    sevent
clus2                  0   1
  12Q LOSS MUTATED     7   1
  12Q LOSS WILD-TYPE 115  17
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                 8                132 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                 1                 17 
$`12Q LOSS MUTATED`
TCGA-BR-7715 TCGA-BR-A4J6 TCGA-CD-5802 TCGA-CG-4436 TCGA-CG-4443 TCGA-CG-5725 
        1.05         0.13         0.30        52.96        29.98        15.02 
TCGA-CG-5732 TCGA-FP-8631 
       55.04         0.56 

$`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-BR-8592 
        0.26         1.18         1.55         1.48         0.76         0.20 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
        0.59         0.92         0.39         0.79         0.72         0.79 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PF TCGA-CD-5798 
        0.53         0.43         0.23         0.10         0.72         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-FP-8099 TCGA-FP-8209 TCGA-HJ-7597 TCGA-IN-7806 TCGA-IN-7808 TCGA-IP-7968 
        1.02        59.05        26.43         6.87         3.55         2.53 

  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
              0.13               0.07 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
             55.04              72.23 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
             8.035              1.235 
[1] "0.1 - 55.0 (8.0)" "0.1 - 72.2 (1.2)"
        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-BR-8592         TCGA-BR-A4IU         TCGA-BR-A4IV 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-BR-A4IY         TCGA-BR-A4IZ         TCGA-BR-A4J1 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-BR-A4J2         TCGA-BR-A4J4         TCGA-BR-A4J5 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-BR-A4J6         TCGA-BR-A4J8         TCGA-BR-A4J9 
  "12Q LOSS MUTATED" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-BR-A4PF         TCGA-CD-5798         TCGA-CD-5799 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-CD-5800         TCGA-CD-5801         TCGA-CD-5802 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE"   "12Q LOSS MUTATED" 
        TCGA-CD-5803         TCGA-CG-4300         TCGA-CG-4301 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-CG-4304         TCGA-CG-4305         TCGA-CG-4306 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-CG-4436         TCGA-CG-4437         TCGA-CG-4438 
  "12Q LOSS MUTATED" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-CG-4440         TCGA-CG-4441         TCGA-CG-4443 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE"   "12Q LOSS MUTATED" 
        TCGA-CG-4444         TCGA-CG-4449         TCGA-CG-4455 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-CG-4460         TCGA-CG-4462         TCGA-CG-4465 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-CG-4466         TCGA-CG-4469         TCGA-CG-4472 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-CG-4474         TCGA-CG-4477         TCGA-CG-5716 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-CG-5717         TCGA-CG-5718         TCGA-CG-5719 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-CG-5720         TCGA-CG-5721         TCGA-CG-5722 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-CG-5723         TCGA-CG-5724         TCGA-CG-5725 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE"   "12Q LOSS MUTATED" 
        TCGA-CG-5726         TCGA-CG-5727         TCGA-CG-5728 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-CG-5730         TCGA-CG-5732         TCGA-CG-5733 
"12Q LOSS WILD-TYPE"   "12Q LOSS MUTATED" "12Q LOSS WILD-TYPE" 
        TCGA-CG-5734         TCGA-D7-5577         TCGA-D7-5578 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-D7-5579         TCGA-D7-6518         TCGA-D7-6519 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-D7-6520         TCGA-D7-6521         TCGA-D7-6522 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-D7-6524         TCGA-D7-6525         TCGA-D7-6526 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-D7-6527         TCGA-D7-6528         TCGA-D7-6815 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-D7-6817         TCGA-D7-6818         TCGA-D7-6820 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-D7-6822         TCGA-EQ-5647         TCGA-EQ-8122 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-F1-6177         TCGA-F1-6874         TCGA-F1-6875 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-FP-7735         TCGA-FP-7829         TCGA-FP-7916 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-FP-7998         TCGA-FP-8099         TCGA-FP-8209 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-FP-8631         TCGA-HJ-7597         TCGA-IN-7806 
  "12Q LOSS MUTATED" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-IN-7808         TCGA-IP-7968 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
  "12Q LOSS MUTATED" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-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-BR-8592         TCGA-BR-A4IU         TCGA-BR-A4IV 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-BR-A4IY         TCGA-BR-A4IZ         TCGA-BR-A4J1 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-BR-A4J2         TCGA-BR-A4J4         TCGA-BR-A4J5 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-BR-A4J6         TCGA-BR-A4J8         TCGA-BR-A4J9 
  "12Q LOSS MUTATED" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-BR-A4PF         TCGA-CD-5798         TCGA-CD-5799 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-CD-5800         TCGA-CD-5801         TCGA-CD-5802 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE"   "12Q LOSS MUTATED" 
        TCGA-CD-5803         TCGA-CG-4300         TCGA-CG-4301 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-CG-4304         TCGA-CG-4305         TCGA-CG-4306 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-CG-4436         TCGA-CG-4437         TCGA-CG-4438 
  "12Q LOSS MUTATED" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-CG-4440         TCGA-CG-4441         TCGA-CG-4443 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE"   "12Q LOSS MUTATED" 
        TCGA-CG-4444         TCGA-CG-4449         TCGA-CG-4455 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-CG-4460         TCGA-CG-4462         TCGA-CG-4465 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-CG-4466         TCGA-CG-4469         TCGA-CG-4472 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-CG-4474         TCGA-CG-4477         TCGA-CG-5716 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-CG-5717         TCGA-CG-5718         TCGA-CG-5719 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-CG-5720         TCGA-CG-5721         TCGA-CG-5722 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-CG-5723         TCGA-CG-5724         TCGA-CG-5725 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE"   "12Q LOSS MUTATED" 
        TCGA-CG-5726         TCGA-CG-5727         TCGA-CG-5728 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-CG-5730         TCGA-CG-5732         TCGA-CG-5733 
"12Q LOSS WILD-TYPE"   "12Q LOSS MUTATED" "12Q LOSS WILD-TYPE" 
        TCGA-CG-5734         TCGA-D7-5577         TCGA-D7-5578 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-D7-5579         TCGA-D7-6518         TCGA-D7-6519 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-D7-6520         TCGA-D7-6521         TCGA-D7-6522 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-D7-6524         TCGA-D7-6525         TCGA-D7-6526 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-D7-6527         TCGA-D7-6528         TCGA-D7-6815 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-D7-6817         TCGA-D7-6818         TCGA-D7-6820 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-D7-6822         TCGA-EQ-5647         TCGA-EQ-8122 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-F1-6177         TCGA-F1-6874         TCGA-F1-6875 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-FP-7735         TCGA-FP-7829         TCGA-FP-7916 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-FP-7998         TCGA-FP-8099         TCGA-FP-8209 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-FP-8631         TCGA-HJ-7597         TCGA-IN-7806 
  "12Q LOSS MUTATED" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-IN-7808         TCGA-IP-7968 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
  "12Q LOSS MUTATED" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-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-BR-8592         TCGA-BR-A4IU         TCGA-BR-A4IV 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-BR-A4IY         TCGA-BR-A4IZ         TCGA-BR-A4J1 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-BR-A4J2         TCGA-BR-A4J4         TCGA-BR-A4J5 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-BR-A4J6         TCGA-BR-A4J8         TCGA-BR-A4J9 
  "12Q LOSS MUTATED" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-BR-A4PF         TCGA-CD-5798         TCGA-CD-5799 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-CD-5800         TCGA-CD-5801         TCGA-CD-5802 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE"   "12Q LOSS MUTATED" 
        TCGA-CD-5803         TCGA-CG-4300         TCGA-CG-4301 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-CG-4304         TCGA-CG-4305         TCGA-CG-4306 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-CG-4436         TCGA-CG-4437         TCGA-CG-4438 
  "12Q LOSS MUTATED" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-CG-4440         TCGA-CG-4441         TCGA-CG-4443 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE"   "12Q LOSS MUTATED" 
        TCGA-CG-4444         TCGA-CG-4449         TCGA-CG-4455 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-CG-4460         TCGA-CG-4462         TCGA-CG-4465 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-CG-4466         TCGA-CG-4469         TCGA-CG-4472 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-CG-4474         TCGA-CG-4477         TCGA-CG-5716 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-CG-5717         TCGA-CG-5718         TCGA-CG-5719 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-CG-5720         TCGA-CG-5721         TCGA-CG-5722 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-CG-5723         TCGA-CG-5724         TCGA-CG-5725 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE"   "12Q LOSS MUTATED" 
        TCGA-CG-5726         TCGA-CG-5727         TCGA-CG-5728 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-CG-5730         TCGA-CG-5732         TCGA-CG-5733 
"12Q LOSS WILD-TYPE"   "12Q LOSS MUTATED" "12Q LOSS WILD-TYPE" 
        TCGA-CG-5734         TCGA-D7-5577         TCGA-D7-5578 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-D7-5579         TCGA-D7-6518         TCGA-D7-6519 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-D7-6520         TCGA-D7-6521         TCGA-D7-6522 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-D7-6524         TCGA-D7-6525         TCGA-D7-6526 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-D7-6527         TCGA-D7-6528         TCGA-D7-6815 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-D7-6817         TCGA-D7-6818         TCGA-D7-6820 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-D7-6822         TCGA-EQ-5647         TCGA-EQ-8122 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-F1-6177         TCGA-F1-6874         TCGA-F1-6875 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-FP-7735         TCGA-FP-7829         TCGA-FP-7916 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-FP-7998         TCGA-FP-8099         TCGA-FP-8209 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-FP-8631         TCGA-HJ-7597         TCGA-IN-7806 
  "12Q LOSS MUTATED" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-IN-7808         TCGA-IP-7968 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
[1] "hr=" "2.5"
D59V2, continuous
D59V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED      1    7
  12Q LOSS WILD-TYPE   69  100
        clus
vv       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  FEMALE                1                 69
  MALE                  7                100
                    vv
clus                 STOMACH ADENOCARCINOMA - DIFFUSE TYPE
  12Q LOSS MUTATED                                       0
  12Q LOSS WILD-TYPE                                    25
                    vv
clus                 STOMACH ADENOCARCINOMA - NOT OTHERWISE SPECIFIED (NOS)
  12Q LOSS MUTATED                                                        4
  12Q LOSS WILD-TYPE                                                     83
                    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                                                10
                    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                                                                        4
  12Q LOSS WILD-TYPE                                                                     32
D59V4, multiclass
                    vv
clus                 T1 T2 T3 T4
  12Q LOSS MUTATED    1  3  4  0
  12Q LOSS WILD-TYPE  5 51 60 43
D59V5, multiclass
    clus
vv   12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  T1                1                  5
  T2                3                 51
  T3                4                 60
  T4                0                 43
                    vv
clus                 N0 N1 N2 N3
  12Q LOSS MUTATED    6  0  1  1
  12Q LOSS WILD-TYPE 50 61 28 19
D59V6, multiclass
    clus
vv   12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  N0                6                 50
  N1                0                 61
  N2                1                 28
  N3                1                 19
                    vv
clus                  M0  M1  MX
  12Q LOSS MUTATED     7   0   1
  12Q LOSS WILD-TYPE 139  18  12
D59V7, multiclass
    clus
vv   12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  M0                7                139
  M1                0                 18
  MX                1                 12
                    vv
clus                  I II III IV
  12Q LOSS MUTATED    3  3   1  1
  12Q LOSS WILD-TYPE 23 45  57 28
D59V8, multiclass
     clus
vv    12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  I                  3                 23
  II                 3                 45
  III                1                 57
  IV                 1                 28
D59V9, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED      0    8
  12Q LOSS WILD-TYPE    5  164
     clus
vv    12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  NO                 0                  5
  YES                8                164
                    vv
clus                  R0  R1  R2  RX
  12Q LOSS MUTATED     7   0   0   0
  12Q LOSS WILD-TYPE 116   7  12  25
D59V10, multiclass
    clus
vv   12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  R0                7                116
  R1                0                  7
  R2                0                 12
  RX                0                 25
D59V11, continuous

Clustering(60) Variable = 13q loss mutation analysis
D60V1, survival
                    sevent
clus2                  0   1
  13Q LOSS MUTATED     3   0
  13Q LOSS WILD-TYPE 119  18
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                 3                137 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                 0                 18 
$`13Q LOSS MUTATED`
TCGA-CG-4301 TCGA-D7-6525 TCGA-FP-8099 
        3.02         5.95         1.02 

$`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-BR-8592 TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        0.20         0.59         0.92         0.39         0.79         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J8 TCGA-BR-A4J9 
        0.79         0.53         0.43         0.13         0.23         0.10 
TCGA-BR-A4PF TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        0.72         0.82         0.69         0.36         0.49         0.30 
TCGA-CD-5803 TCGA-CG-4300 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
        0.07        20.02        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-D7-6526 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-FP-8209 
       72.23         0.39         0.20         3.02         3.58        59.05 
TCGA-FP-8631 TCGA-HJ-7597 TCGA-IN-7806 TCGA-IN-7808 TCGA-IP-7968 
        0.56        26.43         6.87         3.55         2.53 

  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
              1.02               0.07 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
              5.95              72.23 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
              3.02               1.22 
[1] "1.0 - 6.0 (3.0)"  "0.1 - 72.2 (1.2)"
        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-BR-8592         TCGA-BR-A4IU         TCGA-BR-A4IV 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BR-A4IY         TCGA-BR-A4IZ         TCGA-BR-A4J1 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BR-A4J2         TCGA-BR-A4J4         TCGA-BR-A4J5 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BR-A4J6         TCGA-BR-A4J8         TCGA-BR-A4J9 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BR-A4PF         TCGA-CD-5798         TCGA-CD-5799 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CD-5800         TCGA-CD-5801         TCGA-CD-5802 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CD-5803         TCGA-CG-4300         TCGA-CG-4301 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" 
        TCGA-CG-4304         TCGA-CG-4305         TCGA-CG-4306 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CG-4436         TCGA-CG-4437         TCGA-CG-4438 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CG-4440         TCGA-CG-4441         TCGA-CG-4443 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CG-4444         TCGA-CG-4449         TCGA-CG-4455 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CG-4460         TCGA-CG-4462         TCGA-CG-4465 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CG-4466         TCGA-CG-4469         TCGA-CG-4472 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CG-4474         TCGA-CG-4477         TCGA-CG-5716 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CG-5717         TCGA-CG-5718         TCGA-CG-5719 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CG-5720         TCGA-CG-5721         TCGA-CG-5722 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CG-5723         TCGA-CG-5724         TCGA-CG-5725 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CG-5726         TCGA-CG-5727         TCGA-CG-5728 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CG-5730         TCGA-CG-5732         TCGA-CG-5733 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CG-5734         TCGA-D7-5577         TCGA-D7-5578 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-D7-5579         TCGA-D7-6518         TCGA-D7-6519 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-D7-6520         TCGA-D7-6521         TCGA-D7-6522 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-D7-6524         TCGA-D7-6525         TCGA-D7-6526 
"13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" "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-FP-8099         TCGA-FP-8209 
"13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" 
        TCGA-FP-8631         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" 
        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-BR-8592         TCGA-BR-A4IU         TCGA-BR-A4IV 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BR-A4IY         TCGA-BR-A4IZ         TCGA-BR-A4J1 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BR-A4J2         TCGA-BR-A4J4         TCGA-BR-A4J5 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BR-A4J6         TCGA-BR-A4J8         TCGA-BR-A4J9 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BR-A4PF         TCGA-CD-5798         TCGA-CD-5799 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CD-5800         TCGA-CD-5801         TCGA-CD-5802 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CD-5803         TCGA-CG-4300         TCGA-CG-4301 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" 
        TCGA-CG-4304         TCGA-CG-4305         TCGA-CG-4306 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CG-4436         TCGA-CG-4437         TCGA-CG-4438 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CG-4440         TCGA-CG-4441         TCGA-CG-4443 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CG-4444         TCGA-CG-4449         TCGA-CG-4455 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CG-4460         TCGA-CG-4462         TCGA-CG-4465 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CG-4466         TCGA-CG-4469         TCGA-CG-4472 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CG-4474         TCGA-CG-4477         TCGA-CG-5716 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CG-5717         TCGA-CG-5718         TCGA-CG-5719 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CG-5720         TCGA-CG-5721         TCGA-CG-5722 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CG-5723         TCGA-CG-5724         TCGA-CG-5725 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CG-5726         TCGA-CG-5727         TCGA-CG-5728 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CG-5730         TCGA-CG-5732         TCGA-CG-5733 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CG-5734         TCGA-D7-5577         TCGA-D7-5578 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-D7-5579         TCGA-D7-6518         TCGA-D7-6519 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-D7-6520         TCGA-D7-6521         TCGA-D7-6522 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-D7-6524         TCGA-D7-6525         TCGA-D7-6526 
"13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" "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-FP-8099         TCGA-FP-8209 
"13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" 
        TCGA-FP-8631         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" 
        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-BR-8592         TCGA-BR-A4IU         TCGA-BR-A4IV 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BR-A4IY         TCGA-BR-A4IZ         TCGA-BR-A4J1 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BR-A4J2         TCGA-BR-A4J4         TCGA-BR-A4J5 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BR-A4J6         TCGA-BR-A4J8         TCGA-BR-A4J9 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BR-A4PF         TCGA-CD-5798         TCGA-CD-5799 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CD-5800         TCGA-CD-5801         TCGA-CD-5802 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CD-5803         TCGA-CG-4300         TCGA-CG-4301 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" 
        TCGA-CG-4304         TCGA-CG-4305         TCGA-CG-4306 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CG-4436         TCGA-CG-4437         TCGA-CG-4438 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CG-4440         TCGA-CG-4441         TCGA-CG-4443 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CG-4444         TCGA-CG-4449         TCGA-CG-4455 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CG-4460         TCGA-CG-4462         TCGA-CG-4465 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CG-4466         TCGA-CG-4469         TCGA-CG-4472 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CG-4474         TCGA-CG-4477         TCGA-CG-5716 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CG-5717         TCGA-CG-5718         TCGA-CG-5719 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CG-5720         TCGA-CG-5721         TCGA-CG-5722 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CG-5723         TCGA-CG-5724         TCGA-CG-5725 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CG-5726         TCGA-CG-5727         TCGA-CG-5728 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CG-5730         TCGA-CG-5732         TCGA-CG-5733 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CG-5734         TCGA-D7-5577         TCGA-D7-5578 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-D7-5579         TCGA-D7-6518         TCGA-D7-6519 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-D7-6520         TCGA-D7-6521         TCGA-D7-6522 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-D7-6524         TCGA-D7-6525         TCGA-D7-6526 
"13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" "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-FP-8099         TCGA-FP-8209 
"13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" 
        TCGA-FP-8631         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" 
[1] "hr="     "9300000"
D60V2, continuous
D60V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED      2    3
  13Q LOSS WILD-TYPE   68  104
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  FEMALE                2                 68
  MALE                  3                104
                    vv
clus                 STOMACH ADENOCARCINOMA - DIFFUSE TYPE
  13Q LOSS MUTATED                                       1
  13Q LOSS WILD-TYPE                                    24
                    vv
clus                 STOMACH ADENOCARCINOMA - NOT OTHERWISE SPECIFIED (NOS)
  13Q LOSS MUTATED                                                        2
  13Q LOSS WILD-TYPE                                                     85
                    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                                                 9
                    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                                                                     36
D60V4, multiclass
                    vv
clus                 T1 T2 T3 T4
  13Q LOSS MUTATED    0  3  1  1
  13Q LOSS WILD-TYPE  6 51 63 42
D60V5, multiclass
    clus
vv   13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  T1                0                  6
  T2                3                 51
  T3                1                 63
  T4                1                 42
                    vv
clus                 N0 N1 N2 N3
  13Q LOSS MUTATED    1  1  1  1
  13Q LOSS WILD-TYPE 55 60 28 19
D60V6, multiclass
    clus
vv   13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  N0                1                 55
  N1                1                 60
  N2                1                 28
  N3                1                 19
                    vv
clus                  M0  M1  MX
  13Q LOSS MUTATED     3   1   1
  13Q LOSS WILD-TYPE 143  17  12
D60V7, multiclass
    clus
vv   13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  M0                3                143
  M1                1                 17
  MX                1                 12
                    vv
clus                  I II III IV
  13Q LOSS MUTATED    0  1   1  2
  13Q LOSS WILD-TYPE 26 47  57 27
D60V8, multiclass
     clus
vv    13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  I                  0                 26
  II                 1                 47
  III                1                 57
  IV                 2                 27
D60V9, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED      1    4
  13Q LOSS WILD-TYPE    4  168
     clus
vv    13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  NO                 1                  4
  YES                4                168
                    vv
clus                  R0  R1  R2  RX
  13Q LOSS MUTATED     2   1   1   1
  13Q LOSS WILD-TYPE 121   6  11  24
D60V10, multiclass
    clus
vv   13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  R0                2                121
  R1                1                  6
  R2                1                 11
  RX                1                 24
D60V11, continuous

Clustering(61) Variable = 14q loss mutation analysis
D61V1, survival
                    sevent
clus2                  0   1
  14Q LOSS MUTATED    11   1
  14Q LOSS WILD-TYPE 111  17
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                12                128 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                 1                 17 
$`14Q LOSS MUTATED`
TCGA-BR-6458 TCGA-BR-7715 TCGA-BR-A4J1 TCGA-BR-A4J6 TCGA-BR-A4PF TCGA-CG-4438 
        1.35         1.05         0.72         0.13         0.72        54.05 
TCGA-CG-4477 TCGA-D7-6519 TCGA-D7-6520 TCGA-EQ-8122 TCGA-FP-8631 TCGA-IN-7806 
        1.02        15.65         9.63         7.79         0.56         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-BR-8592 TCGA-BR-A4IU 
        1.18         1.55         1.48         0.76         0.20         0.59 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
        0.92         0.39         0.79         0.79         0.53         0.43 
TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
        0.23         0.10         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-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-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-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
        9.80         8.19         6.90         0.69         5.95         6.61 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
        4.14         1.68         3.65         4.70         4.04         2.93 
TCGA-D7-6822 TCGA-EQ-5647 TCGA-F1-6177 TCGA-F1-6874 TCGA-F1-6875 TCGA-FP-7735 
        4.27         0.62         6.54         2.01        72.23         0.39 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-HJ-7597 
        0.20         3.02         3.58         1.02        59.05        26.43 
TCGA-IN-7808 TCGA-IP-7968 
        3.55         2.53 

  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
              0.13               0.07 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
             54.05              72.23 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
             1.200              1.235 
[1] "0.1 - 54.0 (1.2)" "0.1 - 72.2 (1.2)"
        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-BR-8592         TCGA-BR-A4IU         TCGA-BR-A4IV 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-BR-A4IY         TCGA-BR-A4IZ         TCGA-BR-A4J1 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-BR-A4J2         TCGA-BR-A4J4         TCGA-BR-A4J5 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-BR-A4J6         TCGA-BR-A4J8         TCGA-BR-A4J9 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-BR-A4PF         TCGA-CD-5798         TCGA-CD-5799 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-CD-5800         TCGA-CD-5801         TCGA-CD-5802 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-CD-5803         TCGA-CG-4300         TCGA-CG-4301 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-CG-4304         TCGA-CG-4305         TCGA-CG-4306 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-CG-4436         TCGA-CG-4437         TCGA-CG-4438 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-CG-4440         TCGA-CG-4441         TCGA-CG-4443 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-CG-4444         TCGA-CG-4449         TCGA-CG-4455 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-CG-4460         TCGA-CG-4462         TCGA-CG-4465 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-CG-4466         TCGA-CG-4469         TCGA-CG-4472 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-CG-4474         TCGA-CG-4477         TCGA-CG-5716 
"14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" 
        TCGA-CG-5717         TCGA-CG-5718         TCGA-CG-5719 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-CG-5720         TCGA-CG-5721         TCGA-CG-5722 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-CG-5723         TCGA-CG-5724         TCGA-CG-5725 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-CG-5726         TCGA-CG-5727         TCGA-CG-5728 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-CG-5730         TCGA-CG-5732         TCGA-CG-5733 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-CG-5734         TCGA-D7-5577         TCGA-D7-5578 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-D7-5579         TCGA-D7-6518         TCGA-D7-6519 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-D7-6520         TCGA-D7-6521         TCGA-D7-6522 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-D7-6524         TCGA-D7-6525         TCGA-D7-6526 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-D7-6527         TCGA-D7-6528         TCGA-D7-6815 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-D7-6817         TCGA-D7-6818         TCGA-D7-6820 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-D7-6822         TCGA-EQ-5647         TCGA-EQ-8122 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-F1-6177         TCGA-F1-6874         TCGA-F1-6875 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-FP-7735         TCGA-FP-7829         TCGA-FP-7916 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-FP-7998         TCGA-FP-8099         TCGA-FP-8209 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-FP-8631         TCGA-HJ-7597         TCGA-IN-7806 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-IN-7808         TCGA-IP-7968 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-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-BR-8592         TCGA-BR-A4IU         TCGA-BR-A4IV 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-BR-A4IY         TCGA-BR-A4IZ         TCGA-BR-A4J1 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-BR-A4J2         TCGA-BR-A4J4         TCGA-BR-A4J5 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-BR-A4J6         TCGA-BR-A4J8         TCGA-BR-A4J9 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-BR-A4PF         TCGA-CD-5798         TCGA-CD-5799 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-CD-5800         TCGA-CD-5801         TCGA-CD-5802 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-CD-5803         TCGA-CG-4300         TCGA-CG-4301 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-CG-4304         TCGA-CG-4305         TCGA-CG-4306 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-CG-4436         TCGA-CG-4437         TCGA-CG-4438 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-CG-4440         TCGA-CG-4441         TCGA-CG-4443 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-CG-4444         TCGA-CG-4449         TCGA-CG-4455 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-CG-4460         TCGA-CG-4462         TCGA-CG-4465 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-CG-4466         TCGA-CG-4469         TCGA-CG-4472 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-CG-4474         TCGA-CG-4477         TCGA-CG-5716 
"14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" 
        TCGA-CG-5717         TCGA-CG-5718         TCGA-CG-5719 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-CG-5720         TCGA-CG-5721         TCGA-CG-5722 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-CG-5723         TCGA-CG-5724         TCGA-CG-5725 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-CG-5726         TCGA-CG-5727         TCGA-CG-5728 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-CG-5730         TCGA-CG-5732         TCGA-CG-5733 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-CG-5734         TCGA-D7-5577         TCGA-D7-5578 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-D7-5579         TCGA-D7-6518         TCGA-D7-6519 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-D7-6520         TCGA-D7-6521         TCGA-D7-6522 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-D7-6524         TCGA-D7-6525         TCGA-D7-6526 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-D7-6527         TCGA-D7-6528         TCGA-D7-6815 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-D7-6817         TCGA-D7-6818         TCGA-D7-6820 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-D7-6822         TCGA-EQ-5647         TCGA-EQ-8122 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-F1-6177         TCGA-F1-6874         TCGA-F1-6875 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-FP-7735         TCGA-FP-7829         TCGA-FP-7916 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-FP-7998         TCGA-FP-8099         TCGA-FP-8209 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-FP-8631         TCGA-HJ-7597         TCGA-IN-7806 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-IN-7808         TCGA-IP-7968 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-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-BR-8592         TCGA-BR-A4IU         TCGA-BR-A4IV 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-BR-A4IY         TCGA-BR-A4IZ         TCGA-BR-A4J1 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-BR-A4J2         TCGA-BR-A4J4         TCGA-BR-A4J5 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-BR-A4J6         TCGA-BR-A4J8         TCGA-BR-A4J9 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-BR-A4PF         TCGA-CD-5798         TCGA-CD-5799 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-CD-5800         TCGA-CD-5801         TCGA-CD-5802 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-CD-5803         TCGA-CG-4300         TCGA-CG-4301 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-CG-4304         TCGA-CG-4305         TCGA-CG-4306 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-CG-4436         TCGA-CG-4437         TCGA-CG-4438 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-CG-4440         TCGA-CG-4441         TCGA-CG-4443 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-CG-4444         TCGA-CG-4449         TCGA-CG-4455 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-CG-4460         TCGA-CG-4462         TCGA-CG-4465 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-CG-4466         TCGA-CG-4469         TCGA-CG-4472 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-CG-4474         TCGA-CG-4477         TCGA-CG-5716 
"14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" 
        TCGA-CG-5717         TCGA-CG-5718         TCGA-CG-5719 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-CG-5720         TCGA-CG-5721         TCGA-CG-5722 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-CG-5723         TCGA-CG-5724         TCGA-CG-5725 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-CG-5726         TCGA-CG-5727         TCGA-CG-5728 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-CG-5730         TCGA-CG-5732         TCGA-CG-5733 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-CG-5734         TCGA-D7-5577         TCGA-D7-5578 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-D7-5579         TCGA-D7-6518         TCGA-D7-6519 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-D7-6520         TCGA-D7-6521         TCGA-D7-6522 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-D7-6524         TCGA-D7-6525         TCGA-D7-6526 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-D7-6527         TCGA-D7-6528         TCGA-D7-6815 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-D7-6817         TCGA-D7-6818         TCGA-D7-6820 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-D7-6822         TCGA-EQ-5647         TCGA-EQ-8122 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-F1-6177         TCGA-F1-6874         TCGA-F1-6875 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-FP-7735         TCGA-FP-7829         TCGA-FP-7916 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-FP-7998         TCGA-FP-8099         TCGA-FP-8209 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-FP-8631         TCGA-HJ-7597         TCGA-IN-7806 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-IN-7808         TCGA-IP-7968 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
[1] "hr=" "1.5"
D61V2, continuous
D61V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED      5    9
  14Q LOSS WILD-TYPE   65   98
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  FEMALE                5                 65
  MALE                  9                 98
                    vv
clus                 STOMACH ADENOCARCINOMA - DIFFUSE TYPE
  14Q LOSS MUTATED                                       2
  14Q LOSS WILD-TYPE                                    23
                    vv
clus                 STOMACH ADENOCARCINOMA - NOT OTHERWISE SPECIFIED (NOS)
  14Q LOSS MUTATED                                                        7
  14Q LOSS WILD-TYPE                                                     80
                    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                                                10
                    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                                                                        4
  14Q LOSS WILD-TYPE                                                                     32
D61V4, multiclass
                    vv
clus                 T1 T2 T3 T4
  14Q LOSS MUTATED    0  4  6  3
  14Q LOSS WILD-TYPE  6 50 58 40
D61V5, multiclass
    clus
vv   14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  T1                0                  6
  T2                4                 50
  T3                6                 58
  T4                3                 40
                    vv
clus                 N0 N1 N2 N3
  14Q LOSS MUTATED    3  6  4  0
  14Q LOSS WILD-TYPE 53 55 25 20
D61V6, multiclass
    clus
vv   14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  N0                3                 53
  N1                6                 55
  N2                4                 25
  N3                0                 20
                    vv
clus                  M0  M1  MX
  14Q LOSS MUTATED    12   0   2
  14Q LOSS WILD-TYPE 134  18  11
D61V7, multiclass
    clus
vv   14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  M0               12                134
  M1                0                 18
  MX                2                 11
                    vv
clus                  I II III IV
  14Q LOSS MUTATED    1  5   6  1
  14Q LOSS WILD-TYPE 25 43  52 28
D61V8, multiclass
     clus
vv    14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  I                  1                 25
  II                 5                 43
  III                6                 52
  IV                 1                 28
D61V9, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED      0   14
  14Q LOSS WILD-TYPE    5  158
     clus
vv    14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  NO                 0                  5
  YES               14                158
                    vv
clus                  R0  R1  R2  RX
  14Q LOSS MUTATED    11   0   0   2
  14Q LOSS WILD-TYPE 112   7  12  23
D61V10, multiclass
    clus
vv   14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  R0               11                112
  R1                0                  7
  R2                0                 12
  RX                2                 23
D61V11, continuous

Clustering(62) Variable = 15q loss mutation analysis
D62V1, survival
                    sevent
clus2                  0   1
  15Q LOSS MUTATED     7   2
  15Q LOSS WILD-TYPE 115  16
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                 9                131 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                 2                 16 
$`15Q LOSS MUTATED`
TCGA-BR-7704 TCGA-BR-A4J1 TCGA-CG-4436 TCGA-CG-4466 TCGA-CG-5724 TCGA-D7-6519 
        1.25         0.72        52.96        18.94        12.03        15.65 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6817 
        4.14         1.68         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-BR-8592 
        0.26         1.18         1.55         1.48         0.76         0.20 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J4 
        0.59         0.92         0.39         0.79         0.79         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PF TCGA-CD-5798 
        0.43         0.13         0.23         0.10         0.72         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-D7-6815 TCGA-D7-6818 TCGA-D7-6820 
        0.69         5.95         6.61         3.65         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-FP-8099 TCGA-FP-8209 
        0.39         0.20         3.02         3.58         1.02        59.05 
TCGA-FP-8631 TCGA-HJ-7597 TCGA-IN-7806 TCGA-IN-7808 TCGA-IP-7968 
        0.56        26.43         6.87         3.55         2.53 

  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
              0.72               0.07 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
             52.96              72.23 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
              4.70               1.12 
[1] "0.7 - 53.0 (4.7)" "0.1 - 72.2 (1.1)"
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-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-BR-8592         TCGA-BR-A4IU         TCGA-BR-A4IV 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BR-A4IY         TCGA-BR-A4IZ         TCGA-BR-A4J1 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" 
        TCGA-BR-A4J2         TCGA-BR-A4J4         TCGA-BR-A4J5 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BR-A4J6         TCGA-BR-A4J8         TCGA-BR-A4J9 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BR-A4PF         TCGA-CD-5798         TCGA-CD-5799 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-CD-5800         TCGA-CD-5801         TCGA-CD-5802 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-CD-5803         TCGA-CG-4300         TCGA-CG-4301 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-CG-4304         TCGA-CG-4305         TCGA-CG-4306 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-CG-4436         TCGA-CG-4437         TCGA-CG-4438 
  "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-CG-4440         TCGA-CG-4441         TCGA-CG-4443 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-CG-4444         TCGA-CG-4449         TCGA-CG-4455 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-CG-4460         TCGA-CG-4462         TCGA-CG-4465 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-CG-4466         TCGA-CG-4469         TCGA-CG-4472 
  "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-CG-4474         TCGA-CG-4477         TCGA-CG-5716 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-CG-5717         TCGA-CG-5718         TCGA-CG-5719 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-CG-5720         TCGA-CG-5721         TCGA-CG-5722 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-CG-5723         TCGA-CG-5724         TCGA-CG-5725 
"15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" 
        TCGA-CG-5726         TCGA-CG-5727         TCGA-CG-5728 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-CG-5730         TCGA-CG-5732         TCGA-CG-5733 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-CG-5734         TCGA-D7-5577         TCGA-D7-5578 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-D7-5579         TCGA-D7-6518         TCGA-D7-6519 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" 
        TCGA-D7-6520         TCGA-D7-6521         TCGA-D7-6522 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-D7-6524         TCGA-D7-6525         TCGA-D7-6526 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-D7-6527         TCGA-D7-6528         TCGA-D7-6815 
  "15Q LOSS MUTATED"   "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" 
        TCGA-D7-6817         TCGA-D7-6818         TCGA-D7-6820 
  "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-D7-6822         TCGA-EQ-5647         TCGA-EQ-8122 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-F1-6177         TCGA-F1-6874         TCGA-F1-6875 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-FP-7735         TCGA-FP-7829         TCGA-FP-7916 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-FP-7998         TCGA-FP-8099         TCGA-FP-8209 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-FP-8631         TCGA-HJ-7597         TCGA-IN-7806 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-IN-7808         TCGA-IP-7968 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-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-BR-8592         TCGA-BR-A4IU         TCGA-BR-A4IV 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BR-A4IY         TCGA-BR-A4IZ         TCGA-BR-A4J1 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" 
        TCGA-BR-A4J2         TCGA-BR-A4J4         TCGA-BR-A4J5 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BR-A4J6         TCGA-BR-A4J8         TCGA-BR-A4J9 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BR-A4PF         TCGA-CD-5798         TCGA-CD-5799 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-CD-5800         TCGA-CD-5801         TCGA-CD-5802 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-CD-5803         TCGA-CG-4300         TCGA-CG-4301 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-CG-4304         TCGA-CG-4305         TCGA-CG-4306 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-CG-4436         TCGA-CG-4437         TCGA-CG-4438 
  "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-CG-4440         TCGA-CG-4441         TCGA-CG-4443 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-CG-4444         TCGA-CG-4449         TCGA-CG-4455 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-CG-4460         TCGA-CG-4462         TCGA-CG-4465 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-CG-4466         TCGA-CG-4469         TCGA-CG-4472 
  "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-CG-4474         TCGA-CG-4477         TCGA-CG-5716 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-CG-5717         TCGA-CG-5718         TCGA-CG-5719 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-CG-5720         TCGA-CG-5721         TCGA-CG-5722 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-CG-5723         TCGA-CG-5724         TCGA-CG-5725 
"15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" 
        TCGA-CG-5726         TCGA-CG-5727         TCGA-CG-5728 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-CG-5730         TCGA-CG-5732         TCGA-CG-5733 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-CG-5734         TCGA-D7-5577         TCGA-D7-5578 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-D7-5579         TCGA-D7-6518         TCGA-D7-6519 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" 
        TCGA-D7-6520         TCGA-D7-6521         TCGA-D7-6522 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-D7-6524         TCGA-D7-6525         TCGA-D7-6526 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-D7-6527         TCGA-D7-6528         TCGA-D7-6815 
  "15Q LOSS MUTATED"   "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" 
        TCGA-D7-6817         TCGA-D7-6818         TCGA-D7-6820 
  "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-D7-6822         TCGA-EQ-5647         TCGA-EQ-8122 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-F1-6177         TCGA-F1-6874         TCGA-F1-6875 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-FP-7735         TCGA-FP-7829         TCGA-FP-7916 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-FP-7998         TCGA-FP-8099         TCGA-FP-8209 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-FP-8631         TCGA-HJ-7597         TCGA-IN-7806 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-IN-7808         TCGA-IP-7968 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-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-BR-8592         TCGA-BR-A4IU         TCGA-BR-A4IV 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BR-A4IY         TCGA-BR-A4IZ         TCGA-BR-A4J1 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" 
        TCGA-BR-A4J2         TCGA-BR-A4J4         TCGA-BR-A4J5 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BR-A4J6         TCGA-BR-A4J8         TCGA-BR-A4J9 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BR-A4PF         TCGA-CD-5798         TCGA-CD-5799 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-CD-5800         TCGA-CD-5801         TCGA-CD-5802 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-CD-5803         TCGA-CG-4300         TCGA-CG-4301 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-CG-4304         TCGA-CG-4305         TCGA-CG-4306 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-CG-4436         TCGA-CG-4437         TCGA-CG-4438 
  "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-CG-4440         TCGA-CG-4441         TCGA-CG-4443 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-CG-4444         TCGA-CG-4449         TCGA-CG-4455 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-CG-4460         TCGA-CG-4462         TCGA-CG-4465 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-CG-4466         TCGA-CG-4469         TCGA-CG-4472 
  "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-CG-4474         TCGA-CG-4477         TCGA-CG-5716 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-CG-5717         TCGA-CG-5718         TCGA-CG-5719 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-CG-5720         TCGA-CG-5721         TCGA-CG-5722 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-CG-5723         TCGA-CG-5724         TCGA-CG-5725 
"15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" 
        TCGA-CG-5726         TCGA-CG-5727         TCGA-CG-5728 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-CG-5730         TCGA-CG-5732         TCGA-CG-5733 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-CG-5734         TCGA-D7-5577         TCGA-D7-5578 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-D7-5579         TCGA-D7-6518         TCGA-D7-6519 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" 
        TCGA-D7-6520         TCGA-D7-6521         TCGA-D7-6522 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-D7-6524         TCGA-D7-6525         TCGA-D7-6526 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-D7-6527         TCGA-D7-6528         TCGA-D7-6815 
  "15Q LOSS MUTATED"   "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" 
        TCGA-D7-6817         TCGA-D7-6818         TCGA-D7-6820 
  "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-D7-6822         TCGA-EQ-5647         TCGA-EQ-8122 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-F1-6177         TCGA-F1-6874         TCGA-F1-6875 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-FP-7735         TCGA-FP-7829         TCGA-FP-7916 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-FP-7998         TCGA-FP-8099         TCGA-FP-8209 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-FP-8631         TCGA-HJ-7597         TCGA-IN-7806 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-IN-7808         TCGA-IP-7968 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
[1] "hr=" "1.2"
D62V2, continuous
D62V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED      5    7
  15Q LOSS WILD-TYPE   65  100
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  FEMALE                5                 65
  MALE                  7                100
                    vv
clus                 STOMACH ADENOCARCINOMA - DIFFUSE TYPE
  15Q LOSS MUTATED                                       2
  15Q LOSS WILD-TYPE                                    23
                    vv
clus                 STOMACH ADENOCARCINOMA - NOT OTHERWISE SPECIFIED (NOS)
  15Q LOSS MUTATED                                                        3
  15Q LOSS WILD-TYPE                                                     84
                    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                                                10
                    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                                                  3
  15Q LOSS WILD-TYPE                                                7
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - TYPE NOT OTHERWISE SPECIFIED (NOS)
  15Q LOSS MUTATED                                                                        3
  15Q LOSS WILD-TYPE                                                                     33
D62V4, multiclass
                    vv
clus                 T1 T2 T3 T4
  15Q LOSS MUTATED    0  8  3  1
  15Q LOSS WILD-TYPE  6 46 61 42
D62V5, multiclass
    clus
vv   15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  T1                0                  6
  T2                8                 46
  T3                3                 61
  T4                1                 42
                    vv
clus                 N0 N1 N2 N3
  15Q LOSS MUTATED    5  4  0  2
  15Q LOSS WILD-TYPE 51 57 29 18
D62V6, multiclass
    clus
vv   15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  N0                5                 51
  N1                4                 57
  N2                0                 29
  N3                2                 18
                    vv
clus                  M0  M1  MX
  15Q LOSS MUTATED    10   1   1
  15Q LOSS WILD-TYPE 136  17  12
D62V7, multiclass
    clus
vv   15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  M0               10                136
  M1                1                 17
  MX                1                 12
                    vv
clus                  I II III IV
  15Q LOSS MUTATED    4  2   4  1
  15Q LOSS WILD-TYPE 22 46  54 28
D62V8, multiclass
     clus
vv    15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  I                  4                 22
  II                 2                 46
  III                4                 54
  IV                 1                 28
D62V9, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED      2   10
  15Q LOSS WILD-TYPE    3  162
     clus
vv    15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  NO                 2                  3
  YES               10                162
                    vv
clus                  R0  R1  R2  RX
  15Q LOSS MUTATED     9   1   1   1
  15Q LOSS WILD-TYPE 114   6  11  24
D62V10, multiclass
    clus
vv   15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  R0                9                114
  R1                1                  6
  R2                1                 11
  RX                1                 24
D62V11, continuous

Clustering(63) Variable = 16p loss mutation analysis
D63V1, survival
                    sevent
clus2                  0   1
  16P LOSS MUTATED     6   1
  16P LOSS WILD-TYPE 116  17
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                 7                133 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                 1                 17 
$`16P LOSS MUTATED`
TCGA-BR-7715 TCGA-BR-A4PF TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-5724 TCGA-D7-6519 
        1.05         0.72        29.98        19.07        12.03        15.65 
TCGA-D7-6822 
        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-BR-8592 
        0.26         1.18         1.55         1.48         0.76         0.20 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
        0.59         0.92         0.39         0.79         0.72         0.79 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-CD-5798 
        0.53         0.43         0.13         0.23         0.10         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-FP-8099 TCGA-FP-8209 TCGA-FP-8631 TCGA-HJ-7597 TCGA-IN-7806 TCGA-IN-7808 
        1.02        59.05         0.56        26.43         6.87         3.55 
TCGA-IP-7968 
        2.53 

  16P LOSS MUTATED 16P LOSS WILD-TYPE 
              0.72               0.07 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
             29.98              72.23 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
             12.03               1.22 
[1] "0.7 - 30.0 (12.0)" "0.1 - 72.2 (1.2)" 
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
  "16P LOSS MUTATED" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-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-BR-8592         TCGA-BR-A4IU         TCGA-BR-A4IV 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BR-A4IY         TCGA-BR-A4IZ         TCGA-BR-A4J1 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BR-A4J2         TCGA-BR-A4J4         TCGA-BR-A4J5 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BR-A4J6         TCGA-BR-A4J8         TCGA-BR-A4J9 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BR-A4PF         TCGA-CD-5798         TCGA-CD-5799 
  "16P LOSS MUTATED" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-CD-5800         TCGA-CD-5801         TCGA-CD-5802 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-CD-5803         TCGA-CG-4300         TCGA-CG-4301 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-CG-4304         TCGA-CG-4305         TCGA-CG-4306 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-CG-4436         TCGA-CG-4437         TCGA-CG-4438 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-CG-4440         TCGA-CG-4441         TCGA-CG-4443 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE"   "16P LOSS MUTATED" 
        TCGA-CG-4444         TCGA-CG-4449         TCGA-CG-4455 
"16P LOSS WILD-TYPE"   "16P LOSS MUTATED" "16P LOSS WILD-TYPE" 
        TCGA-CG-4460         TCGA-CG-4462         TCGA-CG-4465 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-CG-4466         TCGA-CG-4469         TCGA-CG-4472 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-CG-4474         TCGA-CG-4477         TCGA-CG-5716 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-CG-5717         TCGA-CG-5718         TCGA-CG-5719 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-CG-5720         TCGA-CG-5721         TCGA-CG-5722 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-CG-5723         TCGA-CG-5724         TCGA-CG-5725 
"16P LOSS WILD-TYPE"   "16P LOSS MUTATED" "16P LOSS WILD-TYPE" 
        TCGA-CG-5726         TCGA-CG-5727         TCGA-CG-5728 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-CG-5730         TCGA-CG-5732         TCGA-CG-5733 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-CG-5734         TCGA-D7-5577         TCGA-D7-5578 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-D7-5579         TCGA-D7-6518         TCGA-D7-6519 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE"   "16P LOSS MUTATED" 
        TCGA-D7-6520         TCGA-D7-6521         TCGA-D7-6522 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-D7-6524         TCGA-D7-6525         TCGA-D7-6526 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-D7-6527         TCGA-D7-6528         TCGA-D7-6815 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-D7-6817         TCGA-D7-6818         TCGA-D7-6820 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-D7-6822         TCGA-EQ-5647         TCGA-EQ-8122 
  "16P LOSS MUTATED" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-F1-6177         TCGA-F1-6874         TCGA-F1-6875 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-FP-7735         TCGA-FP-7829         TCGA-FP-7916 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-FP-7998         TCGA-FP-8099         TCGA-FP-8209 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-FP-8631         TCGA-HJ-7597         TCGA-IN-7806 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-IN-7808         TCGA-IP-7968 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
  "16P LOSS MUTATED" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-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-BR-8592         TCGA-BR-A4IU         TCGA-BR-A4IV 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BR-A4IY         TCGA-BR-A4IZ         TCGA-BR-A4J1 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BR-A4J2         TCGA-BR-A4J4         TCGA-BR-A4J5 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BR-A4J6         TCGA-BR-A4J8         TCGA-BR-A4J9 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BR-A4PF         TCGA-CD-5798         TCGA-CD-5799 
  "16P LOSS MUTATED" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-CD-5800         TCGA-CD-5801         TCGA-CD-5802 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-CD-5803         TCGA-CG-4300         TCGA-CG-4301 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-CG-4304         TCGA-CG-4305         TCGA-CG-4306 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-CG-4436         TCGA-CG-4437         TCGA-CG-4438 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-CG-4440         TCGA-CG-4441         TCGA-CG-4443 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE"   "16P LOSS MUTATED" 
        TCGA-CG-4444         TCGA-CG-4449         TCGA-CG-4455 
"16P LOSS WILD-TYPE"   "16P LOSS MUTATED" "16P LOSS WILD-TYPE" 
        TCGA-CG-4460         TCGA-CG-4462         TCGA-CG-4465 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-CG-4466         TCGA-CG-4469         TCGA-CG-4472 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-CG-4474         TCGA-CG-4477         TCGA-CG-5716 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-CG-5717         TCGA-CG-5718         TCGA-CG-5719 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-CG-5720         TCGA-CG-5721         TCGA-CG-5722 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-CG-5723         TCGA-CG-5724         TCGA-CG-5725 
"16P LOSS WILD-TYPE"   "16P LOSS MUTATED" "16P LOSS WILD-TYPE" 
        TCGA-CG-5726         TCGA-CG-5727         TCGA-CG-5728 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-CG-5730         TCGA-CG-5732         TCGA-CG-5733 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-CG-5734         TCGA-D7-5577         TCGA-D7-5578 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-D7-5579         TCGA-D7-6518         TCGA-D7-6519 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE"   "16P LOSS MUTATED" 
        TCGA-D7-6520         TCGA-D7-6521         TCGA-D7-6522 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-D7-6524         TCGA-D7-6525         TCGA-D7-6526 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-D7-6527         TCGA-D7-6528         TCGA-D7-6815 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-D7-6817         TCGA-D7-6818         TCGA-D7-6820 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-D7-6822         TCGA-EQ-5647         TCGA-EQ-8122 
  "16P LOSS MUTATED" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-F1-6177         TCGA-F1-6874         TCGA-F1-6875 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-FP-7735         TCGA-FP-7829         TCGA-FP-7916 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-FP-7998         TCGA-FP-8099         TCGA-FP-8209 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-FP-8631         TCGA-HJ-7597         TCGA-IN-7806 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-IN-7808         TCGA-IP-7968 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
  "16P LOSS MUTATED" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-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-BR-8592         TCGA-BR-A4IU         TCGA-BR-A4IV 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BR-A4IY         TCGA-BR-A4IZ         TCGA-BR-A4J1 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BR-A4J2         TCGA-BR-A4J4         TCGA-BR-A4J5 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BR-A4J6         TCGA-BR-A4J8         TCGA-BR-A4J9 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BR-A4PF         TCGA-CD-5798         TCGA-CD-5799 
  "16P LOSS MUTATED" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-CD-5800         TCGA-CD-5801         TCGA-CD-5802 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-CD-5803         TCGA-CG-4300         TCGA-CG-4301 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-CG-4304         TCGA-CG-4305         TCGA-CG-4306 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-CG-4436         TCGA-CG-4437         TCGA-CG-4438 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-CG-4440         TCGA-CG-4441         TCGA-CG-4443 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE"   "16P LOSS MUTATED" 
        TCGA-CG-4444         TCGA-CG-4449         TCGA-CG-4455 
"16P LOSS WILD-TYPE"   "16P LOSS MUTATED" "16P LOSS WILD-TYPE" 
        TCGA-CG-4460         TCGA-CG-4462         TCGA-CG-4465 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-CG-4466         TCGA-CG-4469         TCGA-CG-4472 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-CG-4474         TCGA-CG-4477         TCGA-CG-5716 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-CG-5717         TCGA-CG-5718         TCGA-CG-5719 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-CG-5720         TCGA-CG-5721         TCGA-CG-5722 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-CG-5723         TCGA-CG-5724         TCGA-CG-5725 
"16P LOSS WILD-TYPE"   "16P LOSS MUTATED" "16P LOSS WILD-TYPE" 
        TCGA-CG-5726         TCGA-CG-5727         TCGA-CG-5728 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-CG-5730         TCGA-CG-5732         TCGA-CG-5733 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-CG-5734         TCGA-D7-5577         TCGA-D7-5578 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-D7-5579         TCGA-D7-6518         TCGA-D7-6519 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE"   "16P LOSS MUTATED" 
        TCGA-D7-6520         TCGA-D7-6521         TCGA-D7-6522 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-D7-6524         TCGA-D7-6525         TCGA-D7-6526 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-D7-6527         TCGA-D7-6528         TCGA-D7-6815 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-D7-6817         TCGA-D7-6818         TCGA-D7-6820 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-D7-6822         TCGA-EQ-5647         TCGA-EQ-8122 
  "16P LOSS MUTATED" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-F1-6177         TCGA-F1-6874         TCGA-F1-6875 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-FP-7735         TCGA-FP-7829         TCGA-FP-7916 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-FP-7998         TCGA-FP-8099         TCGA-FP-8209 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-FP-8631         TCGA-HJ-7597         TCGA-IN-7806 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-IN-7808         TCGA-IP-7968 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
[1] "hr=" "1.7"
D63V2, continuous
D63V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED      2    9
  16P LOSS WILD-TYPE   68   98
        clus
vv       16P LOSS MUTATED 16P LOSS WILD-TYPE
  FEMALE                2                 68
  MALE                  9                 98
                    vv
clus                 STOMACH ADENOCARCINOMA - DIFFUSE TYPE
  16P LOSS MUTATED                                       2
  16P LOSS WILD-TYPE                                    23
                    vv
clus                 STOMACH ADENOCARCINOMA - NOT OTHERWISE SPECIFIED (NOS)
  16P LOSS MUTATED                                                        4
  16P LOSS WILD-TYPE                                                     83
                    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                                                   2
  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                                                                     35
D63V4, multiclass
                    vv
clus                 T1 T2 T3 T4
  16P LOSS MUTATED    1  5  3  1
  16P LOSS WILD-TYPE  5 49 61 42
D63V5, multiclass
    clus
vv   16P LOSS MUTATED 16P LOSS WILD-TYPE
  T1                1                  5
  T2                5                 49
  T3                3                 61
  T4                1                 42
                    vv
clus                 N0 N1 N2 N3
  16P LOSS MUTATED    3  3  1  2
  16P LOSS WILD-TYPE 53 58 28 18
D63V6, multiclass
    clus
vv   16P LOSS MUTATED 16P LOSS WILD-TYPE
  N0                3                 53
  N1                3                 58
  N2                1                 28
  N3                2                 18
                    vv
clus                  M0  M1  MX
  16P LOSS MUTATED    10   1   0
  16P LOSS WILD-TYPE 136  17  13
D63V7, multiclass
    clus
vv   16P LOSS MUTATED 16P LOSS WILD-TYPE
  M0               10                136
  M1                1                 17
  MX                0                 13
                    vv
clus                  I II III IV
  16P LOSS MUTATED    2  2   3  2
  16P LOSS WILD-TYPE 24 46  55 27
D63V8, multiclass
     clus
vv    16P LOSS MUTATED 16P LOSS WILD-TYPE
  I                  2                 24
  II                 2                 46
  III                3                 55
  IV                 2                 27
D63V9, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED      1   10
  16P LOSS WILD-TYPE    4  162
     clus
vv    16P LOSS MUTATED 16P LOSS WILD-TYPE
  NO                 1                  4
  YES               10                162
                    vv
clus                  R0  R1  R2  RX
  16P LOSS MUTATED     6   2   1   2
  16P LOSS WILD-TYPE 117   5  11  23
D63V10, multiclass
    clus
vv   16P LOSS MUTATED 16P LOSS WILD-TYPE
  R0                6                117
  R1                2                  5
  R2                1                 11
  RX                2                 23
D63V11, continuous

Clustering(64) Variable = 16q loss mutation analysis
D64V1, survival
                    sevent
clus2                  0   1
  16Q LOSS MUTATED     9   1
  16Q LOSS WILD-TYPE 113  17
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                10                130 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                 1                 17 
$`16Q LOSS MUTATED`
TCGA-BR-7715 TCGA-BR-A4PF TCGA-CD-5802 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4477 
        1.05         0.72         0.30        29.98        19.07         1.02 
TCGA-CG-5724 TCGA-D7-6519 TCGA-D7-6817 TCGA-EQ-8122 
       12.03        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-BR-8592 
        0.26         1.18         1.55         1.48         0.76         0.20 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
        0.59         0.92         0.39         0.79         0.72         0.79 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-CD-5798 
        0.53         0.43         0.13         0.23         0.10         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-FP-8099 TCGA-FP-8209 TCGA-FP-8631 
        0.20         3.02         3.58         1.02        59.05         0.56 
TCGA-HJ-7597 TCGA-IN-7806 TCGA-IN-7808 TCGA-IP-7968 
       26.43         6.87         3.55         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 
             6.245              1.220 
[1] "0.3 - 30.0 (6.2)" "0.1 - 72.2 (1.2)"
        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-BR-8592         TCGA-BR-A4IU         TCGA-BR-A4IV 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BR-A4IY         TCGA-BR-A4IZ         TCGA-BR-A4J1 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BR-A4J2         TCGA-BR-A4J4         TCGA-BR-A4J5 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BR-A4J6         TCGA-BR-A4J8         TCGA-BR-A4J9 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BR-A4PF         TCGA-CD-5798         TCGA-CD-5799 
  "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CD-5800         TCGA-CD-5801         TCGA-CD-5802 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" 
        TCGA-CD-5803         TCGA-CG-4300         TCGA-CG-4301 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CG-4304         TCGA-CG-4305         TCGA-CG-4306 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CG-4436         TCGA-CG-4437         TCGA-CG-4438 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CG-4440         TCGA-CG-4441         TCGA-CG-4443 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" 
        TCGA-CG-4444         TCGA-CG-4449         TCGA-CG-4455 
"16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" 
        TCGA-CG-4460         TCGA-CG-4462         TCGA-CG-4465 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CG-4466         TCGA-CG-4469         TCGA-CG-4472 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CG-4474         TCGA-CG-4477         TCGA-CG-5716 
"16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" 
        TCGA-CG-5717         TCGA-CG-5718         TCGA-CG-5719 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CG-5720         TCGA-CG-5721         TCGA-CG-5722 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CG-5723         TCGA-CG-5724         TCGA-CG-5725 
"16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" 
        TCGA-CG-5726         TCGA-CG-5727         TCGA-CG-5728 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CG-5730         TCGA-CG-5732         TCGA-CG-5733 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CG-5734         TCGA-D7-5577         TCGA-D7-5578 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-D7-5579         TCGA-D7-6518         TCGA-D7-6519 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" 
        TCGA-D7-6520         TCGA-D7-6521         TCGA-D7-6522 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-D7-6524         TCGA-D7-6525         TCGA-D7-6526 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-D7-6527         TCGA-D7-6528         TCGA-D7-6815 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-D7-6817         TCGA-D7-6818         TCGA-D7-6820 
  "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-D7-6822         TCGA-EQ-5647         TCGA-EQ-8122 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" 
        TCGA-F1-6177         TCGA-F1-6874         TCGA-F1-6875 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-FP-7735         TCGA-FP-7829         TCGA-FP-7916 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-FP-7998         TCGA-FP-8099         TCGA-FP-8209 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-FP-8631         TCGA-HJ-7597         TCGA-IN-7806 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-IN-7808         TCGA-IP-7968 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
  "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-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-BR-8592         TCGA-BR-A4IU         TCGA-BR-A4IV 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BR-A4IY         TCGA-BR-A4IZ         TCGA-BR-A4J1 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BR-A4J2         TCGA-BR-A4J4         TCGA-BR-A4J5 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BR-A4J6         TCGA-BR-A4J8         TCGA-BR-A4J9 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BR-A4PF         TCGA-CD-5798         TCGA-CD-5799 
  "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CD-5800         TCGA-CD-5801         TCGA-CD-5802 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" 
        TCGA-CD-5803         TCGA-CG-4300         TCGA-CG-4301 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CG-4304         TCGA-CG-4305         TCGA-CG-4306 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CG-4436         TCGA-CG-4437         TCGA-CG-4438 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CG-4440         TCGA-CG-4441         TCGA-CG-4443 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" 
        TCGA-CG-4444         TCGA-CG-4449         TCGA-CG-4455 
"16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" 
        TCGA-CG-4460         TCGA-CG-4462         TCGA-CG-4465 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CG-4466         TCGA-CG-4469         TCGA-CG-4472 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CG-4474         TCGA-CG-4477         TCGA-CG-5716 
"16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" 
        TCGA-CG-5717         TCGA-CG-5718         TCGA-CG-5719 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CG-5720         TCGA-CG-5721         TCGA-CG-5722 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CG-5723         TCGA-CG-5724         TCGA-CG-5725 
"16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" 
        TCGA-CG-5726         TCGA-CG-5727         TCGA-CG-5728 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CG-5730         TCGA-CG-5732         TCGA-CG-5733 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CG-5734         TCGA-D7-5577         TCGA-D7-5578 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-D7-5579         TCGA-D7-6518         TCGA-D7-6519 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" 
        TCGA-D7-6520         TCGA-D7-6521         TCGA-D7-6522 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-D7-6524         TCGA-D7-6525         TCGA-D7-6526 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-D7-6527         TCGA-D7-6528         TCGA-D7-6815 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-D7-6817         TCGA-D7-6818         TCGA-D7-6820 
  "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-D7-6822         TCGA-EQ-5647         TCGA-EQ-8122 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" 
        TCGA-F1-6177         TCGA-F1-6874         TCGA-F1-6875 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-FP-7735         TCGA-FP-7829         TCGA-FP-7916 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-FP-7998         TCGA-FP-8099         TCGA-FP-8209 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-FP-8631         TCGA-HJ-7597         TCGA-IN-7806 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-IN-7808         TCGA-IP-7968 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
  "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-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-BR-8592         TCGA-BR-A4IU         TCGA-BR-A4IV 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BR-A4IY         TCGA-BR-A4IZ         TCGA-BR-A4J1 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BR-A4J2         TCGA-BR-A4J4         TCGA-BR-A4J5 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BR-A4J6         TCGA-BR-A4J8         TCGA-BR-A4J9 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BR-A4PF         TCGA-CD-5798         TCGA-CD-5799 
  "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CD-5800         TCGA-CD-5801         TCGA-CD-5802 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" 
        TCGA-CD-5803         TCGA-CG-4300         TCGA-CG-4301 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CG-4304         TCGA-CG-4305         TCGA-CG-4306 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CG-4436         TCGA-CG-4437         TCGA-CG-4438 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CG-4440         TCGA-CG-4441         TCGA-CG-4443 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" 
        TCGA-CG-4444         TCGA-CG-4449         TCGA-CG-4455 
"16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" 
        TCGA-CG-4460         TCGA-CG-4462         TCGA-CG-4465 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CG-4466         TCGA-CG-4469         TCGA-CG-4472 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CG-4474         TCGA-CG-4477         TCGA-CG-5716 
"16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" 
        TCGA-CG-5717         TCGA-CG-5718         TCGA-CG-5719 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CG-5720         TCGA-CG-5721         TCGA-CG-5722 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CG-5723         TCGA-CG-5724         TCGA-CG-5725 
"16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" 
        TCGA-CG-5726         TCGA-CG-5727         TCGA-CG-5728 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CG-5730         TCGA-CG-5732         TCGA-CG-5733 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CG-5734         TCGA-D7-5577         TCGA-D7-5578 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-D7-5579         TCGA-D7-6518         TCGA-D7-6519 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" 
        TCGA-D7-6520         TCGA-D7-6521         TCGA-D7-6522 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-D7-6524         TCGA-D7-6525         TCGA-D7-6526 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-D7-6527         TCGA-D7-6528         TCGA-D7-6815 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-D7-6817         TCGA-D7-6818         TCGA-D7-6820 
  "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-D7-6822         TCGA-EQ-5647         TCGA-EQ-8122 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" 
        TCGA-F1-6177         TCGA-F1-6874         TCGA-F1-6875 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-FP-7735         TCGA-FP-7829         TCGA-FP-7916 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-FP-7998         TCGA-FP-8099         TCGA-FP-8209 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-FP-8631         TCGA-HJ-7597         TCGA-IN-7806 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-IN-7808         TCGA-IP-7968 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
[1] "hr=" "1.9"
D64V2, continuous
D64V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED      4   11
  16Q LOSS WILD-TYPE   66   96
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  FEMALE                4                 66
  MALE                 11                 96
                    vv
clus                 STOMACH ADENOCARCINOMA - DIFFUSE TYPE
  16Q LOSS MUTATED                                       2
  16Q LOSS WILD-TYPE                                    23
                    vv
clus                 STOMACH ADENOCARCINOMA - NOT OTHERWISE SPECIFIED (NOS)
  16Q LOSS MUTATED                                                        5
  16Q LOSS WILD-TYPE                                                     82
                    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                                                 8
                    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                                                                     33
D64V4, multiclass
                    vv
clus                 T1 T2 T3 T4
  16Q LOSS MUTATED    1  6  6  1
  16Q LOSS WILD-TYPE  5 48 58 42
D64V5, multiclass
    clus
vv   16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  T1                1                  5
  T2                6                 48
  T3                6                 58
  T4                1                 42
                    vv
clus                 N0 N1 N2 N3
  16Q LOSS MUTATED    4  5  1  3
  16Q LOSS WILD-TYPE 52 56 28 17
D64V6, multiclass
    clus
vv   16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  N0                4                 52
  N1                5                 56
  N2                1                 28
  N3                3                 17
                    vv
clus                  M0  M1  MX
  16Q LOSS MUTATED    13   1   1
  16Q LOSS WILD-TYPE 133  17  12
D64V7, multiclass
    clus
vv   16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  M0               13                133
  M1                1                 17
  MX                1                 12
                    vv
clus                  I II III IV
  16Q LOSS MUTATED    2  5   4  2
  16Q LOSS WILD-TYPE 24 43  54 27
D64V8, multiclass
     clus
vv    16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  I                  2                 24
  II                 5                 43
  III                4                 54
  IV                 2                 27
D64V9, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED      1   14
  16Q LOSS WILD-TYPE    4  158
     clus
vv    16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  NO                 1                  4
  YES               14                158
                    vv
clus                  R0  R1  R2  RX
  16Q LOSS MUTATED     8   2   1   2
  16Q LOSS WILD-TYPE 115   5  11  23
D64V10, multiclass
    clus
vv   16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  R0                8                115
  R1                2                  5
  R2                1                 11
  RX                2                 23
D64V11, continuous

Clustering(65) Variable = 17p loss mutation analysis
D65V1, survival
                    sevent
clus2                  0   1
  17P LOSS MUTATED    22   4
  17P LOSS WILD-TYPE 100  14
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                26                114 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                 4                 14 
$`17P LOSS MUTATED`
TCGA-B7-5818 TCGA-BR-7197 TCGA-BR-7715 TCGA-BR-A4J1 TCGA-CD-5799 TCGA-CG-4300 
        0.10         1.48         1.05         0.72         0.69        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-D7-6526 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6820 TCGA-FP-8099 
        9.63         6.61         1.68         3.65         2.93         1.02 
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-BR-8592 TCGA-BR-A4IU TCGA-BR-A4IV 
        1.55         1.48         0.76         0.20         0.59         0.92 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
        0.39         0.79         0.79         0.53         0.43         0.13 
TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PF TCGA-CD-5798 TCGA-CD-5800 TCGA-CD-5801 
        0.23         0.10         0.72         0.82         0.36         0.49 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4441 
        0.30         0.07        15.95         1.02        52.96        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-4472 TCGA-CG-4474 TCGA-CG-5716 TCGA-CG-5717 TCGA-CG-5718 
       18.94        12.00         1.02         1.02         6.94         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 
        0.99         5.98         0.95        70.06        12.03        28.96 
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-D7-6519 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-D7-6527 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6822 TCGA-EQ-5647 
        5.95         4.14         4.70         4.04         4.27         0.62 
TCGA-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-FP-8209 TCGA-FP-8631 TCGA-HJ-7597 TCGA-IN-7808 
        3.02         3.58        59.05         0.56        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 
              3.83               1.02 
[1] "0.1 - 54.0 (3.8)" "0.1 - 72.2 (1.0)"
        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-BR-8592         TCGA-BR-A4IU         TCGA-BR-A4IV 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-BR-A4IY         TCGA-BR-A4IZ         TCGA-BR-A4J1 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-BR-A4J2         TCGA-BR-A4J4         TCGA-BR-A4J5 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-BR-A4J6         TCGA-BR-A4J8         TCGA-BR-A4J9 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-BR-A4PF         TCGA-CD-5798         TCGA-CD-5799 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-CD-5800         TCGA-CD-5801         TCGA-CD-5802 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-CD-5803         TCGA-CG-4300         TCGA-CG-4301 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED"   "17P LOSS MUTATED" 
        TCGA-CG-4304         TCGA-CG-4305         TCGA-CG-4306 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-CG-4436         TCGA-CG-4437         TCGA-CG-4438 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED"   "17P LOSS MUTATED" 
        TCGA-CG-4440         TCGA-CG-4441         TCGA-CG-4443 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-CG-4444         TCGA-CG-4449         TCGA-CG-4455 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-CG-4460         TCGA-CG-4462         TCGA-CG-4465 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-CG-4466         TCGA-CG-4469         TCGA-CG-4472 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-CG-4474         TCGA-CG-4477         TCGA-CG-5716 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-CG-5717         TCGA-CG-5718         TCGA-CG-5719 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-CG-5720         TCGA-CG-5721         TCGA-CG-5722 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-CG-5723         TCGA-CG-5724         TCGA-CG-5725 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-CG-5726         TCGA-CG-5727         TCGA-CG-5728 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-CG-5730         TCGA-CG-5732         TCGA-CG-5733 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-CG-5734         TCGA-D7-5577         TCGA-D7-5578 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-D7-5579         TCGA-D7-6518         TCGA-D7-6519 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-D7-6520         TCGA-D7-6521         TCGA-D7-6522 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-D7-6524         TCGA-D7-6525         TCGA-D7-6526 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-D7-6527         TCGA-D7-6528         TCGA-D7-6815 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED"   "17P LOSS MUTATED" 
        TCGA-D7-6817         TCGA-D7-6818         TCGA-D7-6820 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-D7-6822         TCGA-EQ-5647         TCGA-EQ-8122 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-F1-6177         TCGA-F1-6874         TCGA-F1-6875 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-FP-7735         TCGA-FP-7829         TCGA-FP-7916 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-FP-7998         TCGA-FP-8099         TCGA-FP-8209 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-FP-8631         TCGA-HJ-7597         TCGA-IN-7806 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-IN-7808         TCGA-IP-7968 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-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-BR-8592         TCGA-BR-A4IU         TCGA-BR-A4IV 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-BR-A4IY         TCGA-BR-A4IZ         TCGA-BR-A4J1 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-BR-A4J2         TCGA-BR-A4J4         TCGA-BR-A4J5 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-BR-A4J6         TCGA-BR-A4J8         TCGA-BR-A4J9 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-BR-A4PF         TCGA-CD-5798         TCGA-CD-5799 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-CD-5800         TCGA-CD-5801         TCGA-CD-5802 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-CD-5803         TCGA-CG-4300         TCGA-CG-4301 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED"   "17P LOSS MUTATED" 
        TCGA-CG-4304         TCGA-CG-4305         TCGA-CG-4306 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-CG-4436         TCGA-CG-4437         TCGA-CG-4438 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED"   "17P LOSS MUTATED" 
        TCGA-CG-4440         TCGA-CG-4441         TCGA-CG-4443 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-CG-4444         TCGA-CG-4449         TCGA-CG-4455 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-CG-4460         TCGA-CG-4462         TCGA-CG-4465 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-CG-4466         TCGA-CG-4469         TCGA-CG-4472 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-CG-4474         TCGA-CG-4477         TCGA-CG-5716 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-CG-5717         TCGA-CG-5718         TCGA-CG-5719 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-CG-5720         TCGA-CG-5721         TCGA-CG-5722 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-CG-5723         TCGA-CG-5724         TCGA-CG-5725 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-CG-5726         TCGA-CG-5727         TCGA-CG-5728 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-CG-5730         TCGA-CG-5732         TCGA-CG-5733 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-CG-5734         TCGA-D7-5577         TCGA-D7-5578 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-D7-5579         TCGA-D7-6518         TCGA-D7-6519 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-D7-6520         TCGA-D7-6521         TCGA-D7-6522 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-D7-6524         TCGA-D7-6525         TCGA-D7-6526 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-D7-6527         TCGA-D7-6528         TCGA-D7-6815 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED"   "17P LOSS MUTATED" 
        TCGA-D7-6817         TCGA-D7-6818         TCGA-D7-6820 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-D7-6822         TCGA-EQ-5647         TCGA-EQ-8122 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-F1-6177         TCGA-F1-6874         TCGA-F1-6875 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-FP-7735         TCGA-FP-7829         TCGA-FP-7916 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-FP-7998         TCGA-FP-8099         TCGA-FP-8209 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-FP-8631         TCGA-HJ-7597         TCGA-IN-7806 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-IN-7808         TCGA-IP-7968 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-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-BR-8592         TCGA-BR-A4IU         TCGA-BR-A4IV 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-BR-A4IY         TCGA-BR-A4IZ         TCGA-BR-A4J1 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-BR-A4J2         TCGA-BR-A4J4         TCGA-BR-A4J5 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-BR-A4J6         TCGA-BR-A4J8         TCGA-BR-A4J9 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-BR-A4PF         TCGA-CD-5798         TCGA-CD-5799 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-CD-5800         TCGA-CD-5801         TCGA-CD-5802 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-CD-5803         TCGA-CG-4300         TCGA-CG-4301 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED"   "17P LOSS MUTATED" 
        TCGA-CG-4304         TCGA-CG-4305         TCGA-CG-4306 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-CG-4436         TCGA-CG-4437         TCGA-CG-4438 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED"   "17P LOSS MUTATED" 
        TCGA-CG-4440         TCGA-CG-4441         TCGA-CG-4443 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-CG-4444         TCGA-CG-4449         TCGA-CG-4455 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-CG-4460         TCGA-CG-4462         TCGA-CG-4465 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-CG-4466         TCGA-CG-4469         TCGA-CG-4472 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-CG-4474         TCGA-CG-4477         TCGA-CG-5716 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-CG-5717         TCGA-CG-5718         TCGA-CG-5719 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-CG-5720         TCGA-CG-5721         TCGA-CG-5722 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-CG-5723         TCGA-CG-5724         TCGA-CG-5725 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-CG-5726         TCGA-CG-5727         TCGA-CG-5728 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-CG-5730         TCGA-CG-5732         TCGA-CG-5733 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-CG-5734         TCGA-D7-5577         TCGA-D7-5578 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-D7-5579         TCGA-D7-6518         TCGA-D7-6519 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-D7-6520         TCGA-D7-6521         TCGA-D7-6522 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-D7-6524         TCGA-D7-6525         TCGA-D7-6526 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-D7-6527         TCGA-D7-6528         TCGA-D7-6815 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED"   "17P LOSS MUTATED" 
        TCGA-D7-6817         TCGA-D7-6818         TCGA-D7-6820 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-D7-6822         TCGA-EQ-5647         TCGA-EQ-8122 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-F1-6177         TCGA-F1-6874         TCGA-F1-6875 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-FP-7735         TCGA-FP-7829         TCGA-FP-7916 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-FP-7998         TCGA-FP-8099         TCGA-FP-8209 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-FP-8631         TCGA-HJ-7597         TCGA-IN-7806 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-IN-7808         TCGA-IP-7968 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
[1] "hr=" "1.1"
D65V2, continuous
D65V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED     10   22
  17P LOSS WILD-TYPE   60   85
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  FEMALE               10                 60
  MALE                 22                 85
                    vv
clus                 STOMACH ADENOCARCINOMA - DIFFUSE TYPE
  17P LOSS MUTATED                                       2
  17P LOSS WILD-TYPE                                    23
                    vv
clus                 STOMACH ADENOCARCINOMA - NOT OTHERWISE SPECIFIED (NOS)
  17P LOSS MUTATED                                                       12
  17P LOSS WILD-TYPE                                                     75
                    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                                                 8
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - PAPILLARY TYPE
  17P LOSS MUTATED                                                    0
  17P LOSS WILD-TYPE                                                  3
                    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                                                                     26
D65V4, multiclass
                    vv
clus                 T1 T2 T3 T4
  17P LOSS MUTATED    1 16 11  4
  17P LOSS WILD-TYPE  5 38 53 39
D65V5, multiclass
    clus
vv   17P LOSS MUTATED 17P LOSS WILD-TYPE
  T1                1                  5
  T2               16                 38
  T3               11                 53
  T4                4                 39
                    vv
clus                 N0 N1 N2 N3
  17P LOSS MUTATED   13  9  6  3
  17P LOSS WILD-TYPE 43 52 23 17
D65V6, multiclass
    clus
vv   17P LOSS MUTATED 17P LOSS WILD-TYPE
  N0               13                 43
  N1                9                 52
  N2                6                 23
  N3                3                 17
                    vv
clus                  M0  M1  MX
  17P LOSS MUTATED    25   4   3
  17P LOSS WILD-TYPE 121  14  10
D65V7, multiclass
    clus
vv   17P LOSS MUTATED 17P LOSS WILD-TYPE
  M0               25                121
  M1                4                 14
  MX                3                 10
                    vv
clus                  I II III IV
  17P LOSS MUTATED    8  8   8  7
  17P LOSS WILD-TYPE 18 40  50 22
D65V8, multiclass
     clus
vv    17P LOSS MUTATED 17P LOSS WILD-TYPE
  I                  8                 18
  II                 8                 40
  III                8                 50
  IV                 7                 22
D65V9, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED      3   29
  17P LOSS WILD-TYPE    2  143
     clus
vv    17P LOSS MUTATED 17P LOSS WILD-TYPE
  NO                 3                  2
  YES               29                143
                    vv
clus                  R0  R1  R2  RX
  17P LOSS MUTATED    22   3   3   2
  17P LOSS WILD-TYPE 101   4   9  23
D65V10, multiclass
    clus
vv   17P LOSS MUTATED 17P LOSS WILD-TYPE
  R0               22                101
  R1                3                  4
  R2                3                  9
  RX                2                 23
D65V11, continuous

Clustering(66) Variable = 17q loss mutation analysis
D66V1, survival
                    sevent
clus2                  0   1
  17Q LOSS MUTATED     7   2
  17Q LOSS WILD-TYPE 115  16
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                 9                131 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                 2                 16 
$`17Q LOSS MUTATED`
TCGA-BR-A4J1 TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4477 
        0.72        20.02         3.02        54.05         4.01         1.02 
TCGA-D7-6526 TCGA-D7-6820 TCGA-FP-8099 
        6.61         2.93         1.02 

$`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-BR-8592 TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J2 
        0.20         0.59         0.92         0.39         0.79         0.79 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PF 
        0.53         0.43         0.13         0.23         0.10         0.72 
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-FP-8209 
       72.23         0.39         0.20         3.02         3.58        59.05 
TCGA-FP-8631 TCGA-HJ-7597 TCGA-IN-7806 TCGA-IN-7808 TCGA-IP-7968 
        0.56        26.43         6.87         3.55         2.53 

  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
              0.72               0.07 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
             54.05              72.23 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
              3.02               1.22 
[1] "0.7 - 54.0 (3.0)" "0.1 - 72.2 (1.2)"
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-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-BR-8592         TCGA-BR-A4IU         TCGA-BR-A4IV 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-BR-A4IY         TCGA-BR-A4IZ         TCGA-BR-A4J1 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE"   "17Q LOSS MUTATED" 
        TCGA-BR-A4J2         TCGA-BR-A4J4         TCGA-BR-A4J5 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-BR-A4J6         TCGA-BR-A4J8         TCGA-BR-A4J9 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-BR-A4PF         TCGA-CD-5798         TCGA-CD-5799 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-CD-5800         TCGA-CD-5801         TCGA-CD-5802 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-CD-5803         TCGA-CG-4300         TCGA-CG-4301 
"17Q LOSS WILD-TYPE"   "17Q LOSS MUTATED"   "17Q LOSS MUTATED" 
        TCGA-CG-4304         TCGA-CG-4305         TCGA-CG-4306 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-CG-4436         TCGA-CG-4437         TCGA-CG-4438 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE"   "17Q LOSS MUTATED" 
        TCGA-CG-4440         TCGA-CG-4441         TCGA-CG-4443 
  "17Q LOSS MUTATED" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-CG-4444         TCGA-CG-4449         TCGA-CG-4455 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-CG-4460         TCGA-CG-4462         TCGA-CG-4465 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-CG-4466         TCGA-CG-4469         TCGA-CG-4472 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-CG-4474         TCGA-CG-4477         TCGA-CG-5716 
"17Q LOSS WILD-TYPE"   "17Q LOSS MUTATED" "17Q LOSS WILD-TYPE" 
        TCGA-CG-5717         TCGA-CG-5718         TCGA-CG-5719 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-CG-5720         TCGA-CG-5721         TCGA-CG-5722 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-CG-5723         TCGA-CG-5724         TCGA-CG-5725 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-CG-5726         TCGA-CG-5727         TCGA-CG-5728 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-CG-5730         TCGA-CG-5732         TCGA-CG-5733 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-CG-5734         TCGA-D7-5577         TCGA-D7-5578 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-D7-5579         TCGA-D7-6518         TCGA-D7-6519 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-D7-6520         TCGA-D7-6521         TCGA-D7-6522 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-D7-6524         TCGA-D7-6525         TCGA-D7-6526 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE"   "17Q LOSS MUTATED" 
        TCGA-D7-6527         TCGA-D7-6528         TCGA-D7-6815 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-D7-6817         TCGA-D7-6818         TCGA-D7-6820 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE"   "17Q LOSS MUTATED" 
        TCGA-D7-6822         TCGA-EQ-5647         TCGA-EQ-8122 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-F1-6177         TCGA-F1-6874         TCGA-F1-6875 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-FP-7735         TCGA-FP-7829         TCGA-FP-7916 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-FP-7998         TCGA-FP-8099         TCGA-FP-8209 
"17Q LOSS WILD-TYPE"   "17Q LOSS MUTATED" "17Q LOSS WILD-TYPE" 
        TCGA-FP-8631         TCGA-HJ-7597         TCGA-IN-7806 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-IN-7808         TCGA-IP-7968 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-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-BR-8592         TCGA-BR-A4IU         TCGA-BR-A4IV 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-BR-A4IY         TCGA-BR-A4IZ         TCGA-BR-A4J1 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE"   "17Q LOSS MUTATED" 
        TCGA-BR-A4J2         TCGA-BR-A4J4         TCGA-BR-A4J5 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-BR-A4J6         TCGA-BR-A4J8         TCGA-BR-A4J9 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-BR-A4PF         TCGA-CD-5798         TCGA-CD-5799 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-CD-5800         TCGA-CD-5801         TCGA-CD-5802 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-CD-5803         TCGA-CG-4300         TCGA-CG-4301 
"17Q LOSS WILD-TYPE"   "17Q LOSS MUTATED"   "17Q LOSS MUTATED" 
        TCGA-CG-4304         TCGA-CG-4305         TCGA-CG-4306 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-CG-4436         TCGA-CG-4437         TCGA-CG-4438 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE"   "17Q LOSS MUTATED" 
        TCGA-CG-4440         TCGA-CG-4441         TCGA-CG-4443 
  "17Q LOSS MUTATED" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-CG-4444         TCGA-CG-4449         TCGA-CG-4455 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-CG-4460         TCGA-CG-4462         TCGA-CG-4465 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-CG-4466         TCGA-CG-4469         TCGA-CG-4472 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-CG-4474         TCGA-CG-4477         TCGA-CG-5716 
"17Q LOSS WILD-TYPE"   "17Q LOSS MUTATED" "17Q LOSS WILD-TYPE" 
        TCGA-CG-5717         TCGA-CG-5718         TCGA-CG-5719 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-CG-5720         TCGA-CG-5721         TCGA-CG-5722 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-CG-5723         TCGA-CG-5724         TCGA-CG-5725 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-CG-5726         TCGA-CG-5727         TCGA-CG-5728 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-CG-5730         TCGA-CG-5732         TCGA-CG-5733 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-CG-5734         TCGA-D7-5577         TCGA-D7-5578 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-D7-5579         TCGA-D7-6518         TCGA-D7-6519 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-D7-6520         TCGA-D7-6521         TCGA-D7-6522 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-D7-6524         TCGA-D7-6525         TCGA-D7-6526 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE"   "17Q LOSS MUTATED" 
        TCGA-D7-6527         TCGA-D7-6528         TCGA-D7-6815 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-D7-6817         TCGA-D7-6818         TCGA-D7-6820 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE"   "17Q LOSS MUTATED" 
        TCGA-D7-6822         TCGA-EQ-5647         TCGA-EQ-8122 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-F1-6177         TCGA-F1-6874         TCGA-F1-6875 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-FP-7735         TCGA-FP-7829         TCGA-FP-7916 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-FP-7998         TCGA-FP-8099         TCGA-FP-8209 
"17Q LOSS WILD-TYPE"   "17Q LOSS MUTATED" "17Q LOSS WILD-TYPE" 
        TCGA-FP-8631         TCGA-HJ-7597         TCGA-IN-7806 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-IN-7808         TCGA-IP-7968 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-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-BR-8592         TCGA-BR-A4IU         TCGA-BR-A4IV 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-BR-A4IY         TCGA-BR-A4IZ         TCGA-BR-A4J1 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE"   "17Q LOSS MUTATED" 
        TCGA-BR-A4J2         TCGA-BR-A4J4         TCGA-BR-A4J5 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-BR-A4J6         TCGA-BR-A4J8         TCGA-BR-A4J9 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-BR-A4PF         TCGA-CD-5798         TCGA-CD-5799 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-CD-5800         TCGA-CD-5801         TCGA-CD-5802 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-CD-5803         TCGA-CG-4300         TCGA-CG-4301 
"17Q LOSS WILD-TYPE"   "17Q LOSS MUTATED"   "17Q LOSS MUTATED" 
        TCGA-CG-4304         TCGA-CG-4305         TCGA-CG-4306 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-CG-4436         TCGA-CG-4437         TCGA-CG-4438 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE"   "17Q LOSS MUTATED" 
        TCGA-CG-4440         TCGA-CG-4441         TCGA-CG-4443 
  "17Q LOSS MUTATED" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-CG-4444         TCGA-CG-4449         TCGA-CG-4455 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-CG-4460         TCGA-CG-4462         TCGA-CG-4465 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-CG-4466         TCGA-CG-4469         TCGA-CG-4472 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-CG-4474         TCGA-CG-4477         TCGA-CG-5716 
"17Q LOSS WILD-TYPE"   "17Q LOSS MUTATED" "17Q LOSS WILD-TYPE" 
        TCGA-CG-5717         TCGA-CG-5718         TCGA-CG-5719 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-CG-5720         TCGA-CG-5721         TCGA-CG-5722 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-CG-5723         TCGA-CG-5724         TCGA-CG-5725 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-CG-5726         TCGA-CG-5727         TCGA-CG-5728 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-CG-5730         TCGA-CG-5732         TCGA-CG-5733 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-CG-5734         TCGA-D7-5577         TCGA-D7-5578 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-D7-5579         TCGA-D7-6518         TCGA-D7-6519 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-D7-6520         TCGA-D7-6521         TCGA-D7-6522 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-D7-6524         TCGA-D7-6525         TCGA-D7-6526 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE"   "17Q LOSS MUTATED" 
        TCGA-D7-6527         TCGA-D7-6528         TCGA-D7-6815 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-D7-6817         TCGA-D7-6818         TCGA-D7-6820 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE"   "17Q LOSS MUTATED" 
        TCGA-D7-6822         TCGA-EQ-5647         TCGA-EQ-8122 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-F1-6177         TCGA-F1-6874         TCGA-F1-6875 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-FP-7735         TCGA-FP-7829         TCGA-FP-7916 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-FP-7998         TCGA-FP-8099         TCGA-FP-8209 
"17Q LOSS WILD-TYPE"   "17Q LOSS MUTATED" "17Q LOSS WILD-TYPE" 
        TCGA-FP-8631         TCGA-HJ-7597         TCGA-IN-7806 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-IN-7808         TCGA-IP-7968 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
[1] "hr=" "1.7"
D66V2, continuous
D66V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED      5    6
  17Q LOSS WILD-TYPE   65  101
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  FEMALE                5                 65
  MALE                  6                101
                    vv
clus                 STOMACH ADENOCARCINOMA - DIFFUSE TYPE
  17Q LOSS MUTATED                                       0
  17Q LOSS WILD-TYPE                                    25
                    vv
clus                 STOMACH ADENOCARCINOMA - NOT OTHERWISE SPECIFIED (NOS)
  17Q LOSS MUTATED                                                        5
  17Q LOSS WILD-TYPE                                                     82
                    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                                                10
                    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                                                                     33
D66V4, multiclass
                    vv
clus                 T1 T2 T3 T4
  17Q LOSS MUTATED    0  4  4  3
  17Q LOSS WILD-TYPE  6 50 60 40
D66V5, multiclass
    clus
vv   17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  T1                0                  6
  T2                4                 50
  T3                4                 60
  T4                3                 40
                    vv
clus                 N0 N1 N2 N3
  17Q LOSS MUTATED    3  3  3  1
  17Q LOSS WILD-TYPE 53 58 26 19
D66V6, multiclass
    clus
vv   17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  N0                3                 53
  N1                3                 58
  N2                3                 26
  N3                1                 19
                    vv
clus                  M0  M1  MX
  17Q LOSS MUTATED     7   2   2
  17Q LOSS WILD-TYPE 139  16  11
D66V7, multiclass
    clus
vv   17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  M0                7                139
  M1                2                 16
  MX                2                 11
                    vv
clus                  I II III IV
  17Q LOSS MUTATED    2  2   3  3
  17Q LOSS WILD-TYPE 24 46  55 26
D66V8, multiclass
     clus
vv    17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  I                  2                 24
  II                 2                 46
  III                3                 55
  IV                 3                 26
D66V9, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED      1   10
  17Q LOSS WILD-TYPE    4  162
     clus
vv    17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  NO                 1                  4
  YES               10                162
                    vv
clus                  R0  R1  R2  RX
  17Q LOSS MUTATED     8   0   2   1
  17Q LOSS WILD-TYPE 115   7  10  24
D66V10, multiclass
    clus
vv   17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  R0                8                115
  R1                0                  7
  R2                2                 10
  RX                1                 24
D66V11, continuous

Clustering(67) Variable = 18p loss mutation analysis
D67V1, survival
                    sevent
clus2                  0   1
  18P LOSS MUTATED     6   5
  18P LOSS WILD-TYPE 116  13
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                11                129 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                 5                 13 
$`18P LOSS MUTATED`
TCGA-BR-7723 TCGA-BR-A4IY TCGA-CG-4440 TCGA-CG-4449 TCGA-CG-4469 TCGA-CG-4477 
        4.54         0.39         4.01        19.07         7.07         1.02 
TCGA-D7-6519 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6875 TCGA-FP-8209 
       15.65         0.62         7.79        72.23        59.05 

$`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-BR-8592 
        0.26         1.18         1.55         1.48         0.76         0.20 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
        0.59         0.92         0.79         0.72         0.79         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PF TCGA-CD-5798 
        0.43         0.13         0.23         0.10         0.72         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-FP-8099 TCGA-FP-8631 TCGA-HJ-7597 
        0.20         3.02         3.58         1.02         0.56        26.43 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IP-7968 
        6.87         3.55         2.53 

  18P LOSS MUTATED 18P LOSS WILD-TYPE 
              0.39               0.07 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
             72.23              70.06 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
              7.07               1.18 
[1] "0.4 - 72.2 (7.1)" "0.1 - 70.1 (1.2)"
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"18P LOSS WILD-TYPE"   "18P LOSS MUTATED" "18P LOSS WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-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-BR-8592         TCGA-BR-A4IU         TCGA-BR-A4IV 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BR-A4IY         TCGA-BR-A4IZ         TCGA-BR-A4J1 
  "18P LOSS MUTATED" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BR-A4J2         TCGA-BR-A4J4         TCGA-BR-A4J5 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BR-A4J6         TCGA-BR-A4J8         TCGA-BR-A4J9 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BR-A4PF         TCGA-CD-5798         TCGA-CD-5799 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-CD-5800         TCGA-CD-5801         TCGA-CD-5802 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-CD-5803         TCGA-CG-4300         TCGA-CG-4301 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-CG-4304         TCGA-CG-4305         TCGA-CG-4306 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-CG-4436         TCGA-CG-4437         TCGA-CG-4438 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-CG-4440         TCGA-CG-4441         TCGA-CG-4443 
  "18P LOSS MUTATED" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-CG-4444         TCGA-CG-4449         TCGA-CG-4455 
"18P LOSS WILD-TYPE"   "18P LOSS MUTATED" "18P LOSS WILD-TYPE" 
        TCGA-CG-4460         TCGA-CG-4462         TCGA-CG-4465 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-CG-4466         TCGA-CG-4469         TCGA-CG-4472 
"18P LOSS WILD-TYPE"   "18P LOSS MUTATED" "18P LOSS WILD-TYPE" 
        TCGA-CG-4474         TCGA-CG-4477         TCGA-CG-5716 
"18P LOSS WILD-TYPE"   "18P LOSS MUTATED" "18P LOSS WILD-TYPE" 
        TCGA-CG-5717         TCGA-CG-5718         TCGA-CG-5719 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-CG-5720         TCGA-CG-5721         TCGA-CG-5722 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-CG-5723         TCGA-CG-5724         TCGA-CG-5725 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-CG-5726         TCGA-CG-5727         TCGA-CG-5728 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-CG-5730         TCGA-CG-5732         TCGA-CG-5733 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-CG-5734         TCGA-D7-5577         TCGA-D7-5578 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-D7-5579         TCGA-D7-6518         TCGA-D7-6519 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE"   "18P LOSS MUTATED" 
        TCGA-D7-6520         TCGA-D7-6521         TCGA-D7-6522 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-D7-6524         TCGA-D7-6525         TCGA-D7-6526 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-D7-6527         TCGA-D7-6528         TCGA-D7-6815 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-D7-6817         TCGA-D7-6818         TCGA-D7-6820 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-D7-6822         TCGA-EQ-5647         TCGA-EQ-8122 
"18P LOSS WILD-TYPE"   "18P LOSS MUTATED"   "18P LOSS MUTATED" 
        TCGA-F1-6177         TCGA-F1-6874         TCGA-F1-6875 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE"   "18P LOSS MUTATED" 
        TCGA-FP-7735         TCGA-FP-7829         TCGA-FP-7916 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-FP-7998         TCGA-FP-8099         TCGA-FP-8209 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE"   "18P LOSS MUTATED" 
        TCGA-FP-8631         TCGA-HJ-7597         TCGA-IN-7806 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-IN-7808         TCGA-IP-7968 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"18P LOSS WILD-TYPE"   "18P LOSS MUTATED" "18P LOSS WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-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-BR-8592         TCGA-BR-A4IU         TCGA-BR-A4IV 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BR-A4IY         TCGA-BR-A4IZ         TCGA-BR-A4J1 
  "18P LOSS MUTATED" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BR-A4J2         TCGA-BR-A4J4         TCGA-BR-A4J5 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BR-A4J6         TCGA-BR-A4J8         TCGA-BR-A4J9 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BR-A4PF         TCGA-CD-5798         TCGA-CD-5799 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-CD-5800         TCGA-CD-5801         TCGA-CD-5802 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-CD-5803         TCGA-CG-4300         TCGA-CG-4301 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-CG-4304         TCGA-CG-4305         TCGA-CG-4306 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-CG-4436         TCGA-CG-4437         TCGA-CG-4438 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-CG-4440         TCGA-CG-4441         TCGA-CG-4443 
  "18P LOSS MUTATED" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-CG-4444         TCGA-CG-4449         TCGA-CG-4455 
"18P LOSS WILD-TYPE"   "18P LOSS MUTATED" "18P LOSS WILD-TYPE" 
        TCGA-CG-4460         TCGA-CG-4462         TCGA-CG-4465 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-CG-4466         TCGA-CG-4469         TCGA-CG-4472 
"18P LOSS WILD-TYPE"   "18P LOSS MUTATED" "18P LOSS WILD-TYPE" 
        TCGA-CG-4474         TCGA-CG-4477         TCGA-CG-5716 
"18P LOSS WILD-TYPE"   "18P LOSS MUTATED" "18P LOSS WILD-TYPE" 
        TCGA-CG-5717         TCGA-CG-5718         TCGA-CG-5719 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-CG-5720         TCGA-CG-5721         TCGA-CG-5722 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-CG-5723         TCGA-CG-5724         TCGA-CG-5725 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-CG-5726         TCGA-CG-5727         TCGA-CG-5728 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-CG-5730         TCGA-CG-5732         TCGA-CG-5733 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-CG-5734         TCGA-D7-5577         TCGA-D7-5578 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-D7-5579         TCGA-D7-6518         TCGA-D7-6519 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE"   "18P LOSS MUTATED" 
        TCGA-D7-6520         TCGA-D7-6521         TCGA-D7-6522 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-D7-6524         TCGA-D7-6525         TCGA-D7-6526 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-D7-6527         TCGA-D7-6528         TCGA-D7-6815 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-D7-6817         TCGA-D7-6818         TCGA-D7-6820 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-D7-6822         TCGA-EQ-5647         TCGA-EQ-8122 
"18P LOSS WILD-TYPE"   "18P LOSS MUTATED"   "18P LOSS MUTATED" 
        TCGA-F1-6177         TCGA-F1-6874         TCGA-F1-6875 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE"   "18P LOSS MUTATED" 
        TCGA-FP-7735         TCGA-FP-7829         TCGA-FP-7916 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-FP-7998         TCGA-FP-8099         TCGA-FP-8209 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE"   "18P LOSS MUTATED" 
        TCGA-FP-8631         TCGA-HJ-7597         TCGA-IN-7806 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-IN-7808         TCGA-IP-7968 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"18P LOSS WILD-TYPE"   "18P LOSS MUTATED" "18P LOSS WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-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-BR-8592         TCGA-BR-A4IU         TCGA-BR-A4IV 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BR-A4IY         TCGA-BR-A4IZ         TCGA-BR-A4J1 
  "18P LOSS MUTATED" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BR-A4J2         TCGA-BR-A4J4         TCGA-BR-A4J5 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BR-A4J6         TCGA-BR-A4J8         TCGA-BR-A4J9 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BR-A4PF         TCGA-CD-5798         TCGA-CD-5799 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-CD-5800         TCGA-CD-5801         TCGA-CD-5802 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-CD-5803         TCGA-CG-4300         TCGA-CG-4301 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-CG-4304         TCGA-CG-4305         TCGA-CG-4306 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-CG-4436         TCGA-CG-4437         TCGA-CG-4438 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-CG-4440         TCGA-CG-4441         TCGA-CG-4443 
  "18P LOSS MUTATED" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-CG-4444         TCGA-CG-4449         TCGA-CG-4455 
"18P LOSS WILD-TYPE"   "18P LOSS MUTATED" "18P LOSS WILD-TYPE" 
        TCGA-CG-4460         TCGA-CG-4462         TCGA-CG-4465 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-CG-4466         TCGA-CG-4469         TCGA-CG-4472 
"18P LOSS WILD-TYPE"   "18P LOSS MUTATED" "18P LOSS WILD-TYPE" 
        TCGA-CG-4474         TCGA-CG-4477         TCGA-CG-5716 
"18P LOSS WILD-TYPE"   "18P LOSS MUTATED" "18P LOSS WILD-TYPE" 
        TCGA-CG-5717         TCGA-CG-5718         TCGA-CG-5719 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-CG-5720         TCGA-CG-5721         TCGA-CG-5722 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-CG-5723         TCGA-CG-5724         TCGA-CG-5725 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-CG-5726         TCGA-CG-5727         TCGA-CG-5728 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-CG-5730         TCGA-CG-5732         TCGA-CG-5733 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-CG-5734         TCGA-D7-5577         TCGA-D7-5578 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-D7-5579         TCGA-D7-6518         TCGA-D7-6519 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE"   "18P LOSS MUTATED" 
        TCGA-D7-6520         TCGA-D7-6521         TCGA-D7-6522 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-D7-6524         TCGA-D7-6525         TCGA-D7-6526 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-D7-6527         TCGA-D7-6528         TCGA-D7-6815 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-D7-6817         TCGA-D7-6818         TCGA-D7-6820 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-D7-6822         TCGA-EQ-5647         TCGA-EQ-8122 
"18P LOSS WILD-TYPE"   "18P LOSS MUTATED"   "18P LOSS MUTATED" 
        TCGA-F1-6177         TCGA-F1-6874         TCGA-F1-6875 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE"   "18P LOSS MUTATED" 
        TCGA-FP-7735         TCGA-FP-7829         TCGA-FP-7916 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-FP-7998         TCGA-FP-8099         TCGA-FP-8209 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE"   "18P LOSS MUTATED" 
        TCGA-FP-8631         TCGA-HJ-7597         TCGA-IN-7806 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-IN-7808         TCGA-IP-7968 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
[1] "hr=" "1.6"
D67V2, continuous
D67V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED      5    9
  18P LOSS WILD-TYPE   65   98
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  FEMALE                5                 65
  MALE                  9                 98
                    vv
clus                 STOMACH ADENOCARCINOMA - DIFFUSE TYPE
  18P LOSS MUTATED                                       2
  18P LOSS WILD-TYPE                                    23
                    vv
clus                 STOMACH ADENOCARCINOMA - NOT OTHERWISE SPECIFIED (NOS)
  18P LOSS MUTATED                                                        6
  18P LOSS WILD-TYPE                                                     81
                    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                                                 9
                    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                                                                     32
D67V4, multiclass
                    vv
clus                 T1 T2 T3 T4
  18P LOSS MUTATED    0  7  4  2
  18P LOSS WILD-TYPE  6 47 60 41
D67V5, multiclass
    clus
vv   18P LOSS MUTATED 18P LOSS WILD-TYPE
  T1                0                  6
  T2                7                 47
  T3                4                 60
  T4                2                 41
                    vv
clus                 N0 N1 N2 N3
  18P LOSS MUTATED    4  4  1  3
  18P LOSS WILD-TYPE 52 57 28 17
D67V6, multiclass
    clus
vv   18P LOSS MUTATED 18P LOSS WILD-TYPE
  N0                4                 52
  N1                4                 57
  N2                1                 28
  N3                3                 17
                    vv
clus                  M0  M1  MX
  18P LOSS MUTATED    11   2   1
  18P LOSS WILD-TYPE 135  16  12
D67V7, multiclass
    clus
vv   18P LOSS MUTATED 18P LOSS WILD-TYPE
  M0               11                135
  M1                2                 16
  MX                1                 12
                    vv
clus                  I II III IV
  18P LOSS MUTATED    3  5   1  3
  18P LOSS WILD-TYPE 23 43  57 26
D67V8, multiclass
     clus
vv    18P LOSS MUTATED 18P LOSS WILD-TYPE
  I                  3                 23
  II                 5                 43
  III                1                 57
  IV                 3                 26
D67V9, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED      0   14
  18P LOSS WILD-TYPE    5  158
     clus
vv    18P LOSS MUTATED 18P LOSS WILD-TYPE
  NO                 0                  5
  YES               14                158
                    vv
clus                  R0  R1  R2  RX
  18P LOSS MUTATED     7   1   2   3
  18P LOSS WILD-TYPE 116   6  10  22
D67V10, multiclass
    clus
vv   18P LOSS MUTATED 18P LOSS WILD-TYPE
  R0                7                116
  R1                1                  6
  R2                2                 10
  RX                3                 22
D67V11, continuous

Clustering(68) Variable = 18q loss mutation analysis
D68V1, survival
                    sevent
clus2                  0   1
  18Q LOSS MUTATED    15   5
  18Q LOSS WILD-TYPE 107  13
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                20                120 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                 5                 13 
$`18Q LOSS MUTATED`
TCGA-B7-5818 TCGA-BR-7723 TCGA-BR-A4IY TCGA-BR-A4J6 TCGA-CD-5802 TCGA-CG-4301 
        0.10         4.54         0.39         0.13         0.30         3.02 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4449 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5724 
       54.05         4.01        19.07         7.07         1.02        12.03 
TCGA-CG-5730 TCGA-D7-5577 TCGA-D7-6519 TCGA-D7-6521 TCGA-EQ-5647 TCGA-EQ-8122 
        4.01         8.65        15.65         8.19         0.62         7.79 
TCGA-FP-7829 TCGA-FP-8209 
        0.20        59.05 

$`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-BR-8592 TCGA-BR-A4IU 
        1.18         1.55         1.48         0.76         0.20         0.59 
TCGA-BR-A4IV TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
        0.92         0.79         0.72         0.79         0.53         0.43 
TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PF TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
        0.23         0.10         0.72         0.82         0.69         0.36 
TCGA-CD-5801 TCGA-CD-5803 TCGA-CG-4300 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
        0.49         0.07        20.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4455 
       52.96         8.05        14.01        29.98        47.05        12.03 
TCGA-CG-4460 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4472 TCGA-CG-4474 
       21.99         1.02         8.98        18.94        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-5725 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 
        0.95        70.06        15.02        28.96        31.04        65.10 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       55.04        21.07         7.99         3.58         4.54         9.80 
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-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-FP-8099 TCGA-FP-8631 TCGA-HJ-7597 TCGA-IN-7806 TCGA-IN-7808 TCGA-IP-7968 
        1.02         0.56        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 
             59.05              72.23 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
             4.275              1.150 
[1] "0.1 - 59.0 (4.3)" "0.1 - 72.2 (1.1)"
        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-BR-8592         TCGA-BR-A4IU         TCGA-BR-A4IV 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BR-A4IY         TCGA-BR-A4IZ         TCGA-BR-A4J1 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BR-A4J2         TCGA-BR-A4J4         TCGA-BR-A4J5 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BR-A4J6         TCGA-BR-A4J8         TCGA-BR-A4J9 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BR-A4PF         TCGA-CD-5798         TCGA-CD-5799 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-CD-5800         TCGA-CD-5801         TCGA-CD-5802 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" 
        TCGA-CD-5803         TCGA-CG-4300         TCGA-CG-4301 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" 
        TCGA-CG-4304         TCGA-CG-4305         TCGA-CG-4306 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-CG-4436         TCGA-CG-4437         TCGA-CG-4438 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" 
        TCGA-CG-4440         TCGA-CG-4441         TCGA-CG-4443 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-CG-4444         TCGA-CG-4449         TCGA-CG-4455 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" 
        TCGA-CG-4460         TCGA-CG-4462         TCGA-CG-4465 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-CG-4466         TCGA-CG-4469         TCGA-CG-4472 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" 
        TCGA-CG-4474         TCGA-CG-4477         TCGA-CG-5716 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" 
        TCGA-CG-5717         TCGA-CG-5718         TCGA-CG-5719 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-CG-5720         TCGA-CG-5721         TCGA-CG-5722 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-CG-5723         TCGA-CG-5724         TCGA-CG-5725 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" 
        TCGA-CG-5726         TCGA-CG-5727         TCGA-CG-5728 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-CG-5730         TCGA-CG-5732         TCGA-CG-5733 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-CG-5734         TCGA-D7-5577         TCGA-D7-5578 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" 
        TCGA-D7-5579         TCGA-D7-6518         TCGA-D7-6519 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" 
        TCGA-D7-6520         TCGA-D7-6521         TCGA-D7-6522 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" 
        TCGA-D7-6524         TCGA-D7-6525         TCGA-D7-6526 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-D7-6527         TCGA-D7-6528         TCGA-D7-6815 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-D7-6817         TCGA-D7-6818         TCGA-D7-6820 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-D7-6822         TCGA-EQ-5647         TCGA-EQ-8122 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED"   "18Q LOSS MUTATED" 
        TCGA-F1-6177         TCGA-F1-6874         TCGA-F1-6875 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-FP-7735         TCGA-FP-7829         TCGA-FP-7916 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" 
        TCGA-FP-7998         TCGA-FP-8099         TCGA-FP-8209 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" 
        TCGA-FP-8631         TCGA-HJ-7597         TCGA-IN-7806 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-IN-7808         TCGA-IP-7968 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-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-BR-8592         TCGA-BR-A4IU         TCGA-BR-A4IV 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BR-A4IY         TCGA-BR-A4IZ         TCGA-BR-A4J1 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BR-A4J2         TCGA-BR-A4J4         TCGA-BR-A4J5 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BR-A4J6         TCGA-BR-A4J8         TCGA-BR-A4J9 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BR-A4PF         TCGA-CD-5798         TCGA-CD-5799 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-CD-5800         TCGA-CD-5801         TCGA-CD-5802 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" 
        TCGA-CD-5803         TCGA-CG-4300         TCGA-CG-4301 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" 
        TCGA-CG-4304         TCGA-CG-4305         TCGA-CG-4306 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-CG-4436         TCGA-CG-4437         TCGA-CG-4438 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" 
        TCGA-CG-4440         TCGA-CG-4441         TCGA-CG-4443 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-CG-4444         TCGA-CG-4449         TCGA-CG-4455 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" 
        TCGA-CG-4460         TCGA-CG-4462         TCGA-CG-4465 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-CG-4466         TCGA-CG-4469         TCGA-CG-4472 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" 
        TCGA-CG-4474         TCGA-CG-4477         TCGA-CG-5716 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" 
        TCGA-CG-5717         TCGA-CG-5718         TCGA-CG-5719 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-CG-5720         TCGA-CG-5721         TCGA-CG-5722 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-CG-5723         TCGA-CG-5724         TCGA-CG-5725 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" 
        TCGA-CG-5726         TCGA-CG-5727         TCGA-CG-5728 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-CG-5730         TCGA-CG-5732         TCGA-CG-5733 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-CG-5734         TCGA-D7-5577         TCGA-D7-5578 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" 
        TCGA-D7-5579         TCGA-D7-6518         TCGA-D7-6519 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" 
        TCGA-D7-6520         TCGA-D7-6521         TCGA-D7-6522 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" 
        TCGA-D7-6524         TCGA-D7-6525         TCGA-D7-6526 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-D7-6527         TCGA-D7-6528         TCGA-D7-6815 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-D7-6817         TCGA-D7-6818         TCGA-D7-6820 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-D7-6822         TCGA-EQ-5647         TCGA-EQ-8122 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED"   "18Q LOSS MUTATED" 
        TCGA-F1-6177         TCGA-F1-6874         TCGA-F1-6875 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-FP-7735         TCGA-FP-7829         TCGA-FP-7916 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" 
        TCGA-FP-7998         TCGA-FP-8099         TCGA-FP-8209 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" 
        TCGA-FP-8631         TCGA-HJ-7597         TCGA-IN-7806 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-IN-7808         TCGA-IP-7968 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-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-BR-8592         TCGA-BR-A4IU         TCGA-BR-A4IV 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BR-A4IY         TCGA-BR-A4IZ         TCGA-BR-A4J1 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BR-A4J2         TCGA-BR-A4J4         TCGA-BR-A4J5 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BR-A4J6         TCGA-BR-A4J8         TCGA-BR-A4J9 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BR-A4PF         TCGA-CD-5798         TCGA-CD-5799 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-CD-5800         TCGA-CD-5801         TCGA-CD-5802 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" 
        TCGA-CD-5803         TCGA-CG-4300         TCGA-CG-4301 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" 
        TCGA-CG-4304         TCGA-CG-4305         TCGA-CG-4306 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-CG-4436         TCGA-CG-4437         TCGA-CG-4438 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" 
        TCGA-CG-4440         TCGA-CG-4441         TCGA-CG-4443 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-CG-4444         TCGA-CG-4449         TCGA-CG-4455 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" 
        TCGA-CG-4460         TCGA-CG-4462         TCGA-CG-4465 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-CG-4466         TCGA-CG-4469         TCGA-CG-4472 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" 
        TCGA-CG-4474         TCGA-CG-4477         TCGA-CG-5716 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" 
        TCGA-CG-5717         TCGA-CG-5718         TCGA-CG-5719 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-CG-5720         TCGA-CG-5721         TCGA-CG-5722 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-CG-5723         TCGA-CG-5724         TCGA-CG-5725 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" 
        TCGA-CG-5726         TCGA-CG-5727         TCGA-CG-5728 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-CG-5730         TCGA-CG-5732         TCGA-CG-5733 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-CG-5734         TCGA-D7-5577         TCGA-D7-5578 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" 
        TCGA-D7-5579         TCGA-D7-6518         TCGA-D7-6519 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" 
        TCGA-D7-6520         TCGA-D7-6521         TCGA-D7-6522 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" 
        TCGA-D7-6524         TCGA-D7-6525         TCGA-D7-6526 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-D7-6527         TCGA-D7-6528         TCGA-D7-6815 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-D7-6817         TCGA-D7-6818         TCGA-D7-6820 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-D7-6822         TCGA-EQ-5647         TCGA-EQ-8122 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED"   "18Q LOSS MUTATED" 
        TCGA-F1-6177         TCGA-F1-6874         TCGA-F1-6875 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-FP-7735         TCGA-FP-7829         TCGA-FP-7916 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" 
        TCGA-FP-7998         TCGA-FP-8099         TCGA-FP-8209 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" 
        TCGA-FP-8631         TCGA-HJ-7597         TCGA-IN-7806 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-IN-7808         TCGA-IP-7968 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
[1] "hr=" "1.8"
D68V2, continuous
D68V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED      9   18
  18Q LOSS WILD-TYPE   61   89
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  FEMALE                9                 61
  MALE                 18                 89
                    vv
clus                 STOMACH ADENOCARCINOMA - DIFFUSE TYPE
  18Q LOSS MUTATED                                       5
  18Q LOSS WILD-TYPE                                    20
                    vv
clus                 STOMACH ADENOCARCINOMA - NOT OTHERWISE SPECIFIED (NOS)
  18Q LOSS MUTATED                                                       11
  18Q LOSS WILD-TYPE                                                     76
                    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                                                 8
                    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                                                                     30
D68V4, multiclass
                    vv
clus                 T1 T2 T3 T4
  18Q LOSS MUTATED    0 11 10  4
  18Q LOSS WILD-TYPE  6 43 54 39
D68V5, multiclass
    clus
vv   18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  T1                0                  6
  T2               11                 43
  T3               10                 54
  T4                4                 39
                    vv
clus                 N0 N1 N2 N3
  18Q LOSS MUTATED    7 10  3  5
  18Q LOSS WILD-TYPE 49 51 26 15
D68V6, multiclass
    clus
vv   18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  N0                7                 49
  N1               10                 51
  N2                3                 26
  N3                5                 15
                    vv
clus                  M0  M1  MX
  18Q LOSS MUTATED    21   5   1
  18Q LOSS WILD-TYPE 125  13  12
D68V7, multiclass
    clus
vv   18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  M0               21                125
  M1                5                 13
  MX                1                 12
                    vv
clus                  I II III IV
  18Q LOSS MUTATED    4  8   5  7
  18Q LOSS WILD-TYPE 22 40  53 22
D68V8, multiclass
     clus
vv    18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  I                  4                 22
  II                 8                 40
  III                5                 53
  IV                 7                 22
D68V9, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED      0   27
  18Q LOSS WILD-TYPE    5  145
     clus
vv    18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  NO                 0                  5
  YES               27                145
                    vv
clus                  R0  R1  R2  RX
  18Q LOSS MUTATED    13   2   5   5
  18Q LOSS WILD-TYPE 110   5   7  20
D68V10, multiclass
    clus
vv   18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  R0               13                110
  R1                2                  5
  R2                5                  7
  RX                5                 20
D68V11, continuous

Clustering(69) Variable = 19p loss mutation analysis
D69V1, survival
                    sevent
clus2                  0   1
  19P LOSS MUTATED    12   4
  19P LOSS WILD-TYPE 110  14
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                16                124 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                 4                 14 
$`19P LOSS MUTATED`
TCGA-BR-6458 TCGA-BR-6565 TCGA-BR-7723 TCGA-BR-A4J1 TCGA-CG-4436 TCGA-CG-4438 
        1.35         0.62         4.54         0.72        52.96        54.05 
TCGA-CG-4440 TCGA-CG-4443 TCGA-CG-4466 TCGA-CG-5725 TCGA-CG-5732 TCGA-D7-6520 
        4.01        29.98        18.94        15.02        55.04         9.63 
TCGA-D7-6525 TCGA-D7-6820 TCGA-EQ-5647 TCGA-FP-8631 
        5.95         2.93         0.62         0.56 

$`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-BR-8592 TCGA-BR-A4IU TCGA-BR-A4IV 
        1.55         1.48         0.76         0.20         0.59         0.92 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
        0.39         0.79         0.79         0.53         0.43         0.13 
TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PF TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
        0.23         0.10         0.72         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-FP-8099 TCGA-FP-8209 
        0.39         0.20         3.02         3.58         1.02        59.05 
TCGA-HJ-7597 TCGA-IN-7806 TCGA-IN-7808 TCGA-IP-7968 
       26.43         6.87         3.55         2.53 

  19P LOSS MUTATED 19P LOSS WILD-TYPE 
              0.56               0.07 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
             55.04              72.23 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
             5.245              1.100 
[1] "0.6 - 55.0 (5.2)" "0.1 - 72.2 (1.1)"
        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-BR-8592         TCGA-BR-A4IU         TCGA-BR-A4IV 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BR-A4IY         TCGA-BR-A4IZ         TCGA-BR-A4J1 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE"   "19P LOSS MUTATED" 
        TCGA-BR-A4J2         TCGA-BR-A4J4         TCGA-BR-A4J5 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BR-A4J6         TCGA-BR-A4J8         TCGA-BR-A4J9 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BR-A4PF         TCGA-CD-5798         TCGA-CD-5799 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-CD-5800         TCGA-CD-5801         TCGA-CD-5802 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-CD-5803         TCGA-CG-4300         TCGA-CG-4301 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-CG-4304         TCGA-CG-4305         TCGA-CG-4306 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-CG-4436         TCGA-CG-4437         TCGA-CG-4438 
  "19P LOSS MUTATED" "19P LOSS WILD-TYPE"   "19P LOSS MUTATED" 
        TCGA-CG-4440         TCGA-CG-4441         TCGA-CG-4443 
  "19P LOSS MUTATED" "19P LOSS WILD-TYPE"   "19P LOSS MUTATED" 
        TCGA-CG-4444         TCGA-CG-4449         TCGA-CG-4455 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-CG-4460         TCGA-CG-4462         TCGA-CG-4465 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-CG-4466         TCGA-CG-4469         TCGA-CG-4472 
  "19P LOSS MUTATED" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-CG-4474         TCGA-CG-4477         TCGA-CG-5716 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-CG-5717         TCGA-CG-5718         TCGA-CG-5719 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-CG-5720         TCGA-CG-5721         TCGA-CG-5722 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-CG-5723         TCGA-CG-5724         TCGA-CG-5725 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE"   "19P LOSS MUTATED" 
        TCGA-CG-5726         TCGA-CG-5727         TCGA-CG-5728 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-CG-5730         TCGA-CG-5732         TCGA-CG-5733 
"19P LOSS WILD-TYPE"   "19P LOSS MUTATED" "19P LOSS WILD-TYPE" 
        TCGA-CG-5734         TCGA-D7-5577         TCGA-D7-5578 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-D7-5579         TCGA-D7-6518         TCGA-D7-6519 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-D7-6520         TCGA-D7-6521         TCGA-D7-6522 
  "19P LOSS MUTATED" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-D7-6524         TCGA-D7-6525         TCGA-D7-6526 
"19P LOSS WILD-TYPE"   "19P LOSS MUTATED" "19P LOSS WILD-TYPE" 
        TCGA-D7-6527         TCGA-D7-6528         TCGA-D7-6815 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-D7-6817         TCGA-D7-6818         TCGA-D7-6820 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE"   "19P LOSS MUTATED" 
        TCGA-D7-6822         TCGA-EQ-5647         TCGA-EQ-8122 
"19P LOSS WILD-TYPE"   "19P LOSS MUTATED" "19P LOSS WILD-TYPE" 
        TCGA-F1-6177         TCGA-F1-6874         TCGA-F1-6875 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-FP-7735         TCGA-FP-7829         TCGA-FP-7916 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-FP-7998         TCGA-FP-8099         TCGA-FP-8209 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-FP-8631         TCGA-HJ-7597         TCGA-IN-7806 
  "19P LOSS MUTATED" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-IN-7808         TCGA-IP-7968 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE"   "19P LOSS MUTATED" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE"   "19P LOSS MUTATED" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"19P LOSS WILD-TYPE"   "19P LOSS MUTATED" "19P LOSS WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-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-BR-8592         TCGA-BR-A4IU         TCGA-BR-A4IV 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BR-A4IY         TCGA-BR-A4IZ         TCGA-BR-A4J1 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE"   "19P LOSS MUTATED" 
        TCGA-BR-A4J2         TCGA-BR-A4J4         TCGA-BR-A4J5 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BR-A4J6         TCGA-BR-A4J8         TCGA-BR-A4J9 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BR-A4PF         TCGA-CD-5798         TCGA-CD-5799 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-CD-5800         TCGA-CD-5801         TCGA-CD-5802 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-CD-5803         TCGA-CG-4300         TCGA-CG-4301 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-CG-4304         TCGA-CG-4305         TCGA-CG-4306 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-CG-4436         TCGA-CG-4437         TCGA-CG-4438 
  "19P LOSS MUTATED" "19P LOSS WILD-TYPE"   "19P LOSS MUTATED" 
        TCGA-CG-4440         TCGA-CG-4441         TCGA-CG-4443 
  "19P LOSS MUTATED" "19P LOSS WILD-TYPE"   "19P LOSS MUTATED" 
        TCGA-CG-4444         TCGA-CG-4449         TCGA-CG-4455 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-CG-4460         TCGA-CG-4462         TCGA-CG-4465 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-CG-4466         TCGA-CG-4469         TCGA-CG-4472 
  "19P LOSS MUTATED" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-CG-4474         TCGA-CG-4477         TCGA-CG-5716 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-CG-5717         TCGA-CG-5718         TCGA-CG-5719 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-CG-5720         TCGA-CG-5721         TCGA-CG-5722 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-CG-5723         TCGA-CG-5724         TCGA-CG-5725 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE"   "19P LOSS MUTATED" 
        TCGA-CG-5726         TCGA-CG-5727         TCGA-CG-5728 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-CG-5730         TCGA-CG-5732         TCGA-CG-5733 
"19P LOSS WILD-TYPE"   "19P LOSS MUTATED" "19P LOSS WILD-TYPE" 
        TCGA-CG-5734         TCGA-D7-5577         TCGA-D7-5578 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-D7-5579         TCGA-D7-6518         TCGA-D7-6519 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-D7-6520         TCGA-D7-6521         TCGA-D7-6522 
  "19P LOSS MUTATED" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-D7-6524         TCGA-D7-6525         TCGA-D7-6526 
"19P LOSS WILD-TYPE"   "19P LOSS MUTATED" "19P LOSS WILD-TYPE" 
        TCGA-D7-6527         TCGA-D7-6528         TCGA-D7-6815 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-D7-6817         TCGA-D7-6818         TCGA-D7-6820 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE"   "19P LOSS MUTATED" 
        TCGA-D7-6822         TCGA-EQ-5647         TCGA-EQ-8122 
"19P LOSS WILD-TYPE"   "19P LOSS MUTATED" "19P LOSS WILD-TYPE" 
        TCGA-F1-6177         TCGA-F1-6874         TCGA-F1-6875 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-FP-7735         TCGA-FP-7829         TCGA-FP-7916 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-FP-7998         TCGA-FP-8099         TCGA-FP-8209 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-FP-8631         TCGA-HJ-7597         TCGA-IN-7806 
  "19P LOSS MUTATED" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-IN-7808         TCGA-IP-7968 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE"   "19P LOSS MUTATED" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE"   "19P LOSS MUTATED" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"19P LOSS WILD-TYPE"   "19P LOSS MUTATED" "19P LOSS WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-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-BR-8592         TCGA-BR-A4IU         TCGA-BR-A4IV 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BR-A4IY         TCGA-BR-A4IZ         TCGA-BR-A4J1 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE"   "19P LOSS MUTATED" 
        TCGA-BR-A4J2         TCGA-BR-A4J4         TCGA-BR-A4J5 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BR-A4J6         TCGA-BR-A4J8         TCGA-BR-A4J9 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BR-A4PF         TCGA-CD-5798         TCGA-CD-5799 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-CD-5800         TCGA-CD-5801         TCGA-CD-5802 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-CD-5803         TCGA-CG-4300         TCGA-CG-4301 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-CG-4304         TCGA-CG-4305         TCGA-CG-4306 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-CG-4436         TCGA-CG-4437         TCGA-CG-4438 
  "19P LOSS MUTATED" "19P LOSS WILD-TYPE"   "19P LOSS MUTATED" 
        TCGA-CG-4440         TCGA-CG-4441         TCGA-CG-4443 
  "19P LOSS MUTATED" "19P LOSS WILD-TYPE"   "19P LOSS MUTATED" 
        TCGA-CG-4444         TCGA-CG-4449         TCGA-CG-4455 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-CG-4460         TCGA-CG-4462         TCGA-CG-4465 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-CG-4466         TCGA-CG-4469         TCGA-CG-4472 
  "19P LOSS MUTATED" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-CG-4474         TCGA-CG-4477         TCGA-CG-5716 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-CG-5717         TCGA-CG-5718         TCGA-CG-5719 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-CG-5720         TCGA-CG-5721         TCGA-CG-5722 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-CG-5723         TCGA-CG-5724         TCGA-CG-5725 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE"   "19P LOSS MUTATED" 
        TCGA-CG-5726         TCGA-CG-5727         TCGA-CG-5728 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-CG-5730         TCGA-CG-5732         TCGA-CG-5733 
"19P LOSS WILD-TYPE"   "19P LOSS MUTATED" "19P LOSS WILD-TYPE" 
        TCGA-CG-5734         TCGA-D7-5577         TCGA-D7-5578 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-D7-5579         TCGA-D7-6518         TCGA-D7-6519 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-D7-6520         TCGA-D7-6521         TCGA-D7-6522 
  "19P LOSS MUTATED" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-D7-6524         TCGA-D7-6525         TCGA-D7-6526 
"19P LOSS WILD-TYPE"   "19P LOSS MUTATED" "19P LOSS WILD-TYPE" 
        TCGA-D7-6527         TCGA-D7-6528         TCGA-D7-6815 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-D7-6817         TCGA-D7-6818         TCGA-D7-6820 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE"   "19P LOSS MUTATED" 
        TCGA-D7-6822         TCGA-EQ-5647         TCGA-EQ-8122 
"19P LOSS WILD-TYPE"   "19P LOSS MUTATED" "19P LOSS WILD-TYPE" 
        TCGA-F1-6177         TCGA-F1-6874         TCGA-F1-6875 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-FP-7735         TCGA-FP-7829         TCGA-FP-7916 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-FP-7998         TCGA-FP-8099         TCGA-FP-8209 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-FP-8631         TCGA-HJ-7597         TCGA-IN-7806 
  "19P LOSS MUTATED" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-IN-7808         TCGA-IP-7968 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
[1] "hr=" "1.1"
D69V2, continuous
D69V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED      4   14
  19P LOSS WILD-TYPE   66   93
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  FEMALE                4                 66
  MALE                 14                 93
                    vv
clus                 STOMACH ADENOCARCINOMA - DIFFUSE TYPE
  19P LOSS MUTATED                                       1
  19P LOSS WILD-TYPE                                    24
                    vv
clus                 STOMACH ADENOCARCINOMA - NOT OTHERWISE SPECIFIED (NOS)
  19P LOSS MUTATED                                                        8
  19P LOSS WILD-TYPE                                                     79
                    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                                                10
                    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                                                                        7
  19P LOSS WILD-TYPE                                                                     29
D69V4, multiclass
                    vv
clus                 T1 T2 T3 T4
  19P LOSS MUTATED    1  7  6  3
  19P LOSS WILD-TYPE  5 47 58 40
D69V5, multiclass
    clus
vv   19P LOSS MUTATED 19P LOSS WILD-TYPE
  T1                1                  5
  T2                7                 47
  T3                6                 58
  T4                3                 40
                    vv
clus                 N0 N1 N2 N3
  19P LOSS MUTATED    5  4  5  3
  19P LOSS WILD-TYPE 51 57 24 17
D69V6, multiclass
    clus
vv   19P LOSS MUTATED 19P LOSS WILD-TYPE
  N0                5                 51
  N1                4                 57
  N2                5                 24
  N3                3                 17
                    vv
clus                  M0  M1  MX
  19P LOSS MUTATED    15   2   1
  19P LOSS WILD-TYPE 131  16  12
D69V7, multiclass
    clus
vv   19P LOSS MUTATED 19P LOSS WILD-TYPE
  M0               15                131
  M1                2                 16
  MX                1                 12
                    vv
clus                  I II III IV
  19P LOSS MUTATED    4  4   5  4
  19P LOSS WILD-TYPE 22 44  53 25
D69V8, multiclass
     clus
vv    19P LOSS MUTATED 19P LOSS WILD-TYPE
  I                  4                 22
  II                 4                 44
  III                5                 53
  IV                 4                 25
D69V9, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED      0   18
  19P LOSS WILD-TYPE    5  154
     clus
vv    19P LOSS MUTATED 19P LOSS WILD-TYPE
  NO                 0                  5
  YES               18                154
                    vv
clus                  R0  R1  R2  RX
  19P LOSS MUTATED    15   0   2   1
  19P LOSS WILD-TYPE 108   7  10  24
D69V10, multiclass
    clus
vv   19P LOSS MUTATED 19P LOSS WILD-TYPE
  R0               15                108
  R1                0                  7
  R2                2                 10
  RX                1                 24
D69V11, continuous

Clustering(70) Variable = 19q loss mutation analysis
D70V1, survival
                    sevent
clus2                  0   1
  19Q LOSS MUTATED     8   3
  19Q LOSS WILD-TYPE 114  15
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                11                129 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                 3                 15 
$`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 TCGA-FP-8631 
       15.02        55.04         2.93         0.62         0.56 

$`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-BR-8592 TCGA-BR-A4IU 
        1.18         1.55         1.48         0.76         0.20         0.59 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
        0.92         0.39         0.79         0.72         0.79         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PF TCGA-CD-5798 
        0.43         0.13         0.23         0.10         0.72         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-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-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-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 
       70.06        12.03        28.96        31.04        65.10         4.01 
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-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-FP-8099 TCGA-FP-8209 TCGA-HJ-7597 
        0.20         3.02         3.58         1.02        59.05        26.43 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IP-7968 
        6.87         3.55         2.53 

  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
              0.56               0.07 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
             55.04              72.23 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
              4.54               1.18 
[1] "0.6 - 55.0 (4.5)" "0.1 - 72.2 (1.2)"
        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-BR-8592         TCGA-BR-A4IU         TCGA-BR-A4IV 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BR-A4IY         TCGA-BR-A4IZ         TCGA-BR-A4J1 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BR-A4J2         TCGA-BR-A4J4         TCGA-BR-A4J5 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BR-A4J6         TCGA-BR-A4J8         TCGA-BR-A4J9 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BR-A4PF         TCGA-CD-5798         TCGA-CD-5799 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-CD-5800         TCGA-CD-5801         TCGA-CD-5802 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-CD-5803         TCGA-CG-4300         TCGA-CG-4301 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-CG-4304         TCGA-CG-4305         TCGA-CG-4306 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-CG-4436         TCGA-CG-4437         TCGA-CG-4438 
  "19Q LOSS MUTATED" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-CG-4440         TCGA-CG-4441         TCGA-CG-4443 
  "19Q LOSS MUTATED" "19Q LOSS WILD-TYPE"   "19Q LOSS MUTATED" 
        TCGA-CG-4444         TCGA-CG-4449         TCGA-CG-4455 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-CG-4460         TCGA-CG-4462         TCGA-CG-4465 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-CG-4466         TCGA-CG-4469         TCGA-CG-4472 
  "19Q LOSS MUTATED" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-CG-4474         TCGA-CG-4477         TCGA-CG-5716 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-CG-5717         TCGA-CG-5718         TCGA-CG-5719 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-CG-5720         TCGA-CG-5721         TCGA-CG-5722 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-CG-5723         TCGA-CG-5724         TCGA-CG-5725 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE"   "19Q LOSS MUTATED" 
        TCGA-CG-5726         TCGA-CG-5727         TCGA-CG-5728 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-CG-5730         TCGA-CG-5732         TCGA-CG-5733 
"19Q LOSS WILD-TYPE"   "19Q LOSS MUTATED" "19Q LOSS WILD-TYPE" 
        TCGA-CG-5734         TCGA-D7-5577         TCGA-D7-5578 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-D7-5579         TCGA-D7-6518         TCGA-D7-6519 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-D7-6520         TCGA-D7-6521         TCGA-D7-6522 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-D7-6524         TCGA-D7-6525         TCGA-D7-6526 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-D7-6527         TCGA-D7-6528         TCGA-D7-6815 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-D7-6817         TCGA-D7-6818         TCGA-D7-6820 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE"   "19Q LOSS MUTATED" 
        TCGA-D7-6822         TCGA-EQ-5647         TCGA-EQ-8122 
"19Q LOSS WILD-TYPE"   "19Q LOSS MUTATED" "19Q LOSS WILD-TYPE" 
        TCGA-F1-6177         TCGA-F1-6874         TCGA-F1-6875 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-FP-7735         TCGA-FP-7829         TCGA-FP-7916 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-FP-7998         TCGA-FP-8099         TCGA-FP-8209 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-FP-8631         TCGA-HJ-7597         TCGA-IN-7806 
  "19Q LOSS MUTATED" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-IN-7808         TCGA-IP-7968 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE"   "19Q LOSS MUTATED" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"19Q LOSS WILD-TYPE"   "19Q LOSS MUTATED" "19Q LOSS WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-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-BR-8592         TCGA-BR-A4IU         TCGA-BR-A4IV 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BR-A4IY         TCGA-BR-A4IZ         TCGA-BR-A4J1 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BR-A4J2         TCGA-BR-A4J4         TCGA-BR-A4J5 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BR-A4J6         TCGA-BR-A4J8         TCGA-BR-A4J9 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BR-A4PF         TCGA-CD-5798         TCGA-CD-5799 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-CD-5800         TCGA-CD-5801         TCGA-CD-5802 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-CD-5803         TCGA-CG-4300         TCGA-CG-4301 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-CG-4304         TCGA-CG-4305         TCGA-CG-4306 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-CG-4436         TCGA-CG-4437         TCGA-CG-4438 
  "19Q LOSS MUTATED" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-CG-4440         TCGA-CG-4441         TCGA-CG-4443 
  "19Q LOSS MUTATED" "19Q LOSS WILD-TYPE"   "19Q LOSS MUTATED" 
        TCGA-CG-4444         TCGA-CG-4449         TCGA-CG-4455 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-CG-4460         TCGA-CG-4462         TCGA-CG-4465 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-CG-4466         TCGA-CG-4469         TCGA-CG-4472 
  "19Q LOSS MUTATED" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-CG-4474         TCGA-CG-4477         TCGA-CG-5716 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-CG-5717         TCGA-CG-5718         TCGA-CG-5719 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-CG-5720         TCGA-CG-5721         TCGA-CG-5722 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-CG-5723         TCGA-CG-5724         TCGA-CG-5725 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE"   "19Q LOSS MUTATED" 
        TCGA-CG-5726         TCGA-CG-5727         TCGA-CG-5728 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-CG-5730         TCGA-CG-5732         TCGA-CG-5733 
"19Q LOSS WILD-TYPE"   "19Q LOSS MUTATED" "19Q LOSS WILD-TYPE" 
        TCGA-CG-5734         TCGA-D7-5577         TCGA-D7-5578 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-D7-5579         TCGA-D7-6518         TCGA-D7-6519 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-D7-6520         TCGA-D7-6521         TCGA-D7-6522 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-D7-6524         TCGA-D7-6525         TCGA-D7-6526 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-D7-6527         TCGA-D7-6528         TCGA-D7-6815 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-D7-6817         TCGA-D7-6818         TCGA-D7-6820 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE"   "19Q LOSS MUTATED" 
        TCGA-D7-6822         TCGA-EQ-5647         TCGA-EQ-8122 
"19Q LOSS WILD-TYPE"   "19Q LOSS MUTATED" "19Q LOSS WILD-TYPE" 
        TCGA-F1-6177         TCGA-F1-6874         TCGA-F1-6875 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-FP-7735         TCGA-FP-7829         TCGA-FP-7916 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-FP-7998         TCGA-FP-8099         TCGA-FP-8209 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-FP-8631         TCGA-HJ-7597         TCGA-IN-7806 
  "19Q LOSS MUTATED" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-IN-7808         TCGA-IP-7968 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE"   "19Q LOSS MUTATED" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"19Q LOSS WILD-TYPE"   "19Q LOSS MUTATED" "19Q LOSS WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-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-BR-8592         TCGA-BR-A4IU         TCGA-BR-A4IV 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BR-A4IY         TCGA-BR-A4IZ         TCGA-BR-A4J1 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BR-A4J2         TCGA-BR-A4J4         TCGA-BR-A4J5 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BR-A4J6         TCGA-BR-A4J8         TCGA-BR-A4J9 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BR-A4PF         TCGA-CD-5798         TCGA-CD-5799 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-CD-5800         TCGA-CD-5801         TCGA-CD-5802 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-CD-5803         TCGA-CG-4300         TCGA-CG-4301 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-CG-4304         TCGA-CG-4305         TCGA-CG-4306 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-CG-4436         TCGA-CG-4437         TCGA-CG-4438 
  "19Q LOSS MUTATED" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-CG-4440         TCGA-CG-4441         TCGA-CG-4443 
  "19Q LOSS MUTATED" "19Q LOSS WILD-TYPE"   "19Q LOSS MUTATED" 
        TCGA-CG-4444         TCGA-CG-4449         TCGA-CG-4455 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-CG-4460         TCGA-CG-4462         TCGA-CG-4465 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-CG-4466         TCGA-CG-4469         TCGA-CG-4472 
  "19Q LOSS MUTATED" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-CG-4474         TCGA-CG-4477         TCGA-CG-5716 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-CG-5717         TCGA-CG-5718         TCGA-CG-5719 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-CG-5720         TCGA-CG-5721         TCGA-CG-5722 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-CG-5723         TCGA-CG-5724         TCGA-CG-5725 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE"   "19Q LOSS MUTATED" 
        TCGA-CG-5726         TCGA-CG-5727         TCGA-CG-5728 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-CG-5730         TCGA-CG-5732         TCGA-CG-5733 
"19Q LOSS WILD-TYPE"   "19Q LOSS MUTATED" "19Q LOSS WILD-TYPE" 
        TCGA-CG-5734         TCGA-D7-5577         TCGA-D7-5578 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-D7-5579         TCGA-D7-6518         TCGA-D7-6519 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-D7-6520         TCGA-D7-6521         TCGA-D7-6522 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-D7-6524         TCGA-D7-6525         TCGA-D7-6526 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-D7-6527         TCGA-D7-6528         TCGA-D7-6815 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-D7-6817         TCGA-D7-6818         TCGA-D7-6820 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE"   "19Q LOSS MUTATED" 
        TCGA-D7-6822         TCGA-EQ-5647         TCGA-EQ-8122 
"19Q LOSS WILD-TYPE"   "19Q LOSS MUTATED" "19Q LOSS WILD-TYPE" 
        TCGA-F1-6177         TCGA-F1-6874         TCGA-F1-6875 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-FP-7735         TCGA-FP-7829         TCGA-FP-7916 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-FP-7998         TCGA-FP-8099         TCGA-FP-8209 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-FP-8631         TCGA-HJ-7597         TCGA-IN-7806 
  "19Q LOSS MUTATED" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-IN-7808         TCGA-IP-7968 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
[1] "hr=" "1.1"
D70V2, continuous
D70V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED      3   10
  19Q LOSS WILD-TYPE   67   97
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  FEMALE                3                 67
  MALE                 10                 97
                    vv
clus                 STOMACH ADENOCARCINOMA - DIFFUSE TYPE
  19Q LOSS MUTATED                                       0
  19Q LOSS WILD-TYPE                                    25
                    vv
clus                 STOMACH ADENOCARCINOMA - NOT OTHERWISE SPECIFIED (NOS)
  19Q LOSS MUTATED                                                        6
  19Q LOSS WILD-TYPE                                                     81
                    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                                                10
                    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                                                                        6
  19Q LOSS WILD-TYPE                                                                     30
D70V4, multiclass
                    vv
clus                 T1 T2 T3 T4
  19Q LOSS MUTATED    1  5  5  1
  19Q LOSS WILD-TYPE  5 49 59 42
D70V5, multiclass
    clus
vv   19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  T1                1                  5
  T2                5                 49
  T3                5                 59
  T4                1                 42
                    vv
clus                 N0 N1 N2 N3
  19Q LOSS MUTATED    5  2  2  3
  19Q LOSS WILD-TYPE 51 59 27 17
D70V6, multiclass
    clus
vv   19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  N0                5                 51
  N1                2                 59
  N2                2                 27
  N3                3                 17
                    vv
clus                  M0  M1  MX
  19Q LOSS MUTATED    10   2   1
  19Q LOSS WILD-TYPE 136  16  12
D70V7, multiclass
    clus
vv   19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  M0               10                136
  M1                2                 16
  MX                1                 12
                    vv
clus                  I II III IV
  19Q LOSS MUTATED    4  3   2  3
  19Q LOSS WILD-TYPE 22 45  56 26
D70V8, multiclass
     clus
vv    19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  I                  4                 22
  II                 3                 45
  III                2                 56
  IV                 3                 26
D70V9, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED      0   13
  19Q LOSS WILD-TYPE    5  159
     clus
vv    19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  NO                 0                  5
  YES               13                159
                    vv
clus                  R0  R1  R2  RX
  19Q LOSS MUTATED    10   0   2   1
  19Q LOSS WILD-TYPE 113   7  10  24
D70V10, multiclass
    clus
vv   19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  R0               10                113
  R1                0                  7
  R2                2                 10
  RX                1                 24
D70V11, continuous

Clustering(71) Variable = 20p loss mutation analysis
D71V1, survival
                    sevent
clus2                  0   1
  20P LOSS MUTATED     2   1
  20P LOSS WILD-TYPE 120  17
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                 3                137 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                 1                 17 
$`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-BR-8592 TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        0.20         0.59         0.92         0.39         0.79         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J8 TCGA-BR-A4J9 
        0.79         0.53         0.43         0.13         0.23         0.10 
TCGA-BR-A4PF TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        0.72         0.82         0.69         0.36         0.49         0.30 
TCGA-CD-5803 TCGA-CG-4300 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
        0.07        20.02        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-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
        9.80         9.63         8.19         6.90         0.69         5.95 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
        6.61         4.14         1.68         3.65         4.70         4.04 
TCGA-D7-6820 TCGA-D7-6822 TCGA-EQ-8122 TCGA-F1-6177 TCGA-F1-6874 TCGA-F1-6875 
        2.93         4.27         7.79         6.54         2.01        72.23 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        0.39         0.20         3.02         3.58         1.02        59.05 
TCGA-FP-8631 TCGA-HJ-7597 TCGA-IN-7806 TCGA-IN-7808 TCGA-IP-7968 
        0.56        26.43         6.87         3.55         2.53 

  20P LOSS MUTATED 20P LOSS WILD-TYPE 
              0.62               0.07 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
             15.65              72.23 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
              3.02               1.22 
[1] "0.6 - 15.7 (3.0)" "0.1 - 72.2 (1.2)"
        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-BR-8592         TCGA-BR-A4IU         TCGA-BR-A4IV 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-BR-A4IY         TCGA-BR-A4IZ         TCGA-BR-A4J1 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-BR-A4J2         TCGA-BR-A4J4         TCGA-BR-A4J5 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-BR-A4J6         TCGA-BR-A4J8         TCGA-BR-A4J9 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-BR-A4PF         TCGA-CD-5798         TCGA-CD-5799 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CD-5800         TCGA-CD-5801         TCGA-CD-5802 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CD-5803         TCGA-CG-4300         TCGA-CG-4301 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE"   "20P LOSS MUTATED" 
        TCGA-CG-4304         TCGA-CG-4305         TCGA-CG-4306 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CG-4436         TCGA-CG-4437         TCGA-CG-4438 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CG-4440         TCGA-CG-4441         TCGA-CG-4443 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CG-4444         TCGA-CG-4449         TCGA-CG-4455 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CG-4460         TCGA-CG-4462         TCGA-CG-4465 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CG-4466         TCGA-CG-4469         TCGA-CG-4472 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CG-4474         TCGA-CG-4477         TCGA-CG-5716 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CG-5717         TCGA-CG-5718         TCGA-CG-5719 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CG-5720         TCGA-CG-5721         TCGA-CG-5722 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CG-5723         TCGA-CG-5724         TCGA-CG-5725 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CG-5726         TCGA-CG-5727         TCGA-CG-5728 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CG-5730         TCGA-CG-5732         TCGA-CG-5733 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CG-5734         TCGA-D7-5577         TCGA-D7-5578 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-D7-5579         TCGA-D7-6518         TCGA-D7-6519 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE"   "20P LOSS MUTATED" 
        TCGA-D7-6520         TCGA-D7-6521         TCGA-D7-6522 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-D7-6524         TCGA-D7-6525         TCGA-D7-6526 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-D7-6527         TCGA-D7-6528         TCGA-D7-6815 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-D7-6817         TCGA-D7-6818         TCGA-D7-6820 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-D7-6822         TCGA-EQ-5647         TCGA-EQ-8122 
"20P LOSS WILD-TYPE"   "20P LOSS MUTATED" "20P LOSS WILD-TYPE" 
        TCGA-F1-6177         TCGA-F1-6874         TCGA-F1-6875 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-FP-7735         TCGA-FP-7829         TCGA-FP-7916 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-FP-7998         TCGA-FP-8099         TCGA-FP-8209 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-FP-8631         TCGA-HJ-7597         TCGA-IN-7806 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-IN-7808         TCGA-IP-7968 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-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-BR-8592         TCGA-BR-A4IU         TCGA-BR-A4IV 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-BR-A4IY         TCGA-BR-A4IZ         TCGA-BR-A4J1 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-BR-A4J2         TCGA-BR-A4J4         TCGA-BR-A4J5 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-BR-A4J6         TCGA-BR-A4J8         TCGA-BR-A4J9 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-BR-A4PF         TCGA-CD-5798         TCGA-CD-5799 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CD-5800         TCGA-CD-5801         TCGA-CD-5802 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CD-5803         TCGA-CG-4300         TCGA-CG-4301 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE"   "20P LOSS MUTATED" 
        TCGA-CG-4304         TCGA-CG-4305         TCGA-CG-4306 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CG-4436         TCGA-CG-4437         TCGA-CG-4438 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CG-4440         TCGA-CG-4441         TCGA-CG-4443 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CG-4444         TCGA-CG-4449         TCGA-CG-4455 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CG-4460         TCGA-CG-4462         TCGA-CG-4465 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CG-4466         TCGA-CG-4469         TCGA-CG-4472 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CG-4474         TCGA-CG-4477         TCGA-CG-5716 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CG-5717         TCGA-CG-5718         TCGA-CG-5719 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CG-5720         TCGA-CG-5721         TCGA-CG-5722 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CG-5723         TCGA-CG-5724         TCGA-CG-5725 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CG-5726         TCGA-CG-5727         TCGA-CG-5728 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CG-5730         TCGA-CG-5732         TCGA-CG-5733 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CG-5734         TCGA-D7-5577         TCGA-D7-5578 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-D7-5579         TCGA-D7-6518         TCGA-D7-6519 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE"   "20P LOSS MUTATED" 
        TCGA-D7-6520         TCGA-D7-6521         TCGA-D7-6522 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-D7-6524         TCGA-D7-6525         TCGA-D7-6526 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-D7-6527         TCGA-D7-6528         TCGA-D7-6815 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-D7-6817         TCGA-D7-6818         TCGA-D7-6820 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-D7-6822         TCGA-EQ-5647         TCGA-EQ-8122 
"20P LOSS WILD-TYPE"   "20P LOSS MUTATED" "20P LOSS WILD-TYPE" 
        TCGA-F1-6177         TCGA-F1-6874         TCGA-F1-6875 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-FP-7735         TCGA-FP-7829         TCGA-FP-7916 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-FP-7998         TCGA-FP-8099         TCGA-FP-8209 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-FP-8631         TCGA-HJ-7597         TCGA-IN-7806 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-IN-7808         TCGA-IP-7968 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-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-BR-8592         TCGA-BR-A4IU         TCGA-BR-A4IV 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-BR-A4IY         TCGA-BR-A4IZ         TCGA-BR-A4J1 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-BR-A4J2         TCGA-BR-A4J4         TCGA-BR-A4J5 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-BR-A4J6         TCGA-BR-A4J8         TCGA-BR-A4J9 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-BR-A4PF         TCGA-CD-5798         TCGA-CD-5799 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CD-5800         TCGA-CD-5801         TCGA-CD-5802 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CD-5803         TCGA-CG-4300         TCGA-CG-4301 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE"   "20P LOSS MUTATED" 
        TCGA-CG-4304         TCGA-CG-4305         TCGA-CG-4306 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CG-4436         TCGA-CG-4437         TCGA-CG-4438 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CG-4440         TCGA-CG-4441         TCGA-CG-4443 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CG-4444         TCGA-CG-4449         TCGA-CG-4455 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CG-4460         TCGA-CG-4462         TCGA-CG-4465 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CG-4466         TCGA-CG-4469         TCGA-CG-4472 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CG-4474         TCGA-CG-4477         TCGA-CG-5716 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CG-5717         TCGA-CG-5718         TCGA-CG-5719 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CG-5720         TCGA-CG-5721         TCGA-CG-5722 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CG-5723         TCGA-CG-5724         TCGA-CG-5725 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CG-5726         TCGA-CG-5727         TCGA-CG-5728 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CG-5730         TCGA-CG-5732         TCGA-CG-5733 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CG-5734         TCGA-D7-5577         TCGA-D7-5578 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-D7-5579         TCGA-D7-6518         TCGA-D7-6519 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE"   "20P LOSS MUTATED" 
        TCGA-D7-6520         TCGA-D7-6521         TCGA-D7-6522 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-D7-6524         TCGA-D7-6525         TCGA-D7-6526 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-D7-6527         TCGA-D7-6528         TCGA-D7-6815 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-D7-6817         TCGA-D7-6818         TCGA-D7-6820 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-D7-6822         TCGA-EQ-5647         TCGA-EQ-8122 
"20P LOSS WILD-TYPE"   "20P LOSS MUTATED" "20P LOSS WILD-TYPE" 
        TCGA-F1-6177         TCGA-F1-6874         TCGA-F1-6875 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-FP-7735         TCGA-FP-7829         TCGA-FP-7916 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-FP-7998         TCGA-FP-8099         TCGA-FP-8209 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-FP-8631         TCGA-HJ-7597         TCGA-IN-7806 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-IN-7808         TCGA-IP-7968 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
[1] "hr=" "2.9"
D71V2, continuous
D71V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED      4    1
  20P LOSS WILD-TYPE   66  106
        clus
vv       20P LOSS MUTATED 20P LOSS WILD-TYPE
  FEMALE                4                 66
  MALE                  1                106
                    vv
clus                 STOMACH ADENOCARCINOMA - DIFFUSE TYPE
  20P LOSS MUTATED                                       1
  20P LOSS WILD-TYPE                                    24
                    vv
clus                 STOMACH ADENOCARCINOMA - NOT OTHERWISE SPECIFIED (NOS)
  20P LOSS MUTATED                                                        3
  20P LOSS WILD-TYPE                                                     84
                    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                                                   1
  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                                                                     36
D71V4, multiclass
                    vv
clus                 T1 T2 T3 T4
  20P LOSS MUTATED    0  3  0  2
  20P LOSS WILD-TYPE  6 51 64 41
D71V5, multiclass
    clus
vv   20P LOSS MUTATED 20P LOSS WILD-TYPE
  T1                0                  6
  T2                3                 51
  T3                0                 64
  T4                2                 41
                    vv
clus                 N0 N1 N2 N3
  20P LOSS MUTATED    1  2  0  2
  20P LOSS WILD-TYPE 55 59 29 18
D71V6, multiclass
    clus
vv   20P LOSS MUTATED 20P LOSS WILD-TYPE
  N0                1                 55
  N1                2                 59
  N2                0                 29
  N3                2                 18
                    vv
clus                  M0  M1  MX
  20P LOSS MUTATED     3   2   0
  20P LOSS WILD-TYPE 143  16  13
D71V7, multiclass
    clus
vv   20P LOSS MUTATED 20P LOSS WILD-TYPE
  M0                3                143
  M1                2                 16
  MX                0                 13
                    vv
clus                  I II III IV
  20P LOSS MUTATED    1  0   1  3
  20P LOSS WILD-TYPE 25 48  57 26
D71V8, multiclass
     clus
vv    20P LOSS MUTATED 20P LOSS WILD-TYPE
  I                  1                 25
  II                 0                 48
  III                1                 57
  IV                 3                 26
D71V9, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED      1    4
  20P LOSS WILD-TYPE    4  168
     clus
vv    20P LOSS MUTATED 20P LOSS WILD-TYPE
  NO                 1                  4
  YES                4                168
                    vv
clus                  R0  R1  R2  RX
  20P LOSS MUTATED     1   1   2   1
  20P LOSS WILD-TYPE 122   6  10  24
D71V10, multiclass
    clus
vv   20P LOSS MUTATED 20P LOSS WILD-TYPE
  R0                1                122
  R1                1                  6
  R2                2                 10
  RX                1                 24
D71V11, continuous

Clustering(72) Variable = 21q loss mutation analysis
D72V1, survival
                    sevent
clus2                  0   1
  21Q LOSS MUTATED    17   4
  21Q LOSS WILD-TYPE 105  14
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                21                119 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                 4                 14 
$`21Q LOSS MUTATED`
TCGA-B7-5818 TCGA-BR-6458 TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-A4J1 TCGA-BR-A4J8 
        0.10         1.35         1.25         1.05         0.72         0.23 
TCGA-BR-A4PF TCGA-CG-4438 TCGA-CG-4466 TCGA-CG-4477 TCGA-CG-5719 TCGA-CG-5724 
        0.72        54.05        18.94         1.02         1.02        12.03 
TCGA-CG-5725 TCGA-CG-5728 TCGA-CG-5730 TCGA-D7-5579 TCGA-D7-6526 TCGA-D7-6817 
       15.02        65.10         4.01         4.54         6.61         4.70 
TCGA-EQ-5647 TCGA-FP-7829 TCGA-IN-7806 
        0.62         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-BR-8592 TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        1.48         0.76         0.20         0.59         0.92         0.39 
TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J9 
        0.79         0.79         0.53         0.43         0.13         0.10 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
        0.82         0.69         0.36         0.49         0.30         0.07 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02        52.96 
TCGA-CG-4437 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 
        8.05         4.01        14.01        29.98        47.05        19.07 
TCGA-CG-4455 TCGA-CG-4460 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4469 TCGA-CG-4472 
       12.03        21.99         1.02         8.98         7.07        12.00 
TCGA-CG-4474 TCGA-CG-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-5726 TCGA-CG-5727 TCGA-CG-5732 TCGA-CG-5733 
        0.95        70.06        28.96        31.04        55.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
        7.99         8.65         3.58         9.80        15.65         9.63 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6527 TCGA-D7-6528 
        8.19         6.90         0.69         5.95         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-FP-8099 
        2.01        72.23         0.39         3.02         3.58         1.02 
TCGA-FP-8209 TCGA-FP-8631 TCGA-HJ-7597 TCGA-IN-7808 TCGA-IP-7968 
       59.05         0.56        26.43         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 
              1.35               1.22 
[1] "0.1 - 65.1 (1.4)" "0.1 - 72.2 (1.2)"
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
  "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-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-BR-8592         TCGA-BR-A4IU         TCGA-BR-A4IV 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-BR-A4IY         TCGA-BR-A4IZ         TCGA-BR-A4J1 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" 
        TCGA-BR-A4J2         TCGA-BR-A4J4         TCGA-BR-A4J5 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-BR-A4J6         TCGA-BR-A4J8         TCGA-BR-A4J9 
"21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-BR-A4PF         TCGA-CD-5798         TCGA-CD-5799 
  "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-CD-5800         TCGA-CD-5801         TCGA-CD-5802 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-CD-5803         TCGA-CG-4300         TCGA-CG-4301 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-CG-4304         TCGA-CG-4305         TCGA-CG-4306 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-CG-4436         TCGA-CG-4437         TCGA-CG-4438 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" 
        TCGA-CG-4440         TCGA-CG-4441         TCGA-CG-4443 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-CG-4444         TCGA-CG-4449         TCGA-CG-4455 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-CG-4460         TCGA-CG-4462         TCGA-CG-4465 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-CG-4466         TCGA-CG-4469         TCGA-CG-4472 
  "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-CG-4474         TCGA-CG-4477         TCGA-CG-5716 
"21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-CG-5717         TCGA-CG-5718         TCGA-CG-5719 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" 
        TCGA-CG-5720         TCGA-CG-5721         TCGA-CG-5722 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-CG-5723         TCGA-CG-5724         TCGA-CG-5725 
"21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED"   "21Q LOSS MUTATED" 
        TCGA-CG-5726         TCGA-CG-5727         TCGA-CG-5728 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" 
        TCGA-CG-5730         TCGA-CG-5732         TCGA-CG-5733 
  "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-CG-5734         TCGA-D7-5577         TCGA-D7-5578 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-D7-5579         TCGA-D7-6518         TCGA-D7-6519 
  "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-D7-6520         TCGA-D7-6521         TCGA-D7-6522 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-D7-6524         TCGA-D7-6525         TCGA-D7-6526 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" 
        TCGA-D7-6527         TCGA-D7-6528         TCGA-D7-6815 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-D7-6817         TCGA-D7-6818         TCGA-D7-6820 
  "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-D7-6822         TCGA-EQ-5647         TCGA-EQ-8122 
"21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-F1-6177         TCGA-F1-6874         TCGA-F1-6875 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-FP-7735         TCGA-FP-7829         TCGA-FP-7916 
"21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-FP-7998         TCGA-FP-8099         TCGA-FP-8209 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-FP-8631         TCGA-HJ-7597         TCGA-IN-7806 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" 
        TCGA-IN-7808         TCGA-IP-7968 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
  "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-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-BR-8592         TCGA-BR-A4IU         TCGA-BR-A4IV 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-BR-A4IY         TCGA-BR-A4IZ         TCGA-BR-A4J1 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" 
        TCGA-BR-A4J2         TCGA-BR-A4J4         TCGA-BR-A4J5 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-BR-A4J6         TCGA-BR-A4J8         TCGA-BR-A4J9 
"21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-BR-A4PF         TCGA-CD-5798         TCGA-CD-5799 
  "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-CD-5800         TCGA-CD-5801         TCGA-CD-5802 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-CD-5803         TCGA-CG-4300         TCGA-CG-4301 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-CG-4304         TCGA-CG-4305         TCGA-CG-4306 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-CG-4436         TCGA-CG-4437         TCGA-CG-4438 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" 
        TCGA-CG-4440         TCGA-CG-4441         TCGA-CG-4443 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-CG-4444         TCGA-CG-4449         TCGA-CG-4455 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-CG-4460         TCGA-CG-4462         TCGA-CG-4465 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-CG-4466         TCGA-CG-4469         TCGA-CG-4472 
  "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-CG-4474         TCGA-CG-4477         TCGA-CG-5716 
"21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-CG-5717         TCGA-CG-5718         TCGA-CG-5719 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" 
        TCGA-CG-5720         TCGA-CG-5721         TCGA-CG-5722 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-CG-5723         TCGA-CG-5724         TCGA-CG-5725 
"21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED"   "21Q LOSS MUTATED" 
        TCGA-CG-5726         TCGA-CG-5727         TCGA-CG-5728 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" 
        TCGA-CG-5730         TCGA-CG-5732         TCGA-CG-5733 
  "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-CG-5734         TCGA-D7-5577         TCGA-D7-5578 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-D7-5579         TCGA-D7-6518         TCGA-D7-6519 
  "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-D7-6520         TCGA-D7-6521         TCGA-D7-6522 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-D7-6524         TCGA-D7-6525         TCGA-D7-6526 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" 
        TCGA-D7-6527         TCGA-D7-6528         TCGA-D7-6815 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-D7-6817         TCGA-D7-6818         TCGA-D7-6820 
  "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-D7-6822         TCGA-EQ-5647         TCGA-EQ-8122 
"21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-F1-6177         TCGA-F1-6874         TCGA-F1-6875 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-FP-7735         TCGA-FP-7829         TCGA-FP-7916 
"21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-FP-7998         TCGA-FP-8099         TCGA-FP-8209 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-FP-8631         TCGA-HJ-7597         TCGA-IN-7806 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" 
        TCGA-IN-7808         TCGA-IP-7968 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
  "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-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-BR-8592         TCGA-BR-A4IU         TCGA-BR-A4IV 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-BR-A4IY         TCGA-BR-A4IZ         TCGA-BR-A4J1 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" 
        TCGA-BR-A4J2         TCGA-BR-A4J4         TCGA-BR-A4J5 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-BR-A4J6         TCGA-BR-A4J8         TCGA-BR-A4J9 
"21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-BR-A4PF         TCGA-CD-5798         TCGA-CD-5799 
  "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-CD-5800         TCGA-CD-5801         TCGA-CD-5802 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-CD-5803         TCGA-CG-4300         TCGA-CG-4301 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-CG-4304         TCGA-CG-4305         TCGA-CG-4306 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-CG-4436         TCGA-CG-4437         TCGA-CG-4438 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" 
        TCGA-CG-4440         TCGA-CG-4441         TCGA-CG-4443 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-CG-4444         TCGA-CG-4449         TCGA-CG-4455 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-CG-4460         TCGA-CG-4462         TCGA-CG-4465 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-CG-4466         TCGA-CG-4469         TCGA-CG-4472 
  "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-CG-4474         TCGA-CG-4477         TCGA-CG-5716 
"21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-CG-5717         TCGA-CG-5718         TCGA-CG-5719 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" 
        TCGA-CG-5720         TCGA-CG-5721         TCGA-CG-5722 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-CG-5723         TCGA-CG-5724         TCGA-CG-5725 
"21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED"   "21Q LOSS MUTATED" 
        TCGA-CG-5726         TCGA-CG-5727         TCGA-CG-5728 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" 
        TCGA-CG-5730         TCGA-CG-5732         TCGA-CG-5733 
  "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-CG-5734         TCGA-D7-5577         TCGA-D7-5578 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-D7-5579         TCGA-D7-6518         TCGA-D7-6519 
  "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-D7-6520         TCGA-D7-6521         TCGA-D7-6522 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-D7-6524         TCGA-D7-6525         TCGA-D7-6526 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" 
        TCGA-D7-6527         TCGA-D7-6528         TCGA-D7-6815 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-D7-6817         TCGA-D7-6818         TCGA-D7-6820 
  "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-D7-6822         TCGA-EQ-5647         TCGA-EQ-8122 
"21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-F1-6177         TCGA-F1-6874         TCGA-F1-6875 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-FP-7735         TCGA-FP-7829         TCGA-FP-7916 
"21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-FP-7998         TCGA-FP-8099         TCGA-FP-8209 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-FP-8631         TCGA-HJ-7597         TCGA-IN-7806 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" 
        TCGA-IN-7808         TCGA-IP-7968 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
[1] "hr=" "1.5"
D72V2, continuous
D72V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED     12   18
  21Q LOSS WILD-TYPE   58   89
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  FEMALE               12                 58
  MALE                 18                 89
                    vv
clus                 STOMACH ADENOCARCINOMA - DIFFUSE TYPE
  21Q LOSS MUTATED                                       3
  21Q LOSS WILD-TYPE                                    22
                    vv
clus                 STOMACH ADENOCARCINOMA - NOT OTHERWISE SPECIFIED (NOS)
  21Q LOSS MUTATED                                                       14
  21Q LOSS WILD-TYPE                                                     73
                    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                                                 7
                    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                                                                     29
D72V4, multiclass
                    vv
clus                 T1 T2 T3 T4
  21Q LOSS MUTATED    0  8 13  5
  21Q LOSS WILD-TYPE  6 46 51 38
D72V5, multiclass
    clus
vv   21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  T1                0                  6
  T2                8                 46
  T3               13                 51
  T4                5                 38
                    vv
clus                 N0 N1 N2 N3
  21Q LOSS MUTATED    8 10  4  5
  21Q LOSS WILD-TYPE 48 51 25 15
D72V6, multiclass
    clus
vv   21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  N0                8                 48
  N1               10                 51
  N2                4                 25
  N3                5                 15
                    vv
clus                  M0  M1  MX
  21Q LOSS MUTATED    24   4   2
  21Q LOSS WILD-TYPE 122  14  11
D72V7, multiclass
    clus
vv   21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  M0               24                122
  M1                4                 14
  MX                2                 11
                    vv
clus                  I II III IV
  21Q LOSS MUTATED    5  5   9  6
  21Q LOSS WILD-TYPE 21 43  49 23
D72V8, multiclass
     clus
vv    21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  I                  5                 21
  II                 5                 43
  III                9                 49
  IV                 6                 23
D72V9, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED      1   29
  21Q LOSS WILD-TYPE    4  143
     clus
vv    21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  NO                 1                  4
  YES               29                143
                    vv
clus                  R0  R1  R2  RX
  21Q LOSS MUTATED    18   3   3   6
  21Q LOSS WILD-TYPE 105   4   9  19
D72V10, multiclass
    clus
vv   21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  R0               18                105
  R1                3                  4
  R2                3                  9
  RX                6                 19
D72V11, continuous

Clustering(73) Variable = 22q loss mutation analysis
D73V1, survival
                    sevent
clus2                  0   1
  22Q LOSS MUTATED    14   5
  22Q LOSS WILD-TYPE 108  13
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                19                121 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                 5                 13 
$`22Q LOSS MUTATED`
TCGA-BR-6458 TCGA-BR-7715 TCGA-BR-A4J1 TCGA-CD-5800 TCGA-CD-5802 TCGA-CG-4438 
        1.35         1.05         0.72         0.36         0.30        54.05 
TCGA-CG-4460 TCGA-CG-4466 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5732 TCGA-D7-5578 
       21.99        18.94        12.03        15.02        55.04         3.58 
TCGA-D7-6519 TCGA-D7-6817 TCGA-D7-6820 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-FP-8099 
       15.65         4.70         2.93         0.62         7.79         1.02 
TCGA-FP-8631 
        0.56 

$`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-BR-8592 TCGA-BR-A4IU 
        1.18         1.55         1.48         0.76         0.20         0.59 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
        0.92         0.39         0.79         0.79         0.53         0.43 
TCGA-BR-A4J6 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PF TCGA-CD-5798 TCGA-CD-5799 
        0.13         0.23         0.10         0.72         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-FP-8209 TCGA-HJ-7597 TCGA-IN-7806 TCGA-IN-7808 
        3.02         3.58        59.05        26.43         6.87         3.55 
TCGA-IP-7968 
        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 
              3.58               1.18 
[1] "0.3 - 55.0 (3.6)" "0.1 - 72.2 (1.2)"
        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-BR-8592         TCGA-BR-A4IU         TCGA-BR-A4IV 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-BR-A4IY         TCGA-BR-A4IZ         TCGA-BR-A4J1 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" 
        TCGA-BR-A4J2         TCGA-BR-A4J4         TCGA-BR-A4J5 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-BR-A4J6         TCGA-BR-A4J8         TCGA-BR-A4J9 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-BR-A4PF         TCGA-CD-5798         TCGA-CD-5799 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-CD-5800         TCGA-CD-5801         TCGA-CD-5802 
  "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" 
        TCGA-CD-5803         TCGA-CG-4300         TCGA-CG-4301 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-CG-4304         TCGA-CG-4305         TCGA-CG-4306 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-CG-4436         TCGA-CG-4437         TCGA-CG-4438 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" 
        TCGA-CG-4440         TCGA-CG-4441         TCGA-CG-4443 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-CG-4444         TCGA-CG-4449         TCGA-CG-4455 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-CG-4460         TCGA-CG-4462         TCGA-CG-4465 
  "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-CG-4466         TCGA-CG-4469         TCGA-CG-4472 
  "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-CG-4474         TCGA-CG-4477         TCGA-CG-5716 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-CG-5717         TCGA-CG-5718         TCGA-CG-5719 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-CG-5720         TCGA-CG-5721         TCGA-CG-5722 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-CG-5723         TCGA-CG-5724         TCGA-CG-5725 
"22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED"   "22Q LOSS MUTATED" 
        TCGA-CG-5726         TCGA-CG-5727         TCGA-CG-5728 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-CG-5730         TCGA-CG-5732         TCGA-CG-5733 
"22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" 
        TCGA-CG-5734         TCGA-D7-5577         TCGA-D7-5578 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" 
        TCGA-D7-5579         TCGA-D7-6518         TCGA-D7-6519 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" 
        TCGA-D7-6520         TCGA-D7-6521         TCGA-D7-6522 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-D7-6524         TCGA-D7-6525         TCGA-D7-6526 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-D7-6527         TCGA-D7-6528         TCGA-D7-6815 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-D7-6817         TCGA-D7-6818         TCGA-D7-6820 
  "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" 
        TCGA-D7-6822         TCGA-EQ-5647         TCGA-EQ-8122 
"22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED"   "22Q LOSS MUTATED" 
        TCGA-F1-6177         TCGA-F1-6874         TCGA-F1-6875 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-FP-7735         TCGA-FP-7829         TCGA-FP-7916 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-FP-7998         TCGA-FP-8099         TCGA-FP-8209 
"22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" 
        TCGA-FP-8631         TCGA-HJ-7597         TCGA-IN-7806 
  "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-IN-7808         TCGA-IP-7968 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
  "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-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-BR-8592         TCGA-BR-A4IU         TCGA-BR-A4IV 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-BR-A4IY         TCGA-BR-A4IZ         TCGA-BR-A4J1 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" 
        TCGA-BR-A4J2         TCGA-BR-A4J4         TCGA-BR-A4J5 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-BR-A4J6         TCGA-BR-A4J8         TCGA-BR-A4J9 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-BR-A4PF         TCGA-CD-5798         TCGA-CD-5799 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-CD-5800         TCGA-CD-5801         TCGA-CD-5802 
  "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" 
        TCGA-CD-5803         TCGA-CG-4300         TCGA-CG-4301 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-CG-4304         TCGA-CG-4305         TCGA-CG-4306 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-CG-4436         TCGA-CG-4437         TCGA-CG-4438 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" 
        TCGA-CG-4440         TCGA-CG-4441         TCGA-CG-4443 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-CG-4444         TCGA-CG-4449         TCGA-CG-4455 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-CG-4460         TCGA-CG-4462         TCGA-CG-4465 
  "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-CG-4466         TCGA-CG-4469         TCGA-CG-4472 
  "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-CG-4474         TCGA-CG-4477         TCGA-CG-5716 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-CG-5717         TCGA-CG-5718         TCGA-CG-5719 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-CG-5720         TCGA-CG-5721         TCGA-CG-5722 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-CG-5723         TCGA-CG-5724         TCGA-CG-5725 
"22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED"   "22Q LOSS MUTATED" 
        TCGA-CG-5726         TCGA-CG-5727         TCGA-CG-5728 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-CG-5730         TCGA-CG-5732         TCGA-CG-5733 
"22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" 
        TCGA-CG-5734         TCGA-D7-5577         TCGA-D7-5578 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" 
        TCGA-D7-5579         TCGA-D7-6518         TCGA-D7-6519 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" 
        TCGA-D7-6520         TCGA-D7-6521         TCGA-D7-6522 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-D7-6524         TCGA-D7-6525         TCGA-D7-6526 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-D7-6527         TCGA-D7-6528         TCGA-D7-6815 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-D7-6817         TCGA-D7-6818         TCGA-D7-6820 
  "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" 
        TCGA-D7-6822         TCGA-EQ-5647         TCGA-EQ-8122 
"22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED"   "22Q LOSS MUTATED" 
        TCGA-F1-6177         TCGA-F1-6874         TCGA-F1-6875 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-FP-7735         TCGA-FP-7829         TCGA-FP-7916 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-FP-7998         TCGA-FP-8099         TCGA-FP-8209 
"22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" 
        TCGA-FP-8631         TCGA-HJ-7597         TCGA-IN-7806 
  "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-IN-7808         TCGA-IP-7968 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
  "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-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-BR-8592         TCGA-BR-A4IU         TCGA-BR-A4IV 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-BR-A4IY         TCGA-BR-A4IZ         TCGA-BR-A4J1 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" 
        TCGA-BR-A4J2         TCGA-BR-A4J4         TCGA-BR-A4J5 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-BR-A4J6         TCGA-BR-A4J8         TCGA-BR-A4J9 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-BR-A4PF         TCGA-CD-5798         TCGA-CD-5799 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-CD-5800         TCGA-CD-5801         TCGA-CD-5802 
  "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" 
        TCGA-CD-5803         TCGA-CG-4300         TCGA-CG-4301 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-CG-4304         TCGA-CG-4305         TCGA-CG-4306 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-CG-4436         TCGA-CG-4437         TCGA-CG-4438 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" 
        TCGA-CG-4440         TCGA-CG-4441         TCGA-CG-4443 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-CG-4444         TCGA-CG-4449         TCGA-CG-4455 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-CG-4460         TCGA-CG-4462         TCGA-CG-4465 
  "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-CG-4466         TCGA-CG-4469         TCGA-CG-4472 
  "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-CG-4474         TCGA-CG-4477         TCGA-CG-5716 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-CG-5717         TCGA-CG-5718         TCGA-CG-5719 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-CG-5720         TCGA-CG-5721         TCGA-CG-5722 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-CG-5723         TCGA-CG-5724         TCGA-CG-5725 
"22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED"   "22Q LOSS MUTATED" 
        TCGA-CG-5726         TCGA-CG-5727         TCGA-CG-5728 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-CG-5730         TCGA-CG-5732         TCGA-CG-5733 
"22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" 
        TCGA-CG-5734         TCGA-D7-5577         TCGA-D7-5578 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" 
        TCGA-D7-5579         TCGA-D7-6518         TCGA-D7-6519 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" 
        TCGA-D7-6520         TCGA-D7-6521         TCGA-D7-6522 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-D7-6524         TCGA-D7-6525         TCGA-D7-6526 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-D7-6527         TCGA-D7-6528         TCGA-D7-6815 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-D7-6817         TCGA-D7-6818         TCGA-D7-6820 
  "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" 
        TCGA-D7-6822         TCGA-EQ-5647         TCGA-EQ-8122 
"22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED"   "22Q LOSS MUTATED" 
        TCGA-F1-6177         TCGA-F1-6874         TCGA-F1-6875 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-FP-7735         TCGA-FP-7829         TCGA-FP-7916 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-FP-7998         TCGA-FP-8099         TCGA-FP-8209 
"22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" 
        TCGA-FP-8631         TCGA-HJ-7597         TCGA-IN-7806 
  "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-IN-7808         TCGA-IP-7968 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
[1] "hr=" "1.7"
D73V2, continuous
D73V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED      9   16
  22Q LOSS WILD-TYPE   61   91
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  FEMALE                9                 61
  MALE                 16                 91
                    vv
clus                 STOMACH ADENOCARCINOMA - DIFFUSE TYPE
  22Q LOSS MUTATED                                       2
  22Q LOSS WILD-TYPE                                    23
                    vv
clus                 STOMACH ADENOCARCINOMA - NOT OTHERWISE SPECIFIED (NOS)
  22Q LOSS MUTATED                                                       12
  22Q LOSS WILD-TYPE                                                     75
                    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                                                10
                    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                                                                        6
  22Q LOSS WILD-TYPE                                                                     30
D73V4, multiclass
                    vv
clus                 T1 T2 T3 T4
  22Q LOSS MUTATED    0  9 11  4
  22Q LOSS WILD-TYPE  6 45 53 39
D73V5, multiclass
    clus
vv   22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  T1                0                  6
  T2                9                 45
  T3               11                 53
  T4                4                 39
                    vv
clus                 N0 N1 N2 N3
  22Q LOSS MUTATED    8  9  3  4
  22Q LOSS WILD-TYPE 48 52 26 16
D73V6, multiclass
    clus
vv   22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  N0                8                 48
  N1                9                 52
  N2                3                 26
  N3                4                 16
                    vv
clus                  M0  M1  MX
  22Q LOSS MUTATED    18   3   4
  22Q LOSS WILD-TYPE 128  15   9
D73V7, multiclass
    clus
vv   22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  M0               18                128
  M1                3                 15
  MX                4                  9
                    vv
clus                  I II III IV
  22Q LOSS MUTATED    4  8   6  5
  22Q LOSS WILD-TYPE 22 40  52 24
D73V8, multiclass
     clus
vv    22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  I                  4                 22
  II                 8                 40
  III                6                 52
  IV                 5                 24
D73V9, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED      1   24
  22Q LOSS WILD-TYPE    4  148
     clus
vv    22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  NO                 1                  4
  YES               24                148
                    vv
clus                  R0  R1  R2  RX
  22Q LOSS MUTATED    14   1   3   4
  22Q LOSS WILD-TYPE 109   6   9  21
D73V10, multiclass
    clus
vv   22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  R0               14                109
  R1                1                  6
  R2                3                  9
  RX                4                 21
D73V11, continuous

Clustering(74) Variable = Xq loss mutation analysis
D74V1, survival
                   sevent
clus2                 0   1
  XQ LOSS MUTATED     1   2
  XQ LOSS WILD-TYPE 121  16
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
                3               137 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
                2                16 
$`XQ LOSS MUTATED`
TCGA-CG-4469 TCGA-CG-5725 TCGA-D7-6519 
        7.07        15.02        15.65 

$`XQ LOSS WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-6452 TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6458 
        5.62         0.10         0.95         1.41         1.35         1.35 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
        0.85         0.82         0.62         0.62         1.71         2.17 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
        0.99         1.22         0.66         1.12         0.76         0.66 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
        0.26         1.22         1.48         0.46         1.25         0.13 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 
        1.05         0.82         0.69         0.16         4.54         0.99 
TCGA-BR-7901 TCGA-BR-7957 TCGA-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-BR-8592 TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        0.20         0.59         0.92         0.39         0.79         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J8 TCGA-BR-A4J9 
        0.79         0.53         0.43         0.13         0.23         0.10 
TCGA-BR-A4PF TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        0.72         0.82         0.69         0.36         0.49         0.30 
TCGA-CD-5803 TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
        0.07        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
       52.96         8.05        54.05         4.01        14.01        29.98 
TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4460 TCGA-CG-4462 TCGA-CG-4465 
       47.05        19.07        12.03        21.99         1.02         8.98 
TCGA-CG-4466 TCGA-CG-4472 TCGA-CG-4474 TCGA-CG-4477 TCGA-CG-5716 TCGA-CG-5717 
       18.94        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-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-D7-6527 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-FP-8099 TCGA-FP-8209 
        0.39         0.20         3.02         3.58         1.02        59.05 
TCGA-FP-8631 TCGA-HJ-7597 TCGA-IN-7806 TCGA-IN-7808 TCGA-IP-7968 
        0.56        26.43         6.87         3.55         2.53 

  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
             7.07              0.07 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
            15.65             72.23 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
            15.02              1.22 
[1] "7.1 - 15.7 (15.0)" "0.1 - 72.2 (1.2)" 
       TCGA-B7-5816        TCGA-B7-5818        TCGA-BR-6452        TCGA-BR-6455 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BR-6457        TCGA-BR-6458        TCGA-BR-6563        TCGA-BR-6564 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BR-6565        TCGA-BR-6566        TCGA-BR-6705        TCGA-BR-6706 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BR-6707        TCGA-BR-6709        TCGA-BR-6710        TCGA-BR-6801 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BR-6802        TCGA-BR-6803        TCGA-BR-6852        TCGA-BR-7196 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BR-7197        TCGA-BR-7703        TCGA-BR-7704        TCGA-BR-7707 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BR-7715        TCGA-BR-7716        TCGA-BR-7717        TCGA-BR-7722 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BR-7723        TCGA-BR-7851        TCGA-BR-7901        TCGA-BR-7957 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-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-BR-8592        TCGA-BR-A4IU        TCGA-BR-A4IV        TCGA-BR-A4IY 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BR-A4IZ        TCGA-BR-A4J1        TCGA-BR-A4J2        TCGA-BR-A4J4 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BR-A4J5        TCGA-BR-A4J6        TCGA-BR-A4J8        TCGA-BR-A4J9 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BR-A4PF        TCGA-CD-5798        TCGA-CD-5799        TCGA-CD-5800 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-CD-5801        TCGA-CD-5802        TCGA-CD-5803        TCGA-CG-4300 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-CG-4301        TCGA-CG-4304        TCGA-CG-4305        TCGA-CG-4306 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-CG-4436        TCGA-CG-4437        TCGA-CG-4438        TCGA-CG-4440 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-CG-4441        TCGA-CG-4443        TCGA-CG-4444        TCGA-CG-4449 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-CG-4455        TCGA-CG-4460        TCGA-CG-4462        TCGA-CG-4465 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-CG-4466        TCGA-CG-4469        TCGA-CG-4472        TCGA-CG-4474 
"XQ LOSS WILD-TYPE"   "XQ LOSS MUTATED" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-CG-4477        TCGA-CG-5716        TCGA-CG-5717        TCGA-CG-5718 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-CG-5719        TCGA-CG-5720        TCGA-CG-5721        TCGA-CG-5722 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-CG-5723        TCGA-CG-5724        TCGA-CG-5725        TCGA-CG-5726 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE"   "XQ LOSS MUTATED" "XQ LOSS WILD-TYPE" 
       TCGA-CG-5727        TCGA-CG-5728        TCGA-CG-5730        TCGA-CG-5732 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-CG-5733        TCGA-CG-5734        TCGA-D7-5577        TCGA-D7-5578 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-D7-5579        TCGA-D7-6518        TCGA-D7-6519        TCGA-D7-6520 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE"   "XQ LOSS MUTATED" "XQ LOSS WILD-TYPE" 
       TCGA-D7-6521        TCGA-D7-6522        TCGA-D7-6524        TCGA-D7-6525 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-D7-6526        TCGA-D7-6527        TCGA-D7-6528        TCGA-D7-6815 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-D7-6817        TCGA-D7-6818        TCGA-D7-6820        TCGA-D7-6822 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EQ-5647        TCGA-EQ-8122        TCGA-F1-6177        TCGA-F1-6874 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-F1-6875        TCGA-FP-7735        TCGA-FP-7829        TCGA-FP-7916 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-FP-7998        TCGA-FP-8099        TCGA-FP-8209        TCGA-FP-8631 
"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 WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BR-7715        TCGA-BR-7716        TCGA-BR-7717        TCGA-BR-7722 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BR-7723        TCGA-BR-7851        TCGA-BR-7901        TCGA-BR-7957 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-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-BR-8592        TCGA-BR-A4IU        TCGA-BR-A4IV        TCGA-BR-A4IY 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BR-A4IZ        TCGA-BR-A4J1        TCGA-BR-A4J2        TCGA-BR-A4J4 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BR-A4J5        TCGA-BR-A4J6        TCGA-BR-A4J8        TCGA-BR-A4J9 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BR-A4PF        TCGA-CD-5798        TCGA-CD-5799        TCGA-CD-5800 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-CD-5801        TCGA-CD-5802        TCGA-CD-5803        TCGA-CG-4300 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-CG-4301        TCGA-CG-4304        TCGA-CG-4305        TCGA-CG-4306 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-CG-4436        TCGA-CG-4437        TCGA-CG-4438        TCGA-CG-4440 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-CG-4441        TCGA-CG-4443        TCGA-CG-4444        TCGA-CG-4449 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-CG-4455        TCGA-CG-4460        TCGA-CG-4462        TCGA-CG-4465 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-CG-4466        TCGA-CG-4469        TCGA-CG-4472        TCGA-CG-4474 
"XQ LOSS WILD-TYPE"   "XQ LOSS MUTATED" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-CG-4477        TCGA-CG-5716        TCGA-CG-5717        TCGA-CG-5718 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-CG-5719        TCGA-CG-5720        TCGA-CG-5721        TCGA-CG-5722 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-CG-5723        TCGA-CG-5724        TCGA-CG-5725        TCGA-CG-5726 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE"   "XQ LOSS MUTATED" "XQ LOSS WILD-TYPE" 
       TCGA-CG-5727        TCGA-CG-5728        TCGA-CG-5730        TCGA-CG-5732 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-CG-5733        TCGA-CG-5734        TCGA-D7-5577        TCGA-D7-5578 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-D7-5579        TCGA-D7-6518        TCGA-D7-6519        TCGA-D7-6520 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE"   "XQ LOSS MUTATED" "XQ LOSS WILD-TYPE" 
       TCGA-D7-6521        TCGA-D7-6522        TCGA-D7-6524        TCGA-D7-6525 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-D7-6526        TCGA-D7-6527        TCGA-D7-6528        TCGA-D7-6815 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-D7-6817        TCGA-D7-6818        TCGA-D7-6820        TCGA-D7-6822 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EQ-5647        TCGA-EQ-8122        TCGA-F1-6177        TCGA-F1-6874 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-F1-6875        TCGA-FP-7735        TCGA-FP-7829        TCGA-FP-7916 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-FP-7998        TCGA-FP-8099        TCGA-FP-8209        TCGA-FP-8631 
"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 WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BR-7715        TCGA-BR-7716        TCGA-BR-7717        TCGA-BR-7722 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BR-7723        TCGA-BR-7851        TCGA-BR-7901        TCGA-BR-7957 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-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-BR-8592        TCGA-BR-A4IU        TCGA-BR-A4IV        TCGA-BR-A4IY 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BR-A4IZ        TCGA-BR-A4J1        TCGA-BR-A4J2        TCGA-BR-A4J4 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BR-A4J5        TCGA-BR-A4J6        TCGA-BR-A4J8        TCGA-BR-A4J9 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BR-A4PF        TCGA-CD-5798        TCGA-CD-5799        TCGA-CD-5800 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-CD-5801        TCGA-CD-5802        TCGA-CD-5803        TCGA-CG-4300 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-CG-4301        TCGA-CG-4304        TCGA-CG-4305        TCGA-CG-4306 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-CG-4436        TCGA-CG-4437        TCGA-CG-4438        TCGA-CG-4440 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-CG-4441        TCGA-CG-4443        TCGA-CG-4444        TCGA-CG-4449 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-CG-4455        TCGA-CG-4460        TCGA-CG-4462        TCGA-CG-4465 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-CG-4466        TCGA-CG-4469        TCGA-CG-4472        TCGA-CG-4474 
"XQ LOSS WILD-TYPE"   "XQ LOSS MUTATED" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-CG-4477        TCGA-CG-5716        TCGA-CG-5717        TCGA-CG-5718 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-CG-5719        TCGA-CG-5720        TCGA-CG-5721        TCGA-CG-5722 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-CG-5723        TCGA-CG-5724        TCGA-CG-5725        TCGA-CG-5726 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE"   "XQ LOSS MUTATED" "XQ LOSS WILD-TYPE" 
       TCGA-CG-5727        TCGA-CG-5728        TCGA-CG-5730        TCGA-CG-5732 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-CG-5733        TCGA-CG-5734        TCGA-D7-5577        TCGA-D7-5578 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-D7-5579        TCGA-D7-6518        TCGA-D7-6519        TCGA-D7-6520 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE"   "XQ LOSS MUTATED" "XQ LOSS WILD-TYPE" 
       TCGA-D7-6521        TCGA-D7-6522        TCGA-D7-6524        TCGA-D7-6525 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-D7-6526        TCGA-D7-6527        TCGA-D7-6528        TCGA-D7-6815 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-D7-6817        TCGA-D7-6818        TCGA-D7-6820        TCGA-D7-6822 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EQ-5647        TCGA-EQ-8122        TCGA-F1-6177        TCGA-F1-6874 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-F1-6875        TCGA-FP-7735        TCGA-FP-7829        TCGA-FP-7916 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-FP-7998        TCGA-FP-8099        TCGA-FP-8209        TCGA-FP-8631 
"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    4
  XQ LOSS WILD-TYPE   68  103
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  FEMALE               2                68
  MALE                 4               103
                   vv
clus                STOMACH ADENOCARCINOMA - DIFFUSE TYPE
  XQ LOSS MUTATED                                       1
  XQ LOSS WILD-TYPE                                    24
                   vv
clus                STOMACH ADENOCARCINOMA - NOT OTHERWISE SPECIFIED (NOS)
  XQ LOSS MUTATED                                                        2
  XQ LOSS WILD-TYPE                                                     85
                   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                                                 9
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - PAPILLARY TYPE
  XQ LOSS MUTATED                                                    0
  XQ LOSS WILD-TYPE                                                  3
                   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                                                                     35
D74V4, multiclass
                   vv
clus                T1 T2 T3 T4
  XQ LOSS MUTATED    0  4  1  0
  XQ LOSS WILD-TYPE  6 50 63 43
D74V5, multiclass
    clus
vv   XQ LOSS MUTATED XQ LOSS WILD-TYPE
  T1               0                 6
  T2               4                50
  T3               1                63
  T4               0                43
                   vv
clus                N0 N1 N2 N3
  XQ LOSS MUTATED    1  2  0  2
  XQ LOSS WILD-TYPE 55 59 29 18
D74V6, multiclass
    clus
vv   XQ LOSS MUTATED XQ LOSS WILD-TYPE
  N0               1                55
  N1               2                59
  N2               0                29
  N3               2                18
                   vv
clus                 M0  M1  MX
  XQ LOSS MUTATED     6   0   0
  XQ LOSS WILD-TYPE 140  18  13
D74V7, multiclass
    clus
vv   XQ LOSS MUTATED XQ LOSS WILD-TYPE
  M0               6               140
  M1               0                18
  MX               0                13
                   vv
clus                 I II III IV
  XQ LOSS MUTATED    1  0   1  2
  XQ LOSS WILD-TYPE 25 48  57 27
D74V8, multiclass
     clus
vv    XQ LOSS MUTATED XQ LOSS WILD-TYPE
  I                 1                25
  II                0                48
  III               1                57
  IV                2                27
D74V9, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED      1    5
  XQ LOSS WILD-TYPE    4  167
     clus
vv    XQ LOSS MUTATED XQ LOSS WILD-TYPE
  NO                1                 4
  YES               5               167
                   vv
clus                 R0  R1  R2  RX
  XQ LOSS MUTATED     2   2   0   2
  XQ LOSS WILD-TYPE 121   5  12  23
D74V10, multiclass
    clus
vv   XQ LOSS MUTATED XQ LOSS WILD-TYPE
  R0               2               121
  R1               2                 5
  R2               0                12
  RX               2                23
D74V11, continuous
                                    V1.D 
                         "Time to Death" 
                                      V2 
                                   "AGE" 
                                      V3 
                                "GENDER" 
                                      V4 
                     "HISTOLOGICAL.TYPE" 
                                      V5 
                           "PATHOLOGY.T" 
                                      V6 
                           "PATHOLOGY.N" 
                                      V7 
                   "PATHOLOGICSPREAD(M)" 
                                      V8 
                           "TUMOR.STAGE" 
                                      V9 
"RADIATIONS.RADIATION.REGIMENINDICATION" 
                                     V10 
             "COMPLETENESS.OF.RESECTION" 
                                     V11 
                 "NUMBER.OF.LYMPH.NODES" 
> q(save="no")
