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

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> source("/xchip/tcga/gdac_prod/applications/process_mgmt/firehose_task_registry/tcga-gdac/GDAC_Correlate_Genomic_Events/broadinstitute.org/cancer.genome.analysis/10441/12/Correlate_Genomic_Events.R")
> result <- main("/xchip/tcga/gdac_prod/applications/process_mgmt/firehose_task_registry/tcga-gdac/GDAC_Correlate_Genomic_Events/broadinstitute.org/cancer.genome.analysis/10441/12/", "-nF=/xchip/tcga/Tools/Nozzle/v1.current", "-tTRUE", "-iD=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/LIHC-TP/4428362/transformed.cor.cli.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPicker/LIHC-TP/4397111/LIHC-TP.clin.merged.picked.txt", "-fF=", "-fC=3", "-fH=5", "-fW=9", "-fP=OUT", "-cP=1", "-cQ=0.25", "-MF=ONLYSIG", "-oT=LIHC-TP", "-nV=Nozzle.R1", "-OP=MUTSIG", "-iT=", "-iX=")
[1] "terrence_modification_tag"
[1] TRUE
[1] "nver"          "-nV=Nozzle.R1"
[1] "nfn"                                 "/xchip/tcga/Tools/Nozzle/v1.current"
[1] "Nozzle.R1"
[1] "successfully load Nozzle.R1"
[1] "ofn"         "-oT=LIHC-TP"
[1] "opt"        "-OP=MUTSIG"
[1] "tl"   "-iT="
[1] "dx"   "-iX="
[1] "opt"    "MUTSIG"
[1] "dx" ""  
[1] "cfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPicker/LIHC-TP/4397111/LIHC-TP.clin.merged.picked.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/LIHC-TP/4428362/transformed.cor.cli.txt"

nPatients in clinical file=127, in cluster file=139, common to both=117
[1]  80 117
[1] "1P GAIN MUTATION ANALYSIS"
[1] 3
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               17               100 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               17               100 
[1] "1Q GAIN MUTATION ANALYSIS"
[1] 3
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               64                53 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               64                53 
[1] "2P GAIN MUTATION ANALYSIS"
[1] 3
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               18                99 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               18                99 
[1] "2Q GAIN MUTATION ANALYSIS"
[1] 3
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               15               102 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               15               102 
[1] "3P GAIN MUTATION ANALYSIS"
[1] 3
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
                8               109 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
                8               109 
[1] "3Q GAIN MUTATION ANALYSIS"
[1] 3
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
                9               108 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
                9               108 
[1] "4P GAIN MUTATION ANALYSIS"
[1] 3
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                8               109 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                8               109 
[1] "4Q GAIN MUTATION ANALYSIS"
[1] 3
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                3               114 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                3               114 
[1] "5P GAIN MUTATION ANALYSIS"
[1] 3
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               47                70 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               47                70 
[1] "5Q GAIN MUTATION ANALYSIS"
[1] 3
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               36                81 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               36                81 
[1] "6P GAIN MUTATION ANALYSIS"
[1] 3
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               29                88 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               29                88 
[1] "6Q GAIN MUTATION ANALYSIS"
[1] 3
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               17               100 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               17               100 
[1] "7P GAIN MUTATION ANALYSIS"
[1] 3
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               37                80 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               37                80 
[1] "7Q GAIN MUTATION ANALYSIS"
[1] 3
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               39                78 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               39                78 
[1] "8P GAIN MUTATION ANALYSIS"
[1] 3
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               22                95 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               22                95 
[1] "8Q GAIN MUTATION ANALYSIS"
[1] 3
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               56                61 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               56                61 
[1] "9P GAIN MUTATION ANALYSIS"
[1] 3
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
                4               113 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
                4               113 
[1] "9Q GAIN MUTATION ANALYSIS"
[1] 3
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
                4               113 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
                4               113 
[1] "10P GAIN MUTATION ANALYSIS"
[1] 3
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                17                100 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                17                100 
[1] "10Q GAIN MUTATION ANALYSIS"
[1] 3
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                10                107 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                10                107 
[1] "11P GAIN MUTATION ANALYSIS"
[1] 3
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 5                112 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 5                112 
[1] "11Q GAIN MUTATION ANALYSIS"
[1] 3
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 4                113 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 4                113 
[1] "12P GAIN MUTATION ANALYSIS"
[1] 3
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                 8                109 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                 8                109 
[1] "12Q GAIN MUTATION ANALYSIS"
[1] 3
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                12                105 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                12                105 
[1] "13Q GAIN MUTATION ANALYSIS"
[1] 3
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                 9                108 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                 9                108 
[1] "14Q GAIN MUTATION ANALYSIS"
[1] 3
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                 8                109 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                 8                109 
[1] "15Q GAIN MUTATION ANALYSIS"
[1] 3
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                10                107 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                10                107 
[1] "16P GAIN MUTATION ANALYSIS"
[1] 3
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                11                106 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                11                106 
[1] "16Q GAIN MUTATION ANALYSIS"
[1] 3
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                 4                113 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                 4                113 
[1] "17P GAIN MUTATION ANALYSIS"
[1] 3
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                10                107 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                10                107 
[1] "17Q GAIN MUTATION ANALYSIS"
[1] 3
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                36                 81 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                36                 81 
[1] "18P GAIN MUTATION ANALYSIS"
[1] 3
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                 9                108 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                 9                108 
[1] "18Q GAIN MUTATION ANALYSIS"
[1] 3
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 9                108 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 9                108 
[1] "19P GAIN MUTATION ANALYSIS"
[1] 3
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                27                 90 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                27                 90 
[1] "19Q GAIN MUTATION ANALYSIS"
[1] 3
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                29                 88 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                29                 88 
[1] "20P GAIN MUTATION ANALYSIS"
[1] 3
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                34                 83 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                34                 83 
[1] "20Q GAIN MUTATION ANALYSIS"
[1] 3
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                36                 81 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                36                 81 
[1] "21Q GAIN MUTATION ANALYSIS"
[1] 3
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                10                107 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                10                107 
[1] "22Q GAIN MUTATION ANALYSIS"
[1] 3
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                16                101 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                16                101 
[1] "XQ GAIN MUTATION ANALYSIS"
[1] 3
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               24                93 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               24                93 
[1] "1P LOSS MUTATION ANALYSIS"
[1] 3
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               28                89 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               28                89 
[1] "1Q LOSS MUTATION ANALYSIS"
[1] 3
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               12               105 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               12               105 
[1] "2P LOSS MUTATION ANALYSIS"
[1] 3
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
                8               109 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
                8               109 
[1] "2Q LOSS MUTATION ANALYSIS"
[1] 3
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               10               107 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               10               107 
[1] "3P LOSS MUTATION ANALYSIS"
[1] 3
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               14               103 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               14               103 
[1] "3Q LOSS MUTATION ANALYSIS"
[1] 3
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
                6               111 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
                6               111 
[1] "4P LOSS MUTATION ANALYSIS"
[1] 3
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               28                89 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               28                89 
[1] "4Q LOSS MUTATION ANALYSIS"
[1] 3
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               37                80 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               37                80 
[1] "5P LOSS MUTATION ANALYSIS"
[1] 3
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
                9               108 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
                9               108 
[1] "5Q LOSS MUTATION ANALYSIS"
[1] 3
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               13               104 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               13               104 
[1] "6P LOSS MUTATION ANALYSIS"
[1] 3
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               13               104 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               13               104 
[1] "6Q LOSS MUTATION ANALYSIS"
[1] 3
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               35                82 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               35                82 
[1] "7P LOSS MUTATION ANALYSIS"
[1] 3
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
                8               109 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
                8               109 
[1] "7Q LOSS MUTATION ANALYSIS"
[1] 3
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
               11               106 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
               11               106 
[1] "8P LOSS MUTATION ANALYSIS"
[1] 3
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               56                61 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               56                61 
[1] "8Q LOSS MUTATION ANALYSIS"
[1] 3
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               14               103 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               14               103 
[1] "9P LOSS MUTATION ANALYSIS"
[1] 3
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               36                81 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               36                81 
[1] "9Q LOSS MUTATION ANALYSIS"
[1] 3
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               37                80 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               37                80 
[1] "10P LOSS MUTATION ANALYSIS"
[1] 3
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                13                104 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                13                104 
[1] "10Q LOSS MUTATION ANALYSIS"
[1] 3
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                26                 91 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                26                 91 
[1] "11P LOSS MUTATION ANALYSIS"
[1] 3
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                20                 97 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                20                 97 
[1] "11Q LOSS MUTATION ANALYSIS"
[1] 3
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                22                 95 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                22                 95 
[1] "12P LOSS MUTATION ANALYSIS"
[1] 3
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                21                 96 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                21                 96 
[1] "12Q LOSS MUTATION ANALYSIS"
[1] 3
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                12                105 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                12                105 
[1] "13Q LOSS MUTATION ANALYSIS"
[1] 3
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                40                 77 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                40                 77 
[1] "14Q LOSS MUTATION ANALYSIS"
[1] 3
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                38                 79 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                38                 79 
[1] "15Q LOSS MUTATION ANALYSIS"
[1] 3
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                22                 95 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                22                 95 
[1] "16P LOSS MUTATION ANALYSIS"
[1] 3
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                33                 84 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                33                 84 
[1] "16Q LOSS MUTATION ANALYSIS"
[1] 3
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                43                 74 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                43                 74 
[1] "17P LOSS MUTATION ANALYSIS"
[1] 3
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                58                 59 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                58                 59 
[1] "17Q LOSS MUTATION ANALYSIS"
[1] 3
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                 9                108 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                 9                108 
[1] "18P LOSS MUTATION ANALYSIS"
[1] 3
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                18                 99 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                18                 99 
[1] "18Q LOSS MUTATION ANALYSIS"
[1] 3
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                19                 98 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                19                 98 
[1] "19P LOSS MUTATION ANALYSIS"
[1] 3
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                14                103 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                14                103 
[1] "19Q LOSS MUTATION ANALYSIS"
[1] 3
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                10                107 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                10                107 
[1] "20P LOSS MUTATION ANALYSIS"
[1] 3
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                 7                110 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                 7                110 
[1] "20Q LOSS MUTATION ANALYSIS"
[1] 3
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 4                113 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 4                113 
[1] "21Q LOSS MUTATION ANALYSIS"
[1] 3
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                29                 88 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                29                 88 
[1] "22Q LOSS MUTATION ANALYSIS"
[1] 3
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                20                 97 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                20                 97 
[1] "XQ LOSS MUTATION ANALYSIS"
[1] 3
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               16               101 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               16               101 
[1] "terrence_modification_tag"
[1] TRUE
[1] "data2feature, selection="
 [1] "YEARSTOBIRTH"                          
 [2] "VITALSTATUS"                           
 [3] "DAYSTODEATH"                           
 [4] "DAYSTOLASTFOLLOWUP"                    
 [5] "PRIMARYSITEOFDESEASE"                  
 [6] "NEOPLASM.DISEASESTAGE"                 
 [7] "PATHOLOGY.T.STAGE"                     
 [8] "PATHOLOGY.N.STAGE"                     
 [9] "PATHOLOGY.M.STAGE"                     
[10] "DCCUPLOADDATE"                         
[11] "GENDER"                                
[12] "DATEOFINITIALPATHOLOGICDIAGNOSIS"      
[13] "DAYSTOLASTKNOWNALIVE"                  
[14] "RADIATIONTHERAPY"                      
[15] "HISTOLOGICALTYPE"                      
[16] "RADIATIONS.RADIATION.REGIMENINDICATION"
[17] "COMPLETENESS.OF.RESECTION"             
[18] "BATCHNUMBER"                           

Input Data has 18 rows and 117 columns.

[1] "Batch" "18"   
[1] "Last Follow UP"
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T 
          NA          849           NA           NA           NA           NA 
TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 
          NA           NA           NA           NA           NA           NA 
TCGA-BC-A112 TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 
          NA         1351          420            8          498          289 
TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-5264 
           2           NA           NA           NA           NA           NA 
TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A113 
          NA            3            2            3            4         2425 
TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A 
          NA           NA           NA         3436           NA           79 
TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB 
          NA          662           NA           NA         2414         2017 
TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EH TCGA-DD-A1EI 
         601         2301          203           NA         1495          183 
TCGA-DD-A1EJ TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A39Z 
         887           NA           NA           NA           NA           NA 
TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 
          NA           NA           NA           NA           NA           NA 
TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4ND 
          NA           NA           NA           NA         1008         2232 
TCGA-DD-A4NE TCGA-DD-A4NF TCGA-DD-A4NG TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ 
          NA          428          454          433          328          458 
TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ 
          NA         1711           NA         1869         2849           NA 
TCGA-ED-A459 TCGA-ED-A5KG TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB 
           7            6          330          236          357           60 
TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A23B 
          19           97           13           NA           NA          987 
TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 
          NA           NA            6           NA           NA            4 
TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T 
           1           10         1836           12           37         1552 
TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A25Z 
        1636          860          934         1779           NA          655 
TCGA-G3-A3CG TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SJ 
         673          780          179          594          585          364 
TCGA-G3-A5SK TCGA-G3-A5SL TCGA-G3-A5SM 
         302          243          133 
Variable 1:'AGE':	nDistinctValues=48,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYSTODEATH':	nDistinctValues=52,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'DAYSTOLASTFOLLOWUP':	nDistinctValues=62,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 5:'PRIMARY.SITE.OF.DISEASE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 6:'NEOPLASM.DISEASESTAGE':	nDistinctValues=9,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'PATHOLOGY.T.STAGE':	nDistinctValues=6,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'PATHOLOGY.N.STAGE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'PATHOLOGY.M.STAGE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'DCCUPLOADDAY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 11:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 12:'DAYOFINITIALPATHOLOGICDIAGNOSIS':	nDistinctValues=17,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 13:'DAYSTOLASTKNOWNALIVE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 14:'RADIATION.THERAPY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 15:'HISTOLOGICAL.TYPE':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 16:'RADIATIONS.RADIATION.REGIMENINDICATION':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 17:'COMPLETENESS.OF.RESECTION':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 18:'BATCH.NUMBER':	nDistinctValues=10,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
[1] "AGE"                       "NEOPLASM.DISEASESTAGE"    
[3] "PATHOLOGY.T.STAGE"         "PATHOLOGY.N.STAGE"        
[5] "PATHOLOGY.M.STAGE"         "GENDER"                   
[7] "COMPLETENESS.OF.RESECTION"
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T" "3"          
[1] "PATHOLOGY.N" "4"          
Output Data has 117 columns, 1 survival variables, and 7 non-survival variables.
AGE, nv=48, binary=FALSE, numeric=TRUE
NEOPLASM.DISEASESTAGE, nv=9, binary=FALSE, numeric=FALSE
PATHOLOGY.T.STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.T',vnm)"
vv
T1 T2 T3 T4 
48 28 34  6 
[1] "table(vv)"
vv
T1 T2 T3 T4 
48 28 34  6 
$ClinVariableName
[1] "PATHOLOGY.T.STAGE"

$Table
vv
T1 T2 T3 T4 
48 28 34  6 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


T1 T2 T3 T4 
48 28 34  6 
PATHOLOGY.N.STAGE, nv=2, binary=FALSE, numeric=TRUE
PATHOLOGY.M.STAGE, nv=3, binary=FALSE, numeric=FALSE
GENDER, nv=2, binary=FALSE, numeric=FALSE
COMPLETENESS.OF.RESECTION, nv=4, binary=FALSE, numeric=FALSE

Clustering(1) Variable = 1P GAIN MUTATION ANALYSIS
D1V1, survival
                   sevent
clus2                0  1
  1P GAIN MUTATED   10  7
  1P GAIN WILD-TYPE 51 46
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               17                97 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
                7                46 
$`1P GAIN MUTATED`
TCGA-BC-A10Q TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A216 TCGA-CC-5262 TCGA-DD-A114 
       37.32        27.52         2.99        44.42         3.39        37.74 
TCGA-DD-A11A TCGA-DD-A39Y TCGA-DD-A4NJ TCGA-DD-A4NN TCGA-ED-A459 TCGA-EP-A12J 
        2.60         5.59        15.06        29.56         0.23        10.85 
TCGA-EP-A26S TCGA-G3-A25W TCGA-G3-A3CJ TCGA-G3-A5SJ TCGA-G3-A5SK 
        7.76        30.71        19.53        11.97         9.93 

$`1P GAIN WILD-TYPE`
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10X 
       48.99        27.91        10.13        46.78        27.52        25.32 
TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A217 TCGA-BC-A3KF 
       23.34         1.12        69.57         5.03        13.81         0.26 
TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5263 
       16.37         9.50         0.07         2.86         3.02         4.24 
TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A113 
        3.32         0.10         0.07         0.10         0.13        79.73 
TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11B TCGA-DD-A11C 
       83.57        53.29       112.96         7.33         0.46        21.76 
TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED 
       51.25        90.67        79.36        66.31        19.76        75.65 
TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EL 
        6.67        12.95        49.15         6.02        29.16        13.64 
TCGA-DD-A39V TCGA-DD-A39X TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 
       21.14        55.66        19.73        25.81         7.66        70.06 
TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A8 
       17.59        20.12       102.74       107.11        13.78         0.36 
TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4ND TCGA-DD-A4NE TCGA-DD-A4NF TCGA-DD-A4NG 
       30.58        33.14        73.38        21.67        14.07        14.93 
TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NO TCGA-DD-A4NP 
       14.24        10.78        39.75        56.25        61.45        93.67 
TCGA-DD-A4NQ TCGA-ED-A5KG TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL 
       12.26         0.20        11.74         1.97         0.62         3.19 
TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-A3I0 
        0.43        23.01        14.40        32.45        19.07         0.20 
TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZP TCGA-FV-A4ZQ 
        6.35         0.13         0.03         0.33        60.36         0.39 
TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25X TCGA-G3-A25Y 
        1.22        51.02        53.79        28.27        58.49        14.86 
TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CK TCGA-G3-A5SL 
       21.53        22.13        25.64         5.88        19.23         7.99 
TCGA-G3-A5SM 
        4.37 

  1P GAIN MUTATED 1P GAIN WILD-TYPE 
             0.23              0.03 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
            44.42            112.96 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
            11.97             17.59 
[1] "0.2 - 44.4 (12.0)"  "0.0 - 113.0 (17.6)"
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE"   "1P GAIN MUTATED" "1P GAIN WILD-TYPE" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE"   "1P GAIN MUTATED"   "1P GAIN MUTATED" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
"1P GAIN WILD-TYPE"   "1P GAIN MUTATED" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-BC-A5W4        TCGA-CC-5258        TCGA-CC-5260 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CC-5261        TCGA-CC-5262        TCGA-CC-5263        TCGA-CC-A1HT 
"1P GAIN WILD-TYPE"   "1P GAIN MUTATED" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CC-A3M9        TCGA-CC-A3MA        TCGA-CC-A3MB        TCGA-CC-A3MC 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DD-A113        TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116 
"1P GAIN WILD-TYPE"   "1P GAIN MUTATED" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DD-A118        TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE"   "1P GAIN MUTATED" "1P GAIN WILD-TYPE" 
       TCGA-DD-A11C        TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EA 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DD-A1EB        TCGA-DD-A1EC        TCGA-DD-A1ED        TCGA-DD-A1EE 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DD-A1EF        TCGA-DD-A1EH        TCGA-DD-A1EI        TCGA-DD-A1EJ 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DD-A1EL        TCGA-DD-A39V        TCGA-DD-A39X        TCGA-DD-A39Y 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE"   "1P GAIN MUTATED" 
       TCGA-DD-A39Z        TCGA-DD-A3A0        TCGA-DD-A3A1        TCGA-DD-A3A2 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DD-A3A3        TCGA-DD-A3A4        TCGA-DD-A3A5        TCGA-DD-A3A6 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DD-A3A7        TCGA-DD-A3A8        TCGA-DD-A3A9        TCGA-DD-A4NA 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DD-A4ND        TCGA-DD-A4NE        TCGA-DD-A4NF        TCGA-DD-A4NG 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DD-A4NH        TCGA-DD-A4NI        TCGA-DD-A4NJ        TCGA-DD-A4NK 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE"   "1P GAIN MUTATED" "1P GAIN WILD-TYPE" 
       TCGA-DD-A4NL        TCGA-DD-A4NN        TCGA-DD-A4NO        TCGA-DD-A4NP 
"1P GAIN WILD-TYPE"   "1P GAIN MUTATED" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DD-A4NQ        TCGA-ED-A459        TCGA-ED-A5KG        TCGA-EP-A12J 
"1P GAIN WILD-TYPE"   "1P GAIN MUTATED" "1P GAIN WILD-TYPE"   "1P GAIN MUTATED" 
       TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC 
  "1P GAIN MUTATED" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-EP-A3JL        TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-FV-A23B        TCGA-FV-A2QR        TCGA-FV-A3I0        TCGA-FV-A3R2 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-FV-A3R3        TCGA-FV-A495        TCGA-FV-A496        TCGA-FV-A4ZP 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-FV-A4ZQ        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"1P GAIN WILD-TYPE"   "1P GAIN MUTATED" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-G3-A3CJ        TCGA-G3-A3CK        TCGA-G3-A5SJ        TCGA-G3-A5SK 
  "1P GAIN MUTATED" "1P GAIN WILD-TYPE"   "1P GAIN MUTATED"   "1P GAIN MUTATED" 
       TCGA-G3-A5SL        TCGA-G3-A5SM 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE"   "1P GAIN MUTATED" "1P GAIN WILD-TYPE" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE"   "1P GAIN MUTATED"   "1P GAIN MUTATED" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
"1P GAIN WILD-TYPE"   "1P GAIN MUTATED" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-BC-A5W4        TCGA-CC-5258        TCGA-CC-5260 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CC-5261        TCGA-CC-5262        TCGA-CC-5263        TCGA-CC-A1HT 
"1P GAIN WILD-TYPE"   "1P GAIN MUTATED" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CC-A3M9        TCGA-CC-A3MA        TCGA-CC-A3MB        TCGA-CC-A3MC 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DD-A113        TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116 
"1P GAIN WILD-TYPE"   "1P GAIN MUTATED" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DD-A118        TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE"   "1P GAIN MUTATED" "1P GAIN WILD-TYPE" 
       TCGA-DD-A11C        TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EA 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DD-A1EB        TCGA-DD-A1EC        TCGA-DD-A1ED        TCGA-DD-A1EE 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DD-A1EF        TCGA-DD-A1EH        TCGA-DD-A1EI        TCGA-DD-A1EJ 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DD-A1EL        TCGA-DD-A39V        TCGA-DD-A39X        TCGA-DD-A39Y 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE"   "1P GAIN MUTATED" 
       TCGA-DD-A39Z        TCGA-DD-A3A0        TCGA-DD-A3A1        TCGA-DD-A3A2 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DD-A3A3        TCGA-DD-A3A4        TCGA-DD-A3A5        TCGA-DD-A3A6 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DD-A3A7        TCGA-DD-A3A8        TCGA-DD-A3A9        TCGA-DD-A4NA 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DD-A4ND        TCGA-DD-A4NE        TCGA-DD-A4NF        TCGA-DD-A4NG 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DD-A4NH        TCGA-DD-A4NI        TCGA-DD-A4NJ        TCGA-DD-A4NK 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE"   "1P GAIN MUTATED" "1P GAIN WILD-TYPE" 
       TCGA-DD-A4NL        TCGA-DD-A4NN        TCGA-DD-A4NO        TCGA-DD-A4NP 
"1P GAIN WILD-TYPE"   "1P GAIN MUTATED" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DD-A4NQ        TCGA-ED-A459        TCGA-ED-A5KG        TCGA-EP-A12J 
"1P GAIN WILD-TYPE"   "1P GAIN MUTATED" "1P GAIN WILD-TYPE"   "1P GAIN MUTATED" 
       TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC 
  "1P GAIN MUTATED" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-EP-A3JL        TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-FV-A23B        TCGA-FV-A2QR        TCGA-FV-A3I0        TCGA-FV-A3R2 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-FV-A3R3        TCGA-FV-A495        TCGA-FV-A496        TCGA-FV-A4ZP 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-FV-A4ZQ        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"1P GAIN WILD-TYPE"   "1P GAIN MUTATED" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-G3-A3CJ        TCGA-G3-A3CK        TCGA-G3-A5SJ        TCGA-G3-A5SK 
  "1P GAIN MUTATED" "1P GAIN WILD-TYPE"   "1P GAIN MUTATED"   "1P GAIN MUTATED" 
       TCGA-G3-A5SL        TCGA-G3-A5SM 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE"   "1P GAIN MUTATED" "1P GAIN WILD-TYPE" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE"   "1P GAIN MUTATED"   "1P GAIN MUTATED" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
"1P GAIN WILD-TYPE"   "1P GAIN MUTATED" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-BC-A5W4        TCGA-CC-5258        TCGA-CC-5260 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CC-5261        TCGA-CC-5262        TCGA-CC-5263        TCGA-CC-A1HT 
"1P GAIN WILD-TYPE"   "1P GAIN MUTATED" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CC-A3M9        TCGA-CC-A3MA        TCGA-CC-A3MB        TCGA-CC-A3MC 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DD-A113        TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116 
"1P GAIN WILD-TYPE"   "1P GAIN MUTATED" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DD-A118        TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE"   "1P GAIN MUTATED" "1P GAIN WILD-TYPE" 
       TCGA-DD-A11C        TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EA 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DD-A1EB        TCGA-DD-A1EC        TCGA-DD-A1ED        TCGA-DD-A1EE 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DD-A1EF        TCGA-DD-A1EH        TCGA-DD-A1EI        TCGA-DD-A1EJ 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DD-A1EL        TCGA-DD-A39V        TCGA-DD-A39X        TCGA-DD-A39Y 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE"   "1P GAIN MUTATED" 
       TCGA-DD-A39Z        TCGA-DD-A3A0        TCGA-DD-A3A1        TCGA-DD-A3A2 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DD-A3A3        TCGA-DD-A3A4        TCGA-DD-A3A5        TCGA-DD-A3A6 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DD-A3A7        TCGA-DD-A3A8        TCGA-DD-A3A9        TCGA-DD-A4NA 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DD-A4ND        TCGA-DD-A4NE        TCGA-DD-A4NF        TCGA-DD-A4NG 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DD-A4NH        TCGA-DD-A4NI        TCGA-DD-A4NJ        TCGA-DD-A4NK 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE"   "1P GAIN MUTATED" "1P GAIN WILD-TYPE" 
       TCGA-DD-A4NL        TCGA-DD-A4NN        TCGA-DD-A4NO        TCGA-DD-A4NP 
"1P GAIN WILD-TYPE"   "1P GAIN MUTATED" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DD-A4NQ        TCGA-ED-A459        TCGA-ED-A5KG        TCGA-EP-A12J 
"1P GAIN WILD-TYPE"   "1P GAIN MUTATED" "1P GAIN WILD-TYPE"   "1P GAIN MUTATED" 
       TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC 
  "1P GAIN MUTATED" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-EP-A3JL        TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-FV-A23B        TCGA-FV-A2QR        TCGA-FV-A3I0        TCGA-FV-A3R2 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-FV-A3R3        TCGA-FV-A495        TCGA-FV-A496        TCGA-FV-A4ZP 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-FV-A4ZQ        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"1P GAIN WILD-TYPE"   "1P GAIN MUTATED" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-G3-A3CJ        TCGA-G3-A3CK        TCGA-G3-A5SJ        TCGA-G3-A5SK 
  "1P GAIN MUTATED" "1P GAIN WILD-TYPE"   "1P GAIN MUTATED"   "1P GAIN MUTATED" 
       TCGA-G3-A5SL        TCGA-G3-A5SM 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
[1] "hr=" "1.3"
D1V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  1P GAIN MUTATED         7        4         0          1          1          1
  1P GAIN WILD-TYPE      38       21         2         24          2          3
                   vv
clus                STAGE IV STAGE IVA STAGE IVB
  1P GAIN MUTATED          0         0         0
  1P GAIN WILD-TYPE        1         1         1
D1V3, multiclass
                   vv
clus                T1 T2 T3 T4
  1P GAIN MUTATED    7  6  2  2
  1P GAIN WILD-TYPE 41 22 32  4
D1V4, multiclass
    clus
vv   1P GAIN MUTATED 1P GAIN WILD-TYPE
  T1               7                41
  T2               6                22
  T3               2                32
  T4               2                 4
D1V5, binary
                   cls
clus                 0  1
  1P GAIN MUTATED    8  0
  1P GAIN WILD-TYPE 66  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED      8    0
  1P GAIN WILD-TYPE   66    3
   clus
vv  1P GAIN MUTATED 1P GAIN WILD-TYPE
  0               8                66
  1               0                 3
                   vv
clus                M0 M1 MX
  1P GAIN MUTATED   12  0  5
  1P GAIN WILD-TYPE 78  2 20
D1V6, multiclass
    clus
vv   1P GAIN MUTATED 1P GAIN WILD-TYPE
  M0              12                78
  M1               0                 2
  MX               5                20
D1V7, binary
                   cls
clus                 0  1
  1P GAIN MUTATED    5 12
  1P GAIN WILD-TYPE 39 61
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED      5   12
  1P GAIN WILD-TYPE   39   61
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  FEMALE               5                39
  MALE                12                61
                   vv
clus                R0 R1 R2 RX
  1P GAIN MUTATED   12  3  0  0
  1P GAIN WILD-TYPE 81  7  1  8
D1V8, multiclass
    clus
vv   1P GAIN MUTATED 1P GAIN WILD-TYPE
  R0              12                81
  R1               3                 7
  R2               0                 1
  RX               0                 8

Clustering(2) Variable = 1Q GAIN MUTATION ANALYSIS
D2V1, survival
                   sevent
clus2                0  1
  1Q GAIN MUTATED   33 29
  1Q GAIN WILD-TYPE 28 24
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               62                52 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               29                24 
$`1Q GAIN MUTATED`
TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10Y TCGA-BC-A112 
       37.32        10.13        27.52         2.99        23.34         5.03 
TCGA-BC-A216 TCGA-BC-A3KG TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-A3MA TCGA-CC-A3MC 
       44.42        16.37         3.02         3.39         0.07         0.13 
TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11C 
       79.73        37.74       112.96         7.33         2.60        21.76 
TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EH TCGA-DD-A1EL 
       90.67        79.36         6.67        12.95        49.15        13.64 
TCGA-DD-A39V TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A3 TCGA-DD-A3A7 
       21.14         5.59        19.73        25.81        17.59        13.78 
TCGA-DD-A3A8 TCGA-DD-A3A9 TCGA-DD-A4NF TCGA-DD-A4NG TCGA-DD-A4NH TCGA-DD-A4NI 
        0.36        30.58        14.07        14.93        14.24        10.78 
TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NQ TCGA-ED-A459 
       15.06        39.75        29.56        61.45        12.26         0.23 
TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL 
       10.85         7.76        11.74         1.97         0.62         3.19 
TCGA-FV-A2QR TCGA-FV-A3R3 TCGA-FV-A495 TCGA-G3-A25S TCGA-G3-A25W TCGA-G3-A25X 
       19.07         0.13         0.03         1.22        30.71        58.49 
TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SK 
       14.86        21.53        22.13        19.53        19.23         9.93 
TCGA-G3-A5SL TCGA-G3-A5SM 
        7.99         4.37 

$`1Q GAIN WILD-TYPE`
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10X TCGA-BC-A10Z 
       48.99        27.91        46.78        27.52        25.32         1.12 
TCGA-BC-A110 TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A5W4 TCGA-CC-5258 TCGA-CC-5260 
       69.57        13.81         0.26         9.50         0.07         2.86 
TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MB TCGA-DD-A115 TCGA-DD-A116 
        4.24         3.32         0.10         0.10        83.57        53.29 
TCGA-DD-A11B TCGA-DD-A11D TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EI 
        0.46        51.25        66.31        19.76        75.65         6.02 
TCGA-DD-A1EJ TCGA-DD-A39X TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A4 TCGA-DD-A3A5 
       29.16        55.66         7.66        70.06        20.12       102.74 
TCGA-DD-A3A6 TCGA-DD-A4NA TCGA-DD-A4ND TCGA-DD-A4NE TCGA-DD-A4NL TCGA-DD-A4NP 
      107.11        33.14        73.38        21.67        56.25        93.67 
TCGA-ED-A5KG TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A3I0 
        0.20         0.43        23.01        14.40        32.45         0.20 
TCGA-FV-A3R2 TCGA-FV-A496 TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25T TCGA-G3-A25U 
        6.35         0.33        60.36         0.39        51.02        53.79 
TCGA-G3-A25V TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A5SJ 
       28.27        25.64         5.88        11.97 

  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
             0.03              0.07 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
           112.96            107.11 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
           14.155            24.165 
[1] "0.0 - 113.0 (14.2)" "0.1 - 107.1 (24.2)"
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
  "1Q GAIN MUTATED"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-BC-A5W4        TCGA-CC-5258        TCGA-CC-5260 
  "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-CC-5261        TCGA-CC-5262        TCGA-CC-5263        TCGA-CC-A1HT 
  "1Q GAIN MUTATED"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-CC-A3M9        TCGA-CC-A3MA        TCGA-CC-A3MB        TCGA-CC-A3MC 
"1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" 
       TCGA-DD-A113        TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116 
  "1Q GAIN MUTATED"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-DD-A118        TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B 
  "1Q GAIN MUTATED"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" 
       TCGA-DD-A11C        TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EA 
  "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED" 
       TCGA-DD-A1EB        TCGA-DD-A1EC        TCGA-DD-A1ED        TCGA-DD-A1EE 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" 
       TCGA-DD-A1EF        TCGA-DD-A1EH        TCGA-DD-A1EI        TCGA-DD-A1EJ 
  "1Q GAIN MUTATED"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-DD-A1EL        TCGA-DD-A39V        TCGA-DD-A39X        TCGA-DD-A39Y 
  "1Q GAIN MUTATED"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" 
       TCGA-DD-A39Z        TCGA-DD-A3A0        TCGA-DD-A3A1        TCGA-DD-A3A2 
  "1Q GAIN MUTATED"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-DD-A3A3        TCGA-DD-A3A4        TCGA-DD-A3A5        TCGA-DD-A3A6 
  "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-DD-A3A7        TCGA-DD-A3A8        TCGA-DD-A3A9        TCGA-DD-A4NA 
  "1Q GAIN MUTATED"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" 
       TCGA-DD-A4ND        TCGA-DD-A4NE        TCGA-DD-A4NF        TCGA-DD-A4NG 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED" 
       TCGA-DD-A4NH        TCGA-DD-A4NI        TCGA-DD-A4NJ        TCGA-DD-A4NK 
  "1Q GAIN MUTATED"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED" 
       TCGA-DD-A4NL        TCGA-DD-A4NN        TCGA-DD-A4NO        TCGA-DD-A4NP 
"1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" 
       TCGA-DD-A4NQ        TCGA-ED-A459        TCGA-ED-A5KG        TCGA-EP-A12J 
  "1Q GAIN MUTATED"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" 
       TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC 
  "1Q GAIN MUTATED"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED" 
       TCGA-EP-A3JL        TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT 
  "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-FV-A23B        TCGA-FV-A2QR        TCGA-FV-A3I0        TCGA-FV-A3R2 
"1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-FV-A3R3        TCGA-FV-A495        TCGA-FV-A496        TCGA-FV-A4ZP 
  "1Q GAIN MUTATED"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-FV-A4ZQ        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI 
  "1Q GAIN MUTATED"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-G3-A3CJ        TCGA-G3-A3CK        TCGA-G3-A5SJ        TCGA-G3-A5SK 
  "1Q GAIN MUTATED"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" 
       TCGA-G3-A5SL        TCGA-G3-A5SM 
  "1Q GAIN MUTATED"   "1Q GAIN MUTATED" 
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
  "1Q GAIN MUTATED"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-BC-A5W4        TCGA-CC-5258        TCGA-CC-5260 
  "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-CC-5261        TCGA-CC-5262        TCGA-CC-5263        TCGA-CC-A1HT 
  "1Q GAIN MUTATED"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-CC-A3M9        TCGA-CC-A3MA        TCGA-CC-A3MB        TCGA-CC-A3MC 
"1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" 
       TCGA-DD-A113        TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116 
  "1Q GAIN MUTATED"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-DD-A118        TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B 
  "1Q GAIN MUTATED"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" 
       TCGA-DD-A11C        TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EA 
  "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED" 
       TCGA-DD-A1EB        TCGA-DD-A1EC        TCGA-DD-A1ED        TCGA-DD-A1EE 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" 
       TCGA-DD-A1EF        TCGA-DD-A1EH        TCGA-DD-A1EI        TCGA-DD-A1EJ 
  "1Q GAIN MUTATED"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-DD-A1EL        TCGA-DD-A39V        TCGA-DD-A39X        TCGA-DD-A39Y 
  "1Q GAIN MUTATED"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" 
       TCGA-DD-A39Z        TCGA-DD-A3A0        TCGA-DD-A3A1        TCGA-DD-A3A2 
  "1Q GAIN MUTATED"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-DD-A3A3        TCGA-DD-A3A4        TCGA-DD-A3A5        TCGA-DD-A3A6 
  "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-DD-A3A7        TCGA-DD-A3A8        TCGA-DD-A3A9        TCGA-DD-A4NA 
  "1Q GAIN MUTATED"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" 
       TCGA-DD-A4ND        TCGA-DD-A4NE        TCGA-DD-A4NF        TCGA-DD-A4NG 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED" 
       TCGA-DD-A4NH        TCGA-DD-A4NI        TCGA-DD-A4NJ        TCGA-DD-A4NK 
  "1Q GAIN MUTATED"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED" 
       TCGA-DD-A4NL        TCGA-DD-A4NN        TCGA-DD-A4NO        TCGA-DD-A4NP 
"1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" 
       TCGA-DD-A4NQ        TCGA-ED-A459        TCGA-ED-A5KG        TCGA-EP-A12J 
  "1Q GAIN MUTATED"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" 
       TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC 
  "1Q GAIN MUTATED"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED" 
       TCGA-EP-A3JL        TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT 
  "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-FV-A23B        TCGA-FV-A2QR        TCGA-FV-A3I0        TCGA-FV-A3R2 
"1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-FV-A3R3        TCGA-FV-A495        TCGA-FV-A496        TCGA-FV-A4ZP 
  "1Q GAIN MUTATED"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-FV-A4ZQ        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI 
  "1Q GAIN MUTATED"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-G3-A3CJ        TCGA-G3-A3CK        TCGA-G3-A5SJ        TCGA-G3-A5SK 
  "1Q GAIN MUTATED"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" 
       TCGA-G3-A5SL        TCGA-G3-A5SM 
  "1Q GAIN MUTATED"   "1Q GAIN MUTATED" 
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
  "1Q GAIN MUTATED"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-BC-A5W4        TCGA-CC-5258        TCGA-CC-5260 
  "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-CC-5261        TCGA-CC-5262        TCGA-CC-5263        TCGA-CC-A1HT 
  "1Q GAIN MUTATED"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-CC-A3M9        TCGA-CC-A3MA        TCGA-CC-A3MB        TCGA-CC-A3MC 
"1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" 
       TCGA-DD-A113        TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116 
  "1Q GAIN MUTATED"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-DD-A118        TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B 
  "1Q GAIN MUTATED"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" 
       TCGA-DD-A11C        TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EA 
  "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED" 
       TCGA-DD-A1EB        TCGA-DD-A1EC        TCGA-DD-A1ED        TCGA-DD-A1EE 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" 
       TCGA-DD-A1EF        TCGA-DD-A1EH        TCGA-DD-A1EI        TCGA-DD-A1EJ 
  "1Q GAIN MUTATED"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-DD-A1EL        TCGA-DD-A39V        TCGA-DD-A39X        TCGA-DD-A39Y 
  "1Q GAIN MUTATED"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" 
       TCGA-DD-A39Z        TCGA-DD-A3A0        TCGA-DD-A3A1        TCGA-DD-A3A2 
  "1Q GAIN MUTATED"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-DD-A3A3        TCGA-DD-A3A4        TCGA-DD-A3A5        TCGA-DD-A3A6 
  "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-DD-A3A7        TCGA-DD-A3A8        TCGA-DD-A3A9        TCGA-DD-A4NA 
  "1Q GAIN MUTATED"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" 
       TCGA-DD-A4ND        TCGA-DD-A4NE        TCGA-DD-A4NF        TCGA-DD-A4NG 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED" 
       TCGA-DD-A4NH        TCGA-DD-A4NI        TCGA-DD-A4NJ        TCGA-DD-A4NK 
  "1Q GAIN MUTATED"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED" 
       TCGA-DD-A4NL        TCGA-DD-A4NN        TCGA-DD-A4NO        TCGA-DD-A4NP 
"1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" 
       TCGA-DD-A4NQ        TCGA-ED-A459        TCGA-ED-A5KG        TCGA-EP-A12J 
  "1Q GAIN MUTATED"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" 
       TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC 
  "1Q GAIN MUTATED"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED" 
       TCGA-EP-A3JL        TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT 
  "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-FV-A23B        TCGA-FV-A2QR        TCGA-FV-A3I0        TCGA-FV-A3R2 
"1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-FV-A3R3        TCGA-FV-A495        TCGA-FV-A496        TCGA-FV-A4ZP 
  "1Q GAIN MUTATED"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-FV-A4ZQ        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI 
  "1Q GAIN MUTATED"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-G3-A3CJ        TCGA-G3-A3CK        TCGA-G3-A5SJ        TCGA-G3-A5SK 
  "1Q GAIN MUTATED"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" 
       TCGA-G3-A5SL        TCGA-G3-A5SM 
  "1Q GAIN MUTATED"   "1Q GAIN MUTATED" 
[1] "hr=" "1.5"
D2V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  1Q GAIN MUTATED        23       19         1          9          3          1
  1Q GAIN WILD-TYPE      22        6         1         16          0          3
                   vv
clus                STAGE IV STAGE IVA STAGE IVB
  1Q GAIN MUTATED          1         0         1
  1Q GAIN WILD-TYPE        0         1         0
D2V3, multiclass
                   vv
clus                T1 T2 T3 T4
  1Q GAIN MUTATED   23 21 16  4
  1Q GAIN WILD-TYPE 25  7 18  2
D2V4, multiclass
    clus
vv   1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  T1              23                25
  T2              21                 7
  T3              16                18
  T4               4                 2
D2V5, binary
                   cls
clus                 0  1
  1Q GAIN MUTATED   40  0
  1Q GAIN WILD-TYPE 34  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED     40    0
  1Q GAIN WILD-TYPE   34    3
   clus
vv  1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  0              40                34
  1               0                 3
                   vv
clus                M0 M1 MX
  1Q GAIN MUTATED   48  2 14
  1Q GAIN WILD-TYPE 42  0 11
D2V6, multiclass
    clus
vv   1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  M0              48                42
  M1               2                 0
  MX              14                11
D2V7, binary
                   cls
clus                 0  1
  1Q GAIN MUTATED   20 44
  1Q GAIN WILD-TYPE 24 29
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED     20   44
  1Q GAIN WILD-TYPE   24   29
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  FEMALE              20                24
  MALE                44                29
                   vv
clus                R0 R1 R2 RX
  1Q GAIN MUTATED   51  5  1  4
  1Q GAIN WILD-TYPE 42  5  0  4
D2V8, multiclass
    clus
vv   1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  R0              51                42
  R1               5                 5
  R2               1                 0
  RX               4                 4

Clustering(3) Variable = 2P GAIN MUTATION ANALYSIS
D3V1, survival
                   sevent
clus2                0  1
  2P GAIN MUTATED    8 10
  2P GAIN WILD-TYPE 53 43
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               18                96 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               10                43 
$`2P GAIN MUTATED`
TCGA-BC-4072 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A5W4 TCGA-CC-A3M9 
       48.99        37.32        10.13        27.52         9.50         0.10 
TCGA-DD-A113 TCGA-DD-A1E9 TCGA-DD-A1EJ TCGA-DD-A1EL TCGA-DD-A39X TCGA-DD-A3A9 
       79.73        90.67        29.16        13.64        55.66        30.58 
TCGA-DD-A4NA TCGA-DD-A4NI TCGA-ES-A2HS TCGA-G3-A25T TCGA-G3-A25W TCGA-G3-A25Z 
       33.14        10.78        23.01        51.02        30.71        21.53 

$`2P GAIN WILD-TYPE`
TCGA-BC-4073 TCGA-BC-A10S TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y 
       27.91        46.78        27.52         2.99        25.32        23.34 
TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KF 
        1.12        69.57         5.03        44.42        13.81         0.26 
TCGA-BC-A3KG TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 
       16.37         0.07         2.86         3.02         3.39         4.24 
TCGA-CC-A1HT TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A114 TCGA-DD-A115 
        3.32         0.07         0.10         0.13        37.74        83.57 
TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C 
       53.29       112.96         7.33         2.60         0.46        21.76 
TCGA-DD-A11D TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE 
       51.25        79.36        66.31        19.76        75.65         6.67 
TCGA-DD-A1EF TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A39V TCGA-DD-A39Y TCGA-DD-A39Z 
       12.95        49.15         6.02        21.14         5.59        19.73 
TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 
       25.81         7.66        70.06        17.59        20.12       102.74 
TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A4ND TCGA-DD-A4NE TCGA-DD-A4NF 
      107.11        13.78         0.36        73.38        21.67        14.07 
TCGA-DD-A4NG TCGA-DD-A4NH TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN 
       14.93        14.24        15.06        39.75        56.25        29.56 
TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-ED-A459 TCGA-ED-A5KG TCGA-EP-A12J 
       61.45        93.67        12.26         0.23         0.20        10.85 
TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK 
        7.76        11.74         1.97         0.62         3.19         0.43 
TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3R2 TCGA-FV-A3R3 
       14.40        32.45        19.07         0.20         6.35         0.13 
TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25U 
        0.03         0.33        60.36         0.39         1.22        53.79 
TCGA-G3-A25V TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A3CG TCGA-G3-A3CH TCGA-G3-A3CI 
       28.27        58.49        14.86        22.13        25.64         5.88 
TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SJ TCGA-G3-A5SK TCGA-G3-A5SL TCGA-G3-A5SM 
       19.53        19.23        11.97         9.93         7.99         4.37 

  2P GAIN MUTATED 2P GAIN WILD-TYPE 
             0.10              0.03 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
            90.67            112.96 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
            29.87             14.32 
[1] "0.1 - 90.7 (29.9)"  "0.0 - 113.0 (14.3)"
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
  "2P GAIN MUTATED" "2P GAIN WILD-TYPE"   "2P GAIN MUTATED"   "2P GAIN MUTATED" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"2P GAIN WILD-TYPE"   "2P GAIN MUTATED" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-BC-A5W4        TCGA-CC-5258        TCGA-CC-5260 
"2P GAIN WILD-TYPE"   "2P GAIN MUTATED" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-CC-5261        TCGA-CC-5262        TCGA-CC-5263        TCGA-CC-A1HT 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-CC-A3M9        TCGA-CC-A3MA        TCGA-CC-A3MB        TCGA-CC-A3MC 
  "2P GAIN MUTATED" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-DD-A113        TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116 
  "2P GAIN MUTATED" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-DD-A118        TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-DD-A11C        TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EA 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE"   "2P GAIN MUTATED" "2P GAIN WILD-TYPE" 
       TCGA-DD-A1EB        TCGA-DD-A1EC        TCGA-DD-A1ED        TCGA-DD-A1EE 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-DD-A1EF        TCGA-DD-A1EH        TCGA-DD-A1EI        TCGA-DD-A1EJ 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE"   "2P GAIN MUTATED" 
       TCGA-DD-A1EL        TCGA-DD-A39V        TCGA-DD-A39X        TCGA-DD-A39Y 
  "2P GAIN MUTATED" "2P GAIN WILD-TYPE"   "2P GAIN MUTATED" "2P GAIN WILD-TYPE" 
       TCGA-DD-A39Z        TCGA-DD-A3A0        TCGA-DD-A3A1        TCGA-DD-A3A2 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-DD-A3A3        TCGA-DD-A3A4        TCGA-DD-A3A5        TCGA-DD-A3A6 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-DD-A3A7        TCGA-DD-A3A8        TCGA-DD-A3A9        TCGA-DD-A4NA 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE"   "2P GAIN MUTATED"   "2P GAIN MUTATED" 
       TCGA-DD-A4ND        TCGA-DD-A4NE        TCGA-DD-A4NF        TCGA-DD-A4NG 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-DD-A4NH        TCGA-DD-A4NI        TCGA-DD-A4NJ        TCGA-DD-A4NK 
"2P GAIN WILD-TYPE"   "2P GAIN MUTATED" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-DD-A4NL        TCGA-DD-A4NN        TCGA-DD-A4NO        TCGA-DD-A4NP 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-DD-A4NQ        TCGA-ED-A459        TCGA-ED-A5KG        TCGA-EP-A12J 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-EP-A3JL        TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE"   "2P GAIN MUTATED" "2P GAIN WILD-TYPE" 
       TCGA-FV-A23B        TCGA-FV-A2QR        TCGA-FV-A3I0        TCGA-FV-A3R2 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-FV-A3R3        TCGA-FV-A495        TCGA-FV-A496        TCGA-FV-A4ZP 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-FV-A4ZQ        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE"   "2P GAIN MUTATED" "2P GAIN WILD-TYPE" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"2P GAIN WILD-TYPE"   "2P GAIN MUTATED" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI 
  "2P GAIN MUTATED" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-G3-A3CJ        TCGA-G3-A3CK        TCGA-G3-A5SJ        TCGA-G3-A5SK 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-G3-A5SL        TCGA-G3-A5SM 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
  "2P GAIN MUTATED" "2P GAIN WILD-TYPE"   "2P GAIN MUTATED"   "2P GAIN MUTATED" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"2P GAIN WILD-TYPE"   "2P GAIN MUTATED" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-BC-A5W4        TCGA-CC-5258        TCGA-CC-5260 
"2P GAIN WILD-TYPE"   "2P GAIN MUTATED" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-CC-5261        TCGA-CC-5262        TCGA-CC-5263        TCGA-CC-A1HT 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-CC-A3M9        TCGA-CC-A3MA        TCGA-CC-A3MB        TCGA-CC-A3MC 
  "2P GAIN MUTATED" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-DD-A113        TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116 
  "2P GAIN MUTATED" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-DD-A118        TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-DD-A11C        TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EA 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE"   "2P GAIN MUTATED" "2P GAIN WILD-TYPE" 
       TCGA-DD-A1EB        TCGA-DD-A1EC        TCGA-DD-A1ED        TCGA-DD-A1EE 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-DD-A1EF        TCGA-DD-A1EH        TCGA-DD-A1EI        TCGA-DD-A1EJ 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE"   "2P GAIN MUTATED" 
       TCGA-DD-A1EL        TCGA-DD-A39V        TCGA-DD-A39X        TCGA-DD-A39Y 
  "2P GAIN MUTATED" "2P GAIN WILD-TYPE"   "2P GAIN MUTATED" "2P GAIN WILD-TYPE" 
       TCGA-DD-A39Z        TCGA-DD-A3A0        TCGA-DD-A3A1        TCGA-DD-A3A2 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-DD-A3A3        TCGA-DD-A3A4        TCGA-DD-A3A5        TCGA-DD-A3A6 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-DD-A3A7        TCGA-DD-A3A8        TCGA-DD-A3A9        TCGA-DD-A4NA 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE"   "2P GAIN MUTATED"   "2P GAIN MUTATED" 
       TCGA-DD-A4ND        TCGA-DD-A4NE        TCGA-DD-A4NF        TCGA-DD-A4NG 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-DD-A4NH        TCGA-DD-A4NI        TCGA-DD-A4NJ        TCGA-DD-A4NK 
"2P GAIN WILD-TYPE"   "2P GAIN MUTATED" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-DD-A4NL        TCGA-DD-A4NN        TCGA-DD-A4NO        TCGA-DD-A4NP 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-DD-A4NQ        TCGA-ED-A459        TCGA-ED-A5KG        TCGA-EP-A12J 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-EP-A3JL        TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE"   "2P GAIN MUTATED" "2P GAIN WILD-TYPE" 
       TCGA-FV-A23B        TCGA-FV-A2QR        TCGA-FV-A3I0        TCGA-FV-A3R2 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-FV-A3R3        TCGA-FV-A495        TCGA-FV-A496        TCGA-FV-A4ZP 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-FV-A4ZQ        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE"   "2P GAIN MUTATED" "2P GAIN WILD-TYPE" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"2P GAIN WILD-TYPE"   "2P GAIN MUTATED" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI 
  "2P GAIN MUTATED" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-G3-A3CJ        TCGA-G3-A3CK        TCGA-G3-A5SJ        TCGA-G3-A5SK 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-G3-A5SL        TCGA-G3-A5SM 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
  "2P GAIN MUTATED" "2P GAIN WILD-TYPE"   "2P GAIN MUTATED"   "2P GAIN MUTATED" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"2P GAIN WILD-TYPE"   "2P GAIN MUTATED" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-BC-A5W4        TCGA-CC-5258        TCGA-CC-5260 
"2P GAIN WILD-TYPE"   "2P GAIN MUTATED" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-CC-5261        TCGA-CC-5262        TCGA-CC-5263        TCGA-CC-A1HT 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-CC-A3M9        TCGA-CC-A3MA        TCGA-CC-A3MB        TCGA-CC-A3MC 
  "2P GAIN MUTATED" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-DD-A113        TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116 
  "2P GAIN MUTATED" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-DD-A118        TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-DD-A11C        TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EA 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE"   "2P GAIN MUTATED" "2P GAIN WILD-TYPE" 
       TCGA-DD-A1EB        TCGA-DD-A1EC        TCGA-DD-A1ED        TCGA-DD-A1EE 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-DD-A1EF        TCGA-DD-A1EH        TCGA-DD-A1EI        TCGA-DD-A1EJ 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE"   "2P GAIN MUTATED" 
       TCGA-DD-A1EL        TCGA-DD-A39V        TCGA-DD-A39X        TCGA-DD-A39Y 
  "2P GAIN MUTATED" "2P GAIN WILD-TYPE"   "2P GAIN MUTATED" "2P GAIN WILD-TYPE" 
       TCGA-DD-A39Z        TCGA-DD-A3A0        TCGA-DD-A3A1        TCGA-DD-A3A2 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-DD-A3A3        TCGA-DD-A3A4        TCGA-DD-A3A5        TCGA-DD-A3A6 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-DD-A3A7        TCGA-DD-A3A8        TCGA-DD-A3A9        TCGA-DD-A4NA 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE"   "2P GAIN MUTATED"   "2P GAIN MUTATED" 
       TCGA-DD-A4ND        TCGA-DD-A4NE        TCGA-DD-A4NF        TCGA-DD-A4NG 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-DD-A4NH        TCGA-DD-A4NI        TCGA-DD-A4NJ        TCGA-DD-A4NK 
"2P GAIN WILD-TYPE"   "2P GAIN MUTATED" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-DD-A4NL        TCGA-DD-A4NN        TCGA-DD-A4NO        TCGA-DD-A4NP 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-DD-A4NQ        TCGA-ED-A459        TCGA-ED-A5KG        TCGA-EP-A12J 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-EP-A3JL        TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE"   "2P GAIN MUTATED" "2P GAIN WILD-TYPE" 
       TCGA-FV-A23B        TCGA-FV-A2QR        TCGA-FV-A3I0        TCGA-FV-A3R2 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-FV-A3R3        TCGA-FV-A495        TCGA-FV-A496        TCGA-FV-A4ZP 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-FV-A4ZQ        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE"   "2P GAIN MUTATED" "2P GAIN WILD-TYPE" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"2P GAIN WILD-TYPE"   "2P GAIN MUTATED" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI 
  "2P GAIN MUTATED" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-G3-A3CJ        TCGA-G3-A3CK        TCGA-G3-A5SJ        TCGA-G3-A5SK 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-G3-A5SL        TCGA-G3-A5SM 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
[1] "hr=" "1.1"
D3V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  2P GAIN MUTATED         4        3         0          3          1          2
  2P GAIN WILD-TYPE      41       22         2         22          2          2
                   vv
clus                STAGE IV STAGE IVA STAGE IVB
  2P GAIN MUTATED          0         0         1
  2P GAIN WILD-TYPE        1         1         0
D3V3, multiclass
                   vv
clus                T1 T2 T3 T4
  2P GAIN MUTATED    5  5  5  2
  2P GAIN WILD-TYPE 43 23 29  4
D3V4, multiclass
    clus
vv   2P GAIN MUTATED 2P GAIN WILD-TYPE
  T1               5                43
  T2               5                23
  T3               5                29
  T4               2                 4
D3V5, binary
                   cls
clus                 0  1
  2P GAIN MUTATED    9  2
  2P GAIN WILD-TYPE 65  1
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED      9    2
  2P GAIN WILD-TYPE   65    1
   clus
vv  2P GAIN MUTATED 2P GAIN WILD-TYPE
  0               9                65
  1               2                 1
                   vv
clus                M0 M1 MX
  2P GAIN MUTATED   13  1  4
  2P GAIN WILD-TYPE 77  1 21
D3V6, multiclass
    clus
vv   2P GAIN MUTATED 2P GAIN WILD-TYPE
  M0              13                77
  M1               1                 1
  MX               4                21
D3V7, binary
                   cls
clus                 0  1
  2P GAIN MUTATED   10  8
  2P GAIN WILD-TYPE 34 65
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED     10    8
  2P GAIN WILD-TYPE   34   65
        clus
vv       2P GAIN MUTATED 2P GAIN WILD-TYPE
  FEMALE              10                34
  MALE                 8                65
                   vv
clus                R0 R1 R2 RX
  2P GAIN MUTATED   14  4  0  0
  2P GAIN WILD-TYPE 79  6  1  8
D3V8, multiclass
    clus
vv   2P GAIN MUTATED 2P GAIN WILD-TYPE
  R0              14                79
  R1               4                 6
  R2               0                 1
  RX               0                 8

Clustering(4) Variable = 2Q GAIN MUTATION ANALYSIS
D4V1, survival
                   sevent
clus2                0  1
  2Q GAIN MUTATED    5 10
  2Q GAIN WILD-TYPE 56 43
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               15                99 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               10                43 
$`2Q GAIN MUTATED`
TCGA-BC-4072 TCGA-BC-A10Q TCGA-BC-A10R TCGA-DD-A113 TCGA-DD-A1E9 TCGA-DD-A1EJ 
       48.99        37.32        10.13        79.73        90.67        29.16 
TCGA-DD-A1EL TCGA-DD-A39X TCGA-DD-A3A9 TCGA-DD-A4NI TCGA-ES-A2HS TCGA-G3-A25S 
       13.64        55.66        30.58        10.78        23.01         1.22 
TCGA-G3-A25T TCGA-G3-A25W TCGA-G3-A25Z 
       51.02        30.71        21.53 

$`2Q GAIN WILD-TYPE`
TCGA-BC-4073 TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X 
       27.91        46.78        27.52        27.52         2.99        25.32 
TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A216 TCGA-BC-A217 
       23.34         1.12        69.57         5.03        44.42        13.81 
TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5261 
        0.26        16.37         9.50         0.07         2.86         3.02 
TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB 
        3.39         4.24         3.32         0.10         0.07         0.10 
TCGA-CC-A3MC TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 
        0.13        37.74        83.57        53.29       112.96         7.33 
TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1EA TCGA-DD-A1EB 
        2.60         0.46        21.76        51.25        79.36        66.31 
TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EH TCGA-DD-A1EI 
       19.76        75.65         6.67        12.95        49.15         6.02 
TCGA-DD-A39V TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 
       21.14         5.59        19.73        25.81         7.66        70.06 
TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A8 
       17.59        20.12       102.74       107.11        13.78         0.36 
TCGA-DD-A4NA TCGA-DD-A4ND TCGA-DD-A4NE TCGA-DD-A4NF TCGA-DD-A4NG TCGA-DD-A4NH 
       33.14        73.38        21.67        14.07        14.93        14.24 
TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP 
       15.06        39.75        56.25        29.56        61.45        93.67 
TCGA-DD-A4NQ TCGA-ED-A459 TCGA-ED-A5KG TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA 
       12.26         0.23         0.20        10.85         7.76        11.74 
TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A23B 
        1.97         0.62         3.19         0.43        14.40        32.45 
TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 
       19.07         0.20         6.35         0.13         0.03         0.33 
TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25X TCGA-G3-A25Y 
       60.36         0.39        53.79        28.27        58.49        14.86 
TCGA-G3-A3CG TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SJ 
       22.13        25.64         5.88        19.53        19.23        11.97 
TCGA-G3-A5SK TCGA-G3-A5SL TCGA-G3-A5SM 
        9.93         7.99         4.37 

  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
             1.22              0.03 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
            90.67            112.96 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
            30.58             14.40 
[1] "1.2 - 90.7 (30.6)"  "0.0 - 113.0 (14.4)"
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
  "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED"   "2Q GAIN MUTATED" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-BC-A5W4        TCGA-CC-5258        TCGA-CC-5260 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-CC-5261        TCGA-CC-5262        TCGA-CC-5263        TCGA-CC-A1HT 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-CC-A3M9        TCGA-CC-A3MA        TCGA-CC-A3MB        TCGA-CC-A3MC 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-DD-A113        TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116 
  "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-DD-A118        TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-DD-A11C        TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EA 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" 
       TCGA-DD-A1EB        TCGA-DD-A1EC        TCGA-DD-A1ED        TCGA-DD-A1EE 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-DD-A1EF        TCGA-DD-A1EH        TCGA-DD-A1EI        TCGA-DD-A1EJ 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" 
       TCGA-DD-A1EL        TCGA-DD-A39V        TCGA-DD-A39X        TCGA-DD-A39Y 
  "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" 
       TCGA-DD-A39Z        TCGA-DD-A3A0        TCGA-DD-A3A1        TCGA-DD-A3A2 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-DD-A3A3        TCGA-DD-A3A4        TCGA-DD-A3A5        TCGA-DD-A3A6 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-DD-A3A7        TCGA-DD-A3A8        TCGA-DD-A3A9        TCGA-DD-A4NA 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" 
       TCGA-DD-A4ND        TCGA-DD-A4NE        TCGA-DD-A4NF        TCGA-DD-A4NG 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-DD-A4NH        TCGA-DD-A4NI        TCGA-DD-A4NJ        TCGA-DD-A4NK 
"2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-DD-A4NL        TCGA-DD-A4NN        TCGA-DD-A4NO        TCGA-DD-A4NP 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-DD-A4NQ        TCGA-ED-A459        TCGA-ED-A5KG        TCGA-EP-A12J 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-EP-A3JL        TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" 
       TCGA-FV-A23B        TCGA-FV-A2QR        TCGA-FV-A3I0        TCGA-FV-A3R2 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-FV-A3R3        TCGA-FV-A495        TCGA-FV-A496        TCGA-FV-A4ZP 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-FV-A4ZQ        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED"   "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI 
  "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-G3-A3CJ        TCGA-G3-A3CK        TCGA-G3-A5SJ        TCGA-G3-A5SK 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-G3-A5SL        TCGA-G3-A5SM 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
  "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED"   "2Q GAIN MUTATED" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-BC-A5W4        TCGA-CC-5258        TCGA-CC-5260 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-CC-5261        TCGA-CC-5262        TCGA-CC-5263        TCGA-CC-A1HT 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-CC-A3M9        TCGA-CC-A3MA        TCGA-CC-A3MB        TCGA-CC-A3MC 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-DD-A113        TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116 
  "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-DD-A118        TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-DD-A11C        TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EA 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" 
       TCGA-DD-A1EB        TCGA-DD-A1EC        TCGA-DD-A1ED        TCGA-DD-A1EE 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-DD-A1EF        TCGA-DD-A1EH        TCGA-DD-A1EI        TCGA-DD-A1EJ 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" 
       TCGA-DD-A1EL        TCGA-DD-A39V        TCGA-DD-A39X        TCGA-DD-A39Y 
  "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" 
       TCGA-DD-A39Z        TCGA-DD-A3A0        TCGA-DD-A3A1        TCGA-DD-A3A2 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-DD-A3A3        TCGA-DD-A3A4        TCGA-DD-A3A5        TCGA-DD-A3A6 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-DD-A3A7        TCGA-DD-A3A8        TCGA-DD-A3A9        TCGA-DD-A4NA 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" 
       TCGA-DD-A4ND        TCGA-DD-A4NE        TCGA-DD-A4NF        TCGA-DD-A4NG 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-DD-A4NH        TCGA-DD-A4NI        TCGA-DD-A4NJ        TCGA-DD-A4NK 
"2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-DD-A4NL        TCGA-DD-A4NN        TCGA-DD-A4NO        TCGA-DD-A4NP 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-DD-A4NQ        TCGA-ED-A459        TCGA-ED-A5KG        TCGA-EP-A12J 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-EP-A3JL        TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" 
       TCGA-FV-A23B        TCGA-FV-A2QR        TCGA-FV-A3I0        TCGA-FV-A3R2 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-FV-A3R3        TCGA-FV-A495        TCGA-FV-A496        TCGA-FV-A4ZP 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-FV-A4ZQ        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED"   "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI 
  "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-G3-A3CJ        TCGA-G3-A3CK        TCGA-G3-A5SJ        TCGA-G3-A5SK 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-G3-A5SL        TCGA-G3-A5SM 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
  "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED"   "2Q GAIN MUTATED" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-BC-A5W4        TCGA-CC-5258        TCGA-CC-5260 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-CC-5261        TCGA-CC-5262        TCGA-CC-5263        TCGA-CC-A1HT 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-CC-A3M9        TCGA-CC-A3MA        TCGA-CC-A3MB        TCGA-CC-A3MC 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-DD-A113        TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116 
  "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-DD-A118        TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-DD-A11C        TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EA 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" 
       TCGA-DD-A1EB        TCGA-DD-A1EC        TCGA-DD-A1ED        TCGA-DD-A1EE 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-DD-A1EF        TCGA-DD-A1EH        TCGA-DD-A1EI        TCGA-DD-A1EJ 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" 
       TCGA-DD-A1EL        TCGA-DD-A39V        TCGA-DD-A39X        TCGA-DD-A39Y 
  "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" 
       TCGA-DD-A39Z        TCGA-DD-A3A0        TCGA-DD-A3A1        TCGA-DD-A3A2 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-DD-A3A3        TCGA-DD-A3A4        TCGA-DD-A3A5        TCGA-DD-A3A6 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-DD-A3A7        TCGA-DD-A3A8        TCGA-DD-A3A9        TCGA-DD-A4NA 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" 
       TCGA-DD-A4ND        TCGA-DD-A4NE        TCGA-DD-A4NF        TCGA-DD-A4NG 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-DD-A4NH        TCGA-DD-A4NI        TCGA-DD-A4NJ        TCGA-DD-A4NK 
"2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-DD-A4NL        TCGA-DD-A4NN        TCGA-DD-A4NO        TCGA-DD-A4NP 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-DD-A4NQ        TCGA-ED-A459        TCGA-ED-A5KG        TCGA-EP-A12J 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-EP-A3JL        TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" 
       TCGA-FV-A23B        TCGA-FV-A2QR        TCGA-FV-A3I0        TCGA-FV-A3R2 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-FV-A3R3        TCGA-FV-A495        TCGA-FV-A496        TCGA-FV-A4ZP 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-FV-A4ZQ        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED"   "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI 
  "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-G3-A3CJ        TCGA-G3-A3CK        TCGA-G3-A5SJ        TCGA-G3-A5SK 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-G3-A5SL        TCGA-G3-A5SM 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
[1] "hr=" "1.1"
D4V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  2Q GAIN MUTATED         5        3         0          1          1          1
  2Q GAIN WILD-TYPE      40       22         2         24          2          3
                   vv
clus                STAGE IV STAGE IVA STAGE IVB
  2Q GAIN MUTATED          0         0         1
  2Q GAIN WILD-TYPE        1         1         0
D4V3, multiclass
                   vv
clus                T1 T2 T3 T4
  2Q GAIN MUTATED    6  4  3  1
  2Q GAIN WILD-TYPE 42 24 31  5
D4V4, multiclass
    clus
vv   2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  T1               6                42
  T2               4                24
  T3               3                31
  T4               1                 5
D4V5, binary
                   cls
clus                 0  1
  2Q GAIN MUTATED    9  1
  2Q GAIN WILD-TYPE 65  2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED      9    1
  2Q GAIN WILD-TYPE   65    2
   clus
vv  2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  0               9                65
  1               1                 2
                   vv
clus                M0 M1 MX
  2Q GAIN MUTATED   11  1  3
  2Q GAIN WILD-TYPE 79  1 22
D4V6, multiclass
    clus
vv   2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  M0              11                79
  M1               1                 1
  MX               3                22
D4V7, binary
                   cls
clus                 0  1
  2Q GAIN MUTATED    9  6
  2Q GAIN WILD-TYPE 35 67
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED      9    6
  2Q GAIN WILD-TYPE   35   67
        clus
vv       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  FEMALE               9                35
  MALE                 6                67
                   vv
clus                R0 R1 R2 RX
  2Q GAIN MUTATED   12  3  0  0
  2Q GAIN WILD-TYPE 81  7  1  8
D4V8, multiclass
    clus
vv   2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  R0              12                81
  R1               3                 7
  R2               0                 1
  RX               0                 8

Clustering(5) Variable = 3P GAIN MUTATION ANALYSIS
D5V1, survival
                   sevent
clus2                0  1
  3P GAIN MUTATED    2  6
  3P GAIN WILD-TYPE 59 47
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
                8               106 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
                6                47 
$`3P GAIN MUTATED`
TCGA-CC-A3M9 TCGA-DD-A114 TCGA-DD-A11C TCGA-DD-A1EF TCGA-DD-A1EJ TCGA-DD-A39Y 
        0.10        37.74        21.76        12.95        29.16         5.59 
TCGA-ES-A2HS TCGA-FV-A3R2 
       23.01         6.35 

$`3P GAIN WILD-TYPE`
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T 
       48.99        27.91        37.32        10.13        46.78        27.52 
TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 
       27.52         2.99        25.32        23.34         1.12        69.57 
TCGA-BC-A112 TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 
        5.03        44.42        13.81         0.26        16.37         9.50 
TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A1HT 
        0.07         2.86         3.02         3.39         4.24         3.32 
TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A113 TCGA-DD-A115 TCGA-DD-A116 
        0.07         0.10         0.13        79.73        83.57        53.29 
TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11D TCGA-DD-A1E9 
      112.96         7.33         2.60         0.46        51.25        90.67 
TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EH 
       79.36        66.31        19.76        75.65         6.67        49.15 
TCGA-DD-A1EI TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39X TCGA-DD-A39Z TCGA-DD-A3A0 
        6.02        13.64        21.14        55.66        19.73        25.81 
TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 
        7.66        70.06        17.59        20.12       102.74       107.11 
TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4ND TCGA-DD-A4NE 
       13.78         0.36        30.58        33.14        73.38        21.67 
TCGA-DD-A4NF TCGA-DD-A4NG TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK 
       14.07        14.93        14.24        10.78        15.06        39.75 
TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-ED-A459 
       56.25        29.56        61.45        93.67        12.26         0.23 
TCGA-ED-A5KG TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC 
        0.20        10.85         7.76        11.74         1.97         0.62 
TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-A3I0 
        3.19         0.43        14.40        32.45        19.07         0.20 
TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25S 
        0.13         0.03         0.33        60.36         0.39         1.22 
TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25X TCGA-G3-A25Y 
       51.02        53.79        28.27        30.71        58.49        14.86 
TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK 
       21.53        22.13        25.64         5.88        19.53        19.23 
TCGA-G3-A5SJ TCGA-G3-A5SK TCGA-G3-A5SL TCGA-G3-A5SM 
       11.97         9.93         7.99         4.37 

  3P GAIN MUTATED 3P GAIN WILD-TYPE 
             0.10              0.03 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
            37.74            112.96 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
           17.355            15.715 
[1] "0.1 - 37.7 (17.4)"  "0.0 - 113.0 (15.7)"
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-BC-A5W4        TCGA-CC-5258        TCGA-CC-5260 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-CC-5261        TCGA-CC-5262        TCGA-CC-5263        TCGA-CC-A1HT 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-CC-A3M9        TCGA-CC-A3MA        TCGA-CC-A3MB        TCGA-CC-A3MC 
  "3P GAIN MUTATED" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DD-A113        TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116 
"3P GAIN WILD-TYPE"   "3P GAIN MUTATED" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DD-A118        TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DD-A11C        TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EA 
  "3P GAIN MUTATED" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DD-A1EB        TCGA-DD-A1EC        TCGA-DD-A1ED        TCGA-DD-A1EE 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DD-A1EF        TCGA-DD-A1EH        TCGA-DD-A1EI        TCGA-DD-A1EJ 
  "3P GAIN MUTATED" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"   "3P GAIN MUTATED" 
       TCGA-DD-A1EL        TCGA-DD-A39V        TCGA-DD-A39X        TCGA-DD-A39Y 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"   "3P GAIN MUTATED" 
       TCGA-DD-A39Z        TCGA-DD-A3A0        TCGA-DD-A3A1        TCGA-DD-A3A2 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DD-A3A3        TCGA-DD-A3A4        TCGA-DD-A3A5        TCGA-DD-A3A6 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DD-A3A7        TCGA-DD-A3A8        TCGA-DD-A3A9        TCGA-DD-A4NA 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DD-A4ND        TCGA-DD-A4NE        TCGA-DD-A4NF        TCGA-DD-A4NG 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DD-A4NH        TCGA-DD-A4NI        TCGA-DD-A4NJ        TCGA-DD-A4NK 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DD-A4NL        TCGA-DD-A4NN        TCGA-DD-A4NO        TCGA-DD-A4NP 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DD-A4NQ        TCGA-ED-A459        TCGA-ED-A5KG        TCGA-EP-A12J 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EP-A3JL        TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"   "3P GAIN MUTATED" "3P GAIN WILD-TYPE" 
       TCGA-FV-A23B        TCGA-FV-A2QR        TCGA-FV-A3I0        TCGA-FV-A3R2 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"   "3P GAIN MUTATED" 
       TCGA-FV-A3R3        TCGA-FV-A495        TCGA-FV-A496        TCGA-FV-A4ZP 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-FV-A4ZQ        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-G3-A3CJ        TCGA-G3-A3CK        TCGA-G3-A5SJ        TCGA-G3-A5SK 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-G3-A5SL        TCGA-G3-A5SM 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-BC-A5W4        TCGA-CC-5258        TCGA-CC-5260 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-CC-5261        TCGA-CC-5262        TCGA-CC-5263        TCGA-CC-A1HT 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-CC-A3M9        TCGA-CC-A3MA        TCGA-CC-A3MB        TCGA-CC-A3MC 
  "3P GAIN MUTATED" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DD-A113        TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116 
"3P GAIN WILD-TYPE"   "3P GAIN MUTATED" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DD-A118        TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DD-A11C        TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EA 
  "3P GAIN MUTATED" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DD-A1EB        TCGA-DD-A1EC        TCGA-DD-A1ED        TCGA-DD-A1EE 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DD-A1EF        TCGA-DD-A1EH        TCGA-DD-A1EI        TCGA-DD-A1EJ 
  "3P GAIN MUTATED" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"   "3P GAIN MUTATED" 
       TCGA-DD-A1EL        TCGA-DD-A39V        TCGA-DD-A39X        TCGA-DD-A39Y 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"   "3P GAIN MUTATED" 
       TCGA-DD-A39Z        TCGA-DD-A3A0        TCGA-DD-A3A1        TCGA-DD-A3A2 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DD-A3A3        TCGA-DD-A3A4        TCGA-DD-A3A5        TCGA-DD-A3A6 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DD-A3A7        TCGA-DD-A3A8        TCGA-DD-A3A9        TCGA-DD-A4NA 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DD-A4ND        TCGA-DD-A4NE        TCGA-DD-A4NF        TCGA-DD-A4NG 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DD-A4NH        TCGA-DD-A4NI        TCGA-DD-A4NJ        TCGA-DD-A4NK 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DD-A4NL        TCGA-DD-A4NN        TCGA-DD-A4NO        TCGA-DD-A4NP 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DD-A4NQ        TCGA-ED-A459        TCGA-ED-A5KG        TCGA-EP-A12J 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EP-A3JL        TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"   "3P GAIN MUTATED" "3P GAIN WILD-TYPE" 
       TCGA-FV-A23B        TCGA-FV-A2QR        TCGA-FV-A3I0        TCGA-FV-A3R2 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"   "3P GAIN MUTATED" 
       TCGA-FV-A3R3        TCGA-FV-A495        TCGA-FV-A496        TCGA-FV-A4ZP 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-FV-A4ZQ        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-G3-A3CJ        TCGA-G3-A3CK        TCGA-G3-A5SJ        TCGA-G3-A5SK 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-G3-A5SL        TCGA-G3-A5SM 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-BC-A5W4        TCGA-CC-5258        TCGA-CC-5260 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-CC-5261        TCGA-CC-5262        TCGA-CC-5263        TCGA-CC-A1HT 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-CC-A3M9        TCGA-CC-A3MA        TCGA-CC-A3MB        TCGA-CC-A3MC 
  "3P GAIN MUTATED" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DD-A113        TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116 
"3P GAIN WILD-TYPE"   "3P GAIN MUTATED" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DD-A118        TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DD-A11C        TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EA 
  "3P GAIN MUTATED" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DD-A1EB        TCGA-DD-A1EC        TCGA-DD-A1ED        TCGA-DD-A1EE 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DD-A1EF        TCGA-DD-A1EH        TCGA-DD-A1EI        TCGA-DD-A1EJ 
  "3P GAIN MUTATED" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"   "3P GAIN MUTATED" 
       TCGA-DD-A1EL        TCGA-DD-A39V        TCGA-DD-A39X        TCGA-DD-A39Y 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"   "3P GAIN MUTATED" 
       TCGA-DD-A39Z        TCGA-DD-A3A0        TCGA-DD-A3A1        TCGA-DD-A3A2 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DD-A3A3        TCGA-DD-A3A4        TCGA-DD-A3A5        TCGA-DD-A3A6 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DD-A3A7        TCGA-DD-A3A8        TCGA-DD-A3A9        TCGA-DD-A4NA 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DD-A4ND        TCGA-DD-A4NE        TCGA-DD-A4NF        TCGA-DD-A4NG 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DD-A4NH        TCGA-DD-A4NI        TCGA-DD-A4NJ        TCGA-DD-A4NK 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DD-A4NL        TCGA-DD-A4NN        TCGA-DD-A4NO        TCGA-DD-A4NP 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DD-A4NQ        TCGA-ED-A459        TCGA-ED-A5KG        TCGA-EP-A12J 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EP-A3JL        TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"   "3P GAIN MUTATED" "3P GAIN WILD-TYPE" 
       TCGA-FV-A23B        TCGA-FV-A2QR        TCGA-FV-A3I0        TCGA-FV-A3R2 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"   "3P GAIN MUTATED" 
       TCGA-FV-A3R3        TCGA-FV-A495        TCGA-FV-A496        TCGA-FV-A4ZP 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-FV-A4ZQ        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-G3-A3CJ        TCGA-G3-A3CK        TCGA-G3-A5SJ        TCGA-G3-A5SK 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-G3-A5SL        TCGA-G3-A5SM 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
[1] "hr=" "2.4"
D5V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  3P GAIN MUTATED         5        1         0          1          0          1
  3P GAIN WILD-TYPE      40       24         2         24          3          3
                   vv
clus                STAGE IV STAGE IVA STAGE IVB
  3P GAIN MUTATED          0         0         0
  3P GAIN WILD-TYPE        1         1         1
D5V3, multiclass
                   vv
clus                T1 T2 T3 T4
  3P GAIN MUTATED    6  1  1  0
  3P GAIN WILD-TYPE 42 27 33  6
D5V4, multiclass
    clus
vv   3P GAIN MUTATED 3P GAIN WILD-TYPE
  T1               6                42
  T2               1                27
  T3               1                33
  T4               0                 6
D5V5, binary
                   cls
clus                 0  1
  3P GAIN MUTATED    3  1
  3P GAIN WILD-TYPE 71  2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED      3    1
  3P GAIN WILD-TYPE   71    2
   clus
vv  3P GAIN MUTATED 3P GAIN WILD-TYPE
  0               3                71
  1               1                 2
                   vv
clus                M0 M1 MX
  3P GAIN MUTATED    6  0  2
  3P GAIN WILD-TYPE 84  2 23
D5V6, multiclass
    clus
vv   3P GAIN MUTATED 3P GAIN WILD-TYPE
  M0               6                84
  M1               0                 2
  MX               2                23
D5V7, binary
                   cls
clus                 0  1
  3P GAIN MUTATED    2  6
  3P GAIN WILD-TYPE 42 67
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED      2    6
  3P GAIN WILD-TYPE   42   67
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  FEMALE               2                42
  MALE                 6                67
                   vv
clus                R0 R1 R2 RX
  3P GAIN MUTATED    7  0  0  1
  3P GAIN WILD-TYPE 86 10  1  7
D5V8, multiclass
    clus
vv   3P GAIN MUTATED 3P GAIN WILD-TYPE
  R0               7                86
  R1               0                10
  R2               0                 1
  RX               1                 7

Clustering(6) Variable = 3Q GAIN MUTATION ANALYSIS
D6V1, survival
                   sevent
clus2                0  1
  3Q GAIN MUTATED    2  7
  3Q GAIN WILD-TYPE 59 46
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
                9               105 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
                7                46 
$`3Q GAIN MUTATED`
TCGA-BC-A10R TCGA-CC-A3M9 TCGA-DD-A114 TCGA-DD-A11C TCGA-DD-A1EF TCGA-DD-A1EJ 
       10.13         0.10        37.74        21.76        12.95        29.16 
TCGA-DD-A39Y TCGA-ES-A2HS TCGA-FV-A3R2 
        5.59        23.01         6.35 

$`3Q GAIN WILD-TYPE`
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U 
       48.99        27.91        37.32        46.78        27.52        27.52 
TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 
        2.99        25.32        23.34         1.12        69.57         5.03 
TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-CC-5258 
       44.42        13.81         0.26        16.37         9.50         0.07 
TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3MA 
        2.86         3.02         3.39         4.24         3.32         0.07 
TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A113 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 
        0.10         0.13        79.73        83.57        53.29       112.96 
TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA 
        7.33         2.60         0.46        51.25        90.67        79.36 
TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EH TCGA-DD-A1EI 
       66.31        19.76        75.65         6.67        49.15         6.02 
TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39X TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 
       13.64        21.14        55.66        19.73        25.81         7.66 
TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 
       70.06        17.59        20.12       102.74       107.11        13.78 
TCGA-DD-A3A8 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4ND TCGA-DD-A4NE TCGA-DD-A4NF 
        0.36        30.58        33.14        73.38        21.67        14.07 
TCGA-DD-A4NG TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL 
       14.93        14.24        10.78        15.06        39.75        56.25 
TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-ED-A459 TCGA-ED-A5KG 
       29.56        61.45        93.67        12.26         0.23         0.20 
TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL 
       10.85         7.76        11.74         1.97         0.62         3.19 
TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3R3 
        0.43        14.40        32.45        19.07         0.20         0.13 
TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T 
        0.03         0.33        60.36         0.39         1.22        51.02 
TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A25Z 
       53.79        28.27        30.71        58.49        14.86        21.53 
TCGA-G3-A3CG TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SJ 
       22.13        25.64         5.88        19.53        19.23        11.97 
TCGA-G3-A5SK TCGA-G3-A5SL TCGA-G3-A5SM 
        9.93         7.99         4.37 

  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
             0.10              0.03 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
            37.74            112.96 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
            12.95             16.37 
[1] "0.1 - 37.7 (12.9)"  "0.0 - 113.0 (16.4)"
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-BC-A5W4        TCGA-CC-5258        TCGA-CC-5260 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-CC-5261        TCGA-CC-5262        TCGA-CC-5263        TCGA-CC-A1HT 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-CC-A3M9        TCGA-CC-A3MA        TCGA-CC-A3MB        TCGA-CC-A3MC 
  "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-DD-A113        TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116 
"3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-DD-A118        TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-DD-A11C        TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EA 
  "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-DD-A1EB        TCGA-DD-A1EC        TCGA-DD-A1ED        TCGA-DD-A1EE 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-DD-A1EF        TCGA-DD-A1EH        TCGA-DD-A1EI        TCGA-DD-A1EJ 
  "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" 
       TCGA-DD-A1EL        TCGA-DD-A39V        TCGA-DD-A39X        TCGA-DD-A39Y 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" 
       TCGA-DD-A39Z        TCGA-DD-A3A0        TCGA-DD-A3A1        TCGA-DD-A3A2 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-DD-A3A3        TCGA-DD-A3A4        TCGA-DD-A3A5        TCGA-DD-A3A6 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-DD-A3A7        TCGA-DD-A3A8        TCGA-DD-A3A9        TCGA-DD-A4NA 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-DD-A4ND        TCGA-DD-A4NE        TCGA-DD-A4NF        TCGA-DD-A4NG 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-DD-A4NH        TCGA-DD-A4NI        TCGA-DD-A4NJ        TCGA-DD-A4NK 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-DD-A4NL        TCGA-DD-A4NN        TCGA-DD-A4NO        TCGA-DD-A4NP 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-DD-A4NQ        TCGA-ED-A459        TCGA-ED-A5KG        TCGA-EP-A12J 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-EP-A3JL        TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" 
       TCGA-FV-A23B        TCGA-FV-A2QR        TCGA-FV-A3I0        TCGA-FV-A3R2 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" 
       TCGA-FV-A3R3        TCGA-FV-A495        TCGA-FV-A496        TCGA-FV-A4ZP 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-FV-A4ZQ        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-G3-A3CJ        TCGA-G3-A3CK        TCGA-G3-A5SJ        TCGA-G3-A5SK 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-G3-A5SL        TCGA-G3-A5SM 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-BC-A5W4        TCGA-CC-5258        TCGA-CC-5260 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-CC-5261        TCGA-CC-5262        TCGA-CC-5263        TCGA-CC-A1HT 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-CC-A3M9        TCGA-CC-A3MA        TCGA-CC-A3MB        TCGA-CC-A3MC 
  "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-DD-A113        TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116 
"3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-DD-A118        TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-DD-A11C        TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EA 
  "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-DD-A1EB        TCGA-DD-A1EC        TCGA-DD-A1ED        TCGA-DD-A1EE 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-DD-A1EF        TCGA-DD-A1EH        TCGA-DD-A1EI        TCGA-DD-A1EJ 
  "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" 
       TCGA-DD-A1EL        TCGA-DD-A39V        TCGA-DD-A39X        TCGA-DD-A39Y 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" 
       TCGA-DD-A39Z        TCGA-DD-A3A0        TCGA-DD-A3A1        TCGA-DD-A3A2 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-DD-A3A3        TCGA-DD-A3A4        TCGA-DD-A3A5        TCGA-DD-A3A6 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-DD-A3A7        TCGA-DD-A3A8        TCGA-DD-A3A9        TCGA-DD-A4NA 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-DD-A4ND        TCGA-DD-A4NE        TCGA-DD-A4NF        TCGA-DD-A4NG 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-DD-A4NH        TCGA-DD-A4NI        TCGA-DD-A4NJ        TCGA-DD-A4NK 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-DD-A4NL        TCGA-DD-A4NN        TCGA-DD-A4NO        TCGA-DD-A4NP 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-DD-A4NQ        TCGA-ED-A459        TCGA-ED-A5KG        TCGA-EP-A12J 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-EP-A3JL        TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" 
       TCGA-FV-A23B        TCGA-FV-A2QR        TCGA-FV-A3I0        TCGA-FV-A3R2 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" 
       TCGA-FV-A3R3        TCGA-FV-A495        TCGA-FV-A496        TCGA-FV-A4ZP 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-FV-A4ZQ        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-G3-A3CJ        TCGA-G3-A3CK        TCGA-G3-A5SJ        TCGA-G3-A5SK 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-G3-A5SL        TCGA-G3-A5SM 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-BC-A5W4        TCGA-CC-5258        TCGA-CC-5260 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-CC-5261        TCGA-CC-5262        TCGA-CC-5263        TCGA-CC-A1HT 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-CC-A3M9        TCGA-CC-A3MA        TCGA-CC-A3MB        TCGA-CC-A3MC 
  "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-DD-A113        TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116 
"3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-DD-A118        TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-DD-A11C        TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EA 
  "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-DD-A1EB        TCGA-DD-A1EC        TCGA-DD-A1ED        TCGA-DD-A1EE 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-DD-A1EF        TCGA-DD-A1EH        TCGA-DD-A1EI        TCGA-DD-A1EJ 
  "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" 
       TCGA-DD-A1EL        TCGA-DD-A39V        TCGA-DD-A39X        TCGA-DD-A39Y 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" 
       TCGA-DD-A39Z        TCGA-DD-A3A0        TCGA-DD-A3A1        TCGA-DD-A3A2 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-DD-A3A3        TCGA-DD-A3A4        TCGA-DD-A3A5        TCGA-DD-A3A6 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-DD-A3A7        TCGA-DD-A3A8        TCGA-DD-A3A9        TCGA-DD-A4NA 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-DD-A4ND        TCGA-DD-A4NE        TCGA-DD-A4NF        TCGA-DD-A4NG 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-DD-A4NH        TCGA-DD-A4NI        TCGA-DD-A4NJ        TCGA-DD-A4NK 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-DD-A4NL        TCGA-DD-A4NN        TCGA-DD-A4NO        TCGA-DD-A4NP 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-DD-A4NQ        TCGA-ED-A459        TCGA-ED-A5KG        TCGA-EP-A12J 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-EP-A3JL        TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" 
       TCGA-FV-A23B        TCGA-FV-A2QR        TCGA-FV-A3I0        TCGA-FV-A3R2 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" 
       TCGA-FV-A3R3        TCGA-FV-A495        TCGA-FV-A496        TCGA-FV-A4ZP 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-FV-A4ZQ        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-G3-A3CJ        TCGA-G3-A3CK        TCGA-G3-A5SJ        TCGA-G3-A5SK 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-G3-A5SL        TCGA-G3-A5SM 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
[1] "hr=" "2.7"
D6V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  3Q GAIN MUTATED         5        1         0          1          0          1
  3Q GAIN WILD-TYPE      40       24         2         24          3          3
                   vv
clus                STAGE IV STAGE IVA STAGE IVB
  3Q GAIN MUTATED          0         0         0
  3Q GAIN WILD-TYPE        1         1         1
D6V3, multiclass
                   vv
clus                T1 T2 T3 T4
  3Q GAIN MUTATED    6  1  2  0
  3Q GAIN WILD-TYPE 42 27 32  6
D6V4, multiclass
    clus
vv   3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  T1               6                42
  T2               1                27
  T3               2                32
  T4               0                 6
D6V5, binary
                   cls
clus                 0  1
  3Q GAIN MUTATED    3  1
  3Q GAIN WILD-TYPE 71  2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED      3    1
  3Q GAIN WILD-TYPE   71    2
   clus
vv  3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  0               3                71
  1               1                 2
                   vv
clus                M0 M1 MX
  3Q GAIN MUTATED    6  0  3
  3Q GAIN WILD-TYPE 84  2 22
D6V6, multiclass
    clus
vv   3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  M0               6                84
  M1               0                 2
  MX               3                22
D6V7, binary
                   cls
clus                 0  1
  3Q GAIN MUTATED    3  6
  3Q GAIN WILD-TYPE 41 67
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED      3    6
  3Q GAIN WILD-TYPE   41   67
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  FEMALE               3                41
  MALE                 6                67
                   vv
clus                R0 R1 R2 RX
  3Q GAIN MUTATED    8  0  0  1
  3Q GAIN WILD-TYPE 85 10  1  7
D6V8, multiclass
    clus
vv   3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  R0               8                85
  R1               0                10
  R2               0                 1
  RX               1                 7

Clustering(7) Variable = 4P GAIN MUTATION ANALYSIS
D7V1, survival
                   sevent
clus2                0  1
  4P GAIN MUTATED    6  2
  4P GAIN WILD-TYPE 55 51
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                8               106 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                2                51 
$`4P GAIN MUTATED`
TCGA-BC-A10R TCGA-CC-5261 TCGA-CC-A3M9 TCGA-CC-A3MB TCGA-DD-A118 TCGA-DD-A11A 
       10.13         3.02         0.10         0.10       112.96         2.60 
TCGA-DD-A1EC TCGA-G3-A3CG 
       19.76        22.13 

$`4P GAIN WILD-TYPE`
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U 
       48.99        27.91        37.32        46.78        27.52        27.52 
TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 
        2.99        25.32        23.34         1.12        69.57         5.03 
TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-CC-5258 
       44.42        13.81         0.26        16.37         9.50         0.07 
TCGA-CC-5260 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3MA TCGA-CC-A3MC 
        2.86         3.39         4.24         3.32         0.07         0.13 
TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A119 TCGA-DD-A11B 
       79.73        37.74        83.57        53.29         7.33         0.46 
TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1ED 
       21.76        51.25        90.67        79.36        66.31        75.65 
TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EL 
        6.67        12.95        49.15         6.02        29.16        13.64 
TCGA-DD-A39V TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 
       21.14        55.66         5.59        19.73        25.81         7.66 
TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 
       70.06        17.59        20.12       102.74       107.11        13.78 
TCGA-DD-A3A8 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4ND TCGA-DD-A4NE TCGA-DD-A4NF 
        0.36        30.58        33.14        73.38        21.67        14.07 
TCGA-DD-A4NG TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL 
       14.93        14.24        10.78        15.06        39.75        56.25 
TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-ED-A459 TCGA-ED-A5KG 
       29.56        61.45        93.67        12.26         0.23         0.20 
TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL 
       10.85         7.76        11.74         1.97         0.62         3.19 
TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-A3I0 
        0.43        23.01        14.40        32.45        19.07         0.20 
TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZP TCGA-FV-A4ZQ 
        6.35         0.13         0.03         0.33        60.36         0.39 
TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25X 
        1.22        51.02        53.79        28.27        30.71        58.49 
TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK 
       14.86        21.53        25.64         5.88        19.53        19.23 
TCGA-G3-A5SJ TCGA-G3-A5SK TCGA-G3-A5SL TCGA-G3-A5SM 
       11.97         9.93         7.99         4.37 

  4P GAIN MUTATED 4P GAIN WILD-TYPE 
             0.10              0.03 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
           112.96            107.11 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
            6.575            16.980 
[1] "0.1 - 113.0 (6.6)"  "0.0 - 107.1 (17.0)"
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE"   "4P GAIN MUTATED" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-BC-A5W4        TCGA-CC-5258        TCGA-CC-5260 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-CC-5261        TCGA-CC-5262        TCGA-CC-5263        TCGA-CC-A1HT 
  "4P GAIN MUTATED" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-CC-A3M9        TCGA-CC-A3MA        TCGA-CC-A3MB        TCGA-CC-A3MC 
  "4P GAIN MUTATED" "4P GAIN WILD-TYPE"   "4P GAIN MUTATED" "4P GAIN WILD-TYPE" 
       TCGA-DD-A113        TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DD-A118        TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B 
  "4P GAIN MUTATED" "4P GAIN WILD-TYPE"   "4P GAIN MUTATED" "4P GAIN WILD-TYPE" 
       TCGA-DD-A11C        TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EA 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DD-A1EB        TCGA-DD-A1EC        TCGA-DD-A1ED        TCGA-DD-A1EE 
"4P GAIN WILD-TYPE"   "4P GAIN MUTATED" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DD-A1EF        TCGA-DD-A1EH        TCGA-DD-A1EI        TCGA-DD-A1EJ 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DD-A1EL        TCGA-DD-A39V        TCGA-DD-A39X        TCGA-DD-A39Y 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DD-A39Z        TCGA-DD-A3A0        TCGA-DD-A3A1        TCGA-DD-A3A2 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DD-A3A3        TCGA-DD-A3A4        TCGA-DD-A3A5        TCGA-DD-A3A6 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DD-A3A7        TCGA-DD-A3A8        TCGA-DD-A3A9        TCGA-DD-A4NA 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DD-A4ND        TCGA-DD-A4NE        TCGA-DD-A4NF        TCGA-DD-A4NG 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DD-A4NH        TCGA-DD-A4NI        TCGA-DD-A4NJ        TCGA-DD-A4NK 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DD-A4NL        TCGA-DD-A4NN        TCGA-DD-A4NO        TCGA-DD-A4NP 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DD-A4NQ        TCGA-ED-A459        TCGA-ED-A5KG        TCGA-EP-A12J 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EP-A3JL        TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-FV-A23B        TCGA-FV-A2QR        TCGA-FV-A3I0        TCGA-FV-A3R2 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-FV-A3R3        TCGA-FV-A495        TCGA-FV-A496        TCGA-FV-A4ZP 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-FV-A4ZQ        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI 
"4P GAIN WILD-TYPE"   "4P GAIN MUTATED" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-G3-A3CJ        TCGA-G3-A3CK        TCGA-G3-A5SJ        TCGA-G3-A5SK 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-G3-A5SL        TCGA-G3-A5SM 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE"   "4P GAIN MUTATED" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-BC-A5W4        TCGA-CC-5258        TCGA-CC-5260 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-CC-5261        TCGA-CC-5262        TCGA-CC-5263        TCGA-CC-A1HT 
  "4P GAIN MUTATED" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-CC-A3M9        TCGA-CC-A3MA        TCGA-CC-A3MB        TCGA-CC-A3MC 
  "4P GAIN MUTATED" "4P GAIN WILD-TYPE"   "4P GAIN MUTATED" "4P GAIN WILD-TYPE" 
       TCGA-DD-A113        TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DD-A118        TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B 
  "4P GAIN MUTATED" "4P GAIN WILD-TYPE"   "4P GAIN MUTATED" "4P GAIN WILD-TYPE" 
       TCGA-DD-A11C        TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EA 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DD-A1EB        TCGA-DD-A1EC        TCGA-DD-A1ED        TCGA-DD-A1EE 
"4P GAIN WILD-TYPE"   "4P GAIN MUTATED" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DD-A1EF        TCGA-DD-A1EH        TCGA-DD-A1EI        TCGA-DD-A1EJ 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DD-A1EL        TCGA-DD-A39V        TCGA-DD-A39X        TCGA-DD-A39Y 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DD-A39Z        TCGA-DD-A3A0        TCGA-DD-A3A1        TCGA-DD-A3A2 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DD-A3A3        TCGA-DD-A3A4        TCGA-DD-A3A5        TCGA-DD-A3A6 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DD-A3A7        TCGA-DD-A3A8        TCGA-DD-A3A9        TCGA-DD-A4NA 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DD-A4ND        TCGA-DD-A4NE        TCGA-DD-A4NF        TCGA-DD-A4NG 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DD-A4NH        TCGA-DD-A4NI        TCGA-DD-A4NJ        TCGA-DD-A4NK 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DD-A4NL        TCGA-DD-A4NN        TCGA-DD-A4NO        TCGA-DD-A4NP 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DD-A4NQ        TCGA-ED-A459        TCGA-ED-A5KG        TCGA-EP-A12J 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EP-A3JL        TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-FV-A23B        TCGA-FV-A2QR        TCGA-FV-A3I0        TCGA-FV-A3R2 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-FV-A3R3        TCGA-FV-A495        TCGA-FV-A496        TCGA-FV-A4ZP 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-FV-A4ZQ        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI 
"4P GAIN WILD-TYPE"   "4P GAIN MUTATED" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-G3-A3CJ        TCGA-G3-A3CK        TCGA-G3-A5SJ        TCGA-G3-A5SK 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-G3-A5SL        TCGA-G3-A5SM 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE"   "4P GAIN MUTATED" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-BC-A5W4        TCGA-CC-5258        TCGA-CC-5260 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-CC-5261        TCGA-CC-5262        TCGA-CC-5263        TCGA-CC-A1HT 
  "4P GAIN MUTATED" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-CC-A3M9        TCGA-CC-A3MA        TCGA-CC-A3MB        TCGA-CC-A3MC 
  "4P GAIN MUTATED" "4P GAIN WILD-TYPE"   "4P GAIN MUTATED" "4P GAIN WILD-TYPE" 
       TCGA-DD-A113        TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DD-A118        TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B 
  "4P GAIN MUTATED" "4P GAIN WILD-TYPE"   "4P GAIN MUTATED" "4P GAIN WILD-TYPE" 
       TCGA-DD-A11C        TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EA 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DD-A1EB        TCGA-DD-A1EC        TCGA-DD-A1ED        TCGA-DD-A1EE 
"4P GAIN WILD-TYPE"   "4P GAIN MUTATED" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DD-A1EF        TCGA-DD-A1EH        TCGA-DD-A1EI        TCGA-DD-A1EJ 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DD-A1EL        TCGA-DD-A39V        TCGA-DD-A39X        TCGA-DD-A39Y 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DD-A39Z        TCGA-DD-A3A0        TCGA-DD-A3A1        TCGA-DD-A3A2 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DD-A3A3        TCGA-DD-A3A4        TCGA-DD-A3A5        TCGA-DD-A3A6 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DD-A3A7        TCGA-DD-A3A8        TCGA-DD-A3A9        TCGA-DD-A4NA 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DD-A4ND        TCGA-DD-A4NE        TCGA-DD-A4NF        TCGA-DD-A4NG 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DD-A4NH        TCGA-DD-A4NI        TCGA-DD-A4NJ        TCGA-DD-A4NK 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DD-A4NL        TCGA-DD-A4NN        TCGA-DD-A4NO        TCGA-DD-A4NP 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DD-A4NQ        TCGA-ED-A459        TCGA-ED-A5KG        TCGA-EP-A12J 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EP-A3JL        TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-FV-A23B        TCGA-FV-A2QR        TCGA-FV-A3I0        TCGA-FV-A3R2 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-FV-A3R3        TCGA-FV-A495        TCGA-FV-A496        TCGA-FV-A4ZP 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-FV-A4ZQ        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI 
"4P GAIN WILD-TYPE"   "4P GAIN MUTATED" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-G3-A3CJ        TCGA-G3-A3CK        TCGA-G3-A5SJ        TCGA-G3-A5SK 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-G3-A5SL        TCGA-G3-A5SM 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
[1] "hr=" "1.9"
D7V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  4P GAIN MUTATED         3        2         0          2          0          0
  4P GAIN WILD-TYPE      42       23         2         23          3          4
                   vv
clus                STAGE IV STAGE IVA STAGE IVB
  4P GAIN MUTATED          0         0         0
  4P GAIN WILD-TYPE        1         1         1
D7V3, multiclass
                   vv
clus                T1 T2 T3 T4
  4P GAIN MUTATED    3  2  3  0
  4P GAIN WILD-TYPE 45 26 31  6
D7V4, multiclass
    clus
vv   4P GAIN MUTATED 4P GAIN WILD-TYPE
  T1               3                45
  T2               2                26
  T3               3                31
  T4               0                 6
D7V5, binary
                   cls
clus                 0  1
  4P GAIN MUTATED    7  0
  4P GAIN WILD-TYPE 67  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED      7    0
  4P GAIN WILD-TYPE   67    3
   clus
vv  4P GAIN MUTATED 4P GAIN WILD-TYPE
  0               7                67
  1               0                 3
                   vv
clus                M0 M1 MX
  4P GAIN MUTATED    7  0  1
  4P GAIN WILD-TYPE 83  2 24
D7V6, multiclass
    clus
vv   4P GAIN MUTATED 4P GAIN WILD-TYPE
  M0               7                83
  M1               0                 2
  MX               1                24
D7V7, binary
                   cls
clus                 0  1
  4P GAIN MUTATED    3  5
  4P GAIN WILD-TYPE 41 68
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED      3    5
  4P GAIN WILD-TYPE   41   68
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  FEMALE               3                41
  MALE                 5                68
                   vv
clus                R0 R1 R2 RX
  4P GAIN MUTATED    6  1  0  1
  4P GAIN WILD-TYPE 87  9  1  7
D7V8, multiclass
    clus
vv   4P GAIN MUTATED 4P GAIN WILD-TYPE
  R0               6                87
  R1               1                 9
  R2               0                 1
  RX               1                 7

Clustering(8) Variable = 4Q GAIN MUTATION ANALYSIS
D8V1, survival
                   sevent
clus2                0  1
  4Q GAIN MUTATED    2  1
  4Q GAIN WILD-TYPE 59 52
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                3               111 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                1                52 
$`4Q GAIN MUTATED`
TCGA-CC-5261 TCGA-DD-A1EC TCGA-G3-A3CG 
        3.02        19.76        22.13 

$`4Q GAIN WILD-TYPE`
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T 
       48.99        27.91        37.32        10.13        46.78        27.52 
TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 
       27.52         2.99        25.32        23.34         1.12        69.57 
TCGA-BC-A112 TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 
        5.03        44.42        13.81         0.26        16.37         9.50 
TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3M9 
        0.07         2.86         3.39         4.24         3.32         0.10 
TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 
        0.07         0.10         0.13        79.73        37.74        83.57 
TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C 
       53.29       112.96         7.33         2.60         0.46        21.76 
TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1ED TCGA-DD-A1EE 
       51.25        90.67        79.36        66.31        75.65         6.67 
TCGA-DD-A1EF TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EL TCGA-DD-A39V 
       12.95        49.15         6.02        29.16        13.64        21.14 
TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 
       55.66         5.59        19.73        25.81         7.66        70.06 
TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A8 
       17.59        20.12       102.74       107.11        13.78         0.36 
TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4ND TCGA-DD-A4NE TCGA-DD-A4NF TCGA-DD-A4NG 
       30.58        33.14        73.38        21.67        14.07        14.93 
TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN 
       14.24        10.78        15.06        39.75        56.25        29.56 
TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-ED-A459 TCGA-ED-A5KG TCGA-EP-A12J 
       61.45        93.67        12.26         0.23         0.20        10.85 
TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK 
        7.76        11.74         1.97         0.62         3.19         0.43 
TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3R2 
       23.01        14.40        32.45        19.07         0.20         6.35 
TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25S 
        0.13         0.03         0.33        60.36         0.39         1.22 
TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25X TCGA-G3-A25Y 
       51.02        53.79        28.27        30.71        58.49        14.86 
TCGA-G3-A25Z TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SJ 
       21.53        25.64         5.88        19.53        19.23        11.97 
TCGA-G3-A5SK TCGA-G3-A5SL TCGA-G3-A5SM 
        9.93         7.99         4.37 

  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
             3.02              0.03 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
            22.13            112.96 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
            19.76             15.06 
[1] "3.0 - 22.1 (19.8)"  "0.0 - 113.0 (15.1)"
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-BC-A5W4        TCGA-CC-5258        TCGA-CC-5260 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-CC-5261        TCGA-CC-5262        TCGA-CC-5263        TCGA-CC-A1HT 
  "4Q GAIN MUTATED" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-CC-A3M9        TCGA-CC-A3MA        TCGA-CC-A3MB        TCGA-CC-A3MC 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DD-A113        TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DD-A118        TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DD-A11C        TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EA 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DD-A1EB        TCGA-DD-A1EC        TCGA-DD-A1ED        TCGA-DD-A1EE 
"4Q GAIN WILD-TYPE"   "4Q GAIN MUTATED" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DD-A1EF        TCGA-DD-A1EH        TCGA-DD-A1EI        TCGA-DD-A1EJ 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DD-A1EL        TCGA-DD-A39V        TCGA-DD-A39X        TCGA-DD-A39Y 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DD-A39Z        TCGA-DD-A3A0        TCGA-DD-A3A1        TCGA-DD-A3A2 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DD-A3A3        TCGA-DD-A3A4        TCGA-DD-A3A5        TCGA-DD-A3A6 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DD-A3A7        TCGA-DD-A3A8        TCGA-DD-A3A9        TCGA-DD-A4NA 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DD-A4ND        TCGA-DD-A4NE        TCGA-DD-A4NF        TCGA-DD-A4NG 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DD-A4NH        TCGA-DD-A4NI        TCGA-DD-A4NJ        TCGA-DD-A4NK 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DD-A4NL        TCGA-DD-A4NN        TCGA-DD-A4NO        TCGA-DD-A4NP 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DD-A4NQ        TCGA-ED-A459        TCGA-ED-A5KG        TCGA-EP-A12J 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EP-A3JL        TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-FV-A23B        TCGA-FV-A2QR        TCGA-FV-A3I0        TCGA-FV-A3R2 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-FV-A3R3        TCGA-FV-A495        TCGA-FV-A496        TCGA-FV-A4ZP 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-FV-A4ZQ        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI 
"4Q GAIN WILD-TYPE"   "4Q GAIN MUTATED" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-G3-A3CJ        TCGA-G3-A3CK        TCGA-G3-A5SJ        TCGA-G3-A5SK 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-G3-A5SL        TCGA-G3-A5SM 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-BC-A5W4        TCGA-CC-5258        TCGA-CC-5260 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-CC-5261        TCGA-CC-5262        TCGA-CC-5263        TCGA-CC-A1HT 
  "4Q GAIN MUTATED" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-CC-A3M9        TCGA-CC-A3MA        TCGA-CC-A3MB        TCGA-CC-A3MC 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DD-A113        TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DD-A118        TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DD-A11C        TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EA 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DD-A1EB        TCGA-DD-A1EC        TCGA-DD-A1ED        TCGA-DD-A1EE 
"4Q GAIN WILD-TYPE"   "4Q GAIN MUTATED" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DD-A1EF        TCGA-DD-A1EH        TCGA-DD-A1EI        TCGA-DD-A1EJ 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DD-A1EL        TCGA-DD-A39V        TCGA-DD-A39X        TCGA-DD-A39Y 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DD-A39Z        TCGA-DD-A3A0        TCGA-DD-A3A1        TCGA-DD-A3A2 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DD-A3A3        TCGA-DD-A3A4        TCGA-DD-A3A5        TCGA-DD-A3A6 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DD-A3A7        TCGA-DD-A3A8        TCGA-DD-A3A9        TCGA-DD-A4NA 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DD-A4ND        TCGA-DD-A4NE        TCGA-DD-A4NF        TCGA-DD-A4NG 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DD-A4NH        TCGA-DD-A4NI        TCGA-DD-A4NJ        TCGA-DD-A4NK 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DD-A4NL        TCGA-DD-A4NN        TCGA-DD-A4NO        TCGA-DD-A4NP 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DD-A4NQ        TCGA-ED-A459        TCGA-ED-A5KG        TCGA-EP-A12J 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EP-A3JL        TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-FV-A23B        TCGA-FV-A2QR        TCGA-FV-A3I0        TCGA-FV-A3R2 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-FV-A3R3        TCGA-FV-A495        TCGA-FV-A496        TCGA-FV-A4ZP 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-FV-A4ZQ        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI 
"4Q GAIN WILD-TYPE"   "4Q GAIN MUTATED" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-G3-A3CJ        TCGA-G3-A3CK        TCGA-G3-A5SJ        TCGA-G3-A5SK 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-G3-A5SL        TCGA-G3-A5SM 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-BC-A5W4        TCGA-CC-5258        TCGA-CC-5260 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-CC-5261        TCGA-CC-5262        TCGA-CC-5263        TCGA-CC-A1HT 
  "4Q GAIN MUTATED" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-CC-A3M9        TCGA-CC-A3MA        TCGA-CC-A3MB        TCGA-CC-A3MC 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DD-A113        TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DD-A118        TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DD-A11C        TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EA 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DD-A1EB        TCGA-DD-A1EC        TCGA-DD-A1ED        TCGA-DD-A1EE 
"4Q GAIN WILD-TYPE"   "4Q GAIN MUTATED" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DD-A1EF        TCGA-DD-A1EH        TCGA-DD-A1EI        TCGA-DD-A1EJ 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DD-A1EL        TCGA-DD-A39V        TCGA-DD-A39X        TCGA-DD-A39Y 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DD-A39Z        TCGA-DD-A3A0        TCGA-DD-A3A1        TCGA-DD-A3A2 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DD-A3A3        TCGA-DD-A3A4        TCGA-DD-A3A5        TCGA-DD-A3A6 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DD-A3A7        TCGA-DD-A3A8        TCGA-DD-A3A9        TCGA-DD-A4NA 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DD-A4ND        TCGA-DD-A4NE        TCGA-DD-A4NF        TCGA-DD-A4NG 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DD-A4NH        TCGA-DD-A4NI        TCGA-DD-A4NJ        TCGA-DD-A4NK 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DD-A4NL        TCGA-DD-A4NN        TCGA-DD-A4NO        TCGA-DD-A4NP 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DD-A4NQ        TCGA-ED-A459        TCGA-ED-A5KG        TCGA-EP-A12J 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EP-A3JL        TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-FV-A23B        TCGA-FV-A2QR        TCGA-FV-A3I0        TCGA-FV-A3R2 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-FV-A3R3        TCGA-FV-A495        TCGA-FV-A496        TCGA-FV-A4ZP 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-FV-A4ZQ        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI 
"4Q GAIN WILD-TYPE"   "4Q GAIN MUTATED" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-G3-A3CJ        TCGA-G3-A3CK        TCGA-G3-A5SJ        TCGA-G3-A5SK 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-G3-A5SL        TCGA-G3-A5SM 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
[1] "hr=" "1.2"
D8V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  4Q GAIN MUTATED         2        1         0          0          0          0
  4Q GAIN WILD-TYPE      43       24         2         25          3          4
                   vv
clus                STAGE IV STAGE IVA STAGE IVB
  4Q GAIN MUTATED          0         0         0
  4Q GAIN WILD-TYPE        1         1         1
D8V3, multiclass
                   vv
clus                T1 T2 T3 T4
  4Q GAIN MUTATED    2  1  0  0
  4Q GAIN WILD-TYPE 46 27 34  6
D8V4, multiclass
    clus
vv   4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  T1               2                46
  T2               1                27
  T3               0                34
  T4               0                 6
D8V5, binary
                   cls
clus                 0  1
  4Q GAIN MUTATED    3  0
  4Q GAIN WILD-TYPE 71  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED      3    0
  4Q GAIN WILD-TYPE   71    3
   clus
vv  4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  0               3                71
  1               0                 3
                   vv
clus                M0 M1 MX
  4Q GAIN MUTATED    3  0  0
  4Q GAIN WILD-TYPE 87  2 25
D8V6, multiclass
    clus
vv   4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  M0               3                87
  M1               0                 2
  MX               0                25
D8V7, binary
                   cls
clus                 0  1
  4Q GAIN MUTATED    1  2
  4Q GAIN WILD-TYPE 43 71
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED      1    2
  4Q GAIN WILD-TYPE   43   71
        clus
vv       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  FEMALE               1                43
  MALE                 2                71
                   vv
clus                R0 R1 R2 RX
  4Q GAIN MUTATED    1  1  0  1
  4Q GAIN WILD-TYPE 92  9  1  7
D8V8, multiclass
    clus
vv   4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  R0               1                92
  R1               1                 9
  R2               0                 1
  RX               1                 7

Clustering(9) Variable = 5P GAIN MUTATION ANALYSIS
D9V1, survival
                   sevent
clus2                0  1
  5P GAIN MUTATED   22 24
  5P GAIN WILD-TYPE 39 29
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               46                68 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               24                29 
$`5P GAIN MUTATED`
TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10W TCGA-BC-A112 TCGA-BC-A217 TCGA-BC-A3KG 
       37.32        10.13         2.99         5.03        13.81        16.37 
TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A115 TCGA-DD-A116 
        4.24         3.32         0.10         0.13        83.57        53.29 
TCGA-DD-A118 TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EE 
      112.96        51.25        90.67        79.36        66.31         6.67 
TCGA-DD-A1EF TCGA-DD-A39V TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A3A1 TCGA-DD-A3A3 
       12.95        21.14        55.66         5.59         7.66        17.59 
TCGA-DD-A3A5 TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A4ND TCGA-DD-A4NI TCGA-DD-A4NK 
      102.74        13.78         0.36        73.38        10.78        39.75 
TCGA-DD-A4NO TCGA-ED-A459 TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL TCGA-ES-A2HT 
       61.45         0.23         1.97         0.62         3.19        14.40 
TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A495 TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25T 
       19.07         0.20         0.03        60.36         0.39        51.02 
TCGA-G3-A25W TCGA-G3-A25X TCGA-G3-A3CG TCGA-G3-A5SM 
       30.71        58.49        22.13         4.37 

$`5P GAIN WILD-TYPE`
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10X 
       48.99        27.91        46.78        27.52        27.52        25.32 
TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A216 TCGA-BC-A3KF TCGA-BC-A5W4 
       23.34         1.12        69.57        44.42         0.26         9.50 
TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-A3M9 TCGA-CC-A3MA 
        0.07         2.86         3.02         3.39         0.10         0.07 
TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C 
       79.73        37.74         7.33         2.60         0.46        21.76 
TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EL 
       19.76        75.65        49.15         6.02        29.16        13.64 
TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A2 TCGA-DD-A3A4 TCGA-DD-A3A6 TCGA-DD-A3A9 
       19.73        25.81        70.06        20.12       107.11        30.58 
TCGA-DD-A4NA TCGA-DD-A4NE TCGA-DD-A4NF TCGA-DD-A4NG TCGA-DD-A4NH TCGA-DD-A4NJ 
       33.14        21.67        14.07        14.93        14.24        15.06 
TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-ED-A5KG TCGA-EP-A12J 
       56.25        29.56        93.67        12.26         0.20        10.85 
TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A3RK TCGA-ES-A2HS TCGA-FV-A23B TCGA-FV-A3R2 
        7.76        11.74         0.43        23.01        32.45         6.35 
TCGA-FV-A3R3 TCGA-FV-A496 TCGA-G3-A25S TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25Y 
        0.13         0.33         1.22        53.79        28.27        14.86 
TCGA-G3-A25Z TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SJ 
       21.53        25.64         5.88        19.53        19.23        11.97 
TCGA-G3-A5SK TCGA-G3-A5SL 
        9.93         7.99 

  5P GAIN MUTATED 5P GAIN WILD-TYPE 
             0.03              0.07 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
           112.96            107.11 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
           14.105            19.380 
[1] "0.0 - 113.0 (14.1)" "0.1 - 107.1 (19.4)"
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED"   "5P GAIN MUTATED" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
  "5P GAIN MUTATED" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-BC-A5W4        TCGA-CC-5258        TCGA-CC-5260 
  "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-CC-5261        TCGA-CC-5262        TCGA-CC-5263        TCGA-CC-A1HT 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED"   "5P GAIN MUTATED" 
       TCGA-CC-A3M9        TCGA-CC-A3MA        TCGA-CC-A3MB        TCGA-CC-A3MC 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED"   "5P GAIN MUTATED" 
       TCGA-DD-A113        TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED"   "5P GAIN MUTATED" 
       TCGA-DD-A118        TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B 
  "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-DD-A11C        TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EA 
"5P GAIN WILD-TYPE"   "5P GAIN MUTATED"   "5P GAIN MUTATED"   "5P GAIN MUTATED" 
       TCGA-DD-A1EB        TCGA-DD-A1EC        TCGA-DD-A1ED        TCGA-DD-A1EE 
  "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" 
       TCGA-DD-A1EF        TCGA-DD-A1EH        TCGA-DD-A1EI        TCGA-DD-A1EJ 
  "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-DD-A1EL        TCGA-DD-A39V        TCGA-DD-A39X        TCGA-DD-A39Y 
"5P GAIN WILD-TYPE"   "5P GAIN MUTATED"   "5P GAIN MUTATED"   "5P GAIN MUTATED" 
       TCGA-DD-A39Z        TCGA-DD-A3A0        TCGA-DD-A3A1        TCGA-DD-A3A2 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" 
       TCGA-DD-A3A3        TCGA-DD-A3A4        TCGA-DD-A3A5        TCGA-DD-A3A6 
  "5P GAIN MUTATED" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" 
       TCGA-DD-A3A7        TCGA-DD-A3A8        TCGA-DD-A3A9        TCGA-DD-A4NA 
  "5P GAIN MUTATED"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-DD-A4ND        TCGA-DD-A4NE        TCGA-DD-A4NF        TCGA-DD-A4NG 
  "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-DD-A4NH        TCGA-DD-A4NI        TCGA-DD-A4NJ        TCGA-DD-A4NK 
"5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" 
       TCGA-DD-A4NL        TCGA-DD-A4NN        TCGA-DD-A4NO        TCGA-DD-A4NP 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" 
       TCGA-DD-A4NQ        TCGA-ED-A459        TCGA-ED-A5KG        TCGA-EP-A12J 
"5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED"   "5P GAIN MUTATED" 
       TCGA-EP-A3JL        TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT 
  "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" 
       TCGA-FV-A23B        TCGA-FV-A2QR        TCGA-FV-A3I0        TCGA-FV-A3R2 
"5P GAIN WILD-TYPE"   "5P GAIN MUTATED"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" 
       TCGA-FV-A3R3        TCGA-FV-A495        TCGA-FV-A496        TCGA-FV-A4ZP 
"5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" 
       TCGA-FV-A4ZQ        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
  "5P GAIN MUTATED" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"5P GAIN WILD-TYPE"   "5P GAIN MUTATED"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI 
"5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-G3-A3CJ        TCGA-G3-A3CK        TCGA-G3-A5SJ        TCGA-G3-A5SK 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-G3-A5SL        TCGA-G3-A5SM 
"5P GAIN WILD-TYPE"   "5P GAIN MUTATED" 
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED"   "5P GAIN MUTATED" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
  "5P GAIN MUTATED" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-BC-A5W4        TCGA-CC-5258        TCGA-CC-5260 
  "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-CC-5261        TCGA-CC-5262        TCGA-CC-5263        TCGA-CC-A1HT 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED"   "5P GAIN MUTATED" 
       TCGA-CC-A3M9        TCGA-CC-A3MA        TCGA-CC-A3MB        TCGA-CC-A3MC 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED"   "5P GAIN MUTATED" 
       TCGA-DD-A113        TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED"   "5P GAIN MUTATED" 
       TCGA-DD-A118        TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B 
  "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-DD-A11C        TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EA 
"5P GAIN WILD-TYPE"   "5P GAIN MUTATED"   "5P GAIN MUTATED"   "5P GAIN MUTATED" 
       TCGA-DD-A1EB        TCGA-DD-A1EC        TCGA-DD-A1ED        TCGA-DD-A1EE 
  "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" 
       TCGA-DD-A1EF        TCGA-DD-A1EH        TCGA-DD-A1EI        TCGA-DD-A1EJ 
  "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-DD-A1EL        TCGA-DD-A39V        TCGA-DD-A39X        TCGA-DD-A39Y 
"5P GAIN WILD-TYPE"   "5P GAIN MUTATED"   "5P GAIN MUTATED"   "5P GAIN MUTATED" 
       TCGA-DD-A39Z        TCGA-DD-A3A0        TCGA-DD-A3A1        TCGA-DD-A3A2 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" 
       TCGA-DD-A3A3        TCGA-DD-A3A4        TCGA-DD-A3A5        TCGA-DD-A3A6 
  "5P GAIN MUTATED" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" 
       TCGA-DD-A3A7        TCGA-DD-A3A8        TCGA-DD-A3A9        TCGA-DD-A4NA 
  "5P GAIN MUTATED"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-DD-A4ND        TCGA-DD-A4NE        TCGA-DD-A4NF        TCGA-DD-A4NG 
  "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-DD-A4NH        TCGA-DD-A4NI        TCGA-DD-A4NJ        TCGA-DD-A4NK 
"5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" 
       TCGA-DD-A4NL        TCGA-DD-A4NN        TCGA-DD-A4NO        TCGA-DD-A4NP 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" 
       TCGA-DD-A4NQ        TCGA-ED-A459        TCGA-ED-A5KG        TCGA-EP-A12J 
"5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED"   "5P GAIN MUTATED" 
       TCGA-EP-A3JL        TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT 
  "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" 
       TCGA-FV-A23B        TCGA-FV-A2QR        TCGA-FV-A3I0        TCGA-FV-A3R2 
"5P GAIN WILD-TYPE"   "5P GAIN MUTATED"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" 
       TCGA-FV-A3R3        TCGA-FV-A495        TCGA-FV-A496        TCGA-FV-A4ZP 
"5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" 
       TCGA-FV-A4ZQ        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
  "5P GAIN MUTATED" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"5P GAIN WILD-TYPE"   "5P GAIN MUTATED"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI 
"5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-G3-A3CJ        TCGA-G3-A3CK        TCGA-G3-A5SJ        TCGA-G3-A5SK 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-G3-A5SL        TCGA-G3-A5SM 
"5P GAIN WILD-TYPE"   "5P GAIN MUTATED" 
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED"   "5P GAIN MUTATED" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
  "5P GAIN MUTATED" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-BC-A5W4        TCGA-CC-5258        TCGA-CC-5260 
  "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-CC-5261        TCGA-CC-5262        TCGA-CC-5263        TCGA-CC-A1HT 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED"   "5P GAIN MUTATED" 
       TCGA-CC-A3M9        TCGA-CC-A3MA        TCGA-CC-A3MB        TCGA-CC-A3MC 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED"   "5P GAIN MUTATED" 
       TCGA-DD-A113        TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED"   "5P GAIN MUTATED" 
       TCGA-DD-A118        TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B 
  "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-DD-A11C        TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EA 
"5P GAIN WILD-TYPE"   "5P GAIN MUTATED"   "5P GAIN MUTATED"   "5P GAIN MUTATED" 
       TCGA-DD-A1EB        TCGA-DD-A1EC        TCGA-DD-A1ED        TCGA-DD-A1EE 
  "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" 
       TCGA-DD-A1EF        TCGA-DD-A1EH        TCGA-DD-A1EI        TCGA-DD-A1EJ 
  "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-DD-A1EL        TCGA-DD-A39V        TCGA-DD-A39X        TCGA-DD-A39Y 
"5P GAIN WILD-TYPE"   "5P GAIN MUTATED"   "5P GAIN MUTATED"   "5P GAIN MUTATED" 
       TCGA-DD-A39Z        TCGA-DD-A3A0        TCGA-DD-A3A1        TCGA-DD-A3A2 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" 
       TCGA-DD-A3A3        TCGA-DD-A3A4        TCGA-DD-A3A5        TCGA-DD-A3A6 
  "5P GAIN MUTATED" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" 
       TCGA-DD-A3A7        TCGA-DD-A3A8        TCGA-DD-A3A9        TCGA-DD-A4NA 
  "5P GAIN MUTATED"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-DD-A4ND        TCGA-DD-A4NE        TCGA-DD-A4NF        TCGA-DD-A4NG 
  "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-DD-A4NH        TCGA-DD-A4NI        TCGA-DD-A4NJ        TCGA-DD-A4NK 
"5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" 
       TCGA-DD-A4NL        TCGA-DD-A4NN        TCGA-DD-A4NO        TCGA-DD-A4NP 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" 
       TCGA-DD-A4NQ        TCGA-ED-A459        TCGA-ED-A5KG        TCGA-EP-A12J 
"5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED"   "5P GAIN MUTATED" 
       TCGA-EP-A3JL        TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT 
  "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" 
       TCGA-FV-A23B        TCGA-FV-A2QR        TCGA-FV-A3I0        TCGA-FV-A3R2 
"5P GAIN WILD-TYPE"   "5P GAIN MUTATED"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" 
       TCGA-FV-A3R3        TCGA-FV-A495        TCGA-FV-A496        TCGA-FV-A4ZP 
"5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" 
       TCGA-FV-A4ZQ        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
  "5P GAIN MUTATED" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"5P GAIN WILD-TYPE"   "5P GAIN MUTATED"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI 
"5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-G3-A3CJ        TCGA-G3-A3CK        TCGA-G3-A5SJ        TCGA-G3-A5SK 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-G3-A5SL        TCGA-G3-A5SM 
"5P GAIN WILD-TYPE"   "5P GAIN MUTATED" 
[1] "hr=" "1"  
D9V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  5P GAIN MUTATED        16       12         1         11          2          0
  5P GAIN WILD-TYPE      29       13         1         14          1          4
                   vv
clus                STAGE IV STAGE IVA STAGE IVB
  5P GAIN MUTATED          0         0         0
  5P GAIN WILD-TYPE        1         1         1
D9V3, multiclass
                   vv
clus                T1 T2 T3 T4
  5P GAIN MUTATED   16 13 16  1
  5P GAIN WILD-TYPE 32 15 18  5
D9V4, multiclass
    clus
vv   5P GAIN MUTATED 5P GAIN WILD-TYPE
  T1              16                32
  T2              13                15
  T3              16                18
  T4               1                 5
D9V5, binary
                   cls
clus                 0  1
  5P GAIN MUTATED   29  0
  5P GAIN WILD-TYPE 45  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED     29    0
  5P GAIN WILD-TYPE   45    3
   clus
vv  5P GAIN MUTATED 5P GAIN WILD-TYPE
  0              29                45
  1               0                 3
                   vv
clus                M0 M1 MX
  5P GAIN MUTATED   39  0  8
  5P GAIN WILD-TYPE 51  2 17
D9V6, multiclass
    clus
vv   5P GAIN MUTATED 5P GAIN WILD-TYPE
  M0              39                51
  M1               0                 2
  MX               8                17
D9V7, binary
                   cls
clus                 0  1
  5P GAIN MUTATED   17 30
  5P GAIN WILD-TYPE 27 43
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED     17   30
  5P GAIN WILD-TYPE   27   43
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  FEMALE              17                27
  MALE                30                43
                   vv
clus                R0 R1 R2 RX
  5P GAIN MUTATED   38  4  0  3
  5P GAIN WILD-TYPE 55  6  1  5
D9V8, multiclass
    clus
vv   5P GAIN MUTATED 5P GAIN WILD-TYPE
  R0              38                55
  R1               4                 6
  R2               0                 1
  RX               3                 5

Clustering(10) Variable = 5Q GAIN MUTATION ANALYSIS
D10V1, survival
                   sevent
clus2                0  1
  5Q GAIN MUTATED   16 19
  5Q GAIN WILD-TYPE 45 34
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               35                79 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               19                34 
$`5Q GAIN MUTATED`
TCGA-BC-A10Q TCGA-BC-A10W TCGA-BC-A112 TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A115 
       37.32         2.99         5.03         0.10         0.13        83.57 
TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EE 
       53.29       112.96        51.25        90.67        79.36         6.67 
TCGA-DD-A39V TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A3A1 TCGA-DD-A3A3 TCGA-DD-A3A5 
       21.14        55.66         5.59         7.66        17.59       102.74 
TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A4ND TCGA-DD-A4NI TCGA-DD-A4NK TCGA-DD-A4NO 
       13.78         0.36        73.38        10.78        39.75        61.45 
TCGA-ED-A459 TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL TCGA-ES-A2HT TCGA-FV-A495 
        0.23         1.97         0.62         3.19        14.40         0.03 
TCGA-FV-A4ZQ TCGA-G3-A25T TCGA-G3-A25W TCGA-G3-A3CG TCGA-G3-A5SM 
        0.39        51.02        30.71        22.13         4.37 

$`5Q GAIN WILD-TYPE`
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U 
       48.99        27.91        10.13        46.78        27.52        27.52 
TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A216 TCGA-BC-A217 
       25.32        23.34         1.12        69.57        44.42        13.81 
TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5261 
        0.26        16.37         9.50         0.07         2.86         3.02 
TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-DD-A113 
        3.39         4.24         3.32         0.10         0.07        79.73 
TCGA-DD-A114 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A1EB 
       37.74         7.33         2.60         0.46        21.76        66.31 
TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EF TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ 
       19.76        75.65        12.95        49.15         6.02        29.16 
TCGA-DD-A1EL TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A2 TCGA-DD-A3A4 TCGA-DD-A3A6 
       13.64        19.73        25.81        70.06        20.12       107.11 
TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NE TCGA-DD-A4NF TCGA-DD-A4NG TCGA-DD-A4NH 
       30.58        33.14        21.67        14.07        14.93        14.24 
TCGA-DD-A4NJ TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-ED-A5KG 
       15.06        56.25        29.56        93.67        12.26         0.20 
TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A3RK TCGA-ES-A2HS TCGA-FV-A23B 
       10.85         7.76        11.74         0.43        23.01        32.45 
TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A496 TCGA-FV-A4ZP 
       19.07         0.20         6.35         0.13         0.33        60.36 
TCGA-G3-A25S TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A25Z 
        1.22        53.79        28.27        58.49        14.86        21.53 
TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SJ TCGA-G3-A5SK 
       25.64         5.88        19.53        19.23        11.97         9.93 
TCGA-G3-A5SL 
        7.99 

  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
             0.03              0.07 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
           112.96            107.11 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
            14.40             16.37 
[1] "0.0 - 113.0 (14.4)" "0.1 - 107.1 (16.4)"
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
  "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-BC-A5W4        TCGA-CC-5258        TCGA-CC-5260 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-CC-5261        TCGA-CC-5262        TCGA-CC-5263        TCGA-CC-A1HT 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-CC-A3M9        TCGA-CC-A3MA        TCGA-CC-A3MB        TCGA-CC-A3MC 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED"   "5Q GAIN MUTATED" 
       TCGA-DD-A113        TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED"   "5Q GAIN MUTATED" 
       TCGA-DD-A118        TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B 
  "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-DD-A11C        TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EA 
"5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED"   "5Q GAIN MUTATED"   "5Q GAIN MUTATED" 
       TCGA-DD-A1EB        TCGA-DD-A1EC        TCGA-DD-A1ED        TCGA-DD-A1EE 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED" 
       TCGA-DD-A1EF        TCGA-DD-A1EH        TCGA-DD-A1EI        TCGA-DD-A1EJ 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-DD-A1EL        TCGA-DD-A39V        TCGA-DD-A39X        TCGA-DD-A39Y 
"5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED"   "5Q GAIN MUTATED"   "5Q GAIN MUTATED" 
       TCGA-DD-A39Z        TCGA-DD-A3A0        TCGA-DD-A3A1        TCGA-DD-A3A2 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE" 
       TCGA-DD-A3A3        TCGA-DD-A3A4        TCGA-DD-A3A5        TCGA-DD-A3A6 
  "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE" 
       TCGA-DD-A3A7        TCGA-DD-A3A8        TCGA-DD-A3A9        TCGA-DD-A4NA 
  "5Q GAIN MUTATED"   "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-DD-A4ND        TCGA-DD-A4NE        TCGA-DD-A4NF        TCGA-DD-A4NG 
  "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-DD-A4NH        TCGA-DD-A4NI        TCGA-DD-A4NJ        TCGA-DD-A4NK 
"5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED" 
       TCGA-DD-A4NL        TCGA-DD-A4NN        TCGA-DD-A4NO        TCGA-DD-A4NP 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE" 
       TCGA-DD-A4NQ        TCGA-ED-A459        TCGA-ED-A5KG        TCGA-EP-A12J 
"5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED"   "5Q GAIN MUTATED" 
       TCGA-EP-A3JL        TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT 
  "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED" 
       TCGA-FV-A23B        TCGA-FV-A2QR        TCGA-FV-A3I0        TCGA-FV-A3R2 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-FV-A3R3        TCGA-FV-A495        TCGA-FV-A496        TCGA-FV-A4ZP 
"5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-FV-A4ZQ        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
  "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI 
"5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-G3-A3CJ        TCGA-G3-A3CK        TCGA-G3-A5SJ        TCGA-G3-A5SK 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-G3-A5SL        TCGA-G3-A5SM 
"5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED" 
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
  "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-BC-A5W4        TCGA-CC-5258        TCGA-CC-5260 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-CC-5261        TCGA-CC-5262        TCGA-CC-5263        TCGA-CC-A1HT 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-CC-A3M9        TCGA-CC-A3MA        TCGA-CC-A3MB        TCGA-CC-A3MC 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED"   "5Q GAIN MUTATED" 
       TCGA-DD-A113        TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED"   "5Q GAIN MUTATED" 
       TCGA-DD-A118        TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B 
  "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-DD-A11C        TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EA 
"5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED"   "5Q GAIN MUTATED"   "5Q GAIN MUTATED" 
       TCGA-DD-A1EB        TCGA-DD-A1EC        TCGA-DD-A1ED        TCGA-DD-A1EE 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED" 
       TCGA-DD-A1EF        TCGA-DD-A1EH        TCGA-DD-A1EI        TCGA-DD-A1EJ 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-DD-A1EL        TCGA-DD-A39V        TCGA-DD-A39X        TCGA-DD-A39Y 
"5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED"   "5Q GAIN MUTATED"   "5Q GAIN MUTATED" 
       TCGA-DD-A39Z        TCGA-DD-A3A0        TCGA-DD-A3A1        TCGA-DD-A3A2 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE" 
       TCGA-DD-A3A3        TCGA-DD-A3A4        TCGA-DD-A3A5        TCGA-DD-A3A6 
  "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE" 
       TCGA-DD-A3A7        TCGA-DD-A3A8        TCGA-DD-A3A9        TCGA-DD-A4NA 
  "5Q GAIN MUTATED"   "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-DD-A4ND        TCGA-DD-A4NE        TCGA-DD-A4NF        TCGA-DD-A4NG 
  "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-DD-A4NH        TCGA-DD-A4NI        TCGA-DD-A4NJ        TCGA-DD-A4NK 
"5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED" 
       TCGA-DD-A4NL        TCGA-DD-A4NN        TCGA-DD-A4NO        TCGA-DD-A4NP 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE" 
       TCGA-DD-A4NQ        TCGA-ED-A459        TCGA-ED-A5KG        TCGA-EP-A12J 
"5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED"   "5Q GAIN MUTATED" 
       TCGA-EP-A3JL        TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT 
  "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED" 
       TCGA-FV-A23B        TCGA-FV-A2QR        TCGA-FV-A3I0        TCGA-FV-A3R2 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-FV-A3R3        TCGA-FV-A495        TCGA-FV-A496        TCGA-FV-A4ZP 
"5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-FV-A4ZQ        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
  "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI 
"5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-G3-A3CJ        TCGA-G3-A3CK        TCGA-G3-A5SJ        TCGA-G3-A5SK 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-G3-A5SL        TCGA-G3-A5SM 
"5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED" 
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
  "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-BC-A5W4        TCGA-CC-5258        TCGA-CC-5260 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-CC-5261        TCGA-CC-5262        TCGA-CC-5263        TCGA-CC-A1HT 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-CC-A3M9        TCGA-CC-A3MA        TCGA-CC-A3MB        TCGA-CC-A3MC 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED"   "5Q GAIN MUTATED" 
       TCGA-DD-A113        TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED"   "5Q GAIN MUTATED" 
       TCGA-DD-A118        TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B 
  "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-DD-A11C        TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EA 
"5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED"   "5Q GAIN MUTATED"   "5Q GAIN MUTATED" 
       TCGA-DD-A1EB        TCGA-DD-A1EC        TCGA-DD-A1ED        TCGA-DD-A1EE 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED" 
       TCGA-DD-A1EF        TCGA-DD-A1EH        TCGA-DD-A1EI        TCGA-DD-A1EJ 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-DD-A1EL        TCGA-DD-A39V        TCGA-DD-A39X        TCGA-DD-A39Y 
"5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED"   "5Q GAIN MUTATED"   "5Q GAIN MUTATED" 
       TCGA-DD-A39Z        TCGA-DD-A3A0        TCGA-DD-A3A1        TCGA-DD-A3A2 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE" 
       TCGA-DD-A3A3        TCGA-DD-A3A4        TCGA-DD-A3A5        TCGA-DD-A3A6 
  "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE" 
       TCGA-DD-A3A7        TCGA-DD-A3A8        TCGA-DD-A3A9        TCGA-DD-A4NA 
  "5Q GAIN MUTATED"   "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-DD-A4ND        TCGA-DD-A4NE        TCGA-DD-A4NF        TCGA-DD-A4NG 
  "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-DD-A4NH        TCGA-DD-A4NI        TCGA-DD-A4NJ        TCGA-DD-A4NK 
"5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED" 
       TCGA-DD-A4NL        TCGA-DD-A4NN        TCGA-DD-A4NO        TCGA-DD-A4NP 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE" 
       TCGA-DD-A4NQ        TCGA-ED-A459        TCGA-ED-A5KG        TCGA-EP-A12J 
"5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED"   "5Q GAIN MUTATED" 
       TCGA-EP-A3JL        TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT 
  "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED" 
       TCGA-FV-A23B        TCGA-FV-A2QR        TCGA-FV-A3I0        TCGA-FV-A3R2 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-FV-A3R3        TCGA-FV-A495        TCGA-FV-A496        TCGA-FV-A4ZP 
"5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-FV-A4ZQ        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
  "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI 
"5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-G3-A3CJ        TCGA-G3-A3CK        TCGA-G3-A5SJ        TCGA-G3-A5SK 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-G3-A5SL        TCGA-G3-A5SM 
"5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED" 
[1] "hr=" "1"  
D10V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  5Q GAIN MUTATED        13        8         1          8          2          0
  5Q GAIN WILD-TYPE      32       17         1         17          1          4
                   vv
clus                STAGE IV STAGE IVA STAGE IVB
  5Q GAIN MUTATED          0         0         0
  5Q GAIN WILD-TYPE        1         1         1
D10V3, multiclass
                   vv
clus                T1 T2 T3 T4
  5Q GAIN MUTATED   13  9 12  1
  5Q GAIN WILD-TYPE 35 19 22  5
D10V4, multiclass
    clus
vv   5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  T1              13                35
  T2               9                19
  T3              12                22
  T4               1                 5
D10V5, binary
                   cls
clus                 0  1
  5Q GAIN MUTATED   22  0
  5Q GAIN WILD-TYPE 52  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED     22    0
  5Q GAIN WILD-TYPE   52    3
   clus
vv  5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  0              22                52
  1               0                 3
                   vv
clus                M0 M1 MX
  5Q GAIN MUTATED   29  0  7
  5Q GAIN WILD-TYPE 61  2 18
D10V6, multiclass
    clus
vv   5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  M0              29                61
  M1               0                 2
  MX               7                18
D10V7, binary
                   cls
clus                 0  1
  5Q GAIN MUTATED   11 25
  5Q GAIN WILD-TYPE 33 48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED     11   25
  5Q GAIN WILD-TYPE   33   48
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  FEMALE              11                33
  MALE                25                48
                   vv
clus                R0 R1 R2 RX
  5Q GAIN MUTATED   31  3  0  1
  5Q GAIN WILD-TYPE 62  7  1  7
D10V8, multiclass
    clus
vv   5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  R0              31                62
  R1               3                 7
  R2               0                 1
  RX               1                 7

Clustering(11) Variable = 6P GAIN MUTATION ANALYSIS
D11V1, survival
                   sevent
clus2                0  1
  6P GAIN MUTATED   14 14
  6P GAIN WILD-TYPE 47 39
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               28                86 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               14                39 
$`6P GAIN MUTATED`
TCGA-BC-A10U TCGA-BC-A217 TCGA-BC-A3KG TCGA-CC-5263 TCGA-CC-A3MC TCGA-DD-A114 
       27.52        13.81        16.37         4.24         0.13        37.74 
TCGA-DD-A119 TCGA-DD-A1EF TCGA-DD-A1EH TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A3A9 
        7.33        12.95        49.15        55.66         5.59        30.58 
TCGA-DD-A4NE TCGA-DD-A4NG TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NN TCGA-EP-A2KB 
       21.67        14.93        14.24        10.78        29.56         1.97 
TCGA-EP-A2KC TCGA-ES-A2HS TCGA-FV-A3I0 TCGA-FV-A3R2 TCGA-G3-A25S TCGA-G3-A25U 
        0.62        23.01         0.20         6.35         1.22        53.79 
TCGA-G3-A25X TCGA-G3-A3CG TCGA-G3-A3CK TCGA-G3-A5SL 
       58.49        22.13        19.23         7.99 

$`6P GAIN WILD-TYPE`
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T 
       48.99        27.91        37.32        10.13        46.78        27.52 
TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 
        2.99        25.32        23.34         1.12        69.57         5.03 
TCGA-BC-A216 TCGA-BC-A3KF TCGA-BC-A5W4 TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5261 
       44.42         0.26         9.50         0.07         2.86         3.02 
TCGA-CC-5262 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-DD-A113 
        3.39         3.32         0.10         0.07         0.10        79.73 
TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C 
       83.57        53.29       112.96         2.60         0.46        21.76 
TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED 
       51.25        90.67        79.36        66.31        19.76        75.65 
TCGA-DD-A1EE TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39Z 
        6.67         6.02        29.16        13.64        21.14        19.73 
TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 
       25.81         7.66        70.06        17.59        20.12       102.74 
TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A4NA TCGA-DD-A4ND TCGA-DD-A4NF 
      107.11        13.78         0.36        33.14        73.38        14.07 
TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ 
       15.06        39.75        56.25        61.45        93.67        12.26 
TCGA-ED-A459 TCGA-ED-A5KG TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A3JL 
        0.23         0.20        10.85         7.76        11.74         3.19 
TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-A3R3 TCGA-FV-A495 
        0.43        14.40        32.45        19.07         0.13         0.03 
TCGA-FV-A496 TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25T TCGA-G3-A25V TCGA-G3-A25W 
        0.33        60.36         0.39        51.02        28.27        30.71 
TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A5SJ 
       14.86        21.53        25.64         5.88        19.53        11.97 
TCGA-G3-A5SK TCGA-G3-A5SM 
        9.93         4.37 

  6P GAIN MUTATED 6P GAIN WILD-TYPE 
             0.13              0.03 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
            58.49            112.96 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
           14.585            18.330 
[1] "0.1 - 58.5 (14.6)"  "0.0 - 113.0 (18.3)"
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-BC-A5W4        TCGA-CC-5258        TCGA-CC-5260 
  "6P GAIN MUTATED" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-CC-5261        TCGA-CC-5262        TCGA-CC-5263        TCGA-CC-A1HT 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" 
       TCGA-CC-A3M9        TCGA-CC-A3MA        TCGA-CC-A3MB        TCGA-CC-A3MC 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" 
       TCGA-DD-A113        TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116 
"6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-DD-A118        TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B 
"6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-DD-A11C        TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EA 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-DD-A1EB        TCGA-DD-A1EC        TCGA-DD-A1ED        TCGA-DD-A1EE 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-DD-A1EF        TCGA-DD-A1EH        TCGA-DD-A1EI        TCGA-DD-A1EJ 
  "6P GAIN MUTATED"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-DD-A1EL        TCGA-DD-A39V        TCGA-DD-A39X        TCGA-DD-A39Y 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED"   "6P GAIN MUTATED" 
       TCGA-DD-A39Z        TCGA-DD-A3A0        TCGA-DD-A3A1        TCGA-DD-A3A2 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-DD-A3A3        TCGA-DD-A3A4        TCGA-DD-A3A5        TCGA-DD-A3A6 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-DD-A3A7        TCGA-DD-A3A8        TCGA-DD-A3A9        TCGA-DD-A4NA 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" 
       TCGA-DD-A4ND        TCGA-DD-A4NE        TCGA-DD-A4NF        TCGA-DD-A4NG 
"6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" 
       TCGA-DD-A4NH        TCGA-DD-A4NI        TCGA-DD-A4NJ        TCGA-DD-A4NK 
  "6P GAIN MUTATED"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-DD-A4NL        TCGA-DD-A4NN        TCGA-DD-A4NO        TCGA-DD-A4NP 
"6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-DD-A4NQ        TCGA-ED-A459        TCGA-ED-A5KG        TCGA-EP-A12J 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED"   "6P GAIN MUTATED" 
       TCGA-EP-A3JL        TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" 
       TCGA-FV-A23B        TCGA-FV-A2QR        TCGA-FV-A3I0        TCGA-FV-A3R2 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED"   "6P GAIN MUTATED" 
       TCGA-FV-A3R3        TCGA-FV-A495        TCGA-FV-A496        TCGA-FV-A4ZP 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-FV-A4ZQ        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI 
"6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-G3-A3CJ        TCGA-G3-A3CK        TCGA-G3-A5SJ        TCGA-G3-A5SK 
"6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-G3-A5SL        TCGA-G3-A5SM 
  "6P GAIN MUTATED" "6P GAIN WILD-TYPE" 
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-BC-A5W4        TCGA-CC-5258        TCGA-CC-5260 
  "6P GAIN MUTATED" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-CC-5261        TCGA-CC-5262        TCGA-CC-5263        TCGA-CC-A1HT 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" 
       TCGA-CC-A3M9        TCGA-CC-A3MA        TCGA-CC-A3MB        TCGA-CC-A3MC 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" 
       TCGA-DD-A113        TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116 
"6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-DD-A118        TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B 
"6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-DD-A11C        TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EA 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-DD-A1EB        TCGA-DD-A1EC        TCGA-DD-A1ED        TCGA-DD-A1EE 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-DD-A1EF        TCGA-DD-A1EH        TCGA-DD-A1EI        TCGA-DD-A1EJ 
  "6P GAIN MUTATED"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-DD-A1EL        TCGA-DD-A39V        TCGA-DD-A39X        TCGA-DD-A39Y 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED"   "6P GAIN MUTATED" 
       TCGA-DD-A39Z        TCGA-DD-A3A0        TCGA-DD-A3A1        TCGA-DD-A3A2 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-DD-A3A3        TCGA-DD-A3A4        TCGA-DD-A3A5        TCGA-DD-A3A6 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-DD-A3A7        TCGA-DD-A3A8        TCGA-DD-A3A9        TCGA-DD-A4NA 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" 
       TCGA-DD-A4ND        TCGA-DD-A4NE        TCGA-DD-A4NF        TCGA-DD-A4NG 
"6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" 
       TCGA-DD-A4NH        TCGA-DD-A4NI        TCGA-DD-A4NJ        TCGA-DD-A4NK 
  "6P GAIN MUTATED"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-DD-A4NL        TCGA-DD-A4NN        TCGA-DD-A4NO        TCGA-DD-A4NP 
"6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-DD-A4NQ        TCGA-ED-A459        TCGA-ED-A5KG        TCGA-EP-A12J 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED"   "6P GAIN MUTATED" 
       TCGA-EP-A3JL        TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" 
       TCGA-FV-A23B        TCGA-FV-A2QR        TCGA-FV-A3I0        TCGA-FV-A3R2 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED"   "6P GAIN MUTATED" 
       TCGA-FV-A3R3        TCGA-FV-A495        TCGA-FV-A496        TCGA-FV-A4ZP 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-FV-A4ZQ        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI 
"6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-G3-A3CJ        TCGA-G3-A3CK        TCGA-G3-A5SJ        TCGA-G3-A5SK 
"6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-G3-A5SL        TCGA-G3-A5SM 
  "6P GAIN MUTATED" "6P GAIN WILD-TYPE" 
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-BC-A5W4        TCGA-CC-5258        TCGA-CC-5260 
  "6P GAIN MUTATED" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-CC-5261        TCGA-CC-5262        TCGA-CC-5263        TCGA-CC-A1HT 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" 
       TCGA-CC-A3M9        TCGA-CC-A3MA        TCGA-CC-A3MB        TCGA-CC-A3MC 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" 
       TCGA-DD-A113        TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116 
"6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-DD-A118        TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B 
"6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-DD-A11C        TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EA 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-DD-A1EB        TCGA-DD-A1EC        TCGA-DD-A1ED        TCGA-DD-A1EE 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-DD-A1EF        TCGA-DD-A1EH        TCGA-DD-A1EI        TCGA-DD-A1EJ 
  "6P GAIN MUTATED"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-DD-A1EL        TCGA-DD-A39V        TCGA-DD-A39X        TCGA-DD-A39Y 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED"   "6P GAIN MUTATED" 
       TCGA-DD-A39Z        TCGA-DD-A3A0        TCGA-DD-A3A1        TCGA-DD-A3A2 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-DD-A3A3        TCGA-DD-A3A4        TCGA-DD-A3A5        TCGA-DD-A3A6 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-DD-A3A7        TCGA-DD-A3A8        TCGA-DD-A3A9        TCGA-DD-A4NA 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" 
       TCGA-DD-A4ND        TCGA-DD-A4NE        TCGA-DD-A4NF        TCGA-DD-A4NG 
"6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" 
       TCGA-DD-A4NH        TCGA-DD-A4NI        TCGA-DD-A4NJ        TCGA-DD-A4NK 
  "6P GAIN MUTATED"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-DD-A4NL        TCGA-DD-A4NN        TCGA-DD-A4NO        TCGA-DD-A4NP 
"6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-DD-A4NQ        TCGA-ED-A459        TCGA-ED-A5KG        TCGA-EP-A12J 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED"   "6P GAIN MUTATED" 
       TCGA-EP-A3JL        TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" 
       TCGA-FV-A23B        TCGA-FV-A2QR        TCGA-FV-A3I0        TCGA-FV-A3R2 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED"   "6P GAIN MUTATED" 
       TCGA-FV-A3R3        TCGA-FV-A495        TCGA-FV-A496        TCGA-FV-A4ZP 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-FV-A4ZQ        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI 
"6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-G3-A3CJ        TCGA-G3-A3CK        TCGA-G3-A5SJ        TCGA-G3-A5SK 
"6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-G3-A5SL        TCGA-G3-A5SM 
  "6P GAIN MUTATED" "6P GAIN WILD-TYPE" 
[1] "hr=" "1.5"
D11V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  6P GAIN MUTATED        12        6         1          6          1          0
  6P GAIN WILD-TYPE      33       19         1         19          2          4
                   vv
clus                STAGE IV STAGE IVA STAGE IVB
  6P GAIN MUTATED          1         0         1
  6P GAIN WILD-TYPE        0         1         0
D11V3, multiclass
                   vv
clus                T1 T2 T3 T4
  6P GAIN MUTATED   12  7  9  1
  6P GAIN WILD-TYPE 36 21 25  5
D11V4, multiclass
    clus
vv   6P GAIN MUTATED 6P GAIN WILD-TYPE
  T1              12                36
  T2               7                21
  T3               9                25
  T4               1                 5
D11V5, binary
                   cls
clus                 0  1
  6P GAIN MUTATED   16  0
  6P GAIN WILD-TYPE 58  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED     16    0
  6P GAIN WILD-TYPE   58    3
   clus
vv  6P GAIN MUTATED 6P GAIN WILD-TYPE
  0              16                58
  1               0                 3
                   vv
clus                M0 M1 MX
  6P GAIN MUTATED   22  2  5
  6P GAIN WILD-TYPE 68  0 20
D11V6, multiclass
    clus
vv   6P GAIN MUTATED 6P GAIN WILD-TYPE
  M0              22                68
  M1               2                 0
  MX               5                20
D11V7, binary
                   cls
clus                 0  1
  6P GAIN MUTATED   11 18
  6P GAIN WILD-TYPE 33 55
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED     11   18
  6P GAIN WILD-TYPE   33   55
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  FEMALE              11                33
  MALE                18                55
                   vv
clus                R0 R1 R2 RX
  6P GAIN MUTATED   23  3  1  2
  6P GAIN WILD-TYPE 70  7  0  6
D11V8, multiclass
    clus
vv   6P GAIN MUTATED 6P GAIN WILD-TYPE
  R0              23                70
  R1               3                 7
  R2               1                 0
  RX               2                 6

Clustering(12) Variable = 6Q GAIN MUTATION ANALYSIS
D12V1, survival
                   sevent
clus2                0  1
  6Q GAIN MUTATED    8  8
  6Q GAIN WILD-TYPE 53 45
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               16                98 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
                8                45 
$`6Q GAIN MUTATED`
TCGA-BC-A3KG TCGA-CC-5263 TCGA-CC-A3MC TCGA-DD-A114 TCGA-DD-A119 TCGA-DD-A1EH 
       16.37         4.24         0.13        37.74         7.33        49.15 
TCGA-DD-A39Y TCGA-DD-A3A9 TCGA-DD-A4NE TCGA-DD-A4NI TCGA-EP-A2KB TCGA-EP-A2KC 
        5.59        30.58        21.67        10.78         1.97         0.62 
TCGA-G3-A25S TCGA-G3-A25U TCGA-G3-A3CG TCGA-G3-A3CK 
        1.22        53.79        22.13        19.23 

$`6Q GAIN WILD-TYPE`
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T 
       48.99        27.91        37.32        10.13        46.78        27.52 
TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 
       27.52         2.99        25.32        23.34         1.12        69.57 
TCGA-BC-A112 TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A5W4 TCGA-CC-5258 
        5.03        44.42        13.81         0.26         9.50         0.07 
TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA 
        2.86         3.02         3.39         3.32         0.10         0.07 
TCGA-CC-A3MB TCGA-DD-A113 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A11A 
        0.10        79.73        83.57        53.29       112.96         2.60 
TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB 
        0.46        21.76        51.25        90.67        79.36        66.31 
TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EI TCGA-DD-A1EJ 
       19.76        75.65         6.67        12.95         6.02        29.16 
TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39X TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 
       13.64        21.14        55.66        19.73        25.81         7.66 
TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 
       70.06        17.59        20.12       102.74       107.11        13.78 
TCGA-DD-A3A8 TCGA-DD-A4NA TCGA-DD-A4ND TCGA-DD-A4NF TCGA-DD-A4NG TCGA-DD-A4NH 
        0.36        33.14        73.38        14.07        14.93        14.24 
TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP 
       15.06        39.75        56.25        29.56        61.45        93.67 
TCGA-DD-A4NQ TCGA-ED-A459 TCGA-ED-A5KG TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA 
       12.26         0.23         0.20        10.85         7.76        11.74 
TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QR 
        3.19         0.43        23.01        14.40        32.45        19.07 
TCGA-FV-A3I0 TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZP 
        0.20         6.35         0.13         0.03         0.33        60.36 
TCGA-FV-A4ZQ TCGA-G3-A25T TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25X TCGA-G3-A25Y 
        0.39        51.02        28.27        30.71        58.49        14.86 
TCGA-G3-A25Z TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A5SJ TCGA-G3-A5SK 
       21.53        25.64         5.88        19.53        11.97         9.93 
TCGA-G3-A5SL TCGA-G3-A5SM 
        7.99         4.37 

  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
             0.13              0.03 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
            53.79            112.96 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
           13.575            16.325 
[1] "0.1 - 53.8 (13.6)"  "0.0 - 113.0 (16.3)"
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-BC-A5W4        TCGA-CC-5258        TCGA-CC-5260 
  "6Q GAIN MUTATED" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-CC-5261        TCGA-CC-5262        TCGA-CC-5263        TCGA-CC-A1HT 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE"   "6Q GAIN MUTATED" "6Q GAIN WILD-TYPE" 
       TCGA-CC-A3M9        TCGA-CC-A3MA        TCGA-CC-A3MB        TCGA-CC-A3MC 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE"   "6Q GAIN MUTATED" 
       TCGA-DD-A113        TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116 
"6Q GAIN WILD-TYPE"   "6Q GAIN MUTATED" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-DD-A118        TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B 
"6Q GAIN WILD-TYPE"   "6Q GAIN MUTATED" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-DD-A11C        TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EA 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-DD-A1EB        TCGA-DD-A1EC        TCGA-DD-A1ED        TCGA-DD-A1EE 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-DD-A1EF        TCGA-DD-A1EH        TCGA-DD-A1EI        TCGA-DD-A1EJ 
"6Q GAIN WILD-TYPE"   "6Q GAIN MUTATED" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-DD-A1EL        TCGA-DD-A39V        TCGA-DD-A39X        TCGA-DD-A39Y 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE"   "6Q GAIN MUTATED" 
       TCGA-DD-A39Z        TCGA-DD-A3A0        TCGA-DD-A3A1        TCGA-DD-A3A2 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-DD-A3A3        TCGA-DD-A3A4        TCGA-DD-A3A5        TCGA-DD-A3A6 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-DD-A3A7        TCGA-DD-A3A8        TCGA-DD-A3A9        TCGA-DD-A4NA 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE"   "6Q GAIN MUTATED" "6Q GAIN WILD-TYPE" 
       TCGA-DD-A4ND        TCGA-DD-A4NE        TCGA-DD-A4NF        TCGA-DD-A4NG 
"6Q GAIN WILD-TYPE"   "6Q GAIN MUTATED" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-DD-A4NH        TCGA-DD-A4NI        TCGA-DD-A4NJ        TCGA-DD-A4NK 
"6Q GAIN WILD-TYPE"   "6Q GAIN MUTATED" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-DD-A4NL        TCGA-DD-A4NN        TCGA-DD-A4NO        TCGA-DD-A4NP 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-DD-A4NQ        TCGA-ED-A459        TCGA-ED-A5KG        TCGA-EP-A12J 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE"   "6Q GAIN MUTATED"   "6Q GAIN MUTATED" 
       TCGA-EP-A3JL        TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-FV-A23B        TCGA-FV-A2QR        TCGA-FV-A3I0        TCGA-FV-A3R2 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-FV-A3R3        TCGA-FV-A495        TCGA-FV-A496        TCGA-FV-A4ZP 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-FV-A4ZQ        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"6Q GAIN WILD-TYPE"   "6Q GAIN MUTATED" "6Q GAIN WILD-TYPE"   "6Q GAIN MUTATED" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI 
"6Q GAIN WILD-TYPE"   "6Q GAIN MUTATED" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-G3-A3CJ        TCGA-G3-A3CK        TCGA-G3-A5SJ        TCGA-G3-A5SK 
"6Q GAIN WILD-TYPE"   "6Q GAIN MUTATED" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-G3-A5SL        TCGA-G3-A5SM 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-BC-A5W4        TCGA-CC-5258        TCGA-CC-5260 
  "6Q GAIN MUTATED" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-CC-5261        TCGA-CC-5262        TCGA-CC-5263        TCGA-CC-A1HT 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE"   "6Q GAIN MUTATED" "6Q GAIN WILD-TYPE" 
       TCGA-CC-A3M9        TCGA-CC-A3MA        TCGA-CC-A3MB        TCGA-CC-A3MC 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE"   "6Q GAIN MUTATED" 
       TCGA-DD-A113        TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116 
"6Q GAIN WILD-TYPE"   "6Q GAIN MUTATED" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-DD-A118        TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B 
"6Q GAIN WILD-TYPE"   "6Q GAIN MUTATED" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-DD-A11C        TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EA 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-DD-A1EB        TCGA-DD-A1EC        TCGA-DD-A1ED        TCGA-DD-A1EE 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-DD-A1EF        TCGA-DD-A1EH        TCGA-DD-A1EI        TCGA-DD-A1EJ 
"6Q GAIN WILD-TYPE"   "6Q GAIN MUTATED" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-DD-A1EL        TCGA-DD-A39V        TCGA-DD-A39X        TCGA-DD-A39Y 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE"   "6Q GAIN MUTATED" 
       TCGA-DD-A39Z        TCGA-DD-A3A0        TCGA-DD-A3A1        TCGA-DD-A3A2 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-DD-A3A3        TCGA-DD-A3A4        TCGA-DD-A3A5        TCGA-DD-A3A6 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-DD-A3A7        TCGA-DD-A3A8        TCGA-DD-A3A9        TCGA-DD-A4NA 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE"   "6Q GAIN MUTATED" "6Q GAIN WILD-TYPE" 
       TCGA-DD-A4ND        TCGA-DD-A4NE        TCGA-DD-A4NF        TCGA-DD-A4NG 
"6Q GAIN WILD-TYPE"   "6Q GAIN MUTATED" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-DD-A4NH        TCGA-DD-A4NI        TCGA-DD-A4NJ        TCGA-DD-A4NK 
"6Q GAIN WILD-TYPE"   "6Q GAIN MUTATED" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-DD-A4NL        TCGA-DD-A4NN        TCGA-DD-A4NO        TCGA-DD-A4NP 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-DD-A4NQ        TCGA-ED-A459        TCGA-ED-A5KG        TCGA-EP-A12J 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE"   "6Q GAIN MUTATED"   "6Q GAIN MUTATED" 
       TCGA-EP-A3JL        TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-FV-A23B        TCGA-FV-A2QR        TCGA-FV-A3I0        TCGA-FV-A3R2 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-FV-A3R3        TCGA-FV-A495        TCGA-FV-A496        TCGA-FV-A4ZP 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-FV-A4ZQ        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"6Q GAIN WILD-TYPE"   "6Q GAIN MUTATED" "6Q GAIN WILD-TYPE"   "6Q GAIN MUTATED" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI 
"6Q GAIN WILD-TYPE"   "6Q GAIN MUTATED" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-G3-A3CJ        TCGA-G3-A3CK        TCGA-G3-A5SJ        TCGA-G3-A5SK 
"6Q GAIN WILD-TYPE"   "6Q GAIN MUTATED" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-G3-A5SL        TCGA-G3-A5SM 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-BC-A5W4        TCGA-CC-5258        TCGA-CC-5260 
  "6Q GAIN MUTATED" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-CC-5261        TCGA-CC-5262        TCGA-CC-5263        TCGA-CC-A1HT 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE"   "6Q GAIN MUTATED" "6Q GAIN WILD-TYPE" 
       TCGA-CC-A3M9        TCGA-CC-A3MA        TCGA-CC-A3MB        TCGA-CC-A3MC 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE"   "6Q GAIN MUTATED" 
       TCGA-DD-A113        TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116 
"6Q GAIN WILD-TYPE"   "6Q GAIN MUTATED" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-DD-A118        TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B 
"6Q GAIN WILD-TYPE"   "6Q GAIN MUTATED" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-DD-A11C        TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EA 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-DD-A1EB        TCGA-DD-A1EC        TCGA-DD-A1ED        TCGA-DD-A1EE 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-DD-A1EF        TCGA-DD-A1EH        TCGA-DD-A1EI        TCGA-DD-A1EJ 
"6Q GAIN WILD-TYPE"   "6Q GAIN MUTATED" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-DD-A1EL        TCGA-DD-A39V        TCGA-DD-A39X        TCGA-DD-A39Y 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE"   "6Q GAIN MUTATED" 
       TCGA-DD-A39Z        TCGA-DD-A3A0        TCGA-DD-A3A1        TCGA-DD-A3A2 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-DD-A3A3        TCGA-DD-A3A4        TCGA-DD-A3A5        TCGA-DD-A3A6 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-DD-A3A7        TCGA-DD-A3A8        TCGA-DD-A3A9        TCGA-DD-A4NA 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE"   "6Q GAIN MUTATED" "6Q GAIN WILD-TYPE" 
       TCGA-DD-A4ND        TCGA-DD-A4NE        TCGA-DD-A4NF        TCGA-DD-A4NG 
"6Q GAIN WILD-TYPE"   "6Q GAIN MUTATED" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-DD-A4NH        TCGA-DD-A4NI        TCGA-DD-A4NJ        TCGA-DD-A4NK 
"6Q GAIN WILD-TYPE"   "6Q GAIN MUTATED" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-DD-A4NL        TCGA-DD-A4NN        TCGA-DD-A4NO        TCGA-DD-A4NP 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-DD-A4NQ        TCGA-ED-A459        TCGA-ED-A5KG        TCGA-EP-A12J 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE"   "6Q GAIN MUTATED"   "6Q GAIN MUTATED" 
       TCGA-EP-A3JL        TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-FV-A23B        TCGA-FV-A2QR        TCGA-FV-A3I0        TCGA-FV-A3R2 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-FV-A3R3        TCGA-FV-A495        TCGA-FV-A496        TCGA-FV-A4ZP 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-FV-A4ZQ        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"6Q GAIN WILD-TYPE"   "6Q GAIN MUTATED" "6Q GAIN WILD-TYPE"   "6Q GAIN MUTATED" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI 
"6Q GAIN WILD-TYPE"   "6Q GAIN MUTATED" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-G3-A3CJ        TCGA-G3-A3CK        TCGA-G3-A5SJ        TCGA-G3-A5SK 
"6Q GAIN WILD-TYPE"   "6Q GAIN MUTATED" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-G3-A5SL        TCGA-G3-A5SM 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
[1] "hr=" "1.6"
D12V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  6Q GAIN MUTATED         7        3         1          4          0          0
  6Q GAIN WILD-TYPE      38       22         1         21          3          4
                   vv
clus                STAGE IV STAGE IVA STAGE IVB
  6Q GAIN MUTATED          1         0         1
  6Q GAIN WILD-TYPE        0         1         0
D12V3, multiclass
                   vv
clus                T1 T2 T3 T4
  6Q GAIN MUTATED    7  3  6  1
  6Q GAIN WILD-TYPE 41 25 28  5
D12V4, multiclass
    clus
vv   6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  T1               7                41
  T2               3                25
  T3               6                28
  T4               1                 5
D12V5, binary
                   cls
clus                 0  1
  6Q GAIN MUTATED   12  0
  6Q GAIN WILD-TYPE 62  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED     12    0
  6Q GAIN WILD-TYPE   62    3
   clus
vv  6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  0              12                62
  1               0                 3
                   vv
clus                M0 M1 MX
  6Q GAIN MUTATED   13  2  2
  6Q GAIN WILD-TYPE 77  0 23
D12V6, multiclass
    clus
vv   6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  M0              13                77
  M1               2                 0
  MX               2                23
D12V7, binary
                   cls
clus                 0  1
  6Q GAIN MUTATED    5 12
  6Q GAIN WILD-TYPE 39 61
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED      5   12
  6Q GAIN WILD-TYPE   39   61
        clus
vv       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  FEMALE               5                39
  MALE                12                61
                   vv
clus                R0 R1 R2 RX
  6Q GAIN MUTATED   12  2  1  2
  6Q GAIN WILD-TYPE 81  8  0  6
D12V8, multiclass
    clus
vv   6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  R0              12                81
  R1               2                 8
  R2               1                 0
  RX               2                 6

Clustering(13) Variable = 7P GAIN MUTATION ANALYSIS
D13V1, survival
                   sevent
clus2                0  1
  7P GAIN MUTATED   17 19
  7P GAIN WILD-TYPE 44 34
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               36                78 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               19                34 
$`7P GAIN MUTATED`
TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10U TCGA-CC-5260 TCGA-CC-A3MB TCGA-DD-A113 
       37.32        10.13        27.52         2.86         0.10        79.73 
TCGA-DD-A118 TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EC TCGA-DD-A1EE TCGA-DD-A1EJ 
      112.96        51.25        90.67        19.76         6.67        29.16 
TCGA-DD-A39V TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A2 TCGA-DD-A3A7 TCGA-DD-A4NA 
       21.14         5.59        19.73        70.06        13.78        33.14 
TCGA-DD-A4ND TCGA-DD-A4NI TCGA-DD-A4NK TCGA-DD-A4NQ TCGA-EP-A2KC TCGA-EP-A3JL 
       73.38        10.78        39.75        12.26         0.62         3.19 
TCGA-ES-A2HS TCGA-FV-A3R2 TCGA-FV-A496 TCGA-FV-A4ZP TCGA-G3-A25S TCGA-G3-A25T 
       23.01         6.35         0.33        60.36         1.22        51.02 
TCGA-G3-A25V TCGA-G3-A25X TCGA-G3-A3CG TCGA-G3-A3CJ TCGA-G3-A5SL TCGA-G3-A5SM 
       28.27        58.49        22.13        19.53         7.99         4.37 

$`7P GAIN WILD-TYPE`
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10W TCGA-BC-A10X 
       48.99        27.91        46.78        27.52         2.99        25.32 
TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A216 TCGA-BC-A217 
       23.34         1.12        69.57         5.03        44.42        13.81 
TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-CC-5258 TCGA-CC-5261 TCGA-CC-5262 
        0.26        16.37         9.50         0.07         3.02         3.39 
TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MC TCGA-DD-A114 
        4.24         3.32         0.10         0.07         0.13        37.74 
TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C 
       83.57        53.29         7.33         2.60         0.46        21.76 
TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1ED TCGA-DD-A1EF TCGA-DD-A1EH TCGA-DD-A1EI 
       79.36        66.31        75.65        12.95        49.15         6.02 
TCGA-DD-A1EL TCGA-DD-A39X TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A3 TCGA-DD-A3A4 
       13.64        55.66        25.81         7.66        17.59        20.12 
TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A8 TCGA-DD-A3A9 TCGA-DD-A4NE TCGA-DD-A4NF 
      102.74       107.11         0.36        30.58        21.67        14.07 
TCGA-DD-A4NG TCGA-DD-A4NH TCGA-DD-A4NJ TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO 
       14.93        14.24        15.06        56.25        29.56        61.45 
TCGA-DD-A4NP TCGA-ED-A459 TCGA-ED-A5KG TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA 
       93.67         0.23         0.20        10.85         7.76        11.74 
TCGA-EP-A2KB TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-A3I0 
        1.97         0.43        14.40        32.45        19.07         0.20 
TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A4ZQ TCGA-G3-A25U TCGA-G3-A25W TCGA-G3-A25Y 
        0.13         0.03         0.39        53.79        30.71        14.86 
TCGA-G3-A25Z TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CK TCGA-G3-A5SJ TCGA-G3-A5SK 
       21.53        25.64         5.88        19.23        11.97         9.93 

  7P GAIN MUTATED 7P GAIN WILD-TYPE 
             0.10              0.03 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
           112.96            107.11 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
            20.45             14.63 
[1] "0.1 - 113.0 (20.5)" "0.0 - 107.1 (14.6)"
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-BC-A5W4        TCGA-CC-5258        TCGA-CC-5260 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       TCGA-CC-5261        TCGA-CC-5262        TCGA-CC-5263        TCGA-CC-A1HT 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-CC-A3M9        TCGA-CC-A3MA        TCGA-CC-A3MB        TCGA-CC-A3MC 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-DD-A113        TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-DD-A118        TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-DD-A11C        TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EA 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-DD-A1EB        TCGA-DD-A1EC        TCGA-DD-A1ED        TCGA-DD-A1EE 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       TCGA-DD-A1EF        TCGA-DD-A1EH        TCGA-DD-A1EI        TCGA-DD-A1EJ 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       TCGA-DD-A1EL        TCGA-DD-A39V        TCGA-DD-A39X        TCGA-DD-A39Y 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       TCGA-DD-A39Z        TCGA-DD-A3A0        TCGA-DD-A3A1        TCGA-DD-A3A2 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       TCGA-DD-A3A3        TCGA-DD-A3A4        TCGA-DD-A3A5        TCGA-DD-A3A6 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-DD-A3A7        TCGA-DD-A3A8        TCGA-DD-A3A9        TCGA-DD-A4NA 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       TCGA-DD-A4ND        TCGA-DD-A4NE        TCGA-DD-A4NF        TCGA-DD-A4NG 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-DD-A4NH        TCGA-DD-A4NI        TCGA-DD-A4NJ        TCGA-DD-A4NK 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       TCGA-DD-A4NL        TCGA-DD-A4NN        TCGA-DD-A4NO        TCGA-DD-A4NP 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-DD-A4NQ        TCGA-ED-A459        TCGA-ED-A5KG        TCGA-EP-A12J 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       TCGA-EP-A3JL        TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-FV-A23B        TCGA-FV-A2QR        TCGA-FV-A3I0        TCGA-FV-A3R2 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       TCGA-FV-A3R3        TCGA-FV-A495        TCGA-FV-A496        TCGA-FV-A4ZP 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-FV-A4ZQ        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-G3-A3CJ        TCGA-G3-A3CK        TCGA-G3-A5SJ        TCGA-G3-A5SK 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-G3-A5SL        TCGA-G3-A5SM 
  "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-BC-A5W4        TCGA-CC-5258        TCGA-CC-5260 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       TCGA-CC-5261        TCGA-CC-5262        TCGA-CC-5263        TCGA-CC-A1HT 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-CC-A3M9        TCGA-CC-A3MA        TCGA-CC-A3MB        TCGA-CC-A3MC 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-DD-A113        TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-DD-A118        TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-DD-A11C        TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EA 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-DD-A1EB        TCGA-DD-A1EC        TCGA-DD-A1ED        TCGA-DD-A1EE 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       TCGA-DD-A1EF        TCGA-DD-A1EH        TCGA-DD-A1EI        TCGA-DD-A1EJ 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       TCGA-DD-A1EL        TCGA-DD-A39V        TCGA-DD-A39X        TCGA-DD-A39Y 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       TCGA-DD-A39Z        TCGA-DD-A3A0        TCGA-DD-A3A1        TCGA-DD-A3A2 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       TCGA-DD-A3A3        TCGA-DD-A3A4        TCGA-DD-A3A5        TCGA-DD-A3A6 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-DD-A3A7        TCGA-DD-A3A8        TCGA-DD-A3A9        TCGA-DD-A4NA 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       TCGA-DD-A4ND        TCGA-DD-A4NE        TCGA-DD-A4NF        TCGA-DD-A4NG 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-DD-A4NH        TCGA-DD-A4NI        TCGA-DD-A4NJ        TCGA-DD-A4NK 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       TCGA-DD-A4NL        TCGA-DD-A4NN        TCGA-DD-A4NO        TCGA-DD-A4NP 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-DD-A4NQ        TCGA-ED-A459        TCGA-ED-A5KG        TCGA-EP-A12J 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       TCGA-EP-A3JL        TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-FV-A23B        TCGA-FV-A2QR        TCGA-FV-A3I0        TCGA-FV-A3R2 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       TCGA-FV-A3R3        TCGA-FV-A495        TCGA-FV-A496        TCGA-FV-A4ZP 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-FV-A4ZQ        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-G3-A3CJ        TCGA-G3-A3CK        TCGA-G3-A5SJ        TCGA-G3-A5SK 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-G3-A5SL        TCGA-G3-A5SM 
  "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-BC-A5W4        TCGA-CC-5258        TCGA-CC-5260 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       TCGA-CC-5261        TCGA-CC-5262        TCGA-CC-5263        TCGA-CC-A1HT 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-CC-A3M9        TCGA-CC-A3MA        TCGA-CC-A3MB        TCGA-CC-A3MC 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-DD-A113        TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-DD-A118        TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-DD-A11C        TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EA 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-DD-A1EB        TCGA-DD-A1EC        TCGA-DD-A1ED        TCGA-DD-A1EE 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       TCGA-DD-A1EF        TCGA-DD-A1EH        TCGA-DD-A1EI        TCGA-DD-A1EJ 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       TCGA-DD-A1EL        TCGA-DD-A39V        TCGA-DD-A39X        TCGA-DD-A39Y 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       TCGA-DD-A39Z        TCGA-DD-A3A0        TCGA-DD-A3A1        TCGA-DD-A3A2 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       TCGA-DD-A3A3        TCGA-DD-A3A4        TCGA-DD-A3A5        TCGA-DD-A3A6 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-DD-A3A7        TCGA-DD-A3A8        TCGA-DD-A3A9        TCGA-DD-A4NA 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       TCGA-DD-A4ND        TCGA-DD-A4NE        TCGA-DD-A4NF        TCGA-DD-A4NG 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-DD-A4NH        TCGA-DD-A4NI        TCGA-DD-A4NJ        TCGA-DD-A4NK 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       TCGA-DD-A4NL        TCGA-DD-A4NN        TCGA-DD-A4NO        TCGA-DD-A4NP 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-DD-A4NQ        TCGA-ED-A459        TCGA-ED-A5KG        TCGA-EP-A12J 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       TCGA-EP-A3JL        TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-FV-A23B        TCGA-FV-A2QR        TCGA-FV-A3I0        TCGA-FV-A3R2 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       TCGA-FV-A3R3        TCGA-FV-A495        TCGA-FV-A496        TCGA-FV-A4ZP 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-FV-A4ZQ        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-G3-A3CJ        TCGA-G3-A3CK        TCGA-G3-A5SJ        TCGA-G3-A5SK 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-G3-A5SL        TCGA-G3-A5SM 
  "7P GAIN MUTATED"   "7P GAIN MUTATED" 
[1] "hr=" "1"  
D13V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  7P GAIN MUTATED        14        9         0          6          1          3
  7P GAIN WILD-TYPE      31       16         2         19          2          1
                   vv
clus                STAGE IV STAGE IVA STAGE IVB
  7P GAIN MUTATED          0         0         0
  7P GAIN WILD-TYPE        1         1         1
D13V3, multiclass
                   vv
clus                T1 T2 T3 T4
  7P GAIN MUTATED   15 12  8  1
  7P GAIN WILD-TYPE 33 16 26  5
D13V4, multiclass
    clus
vv   7P GAIN MUTATED 7P GAIN WILD-TYPE
  T1              15                33
  T2              12                16
  T3               8                26
  T4               1                 5
D13V5, binary
                   cls
clus                 0  1
  7P GAIN MUTATED   20  2
  7P GAIN WILD-TYPE 54  1
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED     20    2
  7P GAIN WILD-TYPE   54    1
   clus
vv  7P GAIN MUTATED 7P GAIN WILD-TYPE
  0              20                54
  1               2                 1
                   vv
clus                M0 M1 MX
  7P GAIN MUTATED   30  0  7
  7P GAIN WILD-TYPE 60  2 18
D13V6, multiclass
    clus
vv   7P GAIN MUTATED 7P GAIN WILD-TYPE
  M0              30                60
  M1               0                 2
  MX               7                18
D13V7, binary
                   cls
clus                 0  1
  7P GAIN MUTATED   15 22
  7P GAIN WILD-TYPE 29 51
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED     15   22
  7P GAIN WILD-TYPE   29   51
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  FEMALE              15                29
  MALE                22                51
                   vv
clus                R0 R1 R2 RX
  7P GAIN MUTATED   29  5  0  2
  7P GAIN WILD-TYPE 64  5  1  6
D13V8, multiclass
    clus
vv   7P GAIN MUTATED 7P GAIN WILD-TYPE
  R0              29                64
  R1               5                 5
  R2               0                 1
  RX               2                 6

Clustering(14) Variable = 7Q GAIN MUTATION ANALYSIS
D14V1, survival
                   sevent
clus2                0  1
  7Q GAIN MUTATED   20 17
  7Q GAIN WILD-TYPE 41 36
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               37                77 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               17                36 
$`7Q GAIN MUTATED`
TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10U TCGA-BC-A5W4 TCGA-CC-5260 TCGA-CC-A3M9 
       37.32        10.13        27.52         9.50         2.86         0.10 
TCGA-CC-A3MB TCGA-DD-A118 TCGA-DD-A11A TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EC 
        0.10       112.96         2.60        51.25        90.67        19.76 
TCGA-DD-A1EE TCGA-DD-A1EJ TCGA-DD-A39V TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A2 
        6.67        29.16        21.14         5.59        19.73        70.06 
TCGA-DD-A4NA TCGA-DD-A4NG TCGA-DD-A4NI TCGA-DD-A4NK TCGA-DD-A4NQ TCGA-ED-A459 
       33.14        14.93        10.78        39.75        12.26         0.23 
TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KC TCGA-EP-A3JL TCGA-ES-A2HS TCGA-FV-A3R2 
        7.76        11.74         0.62         3.19        23.01         6.35 
TCGA-G3-A25T TCGA-G3-A25V TCGA-G3-A25X TCGA-G3-A3CG TCGA-G3-A3CJ TCGA-G3-A5SL 
       51.02        28.27        58.49        22.13        19.53         7.99 
TCGA-G3-A5SM 
        4.37 

$`7Q GAIN WILD-TYPE`
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10W TCGA-BC-A10X 
       48.99        27.91        46.78        27.52         2.99        25.32 
TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A216 TCGA-BC-A217 
       23.34         1.12        69.57         5.03        44.42        13.81 
TCGA-BC-A3KF TCGA-BC-A3KG TCGA-CC-5258 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 
        0.26        16.37         0.07         3.02         3.39         4.24 
TCGA-CC-A1HT TCGA-CC-A3MA TCGA-CC-A3MC TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 
        3.32         0.07         0.13        79.73        37.74        83.57 
TCGA-DD-A116 TCGA-DD-A119 TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A1EA TCGA-DD-A1EB 
       53.29         7.33         0.46        21.76        79.36        66.31 
TCGA-DD-A1ED TCGA-DD-A1EF TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EL TCGA-DD-A39X 
       75.65        12.95        49.15         6.02        13.64        55.66 
TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 
       25.81         7.66        17.59        20.12       102.74       107.11 
TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A3A9 TCGA-DD-A4ND TCGA-DD-A4NE TCGA-DD-A4NF 
       13.78         0.36        30.58        73.38        21.67        14.07 
TCGA-DD-A4NH TCGA-DD-A4NJ TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP 
       14.24        15.06        56.25        29.56        61.45        93.67 
TCGA-ED-A5KG TCGA-EP-A12J TCGA-EP-A2KB TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A23B 
        0.20        10.85         1.97         0.43        14.40        32.45 
TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZP 
       19.07         0.20         0.13         0.03         0.33        60.36 
TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25U TCGA-G3-A25W TCGA-G3-A25Y TCGA-G3-A25Z 
        0.39         1.22        53.79        30.71        14.86        21.53 
TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CK TCGA-G3-A5SJ TCGA-G3-A5SK 
       25.64         5.88        19.23        11.97         9.93 

  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
             0.10              0.03 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
           112.96            107.11 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
            14.93             16.37 
[1] "0.1 - 113.0 (14.9)" "0.0 - 107.1 (16.4)"
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-BC-A5W4        TCGA-CC-5258        TCGA-CC-5260 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-CC-5261        TCGA-CC-5262        TCGA-CC-5263        TCGA-CC-A1HT 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-CC-A3M9        TCGA-CC-A3MA        TCGA-CC-A3MB        TCGA-CC-A3MC 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-DD-A113        TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-DD-A118        TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-DD-A11C        TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EA 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-DD-A1EB        TCGA-DD-A1EC        TCGA-DD-A1ED        TCGA-DD-A1EE 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-DD-A1EF        TCGA-DD-A1EH        TCGA-DD-A1EI        TCGA-DD-A1EJ 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-DD-A1EL        TCGA-DD-A39V        TCGA-DD-A39X        TCGA-DD-A39Y 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-DD-A39Z        TCGA-DD-A3A0        TCGA-DD-A3A1        TCGA-DD-A3A2 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-DD-A3A3        TCGA-DD-A3A4        TCGA-DD-A3A5        TCGA-DD-A3A6 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-DD-A3A7        TCGA-DD-A3A8        TCGA-DD-A3A9        TCGA-DD-A4NA 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-DD-A4ND        TCGA-DD-A4NE        TCGA-DD-A4NF        TCGA-DD-A4NG 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-DD-A4NH        TCGA-DD-A4NI        TCGA-DD-A4NJ        TCGA-DD-A4NK 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-DD-A4NL        TCGA-DD-A4NN        TCGA-DD-A4NO        TCGA-DD-A4NP 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-DD-A4NQ        TCGA-ED-A459        TCGA-ED-A5KG        TCGA-EP-A12J 
  "7Q GAIN MUTATED"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC 
  "7Q GAIN MUTATED"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-EP-A3JL        TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-FV-A23B        TCGA-FV-A2QR        TCGA-FV-A3I0        TCGA-FV-A3R2 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-FV-A3R3        TCGA-FV-A495        TCGA-FV-A496        TCGA-FV-A4ZP 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-FV-A4ZQ        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-G3-A3CJ        TCGA-G3-A3CK        TCGA-G3-A5SJ        TCGA-G3-A5SK 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-G3-A5SL        TCGA-G3-A5SM 
  "7Q GAIN MUTATED"   "7Q GAIN MUTATED" 
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-BC-A5W4        TCGA-CC-5258        TCGA-CC-5260 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-CC-5261        TCGA-CC-5262        TCGA-CC-5263        TCGA-CC-A1HT 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-CC-A3M9        TCGA-CC-A3MA        TCGA-CC-A3MB        TCGA-CC-A3MC 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-DD-A113        TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-DD-A118        TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-DD-A11C        TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EA 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-DD-A1EB        TCGA-DD-A1EC        TCGA-DD-A1ED        TCGA-DD-A1EE 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-DD-A1EF        TCGA-DD-A1EH        TCGA-DD-A1EI        TCGA-DD-A1EJ 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-DD-A1EL        TCGA-DD-A39V        TCGA-DD-A39X        TCGA-DD-A39Y 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-DD-A39Z        TCGA-DD-A3A0        TCGA-DD-A3A1        TCGA-DD-A3A2 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-DD-A3A3        TCGA-DD-A3A4        TCGA-DD-A3A5        TCGA-DD-A3A6 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-DD-A3A7        TCGA-DD-A3A8        TCGA-DD-A3A9        TCGA-DD-A4NA 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-DD-A4ND        TCGA-DD-A4NE        TCGA-DD-A4NF        TCGA-DD-A4NG 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-DD-A4NH        TCGA-DD-A4NI        TCGA-DD-A4NJ        TCGA-DD-A4NK 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-DD-A4NL        TCGA-DD-A4NN        TCGA-DD-A4NO        TCGA-DD-A4NP 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-DD-A4NQ        TCGA-ED-A459        TCGA-ED-A5KG        TCGA-EP-A12J 
  "7Q GAIN MUTATED"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC 
  "7Q GAIN MUTATED"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-EP-A3JL        TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-FV-A23B        TCGA-FV-A2QR        TCGA-FV-A3I0        TCGA-FV-A3R2 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-FV-A3R3        TCGA-FV-A495        TCGA-FV-A496        TCGA-FV-A4ZP 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-FV-A4ZQ        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-G3-A3CJ        TCGA-G3-A3CK        TCGA-G3-A5SJ        TCGA-G3-A5SK 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-G3-A5SL        TCGA-G3-A5SM 
  "7Q GAIN MUTATED"   "7Q GAIN MUTATED" 
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-BC-A5W4        TCGA-CC-5258        TCGA-CC-5260 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-CC-5261        TCGA-CC-5262        TCGA-CC-5263        TCGA-CC-A1HT 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-CC-A3M9        TCGA-CC-A3MA        TCGA-CC-A3MB        TCGA-CC-A3MC 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-DD-A113        TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-DD-A118        TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-DD-A11C        TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EA 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-DD-A1EB        TCGA-DD-A1EC        TCGA-DD-A1ED        TCGA-DD-A1EE 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-DD-A1EF        TCGA-DD-A1EH        TCGA-DD-A1EI        TCGA-DD-A1EJ 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-DD-A1EL        TCGA-DD-A39V        TCGA-DD-A39X        TCGA-DD-A39Y 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-DD-A39Z        TCGA-DD-A3A0        TCGA-DD-A3A1        TCGA-DD-A3A2 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-DD-A3A3        TCGA-DD-A3A4        TCGA-DD-A3A5        TCGA-DD-A3A6 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-DD-A3A7        TCGA-DD-A3A8        TCGA-DD-A3A9        TCGA-DD-A4NA 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-DD-A4ND        TCGA-DD-A4NE        TCGA-DD-A4NF        TCGA-DD-A4NG 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-DD-A4NH        TCGA-DD-A4NI        TCGA-DD-A4NJ        TCGA-DD-A4NK 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-DD-A4NL        TCGA-DD-A4NN        TCGA-DD-A4NO        TCGA-DD-A4NP 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-DD-A4NQ        TCGA-ED-A459        TCGA-ED-A5KG        TCGA-EP-A12J 
  "7Q GAIN MUTATED"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC 
  "7Q GAIN MUTATED"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-EP-A3JL        TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-FV-A23B        TCGA-FV-A2QR        TCGA-FV-A3I0        TCGA-FV-A3R2 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-FV-A3R3        TCGA-FV-A495        TCGA-FV-A496        TCGA-FV-A4ZP 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-FV-A4ZQ        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-G3-A3CJ        TCGA-G3-A3CK        TCGA-G3-A5SJ        TCGA-G3-A5SK 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-G3-A5SL        TCGA-G3-A5SM 
  "7Q GAIN MUTATED"   "7Q GAIN MUTATED" 
[1] "hr=" "1.1"
D14V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  7Q GAIN MUTATED        13       10         0          9          0          3
  7Q GAIN WILD-TYPE      32       15         2         16          3          1
                   vv
clus                STAGE IV STAGE IVA STAGE IVB
  7Q GAIN MUTATED          0         0         0
  7Q GAIN WILD-TYPE        1         1         1
D14V3, multiclass
                   vv
clus                T1 T2 T3 T4
  7Q GAIN MUTATED   14 13 10  1
  7Q GAIN WILD-TYPE 34 15 24  5
D14V4, multiclass
    clus
vv   7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  T1              14                34
  T2              13                15
  T3              10                24
  T4               1                 5
D14V5, binary
                   cls
clus                 0  1
  7Q GAIN MUTATED   21  2
  7Q GAIN WILD-TYPE 53  1
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED     21    2
  7Q GAIN WILD-TYPE   53    1
   clus
vv  7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  0              21                53
  1               2                 1
                   vv
clus                M0 M1 MX
  7Q GAIN MUTATED   29  0 10
  7Q GAIN WILD-TYPE 61  2 15
D14V6, multiclass
    clus
vv   7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  M0              29                61
  M1               0                 2
  MX              10                15
D14V7, binary
                   cls
clus                 0  1
  7Q GAIN MUTATED   14 25
  7Q GAIN WILD-TYPE 30 48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED     14   25
  7Q GAIN WILD-TYPE   30   48
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  FEMALE              14                30
  MALE                25                48
                   vv
clus                R0 R1 R2 RX
  7Q GAIN MUTATED   31  4  0  2
  7Q GAIN WILD-TYPE 62  6  1  6
D14V8, multiclass
    clus
vv   7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  R0              31                62
  R1               4                 6
  R2               0                 1
  RX               2                 6

Clustering(15) Variable = 8P GAIN MUTATION ANALYSIS
D15V1, survival
                   sevent
clus2                0  1
  8P GAIN MUTATED   13  8
  8P GAIN WILD-TYPE 48 45
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               21                93 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
                8                45 
$`8P GAIN MUTATED`
TCGA-BC-A10S TCGA-CC-5258 TCGA-CC-A1HT TCGA-CC-A3MB TCGA-DD-A119 TCGA-DD-A11A 
       46.78         0.07         3.32         0.10         7.33         2.60 
TCGA-DD-A1E9 TCGA-DD-A1EC TCGA-DD-A1EF TCGA-DD-A1EI TCGA-DD-A3A1 TCGA-DD-A4NG 
       90.67        19.76        12.95         6.02         7.66        14.93 
TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NQ TCGA-ED-A459 TCGA-EP-A2KB TCGA-EP-A3JL 
       29.56        61.45        12.26         0.23         1.97         3.19 
TCGA-G3-A25X TCGA-G3-A25Z TCGA-G3-A5SJ 
       58.49        21.53        11.97 

$`8P GAIN WILD-TYPE`
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A10U 
       48.99        27.91        37.32        10.13        27.52        27.52 
TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 
        2.99        25.32        23.34         1.12        69.57         5.03 
TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-CC-5260 
       44.42        13.81         0.26        16.37         9.50         2.86 
TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MC 
        3.02         3.39         4.24         0.10         0.07         0.13 
TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A11B 
       79.73        37.74        83.57        53.29       112.96         0.46 
TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1ED TCGA-DD-A1EE 
       21.76        51.25        79.36        66.31        75.65         6.67 
TCGA-DD-A1EH TCGA-DD-A1EJ TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39X TCGA-DD-A39Y 
       49.15        29.16        13.64        21.14        55.66         5.59 
TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 
       19.73        25.81        70.06        17.59        20.12       102.74 
TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4ND 
      107.11        13.78         0.36        30.58        33.14        73.38 
TCGA-DD-A4NE TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK 
       21.67        14.07        14.24        10.78        15.06        39.75 
TCGA-DD-A4NL TCGA-DD-A4NP TCGA-ED-A5KG TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA 
       56.25        93.67         0.20        10.85         7.76        11.74 
TCGA-EP-A2KC TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QR 
        0.62         0.43        23.01        14.40        32.45        19.07 
TCGA-FV-A3I0 TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZP 
        0.20         6.35         0.13         0.03         0.33        60.36 
TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W 
        0.39         1.22        51.02        53.79        28.27        30.71 
TCGA-G3-A25Y TCGA-G3-A3CG TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK 
       14.86        22.13        25.64         5.88        19.53        19.23 
TCGA-G3-A5SK TCGA-G3-A5SL TCGA-G3-A5SM 
        9.93         7.99         4.37 

  8P GAIN MUTATED 8P GAIN WILD-TYPE 
             0.07              0.03 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
            90.67            112.96 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
            11.97             19.23 
[1] "0.1 - 90.7 (12.0)"  "0.0 - 113.0 (19.2)"
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
  "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-BC-A5W4        TCGA-CC-5258        TCGA-CC-5260 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" 
       TCGA-CC-5261        TCGA-CC-5262        TCGA-CC-5263        TCGA-CC-A1HT 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" 
       TCGA-CC-A3M9        TCGA-CC-A3MA        TCGA-CC-A3MB        TCGA-CC-A3MC 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" 
       TCGA-DD-A113        TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-DD-A118        TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B 
"8P GAIN WILD-TYPE"   "8P GAIN MUTATED"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" 
       TCGA-DD-A11C        TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EA 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" 
       TCGA-DD-A1EB        TCGA-DD-A1EC        TCGA-DD-A1ED        TCGA-DD-A1EE 
"8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-DD-A1EF        TCGA-DD-A1EH        TCGA-DD-A1EI        TCGA-DD-A1EJ 
  "8P GAIN MUTATED" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" 
       TCGA-DD-A1EL        TCGA-DD-A39V        TCGA-DD-A39X        TCGA-DD-A39Y 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-DD-A39Z        TCGA-DD-A3A0        TCGA-DD-A3A1        TCGA-DD-A3A2 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" 
       TCGA-DD-A3A3        TCGA-DD-A3A4        TCGA-DD-A3A5        TCGA-DD-A3A6 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-DD-A3A7        TCGA-DD-A3A8        TCGA-DD-A3A9        TCGA-DD-A4NA 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-DD-A4ND        TCGA-DD-A4NE        TCGA-DD-A4NF        TCGA-DD-A4NG 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" 
       TCGA-DD-A4NH        TCGA-DD-A4NI        TCGA-DD-A4NJ        TCGA-DD-A4NK 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-DD-A4NL        TCGA-DD-A4NN        TCGA-DD-A4NO        TCGA-DD-A4NP 
"8P GAIN WILD-TYPE"   "8P GAIN MUTATED"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" 
       TCGA-DD-A4NQ        TCGA-ED-A459        TCGA-ED-A5KG        TCGA-EP-A12J 
  "8P GAIN MUTATED"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" 
       TCGA-EP-A3JL        TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT 
  "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-FV-A23B        TCGA-FV-A2QR        TCGA-FV-A3I0        TCGA-FV-A3R2 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-FV-A3R3        TCGA-FV-A495        TCGA-FV-A496        TCGA-FV-A4ZP 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-FV-A4ZQ        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI 
  "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-G3-A3CJ        TCGA-G3-A3CK        TCGA-G3-A5SJ        TCGA-G3-A5SK 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" 
       TCGA-G3-A5SL        TCGA-G3-A5SM 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
  "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-BC-A5W4        TCGA-CC-5258        TCGA-CC-5260 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" 
       TCGA-CC-5261        TCGA-CC-5262        TCGA-CC-5263        TCGA-CC-A1HT 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" 
       TCGA-CC-A3M9        TCGA-CC-A3MA        TCGA-CC-A3MB        TCGA-CC-A3MC 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" 
       TCGA-DD-A113        TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-DD-A118        TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B 
"8P GAIN WILD-TYPE"   "8P GAIN MUTATED"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" 
       TCGA-DD-A11C        TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EA 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" 
       TCGA-DD-A1EB        TCGA-DD-A1EC        TCGA-DD-A1ED        TCGA-DD-A1EE 
"8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-DD-A1EF        TCGA-DD-A1EH        TCGA-DD-A1EI        TCGA-DD-A1EJ 
  "8P GAIN MUTATED" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" 
       TCGA-DD-A1EL        TCGA-DD-A39V        TCGA-DD-A39X        TCGA-DD-A39Y 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-DD-A39Z        TCGA-DD-A3A0        TCGA-DD-A3A1        TCGA-DD-A3A2 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" 
       TCGA-DD-A3A3        TCGA-DD-A3A4        TCGA-DD-A3A5        TCGA-DD-A3A6 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-DD-A3A7        TCGA-DD-A3A8        TCGA-DD-A3A9        TCGA-DD-A4NA 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-DD-A4ND        TCGA-DD-A4NE        TCGA-DD-A4NF        TCGA-DD-A4NG 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" 
       TCGA-DD-A4NH        TCGA-DD-A4NI        TCGA-DD-A4NJ        TCGA-DD-A4NK 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-DD-A4NL        TCGA-DD-A4NN        TCGA-DD-A4NO        TCGA-DD-A4NP 
"8P GAIN WILD-TYPE"   "8P GAIN MUTATED"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" 
       TCGA-DD-A4NQ        TCGA-ED-A459        TCGA-ED-A5KG        TCGA-EP-A12J 
  "8P GAIN MUTATED"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" 
       TCGA-EP-A3JL        TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT 
  "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-FV-A23B        TCGA-FV-A2QR        TCGA-FV-A3I0        TCGA-FV-A3R2 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-FV-A3R3        TCGA-FV-A495        TCGA-FV-A496        TCGA-FV-A4ZP 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-FV-A4ZQ        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI 
  "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-G3-A3CJ        TCGA-G3-A3CK        TCGA-G3-A5SJ        TCGA-G3-A5SK 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" 
       TCGA-G3-A5SL        TCGA-G3-A5SM 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
  "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-BC-A5W4        TCGA-CC-5258        TCGA-CC-5260 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" 
       TCGA-CC-5261        TCGA-CC-5262        TCGA-CC-5263        TCGA-CC-A1HT 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" 
       TCGA-CC-A3M9        TCGA-CC-A3MA        TCGA-CC-A3MB        TCGA-CC-A3MC 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" 
       TCGA-DD-A113        TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-DD-A118        TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B 
"8P GAIN WILD-TYPE"   "8P GAIN MUTATED"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" 
       TCGA-DD-A11C        TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EA 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" 
       TCGA-DD-A1EB        TCGA-DD-A1EC        TCGA-DD-A1ED        TCGA-DD-A1EE 
"8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-DD-A1EF        TCGA-DD-A1EH        TCGA-DD-A1EI        TCGA-DD-A1EJ 
  "8P GAIN MUTATED" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" 
       TCGA-DD-A1EL        TCGA-DD-A39V        TCGA-DD-A39X        TCGA-DD-A39Y 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-DD-A39Z        TCGA-DD-A3A0        TCGA-DD-A3A1        TCGA-DD-A3A2 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" 
       TCGA-DD-A3A3        TCGA-DD-A3A4        TCGA-DD-A3A5        TCGA-DD-A3A6 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-DD-A3A7        TCGA-DD-A3A8        TCGA-DD-A3A9        TCGA-DD-A4NA 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-DD-A4ND        TCGA-DD-A4NE        TCGA-DD-A4NF        TCGA-DD-A4NG 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" 
       TCGA-DD-A4NH        TCGA-DD-A4NI        TCGA-DD-A4NJ        TCGA-DD-A4NK 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-DD-A4NL        TCGA-DD-A4NN        TCGA-DD-A4NO        TCGA-DD-A4NP 
"8P GAIN WILD-TYPE"   "8P GAIN MUTATED"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" 
       TCGA-DD-A4NQ        TCGA-ED-A459        TCGA-ED-A5KG        TCGA-EP-A12J 
  "8P GAIN MUTATED"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" 
       TCGA-EP-A3JL        TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT 
  "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-FV-A23B        TCGA-FV-A2QR        TCGA-FV-A3I0        TCGA-FV-A3R2 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-FV-A3R3        TCGA-FV-A495        TCGA-FV-A496        TCGA-FV-A4ZP 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-FV-A4ZQ        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI 
  "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-G3-A3CJ        TCGA-G3-A3CK        TCGA-G3-A5SJ        TCGA-G3-A5SK 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" 
       TCGA-G3-A5SL        TCGA-G3-A5SM 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
[1] "hr=" "1.1"
D15V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  8P GAIN MUTATED        11        4         0          5          0          0
  8P GAIN WILD-TYPE      34       21         2         20          3          4
                   vv
clus                STAGE IV STAGE IVA STAGE IVB
  8P GAIN MUTATED          1         0         0
  8P GAIN WILD-TYPE        0         1         1
D15V3, multiclass
                   vv
clus                T1 T2 T3 T4
  8P GAIN MUTATED   11  4  7  0
  8P GAIN WILD-TYPE 37 24 27  6
D15V4, multiclass
    clus
vv   8P GAIN MUTATED 8P GAIN WILD-TYPE
  T1              11                37
  T2               4                24
  T3               7                27
  T4               0                 6
D15V5, binary
                   cls
clus                 0  1
  8P GAIN MUTATED   17  0
  8P GAIN WILD-TYPE 57  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED     17    0
  8P GAIN WILD-TYPE   57    3
   clus
vv  8P GAIN MUTATED 8P GAIN WILD-TYPE
  0              17                57
  1               0                 3
                   vv
clus                M0 M1 MX
  8P GAIN MUTATED   18  1  3
  8P GAIN WILD-TYPE 72  1 22
D15V6, multiclass
    clus
vv   8P GAIN MUTATED 8P GAIN WILD-TYPE
  M0              18                72
  M1               1                 1
  MX               3                22
D15V7, binary
                   cls
clus                 0  1
  8P GAIN MUTATED    4 18
  8P GAIN WILD-TYPE 40 55
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED      4   18
  8P GAIN WILD-TYPE   40   55
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  FEMALE               4                40
  MALE                18                55
                   vv
clus                R0 R1 R2 RX
  8P GAIN MUTATED   17  0  1  2
  8P GAIN WILD-TYPE 76 10  0  6
D15V8, multiclass
    clus
vv   8P GAIN MUTATED 8P GAIN WILD-TYPE
  R0              17                76
  R1               0                10
  R2               1                 0
  RX               2                 6

Clustering(16) Variable = 8Q GAIN MUTATION ANALYSIS
D16V1, survival
                   sevent
clus2                0  1
  8Q GAIN MUTATED   31 22
  8Q GAIN WILD-TYPE 30 31
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               53                61 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               22                31 
$`8Q GAIN MUTATED`
TCGA-BC-4072 TCGA-BC-A10S TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A3KF TCGA-CC-5258 
       48.99        46.78        27.52         2.99         0.26         0.07 
TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A113 TCGA-DD-A116 
        3.32         0.10         0.10         0.13        79.73        53.29 
TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11C TCGA-DD-A1E9 TCGA-DD-A1EC 
      112.96         7.33         2.60        21.76        90.67        19.76 
TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EI TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39Y 
        6.67        12.95         6.02        13.64        21.14         5.59 
TCGA-DD-A3A1 TCGA-DD-A3A3 TCGA-DD-A3A8 TCGA-DD-A4ND TCGA-DD-A4NF TCGA-DD-A4NG 
        7.66        17.59         0.36        73.38        14.07        14.93 
TCGA-DD-A4NJ TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NQ TCGA-ED-A459 TCGA-EP-A12J 
       15.06        29.56        61.45        12.26         0.23        10.85 
TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS 
       11.74         1.97         0.62         3.19         0.43        23.01 
TCGA-ES-A2HT TCGA-FV-A3R2 TCGA-FV-A4ZP TCGA-G3-A25T TCGA-G3-A25W TCGA-G3-A25X 
       14.40         6.35        60.36        51.02        30.71        58.49 
TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CJ TCGA-G3-A5SJ TCGA-G3-A5SL 
       21.53        22.13        19.53        11.97         7.99 

$`8Q GAIN WILD-TYPE`
TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A10X TCGA-BC-A10Y 
       27.91        37.32        10.13        27.52        25.32        23.34 
TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KG 
        1.12        69.57         5.03        44.42        13.81        16.37 
TCGA-BC-A5W4 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A3MA 
        9.50         2.86         3.02         3.39         4.24         0.07 
TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A11B TCGA-DD-A11D TCGA-DD-A1EA TCGA-DD-A1EB 
       37.74        83.57         0.46        51.25        79.36        66.31 
TCGA-DD-A1ED TCGA-DD-A1EH TCGA-DD-A1EJ TCGA-DD-A39X TCGA-DD-A39Z TCGA-DD-A3A0 
       75.65        49.15        29.16        55.66        19.73        25.81 
TCGA-DD-A3A2 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A9 
       70.06        20.12       102.74       107.11        13.78        30.58 
TCGA-DD-A4NA TCGA-DD-A4NE TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NK TCGA-DD-A4NL 
       33.14        21.67        14.24        10.78        39.75        56.25 
TCGA-DD-A4NP TCGA-ED-A5KG TCGA-EP-A26S TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-A3I0 
       93.67         0.20         7.76        32.45        19.07         0.20 
TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25U 
        0.13         0.03         0.33         0.39         1.22        53.79 
TCGA-G3-A25V TCGA-G3-A25Y TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CK TCGA-G3-A5SK 
       28.27        14.86        25.64         5.88        19.23         9.93 
TCGA-G3-A5SM 
        4.37 

  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
             0.07              0.03 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
           112.96            107.11 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
            13.64             20.12 
[1] "0.1 - 113.0 (13.6)" "0.0 - 107.1 (20.1)"
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
       TCGA-BC-A3KG        TCGA-BC-A5W4        TCGA-CC-5258        TCGA-CC-5260 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-CC-5261        TCGA-CC-5262        TCGA-CC-5263        TCGA-CC-A1HT 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
       TCGA-CC-A3M9        TCGA-CC-A3MA        TCGA-CC-A3MB        TCGA-CC-A3MC 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" 
       TCGA-DD-A113        TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
       TCGA-DD-A118        TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B 
  "8Q GAIN MUTATED"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-DD-A11C        TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EA 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-DD-A1EB        TCGA-DD-A1EC        TCGA-DD-A1ED        TCGA-DD-A1EE 
"8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
       TCGA-DD-A1EF        TCGA-DD-A1EH        TCGA-DD-A1EI        TCGA-DD-A1EJ 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-DD-A1EL        TCGA-DD-A39V        TCGA-DD-A39X        TCGA-DD-A39Y 
  "8Q GAIN MUTATED"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
       TCGA-DD-A39Z        TCGA-DD-A3A0        TCGA-DD-A3A1        TCGA-DD-A3A2 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-DD-A3A3        TCGA-DD-A3A4        TCGA-DD-A3A5        TCGA-DD-A3A6 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-DD-A3A7        TCGA-DD-A3A8        TCGA-DD-A3A9        TCGA-DD-A4NA 
"8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-DD-A4ND        TCGA-DD-A4NE        TCGA-DD-A4NF        TCGA-DD-A4NG 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" 
       TCGA-DD-A4NH        TCGA-DD-A4NI        TCGA-DD-A4NJ        TCGA-DD-A4NK 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-DD-A4NL        TCGA-DD-A4NN        TCGA-DD-A4NO        TCGA-DD-A4NP 
"8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-DD-A4NQ        TCGA-ED-A459        TCGA-ED-A5KG        TCGA-EP-A12J 
  "8Q GAIN MUTATED"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
       TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC 
"8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" 
       TCGA-EP-A3JL        TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT 
  "8Q GAIN MUTATED"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" 
       TCGA-FV-A23B        TCGA-FV-A2QR        TCGA-FV-A3I0        TCGA-FV-A3R2 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
       TCGA-FV-A3R3        TCGA-FV-A495        TCGA-FV-A496        TCGA-FV-A4ZP 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
       TCGA-FV-A4ZQ        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI 
  "8Q GAIN MUTATED"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-G3-A3CJ        TCGA-G3-A3CK        TCGA-G3-A5SJ        TCGA-G3-A5SK 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-G3-A5SL        TCGA-G3-A5SM 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
       TCGA-BC-A3KG        TCGA-BC-A5W4        TCGA-CC-5258        TCGA-CC-5260 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-CC-5261        TCGA-CC-5262        TCGA-CC-5263        TCGA-CC-A1HT 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
       TCGA-CC-A3M9        TCGA-CC-A3MA        TCGA-CC-A3MB        TCGA-CC-A3MC 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" 
       TCGA-DD-A113        TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
       TCGA-DD-A118        TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B 
  "8Q GAIN MUTATED"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-DD-A11C        TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EA 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-DD-A1EB        TCGA-DD-A1EC        TCGA-DD-A1ED        TCGA-DD-A1EE 
"8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
       TCGA-DD-A1EF        TCGA-DD-A1EH        TCGA-DD-A1EI        TCGA-DD-A1EJ 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-DD-A1EL        TCGA-DD-A39V        TCGA-DD-A39X        TCGA-DD-A39Y 
  "8Q GAIN MUTATED"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
       TCGA-DD-A39Z        TCGA-DD-A3A0        TCGA-DD-A3A1        TCGA-DD-A3A2 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-DD-A3A3        TCGA-DD-A3A4        TCGA-DD-A3A5        TCGA-DD-A3A6 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-DD-A3A7        TCGA-DD-A3A8        TCGA-DD-A3A9        TCGA-DD-A4NA 
"8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-DD-A4ND        TCGA-DD-A4NE        TCGA-DD-A4NF        TCGA-DD-A4NG 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" 
       TCGA-DD-A4NH        TCGA-DD-A4NI        TCGA-DD-A4NJ        TCGA-DD-A4NK 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-DD-A4NL        TCGA-DD-A4NN        TCGA-DD-A4NO        TCGA-DD-A4NP 
"8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-DD-A4NQ        TCGA-ED-A459        TCGA-ED-A5KG        TCGA-EP-A12J 
  "8Q GAIN MUTATED"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
       TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC 
"8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" 
       TCGA-EP-A3JL        TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT 
  "8Q GAIN MUTATED"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" 
       TCGA-FV-A23B        TCGA-FV-A2QR        TCGA-FV-A3I0        TCGA-FV-A3R2 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
       TCGA-FV-A3R3        TCGA-FV-A495        TCGA-FV-A496        TCGA-FV-A4ZP 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
       TCGA-FV-A4ZQ        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI 
  "8Q GAIN MUTATED"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-G3-A3CJ        TCGA-G3-A3CK        TCGA-G3-A5SJ        TCGA-G3-A5SK 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-G3-A5SL        TCGA-G3-A5SM 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
       TCGA-BC-A3KG        TCGA-BC-A5W4        TCGA-CC-5258        TCGA-CC-5260 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-CC-5261        TCGA-CC-5262        TCGA-CC-5263        TCGA-CC-A1HT 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
       TCGA-CC-A3M9        TCGA-CC-A3MA        TCGA-CC-A3MB        TCGA-CC-A3MC 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" 
       TCGA-DD-A113        TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
       TCGA-DD-A118        TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B 
  "8Q GAIN MUTATED"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-DD-A11C        TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EA 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-DD-A1EB        TCGA-DD-A1EC        TCGA-DD-A1ED        TCGA-DD-A1EE 
"8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
       TCGA-DD-A1EF        TCGA-DD-A1EH        TCGA-DD-A1EI        TCGA-DD-A1EJ 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-DD-A1EL        TCGA-DD-A39V        TCGA-DD-A39X        TCGA-DD-A39Y 
  "8Q GAIN MUTATED"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
       TCGA-DD-A39Z        TCGA-DD-A3A0        TCGA-DD-A3A1        TCGA-DD-A3A2 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-DD-A3A3        TCGA-DD-A3A4        TCGA-DD-A3A5        TCGA-DD-A3A6 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-DD-A3A7        TCGA-DD-A3A8        TCGA-DD-A3A9        TCGA-DD-A4NA 
"8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-DD-A4ND        TCGA-DD-A4NE        TCGA-DD-A4NF        TCGA-DD-A4NG 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" 
       TCGA-DD-A4NH        TCGA-DD-A4NI        TCGA-DD-A4NJ        TCGA-DD-A4NK 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-DD-A4NL        TCGA-DD-A4NN        TCGA-DD-A4NO        TCGA-DD-A4NP 
"8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-DD-A4NQ        TCGA-ED-A459        TCGA-ED-A5KG        TCGA-EP-A12J 
  "8Q GAIN MUTATED"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
       TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC 
"8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" 
       TCGA-EP-A3JL        TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT 
  "8Q GAIN MUTATED"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" 
       TCGA-FV-A23B        TCGA-FV-A2QR        TCGA-FV-A3I0        TCGA-FV-A3R2 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
       TCGA-FV-A3R3        TCGA-FV-A495        TCGA-FV-A496        TCGA-FV-A4ZP 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
       TCGA-FV-A4ZQ        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI 
  "8Q GAIN MUTATED"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-G3-A3CJ        TCGA-G3-A3CK        TCGA-G3-A5SJ        TCGA-G3-A5SK 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-G3-A5SL        TCGA-G3-A5SM 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
[1] "hr=" "1"  
D16V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  8Q GAIN MUTATED        23       12         0         14          1          0
  8Q GAIN WILD-TYPE      22       13         2         11          2          4
                   vv
clus                STAGE IV STAGE IVA STAGE IVB
  8Q GAIN MUTATED          1         1         0
  8Q GAIN WILD-TYPE        0         0         1
D16V3, multiclass
                   vv
clus                T1 T2 T3 T4
  8Q GAIN MUTATED   24 13 17  1
  8Q GAIN WILD-TYPE 24 15 17  5
D16V4, multiclass
    clus
vv   8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  T1              24                24
  T2              13                15
  T3              17                17
  T4               1                 5
D16V5, binary
                   cls
clus                 0  1
  8Q GAIN MUTATED   36  1
  8Q GAIN WILD-TYPE 38  2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED     36    1
  8Q GAIN WILD-TYPE   38    2
   clus
vv  8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  0              36                38
  1               1                 2
                   vv
clus                M0 M1 MX
  8Q GAIN MUTATED   41  1 14
  8Q GAIN WILD-TYPE 49  1 11
D16V6, multiclass
    clus
vv   8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  M0              41                49
  M1               1                 1
  MX              14                11
D16V7, binary
                   cls
clus                 0  1
  8Q GAIN MUTATED   14 42
  8Q GAIN WILD-TYPE 30 31
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED     14   42
  8Q GAIN WILD-TYPE   30   31
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  FEMALE              14                30
  MALE                42                31
                   vv
clus                R0 R1 R2 RX
  8Q GAIN MUTATED   44  5  1  3
  8Q GAIN WILD-TYPE 49  5  0  5
D16V8, multiclass
    clus
vv   8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  R0              44                49
  R1               5                 5
  R2               1                 0
  RX               3                 5

Clustering(17) Variable = 9P GAIN MUTATION ANALYSIS
D17V1, survival
                   sevent
clus2                0  1
  9P GAIN MUTATED    2  1
  9P GAIN WILD-TYPE 59 52
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
                3               111 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
                1                52 
$`9P GAIN MUTATED`
TCGA-DD-A3A7 TCGA-EP-A2KB TCGA-G3-A25U 
       13.78         1.97        53.79 

$`9P GAIN WILD-TYPE`
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T 
       48.99        27.91        37.32        10.13        46.78        27.52 
TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 
       27.52         2.99        25.32        23.34         1.12        69.57 
TCGA-BC-A112 TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 
        5.03        44.42        13.81         0.26        16.37         9.50 
TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A1HT 
        0.07         2.86         3.02         3.39         4.24         3.32 
TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A113 TCGA-DD-A114 
        0.10         0.07         0.10         0.13        79.73        37.74 
TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B 
       83.57        53.29       112.96         7.33         2.60         0.46 
TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC 
       21.76        51.25        90.67        79.36        66.31        19.76 
TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ 
       75.65         6.67        12.95        49.15         6.02        29.16 
TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A0 
       13.64        21.14        55.66         5.59        19.73        25.81 
TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 
        7.66        70.06        17.59        20.12       102.74       107.11 
TCGA-DD-A3A8 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4ND TCGA-DD-A4NE TCGA-DD-A4NF 
        0.36        30.58        33.14        73.38        21.67        14.07 
TCGA-DD-A4NG TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL 
       14.93        14.24        10.78        15.06        39.75        56.25 
TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-ED-A459 TCGA-ED-A5KG 
       29.56        61.45        93.67        12.26         0.23         0.20 
TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK 
       10.85         7.76        11.74         0.62         3.19         0.43 
TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3R2 
       23.01        14.40        32.45        19.07         0.20         6.35 
TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25S 
        0.13         0.03         0.33        60.36         0.39         1.22 
TCGA-G3-A25T TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A25Z 
       51.02        28.27        30.71        58.49        14.86        21.53 
TCGA-G3-A3CG TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SJ 
       22.13        25.64         5.88        19.53        19.23        11.97 
TCGA-G3-A5SK TCGA-G3-A5SL TCGA-G3-A5SM 
        9.93         7.99         4.37 

  9P GAIN MUTATED 9P GAIN WILD-TYPE 
             1.97              0.03 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
            53.79            112.96 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
            13.78             16.37 
[1] "2.0 - 53.8 (13.8)"  "0.0 - 113.0 (16.4)"
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-BC-A5W4        TCGA-CC-5258        TCGA-CC-5260 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-CC-5261        TCGA-CC-5262        TCGA-CC-5263        TCGA-CC-A1HT 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-CC-A3M9        TCGA-CC-A3MA        TCGA-CC-A3MB        TCGA-CC-A3MC 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DD-A113        TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DD-A118        TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DD-A11C        TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EA 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DD-A1EB        TCGA-DD-A1EC        TCGA-DD-A1ED        TCGA-DD-A1EE 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DD-A1EF        TCGA-DD-A1EH        TCGA-DD-A1EI        TCGA-DD-A1EJ 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DD-A1EL        TCGA-DD-A39V        TCGA-DD-A39X        TCGA-DD-A39Y 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DD-A39Z        TCGA-DD-A3A0        TCGA-DD-A3A1        TCGA-DD-A3A2 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DD-A3A3        TCGA-DD-A3A4        TCGA-DD-A3A5        TCGA-DD-A3A6 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DD-A3A7        TCGA-DD-A3A8        TCGA-DD-A3A9        TCGA-DD-A4NA 
  "9P GAIN MUTATED" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DD-A4ND        TCGA-DD-A4NE        TCGA-DD-A4NF        TCGA-DD-A4NG 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DD-A4NH        TCGA-DD-A4NI        TCGA-DD-A4NJ        TCGA-DD-A4NK 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DD-A4NL        TCGA-DD-A4NN        TCGA-DD-A4NO        TCGA-DD-A4NP 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DD-A4NQ        TCGA-ED-A459        TCGA-ED-A5KG        TCGA-EP-A12J 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE"   "9P GAIN MUTATED" "9P GAIN WILD-TYPE" 
       TCGA-EP-A3JL        TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-FV-A23B        TCGA-FV-A2QR        TCGA-FV-A3I0        TCGA-FV-A3R2 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-FV-A3R3        TCGA-FV-A495        TCGA-FV-A496        TCGA-FV-A4ZP 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-FV-A4ZQ        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE"   "9P GAIN MUTATED" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-G3-A3CJ        TCGA-G3-A3CK        TCGA-G3-A5SJ        TCGA-G3-A5SK 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-G3-A5SL        TCGA-G3-A5SM 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-BC-A5W4        TCGA-CC-5258        TCGA-CC-5260 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-CC-5261        TCGA-CC-5262        TCGA-CC-5263        TCGA-CC-A1HT 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-CC-A3M9        TCGA-CC-A3MA        TCGA-CC-A3MB        TCGA-CC-A3MC 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DD-A113        TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DD-A118        TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DD-A11C        TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EA 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DD-A1EB        TCGA-DD-A1EC        TCGA-DD-A1ED        TCGA-DD-A1EE 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DD-A1EF        TCGA-DD-A1EH        TCGA-DD-A1EI        TCGA-DD-A1EJ 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DD-A1EL        TCGA-DD-A39V        TCGA-DD-A39X        TCGA-DD-A39Y 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DD-A39Z        TCGA-DD-A3A0        TCGA-DD-A3A1        TCGA-DD-A3A2 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DD-A3A3        TCGA-DD-A3A4        TCGA-DD-A3A5        TCGA-DD-A3A6 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DD-A3A7        TCGA-DD-A3A8        TCGA-DD-A3A9        TCGA-DD-A4NA 
  "9P GAIN MUTATED" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DD-A4ND        TCGA-DD-A4NE        TCGA-DD-A4NF        TCGA-DD-A4NG 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DD-A4NH        TCGA-DD-A4NI        TCGA-DD-A4NJ        TCGA-DD-A4NK 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DD-A4NL        TCGA-DD-A4NN        TCGA-DD-A4NO        TCGA-DD-A4NP 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DD-A4NQ        TCGA-ED-A459        TCGA-ED-A5KG        TCGA-EP-A12J 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE"   "9P GAIN MUTATED" "9P GAIN WILD-TYPE" 
       TCGA-EP-A3JL        TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-FV-A23B        TCGA-FV-A2QR        TCGA-FV-A3I0        TCGA-FV-A3R2 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-FV-A3R3        TCGA-FV-A495        TCGA-FV-A496        TCGA-FV-A4ZP 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-FV-A4ZQ        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE"   "9P GAIN MUTATED" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-G3-A3CJ        TCGA-G3-A3CK        TCGA-G3-A5SJ        TCGA-G3-A5SK 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-G3-A5SL        TCGA-G3-A5SM 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-BC-A5W4        TCGA-CC-5258        TCGA-CC-5260 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-CC-5261        TCGA-CC-5262        TCGA-CC-5263        TCGA-CC-A1HT 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-CC-A3M9        TCGA-CC-A3MA        TCGA-CC-A3MB        TCGA-CC-A3MC 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DD-A113        TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DD-A118        TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DD-A11C        TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EA 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DD-A1EB        TCGA-DD-A1EC        TCGA-DD-A1ED        TCGA-DD-A1EE 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DD-A1EF        TCGA-DD-A1EH        TCGA-DD-A1EI        TCGA-DD-A1EJ 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DD-A1EL        TCGA-DD-A39V        TCGA-DD-A39X        TCGA-DD-A39Y 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DD-A39Z        TCGA-DD-A3A0        TCGA-DD-A3A1        TCGA-DD-A3A2 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DD-A3A3        TCGA-DD-A3A4        TCGA-DD-A3A5        TCGA-DD-A3A6 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DD-A3A7        TCGA-DD-A3A8        TCGA-DD-A3A9        TCGA-DD-A4NA 
  "9P GAIN MUTATED" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DD-A4ND        TCGA-DD-A4NE        TCGA-DD-A4NF        TCGA-DD-A4NG 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DD-A4NH        TCGA-DD-A4NI        TCGA-DD-A4NJ        TCGA-DD-A4NK 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DD-A4NL        TCGA-DD-A4NN        TCGA-DD-A4NO        TCGA-DD-A4NP 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DD-A4NQ        TCGA-ED-A459        TCGA-ED-A5KG        TCGA-EP-A12J 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE"   "9P GAIN MUTATED" "9P GAIN WILD-TYPE" 
       TCGA-EP-A3JL        TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-FV-A23B        TCGA-FV-A2QR        TCGA-FV-A3I0        TCGA-FV-A3R2 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-FV-A3R3        TCGA-FV-A495        TCGA-FV-A496        TCGA-FV-A4ZP 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-FV-A4ZQ        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE"   "9P GAIN MUTATED" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-G3-A3CJ        TCGA-G3-A3CK        TCGA-G3-A5SJ        TCGA-G3-A5SK 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-G3-A5SL        TCGA-G3-A5SM 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
[1] "hr=" "1.3"
D17V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  9P GAIN MUTATED         2        0         0          1          1          0
  9P GAIN WILD-TYPE      43       25         2         24          2          4
                   vv
clus                STAGE IV STAGE IVA STAGE IVB
  9P GAIN MUTATED          0         0         0
  9P GAIN WILD-TYPE        1         1         1
D17V3, multiclass
                   vv
clus                T1 T2 T3 T4
  9P GAIN MUTATED    2  0  2  0
  9P GAIN WILD-TYPE 46 28 32  6
D17V4, multiclass
    clus
vv   9P GAIN MUTATED 9P GAIN WILD-TYPE
  T1               2                46
  T2               0                28
  T3               2                32
  T4               0                 6
D17V5, binary
                   cls
clus                 0  1
  9P GAIN MUTATED    3  0
  9P GAIN WILD-TYPE 71  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED      3    0
  9P GAIN WILD-TYPE   71    3
   clus
vv  9P GAIN MUTATED 9P GAIN WILD-TYPE
  0               3                71
  1               0                 3
                   vv
clus                M0 M1 MX
  9P GAIN MUTATED    3  0  1
  9P GAIN WILD-TYPE 87  2 24
D17V6, multiclass
    clus
vv   9P GAIN MUTATED 9P GAIN WILD-TYPE
  M0               3                87
  M1               0                 2
  MX               1                24
D17V7, binary
                   cls
clus                 0  1
  9P GAIN MUTATED    2  2
  9P GAIN WILD-TYPE 42 71
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED      2    2
  9P GAIN WILD-TYPE   42   71
        clus
vv       9P GAIN MUTATED 9P GAIN WILD-TYPE
  FEMALE               2                42
  MALE                 2                71
                   vv
clus                R0 R1 R2 RX
  9P GAIN MUTATED    3  0  0  1
  9P GAIN WILD-TYPE 90 10  1  7
D17V8, multiclass
    clus
vv   9P GAIN MUTATED 9P GAIN WILD-TYPE
  R0               3                90
  R1               0                10
  R2               0                 1
  RX               1                 7

Clustering(18) Variable = 9Q GAIN MUTATION ANALYSIS
D18V1, survival
                   sevent
clus2                0  1
  9Q GAIN MUTATED    2  1
  9Q GAIN WILD-TYPE 59 52
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
                3               111 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
                1                52 
$`9Q GAIN MUTATED`
TCGA-DD-A3A6 TCGA-EP-A2KB TCGA-G3-A25U 
      107.11         1.97        53.79 

$`9Q GAIN WILD-TYPE`
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T 
       48.99        27.91        37.32        10.13        46.78        27.52 
TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 
       27.52         2.99        25.32        23.34         1.12        69.57 
TCGA-BC-A112 TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 
        5.03        44.42        13.81         0.26        16.37         9.50 
TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A1HT 
        0.07         2.86         3.02         3.39         4.24         3.32 
TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A113 TCGA-DD-A114 
        0.10         0.07         0.10         0.13        79.73        37.74 
TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B 
       83.57        53.29       112.96         7.33         2.60         0.46 
TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC 
       21.76        51.25        90.67        79.36        66.31        19.76 
TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ 
       75.65         6.67        12.95        49.15         6.02        29.16 
TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A0 
       13.64        21.14        55.66         5.59        19.73        25.81 
TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A7 
        7.66        70.06        17.59        20.12       102.74        13.78 
TCGA-DD-A3A8 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4ND TCGA-DD-A4NE TCGA-DD-A4NF 
        0.36        30.58        33.14        73.38        21.67        14.07 
TCGA-DD-A4NG TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL 
       14.93        14.24        10.78        15.06        39.75        56.25 
TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-ED-A459 TCGA-ED-A5KG 
       29.56        61.45        93.67        12.26         0.23         0.20 
TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK 
       10.85         7.76        11.74         0.62         3.19         0.43 
TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3R2 
       23.01        14.40        32.45        19.07         0.20         6.35 
TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25S 
        0.13         0.03         0.33        60.36         0.39         1.22 
TCGA-G3-A25T TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A25Z 
       51.02        28.27        30.71        58.49        14.86        21.53 
TCGA-G3-A3CG TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SJ 
       22.13        25.64         5.88        19.53        19.23        11.97 
TCGA-G3-A5SK TCGA-G3-A5SL TCGA-G3-A5SM 
        9.93         7.99         4.37 

  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
             1.97              0.03 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
           107.11            112.96 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
            53.79             15.06 
[1] "2.0 - 107.1 (53.8)" "0.0 - 113.0 (15.1)"
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-BC-A5W4        TCGA-CC-5258        TCGA-CC-5260 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-CC-5261        TCGA-CC-5262        TCGA-CC-5263        TCGA-CC-A1HT 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-CC-A3M9        TCGA-CC-A3MA        TCGA-CC-A3MB        TCGA-CC-A3MC 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-DD-A113        TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-DD-A118        TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-DD-A11C        TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EA 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-DD-A1EB        TCGA-DD-A1EC        TCGA-DD-A1ED        TCGA-DD-A1EE 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-DD-A1EF        TCGA-DD-A1EH        TCGA-DD-A1EI        TCGA-DD-A1EJ 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-DD-A1EL        TCGA-DD-A39V        TCGA-DD-A39X        TCGA-DD-A39Y 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-DD-A39Z        TCGA-DD-A3A0        TCGA-DD-A3A1        TCGA-DD-A3A2 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-DD-A3A3        TCGA-DD-A3A4        TCGA-DD-A3A5        TCGA-DD-A3A6 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE"   "9Q GAIN MUTATED" 
       TCGA-DD-A3A7        TCGA-DD-A3A8        TCGA-DD-A3A9        TCGA-DD-A4NA 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-DD-A4ND        TCGA-DD-A4NE        TCGA-DD-A4NF        TCGA-DD-A4NG 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-DD-A4NH        TCGA-DD-A4NI        TCGA-DD-A4NJ        TCGA-DD-A4NK 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-DD-A4NL        TCGA-DD-A4NN        TCGA-DD-A4NO        TCGA-DD-A4NP 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-DD-A4NQ        TCGA-ED-A459        TCGA-ED-A5KG        TCGA-EP-A12J 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE"   "9Q GAIN MUTATED" "9Q GAIN WILD-TYPE" 
       TCGA-EP-A3JL        TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-FV-A23B        TCGA-FV-A2QR        TCGA-FV-A3I0        TCGA-FV-A3R2 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-FV-A3R3        TCGA-FV-A495        TCGA-FV-A496        TCGA-FV-A4ZP 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-FV-A4ZQ        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE"   "9Q GAIN MUTATED" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-G3-A3CJ        TCGA-G3-A3CK        TCGA-G3-A5SJ        TCGA-G3-A5SK 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-G3-A5SL        TCGA-G3-A5SM 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-BC-A5W4        TCGA-CC-5258        TCGA-CC-5260 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-CC-5261        TCGA-CC-5262        TCGA-CC-5263        TCGA-CC-A1HT 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-CC-A3M9        TCGA-CC-A3MA        TCGA-CC-A3MB        TCGA-CC-A3MC 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-DD-A113        TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-DD-A118        TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-DD-A11C        TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EA 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-DD-A1EB        TCGA-DD-A1EC        TCGA-DD-A1ED        TCGA-DD-A1EE 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-DD-A1EF        TCGA-DD-A1EH        TCGA-DD-A1EI        TCGA-DD-A1EJ 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-DD-A1EL        TCGA-DD-A39V        TCGA-DD-A39X        TCGA-DD-A39Y 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-DD-A39Z        TCGA-DD-A3A0        TCGA-DD-A3A1        TCGA-DD-A3A2 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-DD-A3A3        TCGA-DD-A3A4        TCGA-DD-A3A5        TCGA-DD-A3A6 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE"   "9Q GAIN MUTATED" 
       TCGA-DD-A3A7        TCGA-DD-A3A8        TCGA-DD-A3A9        TCGA-DD-A4NA 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-DD-A4ND        TCGA-DD-A4NE        TCGA-DD-A4NF        TCGA-DD-A4NG 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-DD-A4NH        TCGA-DD-A4NI        TCGA-DD-A4NJ        TCGA-DD-A4NK 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-DD-A4NL        TCGA-DD-A4NN        TCGA-DD-A4NO        TCGA-DD-A4NP 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-DD-A4NQ        TCGA-ED-A459        TCGA-ED-A5KG        TCGA-EP-A12J 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE"   "9Q GAIN MUTATED" "9Q GAIN WILD-TYPE" 
       TCGA-EP-A3JL        TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-FV-A23B        TCGA-FV-A2QR        TCGA-FV-A3I0        TCGA-FV-A3R2 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-FV-A3R3        TCGA-FV-A495        TCGA-FV-A496        TCGA-FV-A4ZP 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-FV-A4ZQ        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE"   "9Q GAIN MUTATED" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-G3-A3CJ        TCGA-G3-A3CK        TCGA-G3-A5SJ        TCGA-G3-A5SK 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-G3-A5SL        TCGA-G3-A5SM 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-BC-A5W4        TCGA-CC-5258        TCGA-CC-5260 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-CC-5261        TCGA-CC-5262        TCGA-CC-5263        TCGA-CC-A1HT 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-CC-A3M9        TCGA-CC-A3MA        TCGA-CC-A3MB        TCGA-CC-A3MC 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-DD-A113        TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-DD-A118        TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-DD-A11C        TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EA 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-DD-A1EB        TCGA-DD-A1EC        TCGA-DD-A1ED        TCGA-DD-A1EE 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-DD-A1EF        TCGA-DD-A1EH        TCGA-DD-A1EI        TCGA-DD-A1EJ 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-DD-A1EL        TCGA-DD-A39V        TCGA-DD-A39X        TCGA-DD-A39Y 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-DD-A39Z        TCGA-DD-A3A0        TCGA-DD-A3A1        TCGA-DD-A3A2 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-DD-A3A3        TCGA-DD-A3A4        TCGA-DD-A3A5        TCGA-DD-A3A6 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE"   "9Q GAIN MUTATED" 
       TCGA-DD-A3A7        TCGA-DD-A3A8        TCGA-DD-A3A9        TCGA-DD-A4NA 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-DD-A4ND        TCGA-DD-A4NE        TCGA-DD-A4NF        TCGA-DD-A4NG 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-DD-A4NH        TCGA-DD-A4NI        TCGA-DD-A4NJ        TCGA-DD-A4NK 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-DD-A4NL        TCGA-DD-A4NN        TCGA-DD-A4NO        TCGA-DD-A4NP 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-DD-A4NQ        TCGA-ED-A459        TCGA-ED-A5KG        TCGA-EP-A12J 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE"   "9Q GAIN MUTATED" "9Q GAIN WILD-TYPE" 
       TCGA-EP-A3JL        TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-FV-A23B        TCGA-FV-A2QR        TCGA-FV-A3I0        TCGA-FV-A3R2 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-FV-A3R3        TCGA-FV-A495        TCGA-FV-A496        TCGA-FV-A4ZP 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-FV-A4ZQ        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE"   "9Q GAIN MUTATED" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-G3-A3CJ        TCGA-G3-A3CK        TCGA-G3-A5SJ        TCGA-G3-A5SK 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-G3-A5SL        TCGA-G3-A5SM 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
[1] "hr=" "3.9"
D18V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  9Q GAIN MUTATED         2        1         0          1          0          0
  9Q GAIN WILD-TYPE      43       24         2         24          3          4
                   vv
clus                STAGE IV STAGE IVA STAGE IVB
  9Q GAIN MUTATED          0         0         0
  9Q GAIN WILD-TYPE        1         1         1
D18V3, multiclass
                   vv
clus                T1 T2 T3 T4
  9Q GAIN MUTATED    2  1  1  0
  9Q GAIN WILD-TYPE 46 27 33  6
D18V4, multiclass
    clus
vv   9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  T1               2                46
  T2               1                27
  T3               1                33
  T4               0                 6
D18V5, binary
                   cls
clus                 0  1
  9Q GAIN MUTATED    3  0
  9Q GAIN WILD-TYPE 71  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED      3    0
  9Q GAIN WILD-TYPE   71    3
   clus
vv  9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  0               3                71
  1               0                 3
                   vv
clus                M0 M1 MX
  9Q GAIN MUTATED    3  0  1
  9Q GAIN WILD-TYPE 87  2 24
D18V6, multiclass
    clus
vv   9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  M0               3                87
  M1               0                 2
  MX               1                24
D18V7, binary
                   cls
clus                 0  1
  9Q GAIN MUTATED    3  1
  9Q GAIN WILD-TYPE 41 72
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED      3    1
  9Q GAIN WILD-TYPE   41   72
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  FEMALE               3                41
  MALE                 1                72
                   vv
clus                R0 R1 R2 RX
  9Q GAIN MUTATED    3  0  0  1
  9Q GAIN WILD-TYPE 90 10  1  7
D18V8, multiclass
    clus
vv   9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  R0               3                90
  R1               0                10
  R2               0                 1
  RX               1                 7

Clustering(19) Variable = 10P GAIN MUTATION ANALYSIS
D19V1, survival
                    sevent
clus2                 0  1
  10P GAIN MUTATED    9  7
  10P GAIN WILD-TYPE 52 46
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                16                 98 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                 7                 46 
$`10P GAIN MUTATED`
TCGA-BC-A10Q TCGA-BC-A10R TCGA-CC-A3MB TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A1EF 
       37.32        10.13         0.10        79.73        37.74        12.95 
TCGA-DD-A1EL TCGA-DD-A3A9 TCGA-DD-A4NG TCGA-ED-A459 TCGA-EP-A2KB TCGA-ES-A2HS 
       13.64        30.58        14.93         0.23         1.97        23.01 
TCGA-FV-A4ZQ TCGA-G3-A5SJ TCGA-G3-A5SL TCGA-G3-A5SM 
        0.39        11.97         7.99         4.37 

$`10P GAIN WILD-TYPE`
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W 
       48.99        27.91        46.78        27.52        27.52         2.99 
TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A216 
       25.32        23.34         1.12        69.57         5.03        44.42 
TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-CC-5258 TCGA-CC-5260 
       13.81         0.26        16.37         9.50         0.07         2.86 
TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA 
        3.02         3.39         4.24         3.32         0.10         0.07 
TCGA-CC-A3MC TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A 
        0.13        83.57        53.29       112.96         7.33         2.60 
TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB 
        0.46        21.76        51.25        90.67        79.36        66.31 
TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ 
       19.76        75.65         6.67        49.15         6.02        29.16 
TCGA-DD-A39V TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 
       21.14        55.66         5.59        19.73        25.81         7.66 
TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 
       70.06        17.59        20.12       102.74       107.11        13.78 
TCGA-DD-A3A8 TCGA-DD-A4NA TCGA-DD-A4ND TCGA-DD-A4NE TCGA-DD-A4NF TCGA-DD-A4NH 
        0.36        33.14        73.38        21.67        14.07        14.24 
TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO 
       10.78        15.06        39.75        56.25        29.56        61.45 
TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-ED-A5KG TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA 
       93.67        12.26         0.20        10.85         7.76        11.74 
TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QR 
        0.62         3.19         0.43        14.40        32.45        19.07 
TCGA-FV-A3I0 TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZP 
        0.20         6.35         0.13         0.03         0.33        60.36 
TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25X 
        1.22        51.02        53.79        28.27        30.71        58.49 
TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ 
       14.86        21.53        22.13        25.64         5.88        19.53 
TCGA-G3-A3CK TCGA-G3-A5SK 
       19.23         9.93 

  10P GAIN MUTATED 10P GAIN WILD-TYPE 
              0.10               0.03 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
             79.73             112.96 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
             12.46              19.15 
[1] "0.1 - 79.7 (12.5)"  "0.0 - 113.0 (19.1)"
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE"   "10P GAIN MUTATED" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
  "10P GAIN MUTATED" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-BC-A5W4 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-CC-5258         TCGA-CC-5260         TCGA-CC-5261 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-CC-5262         TCGA-CC-5263         TCGA-CC-A1HT 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-CC-A3M9         TCGA-CC-A3MA         TCGA-CC-A3MB 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE"   "10P GAIN MUTATED" 
        TCGA-CC-A3MC         TCGA-DD-A113         TCGA-DD-A114 
"10P GAIN WILD-TYPE"   "10P GAIN MUTATED"   "10P GAIN MUTATED" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-DD-A1EA         TCGA-DD-A1EB         TCGA-DD-A1EC 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-DD-A1ED         TCGA-DD-A1EE         TCGA-DD-A1EF 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE"   "10P GAIN MUTATED" 
        TCGA-DD-A1EH         TCGA-DD-A1EI         TCGA-DD-A1EJ 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-DD-A1EL         TCGA-DD-A39V         TCGA-DD-A39X 
  "10P GAIN MUTATED" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-DD-A39Y         TCGA-DD-A39Z         TCGA-DD-A3A0 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-DD-A3A1         TCGA-DD-A3A2         TCGA-DD-A3A3 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-DD-A3A4         TCGA-DD-A3A5         TCGA-DD-A3A6 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-DD-A3A7         TCGA-DD-A3A8         TCGA-DD-A3A9 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE"   "10P GAIN MUTATED" 
        TCGA-DD-A4NA         TCGA-DD-A4ND         TCGA-DD-A4NE 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-DD-A4NF         TCGA-DD-A4NG         TCGA-DD-A4NH 
"10P GAIN WILD-TYPE"   "10P GAIN MUTATED" "10P GAIN WILD-TYPE" 
        TCGA-DD-A4NI         TCGA-DD-A4NJ         TCGA-DD-A4NK 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-DD-A4NL         TCGA-DD-A4NN         TCGA-DD-A4NO 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-DD-A4NP         TCGA-DD-A4NQ         TCGA-ED-A459 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE"   "10P GAIN MUTATED" 
        TCGA-ED-A5KG         TCGA-EP-A12J         TCGA-EP-A26S 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-EP-A2KA         TCGA-EP-A2KB         TCGA-EP-A2KC 
"10P GAIN WILD-TYPE"   "10P GAIN MUTATED" "10P GAIN WILD-TYPE" 
        TCGA-EP-A3JL         TCGA-EP-A3RK         TCGA-ES-A2HS 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE"   "10P GAIN MUTATED" 
        TCGA-ES-A2HT         TCGA-FV-A23B         TCGA-FV-A2QR 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-FV-A3I0         TCGA-FV-A3R2         TCGA-FV-A3R3 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-FV-A495         TCGA-FV-A496         TCGA-FV-A4ZP 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-FV-A4ZQ         TCGA-G3-A25S         TCGA-G3-A25T 
  "10P GAIN MUTATED" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-G3-A25U         TCGA-G3-A25V         TCGA-G3-A25W 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-G3-A25X         TCGA-G3-A25Y         TCGA-G3-A25Z 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-G3-A3CG         TCGA-G3-A3CH         TCGA-G3-A3CI 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK         TCGA-G3-A5SJ 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE"   "10P GAIN MUTATED" 
        TCGA-G3-A5SK         TCGA-G3-A5SL         TCGA-G3-A5SM 
"10P GAIN WILD-TYPE"   "10P GAIN MUTATED"   "10P GAIN MUTATED" 
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE"   "10P GAIN MUTATED" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
  "10P GAIN MUTATED" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-BC-A5W4 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-CC-5258         TCGA-CC-5260         TCGA-CC-5261 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-CC-5262         TCGA-CC-5263         TCGA-CC-A1HT 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-CC-A3M9         TCGA-CC-A3MA         TCGA-CC-A3MB 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE"   "10P GAIN MUTATED" 
        TCGA-CC-A3MC         TCGA-DD-A113         TCGA-DD-A114 
"10P GAIN WILD-TYPE"   "10P GAIN MUTATED"   "10P GAIN MUTATED" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-DD-A1EA         TCGA-DD-A1EB         TCGA-DD-A1EC 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-DD-A1ED         TCGA-DD-A1EE         TCGA-DD-A1EF 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE"   "10P GAIN MUTATED" 
        TCGA-DD-A1EH         TCGA-DD-A1EI         TCGA-DD-A1EJ 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-DD-A1EL         TCGA-DD-A39V         TCGA-DD-A39X 
  "10P GAIN MUTATED" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-DD-A39Y         TCGA-DD-A39Z         TCGA-DD-A3A0 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-DD-A3A1         TCGA-DD-A3A2         TCGA-DD-A3A3 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-DD-A3A4         TCGA-DD-A3A5         TCGA-DD-A3A6 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-DD-A3A7         TCGA-DD-A3A8         TCGA-DD-A3A9 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE"   "10P GAIN MUTATED" 
        TCGA-DD-A4NA         TCGA-DD-A4ND         TCGA-DD-A4NE 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-DD-A4NF         TCGA-DD-A4NG         TCGA-DD-A4NH 
"10P GAIN WILD-TYPE"   "10P GAIN MUTATED" "10P GAIN WILD-TYPE" 
        TCGA-DD-A4NI         TCGA-DD-A4NJ         TCGA-DD-A4NK 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-DD-A4NL         TCGA-DD-A4NN         TCGA-DD-A4NO 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-DD-A4NP         TCGA-DD-A4NQ         TCGA-ED-A459 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE"   "10P GAIN MUTATED" 
        TCGA-ED-A5KG         TCGA-EP-A12J         TCGA-EP-A26S 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-EP-A2KA         TCGA-EP-A2KB         TCGA-EP-A2KC 
"10P GAIN WILD-TYPE"   "10P GAIN MUTATED" "10P GAIN WILD-TYPE" 
        TCGA-EP-A3JL         TCGA-EP-A3RK         TCGA-ES-A2HS 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE"   "10P GAIN MUTATED" 
        TCGA-ES-A2HT         TCGA-FV-A23B         TCGA-FV-A2QR 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-FV-A3I0         TCGA-FV-A3R2         TCGA-FV-A3R3 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-FV-A495         TCGA-FV-A496         TCGA-FV-A4ZP 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-FV-A4ZQ         TCGA-G3-A25S         TCGA-G3-A25T 
  "10P GAIN MUTATED" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-G3-A25U         TCGA-G3-A25V         TCGA-G3-A25W 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-G3-A25X         TCGA-G3-A25Y         TCGA-G3-A25Z 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-G3-A3CG         TCGA-G3-A3CH         TCGA-G3-A3CI 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK         TCGA-G3-A5SJ 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE"   "10P GAIN MUTATED" 
        TCGA-G3-A5SK         TCGA-G3-A5SL         TCGA-G3-A5SM 
"10P GAIN WILD-TYPE"   "10P GAIN MUTATED"   "10P GAIN MUTATED" 
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE"   "10P GAIN MUTATED" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
  "10P GAIN MUTATED" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-BC-A5W4 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-CC-5258         TCGA-CC-5260         TCGA-CC-5261 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-CC-5262         TCGA-CC-5263         TCGA-CC-A1HT 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-CC-A3M9         TCGA-CC-A3MA         TCGA-CC-A3MB 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE"   "10P GAIN MUTATED" 
        TCGA-CC-A3MC         TCGA-DD-A113         TCGA-DD-A114 
"10P GAIN WILD-TYPE"   "10P GAIN MUTATED"   "10P GAIN MUTATED" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-DD-A1EA         TCGA-DD-A1EB         TCGA-DD-A1EC 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-DD-A1ED         TCGA-DD-A1EE         TCGA-DD-A1EF 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE"   "10P GAIN MUTATED" 
        TCGA-DD-A1EH         TCGA-DD-A1EI         TCGA-DD-A1EJ 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-DD-A1EL         TCGA-DD-A39V         TCGA-DD-A39X 
  "10P GAIN MUTATED" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-DD-A39Y         TCGA-DD-A39Z         TCGA-DD-A3A0 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-DD-A3A1         TCGA-DD-A3A2         TCGA-DD-A3A3 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-DD-A3A4         TCGA-DD-A3A5         TCGA-DD-A3A6 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-DD-A3A7         TCGA-DD-A3A8         TCGA-DD-A3A9 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE"   "10P GAIN MUTATED" 
        TCGA-DD-A4NA         TCGA-DD-A4ND         TCGA-DD-A4NE 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-DD-A4NF         TCGA-DD-A4NG         TCGA-DD-A4NH 
"10P GAIN WILD-TYPE"   "10P GAIN MUTATED" "10P GAIN WILD-TYPE" 
        TCGA-DD-A4NI         TCGA-DD-A4NJ         TCGA-DD-A4NK 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-DD-A4NL         TCGA-DD-A4NN         TCGA-DD-A4NO 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-DD-A4NP         TCGA-DD-A4NQ         TCGA-ED-A459 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE"   "10P GAIN MUTATED" 
        TCGA-ED-A5KG         TCGA-EP-A12J         TCGA-EP-A26S 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-EP-A2KA         TCGA-EP-A2KB         TCGA-EP-A2KC 
"10P GAIN WILD-TYPE"   "10P GAIN MUTATED" "10P GAIN WILD-TYPE" 
        TCGA-EP-A3JL         TCGA-EP-A3RK         TCGA-ES-A2HS 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE"   "10P GAIN MUTATED" 
        TCGA-ES-A2HT         TCGA-FV-A23B         TCGA-FV-A2QR 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-FV-A3I0         TCGA-FV-A3R2         TCGA-FV-A3R3 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-FV-A495         TCGA-FV-A496         TCGA-FV-A4ZP 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-FV-A4ZQ         TCGA-G3-A25S         TCGA-G3-A25T 
  "10P GAIN MUTATED" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-G3-A25U         TCGA-G3-A25V         TCGA-G3-A25W 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-G3-A25X         TCGA-G3-A25Y         TCGA-G3-A25Z 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-G3-A3CG         TCGA-G3-A3CH         TCGA-G3-A3CI 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK         TCGA-G3-A5SJ 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE"   "10P GAIN MUTATED" 
        TCGA-G3-A5SK         TCGA-G3-A5SL         TCGA-G3-A5SM 
"10P GAIN WILD-TYPE"   "10P GAIN MUTATED"   "10P GAIN MUTATED" 
[1] "hr=" "1.4"
D19V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  10P GAIN MUTATED         5        5         0          4          0
  10P GAIN WILD-TYPE      40       20         2         21          3
                    vv
clus                 STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  10P GAIN MUTATED            0        0         0         1
  10P GAIN WILD-TYPE          4        1         1         0
D19V3, multiclass
                    vv
clus                 T1 T2 T3 T4
  10P GAIN MUTATED    5  6  5  1
  10P GAIN WILD-TYPE 43 22 29  5
D19V4, multiclass
    clus
vv   10P GAIN MUTATED 10P GAIN WILD-TYPE
  T1                5                 43
  T2                6                 22
  T3                5                 29
  T4                1                  5
D19V5, binary
                    cls
clus                  0  1
  10P GAIN MUTATED    7  0
  10P GAIN WILD-TYPE 67  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED      7    0
  10P GAIN WILD-TYPE   67    3
   clus
vv  10P GAIN MUTATED 10P GAIN WILD-TYPE
  0                7                 67
  1                0                  3
                    vv
clus                 M0 M1 MX
  10P GAIN MUTATED   12  1  4
  10P GAIN WILD-TYPE 78  1 21
D19V6, multiclass
    clus
vv   10P GAIN MUTATED 10P GAIN WILD-TYPE
  M0               12                 78
  M1                1                  1
  MX                4                 21
D19V7, binary
                    cls
clus                  0  1
  10P GAIN MUTATED    6 11
  10P GAIN WILD-TYPE 38 62
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED      6   11
  10P GAIN WILD-TYPE   38   62
        clus
vv       10P GAIN MUTATED 10P GAIN WILD-TYPE
  FEMALE                6                 38
  MALE                 11                 62
                    vv
clus                 R0 R1 R2 RX
  10P GAIN MUTATED   15  1  0  1
  10P GAIN WILD-TYPE 78  9  1  7
D19V8, multiclass
    clus
vv   10P GAIN MUTATED 10P GAIN WILD-TYPE
  R0               15                 78
  R1                1                  9
  R2                0                  1
  RX                1                  7

Clustering(20) Variable = 10Q GAIN MUTATION ANALYSIS
D20V1, survival
                    sevent
clus2                 0  1
  10Q GAIN MUTATED    6  4
  10Q GAIN WILD-TYPE 55 49
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                10                104 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                 4                 49 
$`10Q GAIN MUTATED`
TCGA-DD-A113 TCGA-DD-A1EF TCGA-DD-A39Z TCGA-DD-A3A9 TCGA-DD-A4NG TCGA-EP-A2KB 
       79.73        12.95        19.73        30.58        14.93         1.97 
TCGA-ES-A2HS TCGA-FV-A4ZQ TCGA-G3-A5SL TCGA-G3-A5SM 
       23.01         0.39         7.99         4.37 

$`10Q GAIN WILD-TYPE`
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T 
       48.99        27.91        37.32        10.13        46.78        27.52 
TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 
       27.52         2.99        25.32        23.34         1.12        69.57 
TCGA-BC-A112 TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 
        5.03        44.42        13.81         0.26        16.37         9.50 
TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A1HT 
        0.07         2.86         3.02         3.39         4.24         3.32 
TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A114 TCGA-DD-A115 
        0.10         0.07         0.10         0.13        37.74        83.57 
TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C 
       53.29       112.96         7.33         2.60         0.46        21.76 
TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED 
       51.25        90.67        79.36        66.31        19.76        75.65 
TCGA-DD-A1EE TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EL TCGA-DD-A39V 
        6.67        49.15         6.02        29.16        13.64        21.14 
TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 
       55.66         5.59        25.81         7.66        70.06        17.59 
TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A4NA 
       20.12       102.74       107.11        13.78         0.36        33.14 
TCGA-DD-A4ND TCGA-DD-A4NE TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ 
       73.38        21.67        14.07        14.24        10.78        15.06 
TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ 
       39.75        56.25        29.56        61.45        93.67        12.26 
TCGA-ED-A459 TCGA-ED-A5KG TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KC 
        0.23         0.20        10.85         7.76        11.74         0.62 
TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-A3I0 
        3.19         0.43        14.40        32.45        19.07         0.20 
TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZP TCGA-G3-A25S 
        6.35         0.13         0.03         0.33        60.36         1.22 
TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25X TCGA-G3-A25Y 
       51.02        53.79        28.27        30.71        58.49        14.86 
TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK 
       21.53        22.13        25.64         5.88        19.53        19.23 
TCGA-G3-A5SJ TCGA-G3-A5SK 
       11.97         9.93 

  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
              0.39               0.03 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
             79.73             112.96 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
             13.94              16.98 
[1] "0.4 - 79.7 (13.9)"  "0.0 - 113.0 (17.0)"
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-BC-A5W4 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CC-5258         TCGA-CC-5260         TCGA-CC-5261 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CC-5262         TCGA-CC-5263         TCGA-CC-A1HT 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CC-A3M9         TCGA-CC-A3MA         TCGA-CC-A3MB 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CC-A3MC         TCGA-DD-A113         TCGA-DD-A114 
"10Q GAIN WILD-TYPE"   "10Q GAIN MUTATED" "10Q GAIN WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DD-A1EA         TCGA-DD-A1EB         TCGA-DD-A1EC 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DD-A1ED         TCGA-DD-A1EE         TCGA-DD-A1EF 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE"   "10Q GAIN MUTATED" 
        TCGA-DD-A1EH         TCGA-DD-A1EI         TCGA-DD-A1EJ 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DD-A1EL         TCGA-DD-A39V         TCGA-DD-A39X 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DD-A39Y         TCGA-DD-A39Z         TCGA-DD-A3A0 
"10Q GAIN WILD-TYPE"   "10Q GAIN MUTATED" "10Q GAIN WILD-TYPE" 
        TCGA-DD-A3A1         TCGA-DD-A3A2         TCGA-DD-A3A3 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DD-A3A4         TCGA-DD-A3A5         TCGA-DD-A3A6 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DD-A3A7         TCGA-DD-A3A8         TCGA-DD-A3A9 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE"   "10Q GAIN MUTATED" 
        TCGA-DD-A4NA         TCGA-DD-A4ND         TCGA-DD-A4NE 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DD-A4NF         TCGA-DD-A4NG         TCGA-DD-A4NH 
"10Q GAIN WILD-TYPE"   "10Q GAIN MUTATED" "10Q GAIN WILD-TYPE" 
        TCGA-DD-A4NI         TCGA-DD-A4NJ         TCGA-DD-A4NK 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DD-A4NL         TCGA-DD-A4NN         TCGA-DD-A4NO 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DD-A4NP         TCGA-DD-A4NQ         TCGA-ED-A459 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-ED-A5KG         TCGA-EP-A12J         TCGA-EP-A26S 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-EP-A2KA         TCGA-EP-A2KB         TCGA-EP-A2KC 
"10Q GAIN WILD-TYPE"   "10Q GAIN MUTATED" "10Q GAIN WILD-TYPE" 
        TCGA-EP-A3JL         TCGA-EP-A3RK         TCGA-ES-A2HS 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE"   "10Q GAIN MUTATED" 
        TCGA-ES-A2HT         TCGA-FV-A23B         TCGA-FV-A2QR 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-FV-A3I0         TCGA-FV-A3R2         TCGA-FV-A3R3 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-FV-A495         TCGA-FV-A496         TCGA-FV-A4ZP 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-FV-A4ZQ         TCGA-G3-A25S         TCGA-G3-A25T 
  "10Q GAIN MUTATED" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-G3-A25U         TCGA-G3-A25V         TCGA-G3-A25W 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-G3-A25X         TCGA-G3-A25Y         TCGA-G3-A25Z 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-G3-A3CG         TCGA-G3-A3CH         TCGA-G3-A3CI 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK         TCGA-G3-A5SJ 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-G3-A5SK         TCGA-G3-A5SL         TCGA-G3-A5SM 
"10Q GAIN WILD-TYPE"   "10Q GAIN MUTATED"   "10Q GAIN MUTATED" 
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-BC-A5W4 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CC-5258         TCGA-CC-5260         TCGA-CC-5261 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CC-5262         TCGA-CC-5263         TCGA-CC-A1HT 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CC-A3M9         TCGA-CC-A3MA         TCGA-CC-A3MB 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CC-A3MC         TCGA-DD-A113         TCGA-DD-A114 
"10Q GAIN WILD-TYPE"   "10Q GAIN MUTATED" "10Q GAIN WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DD-A1EA         TCGA-DD-A1EB         TCGA-DD-A1EC 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DD-A1ED         TCGA-DD-A1EE         TCGA-DD-A1EF 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE"   "10Q GAIN MUTATED" 
        TCGA-DD-A1EH         TCGA-DD-A1EI         TCGA-DD-A1EJ 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DD-A1EL         TCGA-DD-A39V         TCGA-DD-A39X 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DD-A39Y         TCGA-DD-A39Z         TCGA-DD-A3A0 
"10Q GAIN WILD-TYPE"   "10Q GAIN MUTATED" "10Q GAIN WILD-TYPE" 
        TCGA-DD-A3A1         TCGA-DD-A3A2         TCGA-DD-A3A3 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DD-A3A4         TCGA-DD-A3A5         TCGA-DD-A3A6 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DD-A3A7         TCGA-DD-A3A8         TCGA-DD-A3A9 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE"   "10Q GAIN MUTATED" 
        TCGA-DD-A4NA         TCGA-DD-A4ND         TCGA-DD-A4NE 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DD-A4NF         TCGA-DD-A4NG         TCGA-DD-A4NH 
"10Q GAIN WILD-TYPE"   "10Q GAIN MUTATED" "10Q GAIN WILD-TYPE" 
        TCGA-DD-A4NI         TCGA-DD-A4NJ         TCGA-DD-A4NK 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DD-A4NL         TCGA-DD-A4NN         TCGA-DD-A4NO 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DD-A4NP         TCGA-DD-A4NQ         TCGA-ED-A459 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-ED-A5KG         TCGA-EP-A12J         TCGA-EP-A26S 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-EP-A2KA         TCGA-EP-A2KB         TCGA-EP-A2KC 
"10Q GAIN WILD-TYPE"   "10Q GAIN MUTATED" "10Q GAIN WILD-TYPE" 
        TCGA-EP-A3JL         TCGA-EP-A3RK         TCGA-ES-A2HS 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE"   "10Q GAIN MUTATED" 
        TCGA-ES-A2HT         TCGA-FV-A23B         TCGA-FV-A2QR 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-FV-A3I0         TCGA-FV-A3R2         TCGA-FV-A3R3 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-FV-A495         TCGA-FV-A496         TCGA-FV-A4ZP 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-FV-A4ZQ         TCGA-G3-A25S         TCGA-G3-A25T 
  "10Q GAIN MUTATED" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-G3-A25U         TCGA-G3-A25V         TCGA-G3-A25W 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-G3-A25X         TCGA-G3-A25Y         TCGA-G3-A25Z 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-G3-A3CG         TCGA-G3-A3CH         TCGA-G3-A3CI 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK         TCGA-G3-A5SJ 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-G3-A5SK         TCGA-G3-A5SL         TCGA-G3-A5SM 
"10Q GAIN WILD-TYPE"   "10Q GAIN MUTATED"   "10Q GAIN MUTATED" 
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-BC-A5W4 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CC-5258         TCGA-CC-5260         TCGA-CC-5261 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CC-5262         TCGA-CC-5263         TCGA-CC-A1HT 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CC-A3M9         TCGA-CC-A3MA         TCGA-CC-A3MB 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CC-A3MC         TCGA-DD-A113         TCGA-DD-A114 
"10Q GAIN WILD-TYPE"   "10Q GAIN MUTATED" "10Q GAIN WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DD-A1EA         TCGA-DD-A1EB         TCGA-DD-A1EC 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DD-A1ED         TCGA-DD-A1EE         TCGA-DD-A1EF 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE"   "10Q GAIN MUTATED" 
        TCGA-DD-A1EH         TCGA-DD-A1EI         TCGA-DD-A1EJ 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DD-A1EL         TCGA-DD-A39V         TCGA-DD-A39X 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DD-A39Y         TCGA-DD-A39Z         TCGA-DD-A3A0 
"10Q GAIN WILD-TYPE"   "10Q GAIN MUTATED" "10Q GAIN WILD-TYPE" 
        TCGA-DD-A3A1         TCGA-DD-A3A2         TCGA-DD-A3A3 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DD-A3A4         TCGA-DD-A3A5         TCGA-DD-A3A6 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DD-A3A7         TCGA-DD-A3A8         TCGA-DD-A3A9 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE"   "10Q GAIN MUTATED" 
        TCGA-DD-A4NA         TCGA-DD-A4ND         TCGA-DD-A4NE 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DD-A4NF         TCGA-DD-A4NG         TCGA-DD-A4NH 
"10Q GAIN WILD-TYPE"   "10Q GAIN MUTATED" "10Q GAIN WILD-TYPE" 
        TCGA-DD-A4NI         TCGA-DD-A4NJ         TCGA-DD-A4NK 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DD-A4NL         TCGA-DD-A4NN         TCGA-DD-A4NO 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DD-A4NP         TCGA-DD-A4NQ         TCGA-ED-A459 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-ED-A5KG         TCGA-EP-A12J         TCGA-EP-A26S 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-EP-A2KA         TCGA-EP-A2KB         TCGA-EP-A2KC 
"10Q GAIN WILD-TYPE"   "10Q GAIN MUTATED" "10Q GAIN WILD-TYPE" 
        TCGA-EP-A3JL         TCGA-EP-A3RK         TCGA-ES-A2HS 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE"   "10Q GAIN MUTATED" 
        TCGA-ES-A2HT         TCGA-FV-A23B         TCGA-FV-A2QR 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-FV-A3I0         TCGA-FV-A3R2         TCGA-FV-A3R3 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-FV-A495         TCGA-FV-A496         TCGA-FV-A4ZP 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-FV-A4ZQ         TCGA-G3-A25S         TCGA-G3-A25T 
  "10Q GAIN MUTATED" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-G3-A25U         TCGA-G3-A25V         TCGA-G3-A25W 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-G3-A25X         TCGA-G3-A25Y         TCGA-G3-A25Z 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-G3-A3CG         TCGA-G3-A3CH         TCGA-G3-A3CI 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK         TCGA-G3-A5SJ 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-G3-A5SK         TCGA-G3-A5SL         TCGA-G3-A5SM 
"10Q GAIN WILD-TYPE"   "10Q GAIN MUTATED"   "10Q GAIN MUTATED" 
[1] "hr=" "1.2"
D20V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  10Q GAIN MUTATED         4        3         0          2          0
  10Q GAIN WILD-TYPE      41       22         2         23          3
                    vv
clus                 STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  10Q GAIN MUTATED            0        0         0         1
  10Q GAIN WILD-TYPE          4        1         1         0
D20V3, multiclass
                    vv
clus                 T1 T2 T3 T4
  10Q GAIN MUTATED    4  3  2  1
  10Q GAIN WILD-TYPE 44 25 32  5
D20V4, multiclass
    clus
vv   10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  T1                4                 44
  T2                3                 25
  T3                2                 32
  T4                1                  5
D20V5, binary
                    cls
clus                  0  1
  10Q GAIN MUTATED    3  0
  10Q GAIN WILD-TYPE 71  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED      3    0
  10Q GAIN WILD-TYPE   71    3
   clus
vv  10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  0                3                 71
  1                0                  3
                    vv
clus                 M0 M1 MX
  10Q GAIN MUTATED    7  1  2
  10Q GAIN WILD-TYPE 83  1 23
D20V6, multiclass
    clus
vv   10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  M0                7                 83
  M1                1                  1
  MX                2                 23
D20V7, binary
                    cls
clus                  0  1
  10Q GAIN MUTATED    5  5
  10Q GAIN WILD-TYPE 39 68
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED      5    5
  10Q GAIN WILD-TYPE   39   68
        clus
vv       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  FEMALE                5                 39
  MALE                  5                 68
                    vv
clus                 R0 R1 R2 RX
  10Q GAIN MUTATED   10  0  0  0
  10Q GAIN WILD-TYPE 83 10  1  8
D20V8, multiclass
    clus
vv   10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  R0               10                 83
  R1                0                 10
  R2                0                  1
  RX                0                  8

Clustering(21) Variable = 11P GAIN MUTATION ANALYSIS
D21V1, survival
                    sevent
clus2                 0  1
  11P GAIN MUTATED    3  2
  11P GAIN WILD-TYPE 58 51
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 5                109 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 2                 51 
$`11P GAIN MUTATED`
TCGA-CC-A3M9 TCGA-DD-A119 TCGA-DD-A39Y TCGA-FV-A4ZQ TCGA-G3-A3CG 
        0.10         7.33         5.59         0.39        22.13 

$`11P GAIN WILD-TYPE`
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T 
       48.99        27.91        37.32        10.13        46.78        27.52 
TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 
       27.52         2.99        25.32        23.34         1.12        69.57 
TCGA-BC-A112 TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 
        5.03        44.42        13.81         0.26        16.37         9.50 
TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A1HT 
        0.07         2.86         3.02         3.39         4.24         3.32 
TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 
        0.07         0.10         0.13        79.73        37.74        83.57 
TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D 
       53.29       112.96         2.60         0.46        21.76        51.25 
TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE 
       90.67        79.36        66.31        19.76        75.65         6.67 
TCGA-DD-A1EF TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EL TCGA-DD-A39V 
       12.95        49.15         6.02        29.16        13.64        21.14 
TCGA-DD-A39X TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 
       55.66        19.73        25.81         7.66        70.06        17.59 
TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A3A9 
       20.12       102.74       107.11        13.78         0.36        30.58 
TCGA-DD-A4NA TCGA-DD-A4ND TCGA-DD-A4NE TCGA-DD-A4NF TCGA-DD-A4NG TCGA-DD-A4NH 
       33.14        73.38        21.67        14.07        14.93        14.24 
TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO 
       10.78        15.06        39.75        56.25        29.56        61.45 
TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-ED-A459 TCGA-ED-A5KG TCGA-EP-A12J TCGA-EP-A26S 
       93.67        12.26         0.23         0.20        10.85         7.76 
TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS 
       11.74         1.97         0.62         3.19         0.43        23.01 
TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3R2 TCGA-FV-A3R3 
       14.40        32.45        19.07         0.20         6.35         0.13 
TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZP TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25U 
        0.03         0.33        60.36         1.22        51.02        53.79 
TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CH 
       28.27        30.71        58.49        14.86        21.53        25.64 
TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SJ TCGA-G3-A5SK TCGA-G3-A5SL 
        5.88        19.53        19.23        11.97         9.93         7.99 
TCGA-G3-A5SM 
        4.37 

  11P GAIN MUTATED 11P GAIN WILD-TYPE 
              0.10               0.03 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
             22.13             112.96 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
              5.59              17.59 
[1] "0.1 - 22.1 (5.6)"   "0.0 - 113.0 (17.6)"
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-BC-A5W4 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-CC-5258         TCGA-CC-5260         TCGA-CC-5261 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-CC-5262         TCGA-CC-5263         TCGA-CC-A1HT 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-CC-A3M9         TCGA-CC-A3MA         TCGA-CC-A3MB 
  "11P GAIN MUTATED" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-CC-A3MC         TCGA-DD-A113         TCGA-DD-A114 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
  "11P GAIN MUTATED" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DD-A1EA         TCGA-DD-A1EB         TCGA-DD-A1EC 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DD-A1ED         TCGA-DD-A1EE         TCGA-DD-A1EF 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DD-A1EH         TCGA-DD-A1EI         TCGA-DD-A1EJ 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DD-A1EL         TCGA-DD-A39V         TCGA-DD-A39X 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DD-A39Y         TCGA-DD-A39Z         TCGA-DD-A3A0 
  "11P GAIN MUTATED" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DD-A3A1         TCGA-DD-A3A2         TCGA-DD-A3A3 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DD-A3A4         TCGA-DD-A3A5         TCGA-DD-A3A6 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DD-A3A7         TCGA-DD-A3A8         TCGA-DD-A3A9 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DD-A4NA         TCGA-DD-A4ND         TCGA-DD-A4NE 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DD-A4NF         TCGA-DD-A4NG         TCGA-DD-A4NH 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DD-A4NI         TCGA-DD-A4NJ         TCGA-DD-A4NK 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DD-A4NL         TCGA-DD-A4NN         TCGA-DD-A4NO 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DD-A4NP         TCGA-DD-A4NQ         TCGA-ED-A459 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-ED-A5KG         TCGA-EP-A12J         TCGA-EP-A26S 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-EP-A2KA         TCGA-EP-A2KB         TCGA-EP-A2KC 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-EP-A3JL         TCGA-EP-A3RK         TCGA-ES-A2HS 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-ES-A2HT         TCGA-FV-A23B         TCGA-FV-A2QR 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-FV-A3I0         TCGA-FV-A3R2         TCGA-FV-A3R3 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-FV-A495         TCGA-FV-A496         TCGA-FV-A4ZP 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-FV-A4ZQ         TCGA-G3-A25S         TCGA-G3-A25T 
  "11P GAIN MUTATED" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-G3-A25U         TCGA-G3-A25V         TCGA-G3-A25W 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-G3-A25X         TCGA-G3-A25Y         TCGA-G3-A25Z 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-G3-A3CG         TCGA-G3-A3CH         TCGA-G3-A3CI 
  "11P GAIN MUTATED" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK         TCGA-G3-A5SJ 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-G3-A5SK         TCGA-G3-A5SL         TCGA-G3-A5SM 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-BC-A5W4 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-CC-5258         TCGA-CC-5260         TCGA-CC-5261 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-CC-5262         TCGA-CC-5263         TCGA-CC-A1HT 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-CC-A3M9         TCGA-CC-A3MA         TCGA-CC-A3MB 
  "11P GAIN MUTATED" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-CC-A3MC         TCGA-DD-A113         TCGA-DD-A114 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
  "11P GAIN MUTATED" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DD-A1EA         TCGA-DD-A1EB         TCGA-DD-A1EC 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DD-A1ED         TCGA-DD-A1EE         TCGA-DD-A1EF 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DD-A1EH         TCGA-DD-A1EI         TCGA-DD-A1EJ 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DD-A1EL         TCGA-DD-A39V         TCGA-DD-A39X 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DD-A39Y         TCGA-DD-A39Z         TCGA-DD-A3A0 
  "11P GAIN MUTATED" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DD-A3A1         TCGA-DD-A3A2         TCGA-DD-A3A3 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DD-A3A4         TCGA-DD-A3A5         TCGA-DD-A3A6 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DD-A3A7         TCGA-DD-A3A8         TCGA-DD-A3A9 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DD-A4NA         TCGA-DD-A4ND         TCGA-DD-A4NE 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DD-A4NF         TCGA-DD-A4NG         TCGA-DD-A4NH 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DD-A4NI         TCGA-DD-A4NJ         TCGA-DD-A4NK 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DD-A4NL         TCGA-DD-A4NN         TCGA-DD-A4NO 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DD-A4NP         TCGA-DD-A4NQ         TCGA-ED-A459 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-ED-A5KG         TCGA-EP-A12J         TCGA-EP-A26S 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-EP-A2KA         TCGA-EP-A2KB         TCGA-EP-A2KC 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-EP-A3JL         TCGA-EP-A3RK         TCGA-ES-A2HS 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-ES-A2HT         TCGA-FV-A23B         TCGA-FV-A2QR 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-FV-A3I0         TCGA-FV-A3R2         TCGA-FV-A3R3 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-FV-A495         TCGA-FV-A496         TCGA-FV-A4ZP 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-FV-A4ZQ         TCGA-G3-A25S         TCGA-G3-A25T 
  "11P GAIN MUTATED" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-G3-A25U         TCGA-G3-A25V         TCGA-G3-A25W 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-G3-A25X         TCGA-G3-A25Y         TCGA-G3-A25Z 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-G3-A3CG         TCGA-G3-A3CH         TCGA-G3-A3CI 
  "11P GAIN MUTATED" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK         TCGA-G3-A5SJ 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-G3-A5SK         TCGA-G3-A5SL         TCGA-G3-A5SM 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-BC-A5W4 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-CC-5258         TCGA-CC-5260         TCGA-CC-5261 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-CC-5262         TCGA-CC-5263         TCGA-CC-A1HT 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-CC-A3M9         TCGA-CC-A3MA         TCGA-CC-A3MB 
  "11P GAIN MUTATED" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-CC-A3MC         TCGA-DD-A113         TCGA-DD-A114 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
  "11P GAIN MUTATED" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DD-A1EA         TCGA-DD-A1EB         TCGA-DD-A1EC 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DD-A1ED         TCGA-DD-A1EE         TCGA-DD-A1EF 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DD-A1EH         TCGA-DD-A1EI         TCGA-DD-A1EJ 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DD-A1EL         TCGA-DD-A39V         TCGA-DD-A39X 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DD-A39Y         TCGA-DD-A39Z         TCGA-DD-A3A0 
  "11P GAIN MUTATED" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DD-A3A1         TCGA-DD-A3A2         TCGA-DD-A3A3 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DD-A3A4         TCGA-DD-A3A5         TCGA-DD-A3A6 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DD-A3A7         TCGA-DD-A3A8         TCGA-DD-A3A9 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DD-A4NA         TCGA-DD-A4ND         TCGA-DD-A4NE 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DD-A4NF         TCGA-DD-A4NG         TCGA-DD-A4NH 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DD-A4NI         TCGA-DD-A4NJ         TCGA-DD-A4NK 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DD-A4NL         TCGA-DD-A4NN         TCGA-DD-A4NO 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DD-A4NP         TCGA-DD-A4NQ         TCGA-ED-A459 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-ED-A5KG         TCGA-EP-A12J         TCGA-EP-A26S 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-EP-A2KA         TCGA-EP-A2KB         TCGA-EP-A2KC 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-EP-A3JL         TCGA-EP-A3RK         TCGA-ES-A2HS 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-ES-A2HT         TCGA-FV-A23B         TCGA-FV-A2QR 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-FV-A3I0         TCGA-FV-A3R2         TCGA-FV-A3R3 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-FV-A495         TCGA-FV-A496         TCGA-FV-A4ZP 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-FV-A4ZQ         TCGA-G3-A25S         TCGA-G3-A25T 
  "11P GAIN MUTATED" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-G3-A25U         TCGA-G3-A25V         TCGA-G3-A25W 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-G3-A25X         TCGA-G3-A25Y         TCGA-G3-A25Z 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-G3-A3CG         TCGA-G3-A3CH         TCGA-G3-A3CI 
  "11P GAIN MUTATED" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK         TCGA-G3-A5SJ 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-G3-A5SK         TCGA-G3-A5SL         TCGA-G3-A5SM 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
[1] "hr=" "2.8"
D21V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  11P GAIN MUTATED         3        0         0          1          0
  11P GAIN WILD-TYPE      42       25         2         24          3
                    vv
clus                 STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  11P GAIN MUTATED            0        1         0         0
  11P GAIN WILD-TYPE          4        0         1         1
D21V3, multiclass
                    vv
clus                 T1 T2 T3 T4
  11P GAIN MUTATED    3  0  2  0
  11P GAIN WILD-TYPE 45 28 32  6
D21V4, multiclass
    clus
vv   11P GAIN MUTATED 11P GAIN WILD-TYPE
  T1                3                 45
  T2                0                 28
  T3                2                 32
  T4                0                  6
D21V5, binary
                    cls
clus                  0  1
  11P GAIN MUTATED    3  0
  11P GAIN WILD-TYPE 71  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED      3    0
  11P GAIN WILD-TYPE   71    3
   clus
vv  11P GAIN MUTATED 11P GAIN WILD-TYPE
  0                3                 71
  1                0                  3
                    vv
clus                 M0 M1 MX
  11P GAIN MUTATED    4  1  0
  11P GAIN WILD-TYPE 86  1 25
D21V6, multiclass
    clus
vv   11P GAIN MUTATED 11P GAIN WILD-TYPE
  M0                4                 86
  M1                1                  1
  MX                0                 25
D21V7, binary
                    cls
clus                  0  1
  11P GAIN MUTATED    0  5
  11P GAIN WILD-TYPE 44 68
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED      0    5
  11P GAIN WILD-TYPE   44   68
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  FEMALE                0                 44
  MALE                  5                 68
                    vv
clus                 R0 R1 R2 RX
  11P GAIN MUTATED    3  1  1  0
  11P GAIN WILD-TYPE 90  9  0  8
D21V8, multiclass
    clus
vv   11P GAIN MUTATED 11P GAIN WILD-TYPE
  R0                3                 90
  R1                1                  9
  R2                1                  0
  RX                0                  8

Clustering(22) Variable = 11Q GAIN MUTATION ANALYSIS
D22V1, survival
                    sevent
clus2                 0  1
  11Q GAIN MUTATED    1  3
  11Q GAIN WILD-TYPE 60 50
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 4                110 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 3                 50 
$`11Q GAIN MUTATED`
TCGA-DD-A119 TCGA-DD-A39Y TCGA-DD-A3A0 TCGA-G3-A3CG 
        7.33         5.59        25.81        22.13 

$`11Q GAIN WILD-TYPE`
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T 
       48.99        27.91        37.32        10.13        46.78        27.52 
TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 
       27.52         2.99        25.32        23.34         1.12        69.57 
TCGA-BC-A112 TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 
        5.03        44.42        13.81         0.26        16.37         9.50 
TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A1HT 
        0.07         2.86         3.02         3.39         4.24         3.32 
TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A113 TCGA-DD-A114 
        0.10         0.07         0.10         0.13        79.73        37.74 
TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C 
       83.57        53.29       112.96         2.60         0.46        21.76 
TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED 
       51.25        90.67        79.36        66.31        19.76        75.65 
TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EL 
        6.67        12.95        49.15         6.02        29.16        13.64 
TCGA-DD-A39V TCGA-DD-A39X TCGA-DD-A39Z TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 
       21.14        55.66        19.73         7.66        70.06        17.59 
TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A3A9 
       20.12       102.74       107.11        13.78         0.36        30.58 
TCGA-DD-A4NA TCGA-DD-A4ND TCGA-DD-A4NE TCGA-DD-A4NF TCGA-DD-A4NG TCGA-DD-A4NH 
       33.14        73.38        21.67        14.07        14.93        14.24 
TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO 
       10.78        15.06        39.75        56.25        29.56        61.45 
TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-ED-A459 TCGA-ED-A5KG TCGA-EP-A12J TCGA-EP-A26S 
       93.67        12.26         0.23         0.20        10.85         7.76 
TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS 
       11.74         1.97         0.62         3.19         0.43        23.01 
TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3R2 TCGA-FV-A3R3 
       14.40        32.45        19.07         0.20         6.35         0.13 
TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T 
        0.03         0.33        60.36         0.39         1.22        51.02 
TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A25Z 
       53.79        28.27        30.71        58.49        14.86        21.53 
TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SJ TCGA-G3-A5SK 
       25.64         5.88        19.53        19.23        11.97         9.93 
TCGA-G3-A5SL TCGA-G3-A5SM 
        7.99         4.37 

  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
              5.59               0.03 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
             25.81             112.96 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
            14.730             15.715 
[1] "5.6 - 25.8 (14.7)"  "0.0 - 113.0 (15.7)"
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-BC-A5W4 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-CC-5258         TCGA-CC-5260         TCGA-CC-5261 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-CC-5262         TCGA-CC-5263         TCGA-CC-A1HT 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-CC-A3M9         TCGA-CC-A3MA         TCGA-CC-A3MB 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-CC-A3MC         TCGA-DD-A113         TCGA-DD-A114 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
  "11Q GAIN MUTATED" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DD-A1EA         TCGA-DD-A1EB         TCGA-DD-A1EC 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DD-A1ED         TCGA-DD-A1EE         TCGA-DD-A1EF 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DD-A1EH         TCGA-DD-A1EI         TCGA-DD-A1EJ 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DD-A1EL         TCGA-DD-A39V         TCGA-DD-A39X 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DD-A39Y         TCGA-DD-A39Z         TCGA-DD-A3A0 
  "11Q GAIN MUTATED" "11Q GAIN WILD-TYPE"   "11Q GAIN MUTATED" 
        TCGA-DD-A3A1         TCGA-DD-A3A2         TCGA-DD-A3A3 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DD-A3A4         TCGA-DD-A3A5         TCGA-DD-A3A6 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DD-A3A7         TCGA-DD-A3A8         TCGA-DD-A3A9 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DD-A4NA         TCGA-DD-A4ND         TCGA-DD-A4NE 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DD-A4NF         TCGA-DD-A4NG         TCGA-DD-A4NH 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DD-A4NI         TCGA-DD-A4NJ         TCGA-DD-A4NK 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DD-A4NL         TCGA-DD-A4NN         TCGA-DD-A4NO 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DD-A4NP         TCGA-DD-A4NQ         TCGA-ED-A459 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-ED-A5KG         TCGA-EP-A12J         TCGA-EP-A26S 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EP-A2KA         TCGA-EP-A2KB         TCGA-EP-A2KC 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EP-A3JL         TCGA-EP-A3RK         TCGA-ES-A2HS 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-ES-A2HT         TCGA-FV-A23B         TCGA-FV-A2QR 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-FV-A3I0         TCGA-FV-A3R2         TCGA-FV-A3R3 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-FV-A495         TCGA-FV-A496         TCGA-FV-A4ZP 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-FV-A4ZQ         TCGA-G3-A25S         TCGA-G3-A25T 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-G3-A25U         TCGA-G3-A25V         TCGA-G3-A25W 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-G3-A25X         TCGA-G3-A25Y         TCGA-G3-A25Z 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-G3-A3CG         TCGA-G3-A3CH         TCGA-G3-A3CI 
  "11Q GAIN MUTATED" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK         TCGA-G3-A5SJ 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-G3-A5SK         TCGA-G3-A5SL         TCGA-G3-A5SM 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-BC-A5W4 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-CC-5258         TCGA-CC-5260         TCGA-CC-5261 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-CC-5262         TCGA-CC-5263         TCGA-CC-A1HT 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-CC-A3M9         TCGA-CC-A3MA         TCGA-CC-A3MB 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-CC-A3MC         TCGA-DD-A113         TCGA-DD-A114 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
  "11Q GAIN MUTATED" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DD-A1EA         TCGA-DD-A1EB         TCGA-DD-A1EC 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DD-A1ED         TCGA-DD-A1EE         TCGA-DD-A1EF 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DD-A1EH         TCGA-DD-A1EI         TCGA-DD-A1EJ 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DD-A1EL         TCGA-DD-A39V         TCGA-DD-A39X 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DD-A39Y         TCGA-DD-A39Z         TCGA-DD-A3A0 
  "11Q GAIN MUTATED" "11Q GAIN WILD-TYPE"   "11Q GAIN MUTATED" 
        TCGA-DD-A3A1         TCGA-DD-A3A2         TCGA-DD-A3A3 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DD-A3A4         TCGA-DD-A3A5         TCGA-DD-A3A6 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DD-A3A7         TCGA-DD-A3A8         TCGA-DD-A3A9 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DD-A4NA         TCGA-DD-A4ND         TCGA-DD-A4NE 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DD-A4NF         TCGA-DD-A4NG         TCGA-DD-A4NH 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DD-A4NI         TCGA-DD-A4NJ         TCGA-DD-A4NK 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DD-A4NL         TCGA-DD-A4NN         TCGA-DD-A4NO 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DD-A4NP         TCGA-DD-A4NQ         TCGA-ED-A459 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-ED-A5KG         TCGA-EP-A12J         TCGA-EP-A26S 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EP-A2KA         TCGA-EP-A2KB         TCGA-EP-A2KC 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EP-A3JL         TCGA-EP-A3RK         TCGA-ES-A2HS 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-ES-A2HT         TCGA-FV-A23B         TCGA-FV-A2QR 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-FV-A3I0         TCGA-FV-A3R2         TCGA-FV-A3R3 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-FV-A495         TCGA-FV-A496         TCGA-FV-A4ZP 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-FV-A4ZQ         TCGA-G3-A25S         TCGA-G3-A25T 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-G3-A25U         TCGA-G3-A25V         TCGA-G3-A25W 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-G3-A25X         TCGA-G3-A25Y         TCGA-G3-A25Z 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-G3-A3CG         TCGA-G3-A3CH         TCGA-G3-A3CI 
  "11Q GAIN MUTATED" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK         TCGA-G3-A5SJ 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-G3-A5SK         TCGA-G3-A5SL         TCGA-G3-A5SM 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-BC-A5W4 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-CC-5258         TCGA-CC-5260         TCGA-CC-5261 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-CC-5262         TCGA-CC-5263         TCGA-CC-A1HT 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-CC-A3M9         TCGA-CC-A3MA         TCGA-CC-A3MB 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-CC-A3MC         TCGA-DD-A113         TCGA-DD-A114 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
  "11Q GAIN MUTATED" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DD-A1EA         TCGA-DD-A1EB         TCGA-DD-A1EC 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DD-A1ED         TCGA-DD-A1EE         TCGA-DD-A1EF 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DD-A1EH         TCGA-DD-A1EI         TCGA-DD-A1EJ 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DD-A1EL         TCGA-DD-A39V         TCGA-DD-A39X 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DD-A39Y         TCGA-DD-A39Z         TCGA-DD-A3A0 
  "11Q GAIN MUTATED" "11Q GAIN WILD-TYPE"   "11Q GAIN MUTATED" 
        TCGA-DD-A3A1         TCGA-DD-A3A2         TCGA-DD-A3A3 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DD-A3A4         TCGA-DD-A3A5         TCGA-DD-A3A6 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DD-A3A7         TCGA-DD-A3A8         TCGA-DD-A3A9 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DD-A4NA         TCGA-DD-A4ND         TCGA-DD-A4NE 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DD-A4NF         TCGA-DD-A4NG         TCGA-DD-A4NH 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DD-A4NI         TCGA-DD-A4NJ         TCGA-DD-A4NK 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DD-A4NL         TCGA-DD-A4NN         TCGA-DD-A4NO 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DD-A4NP         TCGA-DD-A4NQ         TCGA-ED-A459 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-ED-A5KG         TCGA-EP-A12J         TCGA-EP-A26S 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EP-A2KA         TCGA-EP-A2KB         TCGA-EP-A2KC 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EP-A3JL         TCGA-EP-A3RK         TCGA-ES-A2HS 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-ES-A2HT         TCGA-FV-A23B         TCGA-FV-A2QR 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-FV-A3I0         TCGA-FV-A3R2         TCGA-FV-A3R3 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-FV-A495         TCGA-FV-A496         TCGA-FV-A4ZP 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-FV-A4ZQ         TCGA-G3-A25S         TCGA-G3-A25T 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-G3-A25U         TCGA-G3-A25V         TCGA-G3-A25W 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-G3-A25X         TCGA-G3-A25Y         TCGA-G3-A25Z 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-G3-A3CG         TCGA-G3-A3CH         TCGA-G3-A3CI 
  "11Q GAIN MUTATED" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK         TCGA-G3-A5SJ 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-G3-A5SK         TCGA-G3-A5SL         TCGA-G3-A5SM 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
[1] "hr=" "2.6"
D22V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  11Q GAIN MUTATED         3        0         0          0          0
  11Q GAIN WILD-TYPE      42       25         2         25          3
                    vv
clus                 STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  11Q GAIN MUTATED            0        1         0         0
  11Q GAIN WILD-TYPE          4        0         1         1
D22V3, multiclass
                    vv
clus                 T1 T2 T3 T4
  11Q GAIN MUTATED    3  0  1  0
  11Q GAIN WILD-TYPE 45 28 33  6
D22V4, multiclass
    clus
vv   11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  T1                3                 45
  T2                0                 28
  T3                1                 33
  T4                0                  6
D22V5, binary
                    cls
clus                  0  1
  11Q GAIN MUTATED    2  0
  11Q GAIN WILD-TYPE 72  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED      2    0
  11Q GAIN WILD-TYPE   72    3
   clus
vv  11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  0                2                 72
  1                0                  3
                    vv
clus                 M0 M1 MX
  11Q GAIN MUTATED    3  1  0
  11Q GAIN WILD-TYPE 87  1 25
D22V6, multiclass
    clus
vv   11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  M0                3                 87
  M1                1                  1
  MX                0                 25
D22V7, binary
                    cls
clus                  0  1
  11Q GAIN MUTATED    0  4
  11Q GAIN WILD-TYPE 44 69
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED      0    4
  11Q GAIN WILD-TYPE   44   69
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  FEMALE                0                 44
  MALE                  4                 69
                    vv
clus                 R0 R1 R2 RX
  11Q GAIN MUTATED    2  1  1  0
  11Q GAIN WILD-TYPE 91  9  0  8
D22V8, multiclass
    clus
vv   11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  R0                2                 91
  R1                1                  9
  R2                1                  0
  RX                0                  8

Clustering(23) Variable = 12P GAIN MUTATION ANALYSIS
D23V1, survival
                    sevent
clus2                 0  1
  12P GAIN MUTATED    5  2
  12P GAIN WILD-TYPE 56 51
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                 7                107 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                 2                 51 
$`12P GAIN MUTATED`
TCGA-DD-A11A TCGA-DD-A1EF TCGA-DD-A3A7 TCGA-EP-A3JL TCGA-FV-A3I0 TCGA-G3-A25T 
        2.60        12.95        13.78         3.19         0.20        51.02 
TCGA-G3-A25X 
       58.49 

$`12P GAIN WILD-TYPE`
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T 
       48.99        27.91        37.32        10.13        46.78        27.52 
TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 
       27.52         2.99        25.32        23.34         1.12        69.57 
TCGA-BC-A112 TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 
        5.03        44.42        13.81         0.26        16.37         9.50 
TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A1HT 
        0.07         2.86         3.02         3.39         4.24         3.32 
TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A113 TCGA-DD-A114 
        0.10         0.07         0.10         0.13        79.73        37.74 
TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11B TCGA-DD-A11C 
       83.57        53.29       112.96         7.33         0.46        21.76 
TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED 
       51.25        90.67        79.36        66.31        19.76        75.65 
TCGA-DD-A1EE TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EL TCGA-DD-A39V 
        6.67        49.15         6.02        29.16        13.64        21.14 
TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 
       55.66         5.59        19.73        25.81         7.66        70.06 
TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A8 TCGA-DD-A3A9 
       17.59        20.12       102.74       107.11         0.36        30.58 
TCGA-DD-A4NA TCGA-DD-A4ND TCGA-DD-A4NE TCGA-DD-A4NF TCGA-DD-A4NG TCGA-DD-A4NH 
       33.14        73.38        21.67        14.07        14.93        14.24 
TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO 
       10.78        15.06        39.75        56.25        29.56        61.45 
TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-ED-A459 TCGA-ED-A5KG TCGA-EP-A12J TCGA-EP-A26S 
       93.67        12.26         0.23         0.20        10.85         7.76 
TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT 
       11.74         1.97         0.62         0.43        23.01        14.40 
TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 
       32.45        19.07         6.35         0.13         0.03         0.33 
TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W 
       60.36         0.39         1.22        53.79        28.27        30.71 
TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ 
       14.86        21.53        22.13        25.64         5.88        19.53 
TCGA-G3-A3CK TCGA-G3-A5SJ TCGA-G3-A5SK TCGA-G3-A5SL TCGA-G3-A5SM 
       19.23        11.97         9.93         7.99         4.37 

  12P GAIN MUTATED 12P GAIN WILD-TYPE 
              0.20               0.03 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
             58.49             112.96 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
             12.95              17.59 
[1] "0.2 - 58.5 (12.9)"  "0.0 - 113.0 (17.6)"
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-BC-A5W4 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-CC-5258         TCGA-CC-5260         TCGA-CC-5261 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-CC-5262         TCGA-CC-5263         TCGA-CC-A1HT 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-CC-A3M9         TCGA-CC-A3MA         TCGA-CC-A3MB 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-CC-A3MC         TCGA-DD-A113         TCGA-DD-A114 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"12P GAIN WILD-TYPE"   "12P GAIN MUTATED" "12P GAIN WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-DD-A1EA         TCGA-DD-A1EB         TCGA-DD-A1EC 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-DD-A1ED         TCGA-DD-A1EE         TCGA-DD-A1EF 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE"   "12P GAIN MUTATED" 
        TCGA-DD-A1EH         TCGA-DD-A1EI         TCGA-DD-A1EJ 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-DD-A1EL         TCGA-DD-A39V         TCGA-DD-A39X 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-DD-A39Y         TCGA-DD-A39Z         TCGA-DD-A3A0 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-DD-A3A1         TCGA-DD-A3A2         TCGA-DD-A3A3 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-DD-A3A4         TCGA-DD-A3A5         TCGA-DD-A3A6 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-DD-A3A7         TCGA-DD-A3A8         TCGA-DD-A3A9 
  "12P GAIN MUTATED" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-DD-A4NA         TCGA-DD-A4ND         TCGA-DD-A4NE 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-DD-A4NF         TCGA-DD-A4NG         TCGA-DD-A4NH 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-DD-A4NI         TCGA-DD-A4NJ         TCGA-DD-A4NK 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-DD-A4NL         TCGA-DD-A4NN         TCGA-DD-A4NO 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-DD-A4NP         TCGA-DD-A4NQ         TCGA-ED-A459 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-ED-A5KG         TCGA-EP-A12J         TCGA-EP-A26S 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-EP-A2KA         TCGA-EP-A2KB         TCGA-EP-A2KC 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-EP-A3JL         TCGA-EP-A3RK         TCGA-ES-A2HS 
  "12P GAIN MUTATED" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-ES-A2HT         TCGA-FV-A23B         TCGA-FV-A2QR 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-FV-A3I0         TCGA-FV-A3R2         TCGA-FV-A3R3 
  "12P GAIN MUTATED" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-FV-A495         TCGA-FV-A496         TCGA-FV-A4ZP 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-FV-A4ZQ         TCGA-G3-A25S         TCGA-G3-A25T 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE"   "12P GAIN MUTATED" 
        TCGA-G3-A25U         TCGA-G3-A25V         TCGA-G3-A25W 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-G3-A25X         TCGA-G3-A25Y         TCGA-G3-A25Z 
  "12P GAIN MUTATED" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-G3-A3CG         TCGA-G3-A3CH         TCGA-G3-A3CI 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK         TCGA-G3-A5SJ 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-G3-A5SK         TCGA-G3-A5SL         TCGA-G3-A5SM 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-BC-A5W4 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-CC-5258         TCGA-CC-5260         TCGA-CC-5261 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-CC-5262         TCGA-CC-5263         TCGA-CC-A1HT 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-CC-A3M9         TCGA-CC-A3MA         TCGA-CC-A3MB 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-CC-A3MC         TCGA-DD-A113         TCGA-DD-A114 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"12P GAIN WILD-TYPE"   "12P GAIN MUTATED" "12P GAIN WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-DD-A1EA         TCGA-DD-A1EB         TCGA-DD-A1EC 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-DD-A1ED         TCGA-DD-A1EE         TCGA-DD-A1EF 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE"   "12P GAIN MUTATED" 
        TCGA-DD-A1EH         TCGA-DD-A1EI         TCGA-DD-A1EJ 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-DD-A1EL         TCGA-DD-A39V         TCGA-DD-A39X 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-DD-A39Y         TCGA-DD-A39Z         TCGA-DD-A3A0 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-DD-A3A1         TCGA-DD-A3A2         TCGA-DD-A3A3 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-DD-A3A4         TCGA-DD-A3A5         TCGA-DD-A3A6 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-DD-A3A7         TCGA-DD-A3A8         TCGA-DD-A3A9 
  "12P GAIN MUTATED" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-DD-A4NA         TCGA-DD-A4ND         TCGA-DD-A4NE 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-DD-A4NF         TCGA-DD-A4NG         TCGA-DD-A4NH 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-DD-A4NI         TCGA-DD-A4NJ         TCGA-DD-A4NK 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-DD-A4NL         TCGA-DD-A4NN         TCGA-DD-A4NO 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-DD-A4NP         TCGA-DD-A4NQ         TCGA-ED-A459 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-ED-A5KG         TCGA-EP-A12J         TCGA-EP-A26S 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-EP-A2KA         TCGA-EP-A2KB         TCGA-EP-A2KC 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-EP-A3JL         TCGA-EP-A3RK         TCGA-ES-A2HS 
  "12P GAIN MUTATED" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-ES-A2HT         TCGA-FV-A23B         TCGA-FV-A2QR 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-FV-A3I0         TCGA-FV-A3R2         TCGA-FV-A3R3 
  "12P GAIN MUTATED" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-FV-A495         TCGA-FV-A496         TCGA-FV-A4ZP 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-FV-A4ZQ         TCGA-G3-A25S         TCGA-G3-A25T 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE"   "12P GAIN MUTATED" 
        TCGA-G3-A25U         TCGA-G3-A25V         TCGA-G3-A25W 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-G3-A25X         TCGA-G3-A25Y         TCGA-G3-A25Z 
  "12P GAIN MUTATED" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-G3-A3CG         TCGA-G3-A3CH         TCGA-G3-A3CI 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK         TCGA-G3-A5SJ 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-G3-A5SK         TCGA-G3-A5SL         TCGA-G3-A5SM 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-BC-A5W4 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-CC-5258         TCGA-CC-5260         TCGA-CC-5261 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-CC-5262         TCGA-CC-5263         TCGA-CC-A1HT 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-CC-A3M9         TCGA-CC-A3MA         TCGA-CC-A3MB 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-CC-A3MC         TCGA-DD-A113         TCGA-DD-A114 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"12P GAIN WILD-TYPE"   "12P GAIN MUTATED" "12P GAIN WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-DD-A1EA         TCGA-DD-A1EB         TCGA-DD-A1EC 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-DD-A1ED         TCGA-DD-A1EE         TCGA-DD-A1EF 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE"   "12P GAIN MUTATED" 
        TCGA-DD-A1EH         TCGA-DD-A1EI         TCGA-DD-A1EJ 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-DD-A1EL         TCGA-DD-A39V         TCGA-DD-A39X 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-DD-A39Y         TCGA-DD-A39Z         TCGA-DD-A3A0 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-DD-A3A1         TCGA-DD-A3A2         TCGA-DD-A3A3 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-DD-A3A4         TCGA-DD-A3A5         TCGA-DD-A3A6 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-DD-A3A7         TCGA-DD-A3A8         TCGA-DD-A3A9 
  "12P GAIN MUTATED" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-DD-A4NA         TCGA-DD-A4ND         TCGA-DD-A4NE 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-DD-A4NF         TCGA-DD-A4NG         TCGA-DD-A4NH 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-DD-A4NI         TCGA-DD-A4NJ         TCGA-DD-A4NK 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-DD-A4NL         TCGA-DD-A4NN         TCGA-DD-A4NO 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-DD-A4NP         TCGA-DD-A4NQ         TCGA-ED-A459 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-ED-A5KG         TCGA-EP-A12J         TCGA-EP-A26S 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-EP-A2KA         TCGA-EP-A2KB         TCGA-EP-A2KC 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-EP-A3JL         TCGA-EP-A3RK         TCGA-ES-A2HS 
  "12P GAIN MUTATED" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-ES-A2HT         TCGA-FV-A23B         TCGA-FV-A2QR 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-FV-A3I0         TCGA-FV-A3R2         TCGA-FV-A3R3 
  "12P GAIN MUTATED" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-FV-A495         TCGA-FV-A496         TCGA-FV-A4ZP 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-FV-A4ZQ         TCGA-G3-A25S         TCGA-G3-A25T 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE"   "12P GAIN MUTATED" 
        TCGA-G3-A25U         TCGA-G3-A25V         TCGA-G3-A25W 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-G3-A25X         TCGA-G3-A25Y         TCGA-G3-A25Z 
  "12P GAIN MUTATED" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-G3-A3CG         TCGA-G3-A3CH         TCGA-G3-A3CI 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK         TCGA-G3-A5SJ 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-G3-A5SK         TCGA-G3-A5SL         TCGA-G3-A5SM 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
[1] "hr=" "1.2"
D23V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  12P GAIN MUTATED         3        2         0          1          1
  12P GAIN WILD-TYPE      42       23         2         24          2
                    vv
clus                 STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  12P GAIN MUTATED            0        0         0         0
  12P GAIN WILD-TYPE          4        1         1         1
D23V3, multiclass
                    vv
clus                 T1 T2 T3 T4
  12P GAIN MUTATED    3  2  2  0
  12P GAIN WILD-TYPE 45 26 32  6
D23V4, multiclass
    clus
vv   12P GAIN MUTATED 12P GAIN WILD-TYPE
  T1                3                 45
  T2                2                 26
  T3                2                 32
  T4                0                  6
D23V5, binary
                    cls
clus                  0  1
  12P GAIN MUTATED    6  0
  12P GAIN WILD-TYPE 68  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED      6    0
  12P GAIN WILD-TYPE   68    3
   clus
vv  12P GAIN MUTATED 12P GAIN WILD-TYPE
  0                6                 68
  1                0                  3
                    vv
clus                 M0 M1 MX
  12P GAIN MUTATED    7  0  1
  12P GAIN WILD-TYPE 83  2 24
D23V6, multiclass
    clus
vv   12P GAIN MUTATED 12P GAIN WILD-TYPE
  M0                7                 83
  M1                0                  2
  MX                1                 24
D23V7, binary
                    cls
clus                  0  1
  12P GAIN MUTATED    3  5
  12P GAIN WILD-TYPE 41 68
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED      3    5
  12P GAIN WILD-TYPE   41   68
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  FEMALE                3                 41
  MALE                  5                 68
                    vv
clus                 R0 R1 R2 RX
  12P GAIN MUTATED    6  0  0  1
  12P GAIN WILD-TYPE 87 10  1  7
D23V8, multiclass
    clus
vv   12P GAIN MUTATED 12P GAIN WILD-TYPE
  R0                6                 87
  R1                0                 10
  R2                0                  1
  RX                1                  7

Clustering(24) Variable = 12Q GAIN MUTATION ANALYSIS
D24V1, survival
                    sevent
clus2                 0  1
  12Q GAIN MUTATED    8  3
  12Q GAIN WILD-TYPE 53 50
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                11                103 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                 3                 50 
$`12Q GAIN MUTATED`
TCGA-BC-A3KF TCGA-DD-A11A TCGA-DD-A1EF TCGA-DD-A1EJ TCGA-DD-A3A7 TCGA-DD-A4ND 
        0.26         2.60        12.95        29.16        13.78        73.38 
TCGA-DD-A4NH TCGA-EP-A3JL TCGA-FV-A3I0 TCGA-G3-A25T TCGA-G3-A25X 
       14.24         3.19         0.20        51.02        58.49 

$`12Q GAIN WILD-TYPE`
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T 
       48.99        27.91        37.32        10.13        46.78        27.52 
TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 
       27.52         2.99        25.32        23.34         1.12        69.57 
TCGA-BC-A112 TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-CC-5258 
        5.03        44.42        13.81        16.37         9.50         0.07 
TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3M9 
        2.86         3.02         3.39         4.24         3.32         0.10 
TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 
        0.07         0.10         0.13        79.73        37.74        83.57 
TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D 
       53.29       112.96         7.33         0.46        21.76        51.25 
TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE 
       90.67        79.36        66.31        19.76        75.65         6.67 
TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39X TCGA-DD-A39Y 
       49.15         6.02        13.64        21.14        55.66         5.59 
TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 
       19.73        25.81         7.66        70.06        17.59        20.12 
TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A8 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NE 
      102.74       107.11         0.36        30.58        33.14        21.67 
TCGA-DD-A4NF TCGA-DD-A4NG TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL 
       14.07        14.93        10.78        15.06        39.75        56.25 
TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-ED-A459 TCGA-ED-A5KG 
       29.56        61.45        93.67        12.26         0.23         0.20 
TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3RK 
       10.85         7.76        11.74         1.97         0.62         0.43 
TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-A3R2 TCGA-FV-A3R3 
       23.01        14.40        32.45        19.07         6.35         0.13 
TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25U 
        0.03         0.33        60.36         0.39         1.22        53.79 
TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CH 
       28.27        30.71        14.86        21.53        22.13        25.64 
TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SJ TCGA-G3-A5SK TCGA-G3-A5SL 
        5.88        19.53        19.23        11.97         9.93         7.99 
TCGA-G3-A5SM 
        4.37 

  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
              0.20               0.03 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
             73.38             112.96 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
             13.78              17.59 
[1] "0.2 - 73.4 (13.8)"  "0.0 - 113.0 (17.6)"
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-BC-A5W4 
  "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-CC-5258         TCGA-CC-5260         TCGA-CC-5261 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-CC-5262         TCGA-CC-5263         TCGA-CC-A1HT 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-CC-A3M9         TCGA-CC-A3MA         TCGA-CC-A3MB 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-CC-A3MC         TCGA-DD-A113         TCGA-DD-A114 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DD-A1EA         TCGA-DD-A1EB         TCGA-DD-A1EC 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DD-A1ED         TCGA-DD-A1EE         TCGA-DD-A1EF 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" 
        TCGA-DD-A1EH         TCGA-DD-A1EI         TCGA-DD-A1EJ 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" 
        TCGA-DD-A1EL         TCGA-DD-A39V         TCGA-DD-A39X 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DD-A39Y         TCGA-DD-A39Z         TCGA-DD-A3A0 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DD-A3A1         TCGA-DD-A3A2         TCGA-DD-A3A3 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DD-A3A4         TCGA-DD-A3A5         TCGA-DD-A3A6 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DD-A3A7         TCGA-DD-A3A8         TCGA-DD-A3A9 
  "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DD-A4NA         TCGA-DD-A4ND         TCGA-DD-A4NE 
"12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" 
        TCGA-DD-A4NF         TCGA-DD-A4NG         TCGA-DD-A4NH 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" 
        TCGA-DD-A4NI         TCGA-DD-A4NJ         TCGA-DD-A4NK 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DD-A4NL         TCGA-DD-A4NN         TCGA-DD-A4NO 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DD-A4NP         TCGA-DD-A4NQ         TCGA-ED-A459 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-ED-A5KG         TCGA-EP-A12J         TCGA-EP-A26S 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EP-A2KA         TCGA-EP-A2KB         TCGA-EP-A2KC 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EP-A3JL         TCGA-EP-A3RK         TCGA-ES-A2HS 
  "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-ES-A2HT         TCGA-FV-A23B         TCGA-FV-A2QR 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-FV-A3I0         TCGA-FV-A3R2         TCGA-FV-A3R3 
  "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-FV-A495         TCGA-FV-A496         TCGA-FV-A4ZP 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-FV-A4ZQ         TCGA-G3-A25S         TCGA-G3-A25T 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" 
        TCGA-G3-A25U         TCGA-G3-A25V         TCGA-G3-A25W 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-G3-A25X         TCGA-G3-A25Y         TCGA-G3-A25Z 
  "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-G3-A3CG         TCGA-G3-A3CH         TCGA-G3-A3CI 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK         TCGA-G3-A5SJ 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-G3-A5SK         TCGA-G3-A5SL         TCGA-G3-A5SM 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-BC-A5W4 
  "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-CC-5258         TCGA-CC-5260         TCGA-CC-5261 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-CC-5262         TCGA-CC-5263         TCGA-CC-A1HT 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-CC-A3M9         TCGA-CC-A3MA         TCGA-CC-A3MB 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-CC-A3MC         TCGA-DD-A113         TCGA-DD-A114 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DD-A1EA         TCGA-DD-A1EB         TCGA-DD-A1EC 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DD-A1ED         TCGA-DD-A1EE         TCGA-DD-A1EF 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" 
        TCGA-DD-A1EH         TCGA-DD-A1EI         TCGA-DD-A1EJ 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" 
        TCGA-DD-A1EL         TCGA-DD-A39V         TCGA-DD-A39X 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DD-A39Y         TCGA-DD-A39Z         TCGA-DD-A3A0 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DD-A3A1         TCGA-DD-A3A2         TCGA-DD-A3A3 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DD-A3A4         TCGA-DD-A3A5         TCGA-DD-A3A6 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DD-A3A7         TCGA-DD-A3A8         TCGA-DD-A3A9 
  "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DD-A4NA         TCGA-DD-A4ND         TCGA-DD-A4NE 
"12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" 
        TCGA-DD-A4NF         TCGA-DD-A4NG         TCGA-DD-A4NH 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" 
        TCGA-DD-A4NI         TCGA-DD-A4NJ         TCGA-DD-A4NK 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DD-A4NL         TCGA-DD-A4NN         TCGA-DD-A4NO 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DD-A4NP         TCGA-DD-A4NQ         TCGA-ED-A459 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-ED-A5KG         TCGA-EP-A12J         TCGA-EP-A26S 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EP-A2KA         TCGA-EP-A2KB         TCGA-EP-A2KC 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EP-A3JL         TCGA-EP-A3RK         TCGA-ES-A2HS 
  "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-ES-A2HT         TCGA-FV-A23B         TCGA-FV-A2QR 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-FV-A3I0         TCGA-FV-A3R2         TCGA-FV-A3R3 
  "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-FV-A495         TCGA-FV-A496         TCGA-FV-A4ZP 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-FV-A4ZQ         TCGA-G3-A25S         TCGA-G3-A25T 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" 
        TCGA-G3-A25U         TCGA-G3-A25V         TCGA-G3-A25W 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-G3-A25X         TCGA-G3-A25Y         TCGA-G3-A25Z 
  "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-G3-A3CG         TCGA-G3-A3CH         TCGA-G3-A3CI 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK         TCGA-G3-A5SJ 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-G3-A5SK         TCGA-G3-A5SL         TCGA-G3-A5SM 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-BC-A5W4 
  "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-CC-5258         TCGA-CC-5260         TCGA-CC-5261 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-CC-5262         TCGA-CC-5263         TCGA-CC-A1HT 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-CC-A3M9         TCGA-CC-A3MA         TCGA-CC-A3MB 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-CC-A3MC         TCGA-DD-A113         TCGA-DD-A114 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DD-A1EA         TCGA-DD-A1EB         TCGA-DD-A1EC 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DD-A1ED         TCGA-DD-A1EE         TCGA-DD-A1EF 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" 
        TCGA-DD-A1EH         TCGA-DD-A1EI         TCGA-DD-A1EJ 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" 
        TCGA-DD-A1EL         TCGA-DD-A39V         TCGA-DD-A39X 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DD-A39Y         TCGA-DD-A39Z         TCGA-DD-A3A0 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DD-A3A1         TCGA-DD-A3A2         TCGA-DD-A3A3 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DD-A3A4         TCGA-DD-A3A5         TCGA-DD-A3A6 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DD-A3A7         TCGA-DD-A3A8         TCGA-DD-A3A9 
  "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DD-A4NA         TCGA-DD-A4ND         TCGA-DD-A4NE 
"12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" 
        TCGA-DD-A4NF         TCGA-DD-A4NG         TCGA-DD-A4NH 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" 
        TCGA-DD-A4NI         TCGA-DD-A4NJ         TCGA-DD-A4NK 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DD-A4NL         TCGA-DD-A4NN         TCGA-DD-A4NO 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DD-A4NP         TCGA-DD-A4NQ         TCGA-ED-A459 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-ED-A5KG         TCGA-EP-A12J         TCGA-EP-A26S 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EP-A2KA         TCGA-EP-A2KB         TCGA-EP-A2KC 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EP-A3JL         TCGA-EP-A3RK         TCGA-ES-A2HS 
  "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-ES-A2HT         TCGA-FV-A23B         TCGA-FV-A2QR 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-FV-A3I0         TCGA-FV-A3R2         TCGA-FV-A3R3 
  "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-FV-A495         TCGA-FV-A496         TCGA-FV-A4ZP 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-FV-A4ZQ         TCGA-G3-A25S         TCGA-G3-A25T 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" 
        TCGA-G3-A25U         TCGA-G3-A25V         TCGA-G3-A25W 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-G3-A25X         TCGA-G3-A25Y         TCGA-G3-A25Z 
  "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-G3-A3CG         TCGA-G3-A3CH         TCGA-G3-A3CI 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK         TCGA-G3-A5SJ 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-G3-A5SK         TCGA-G3-A5SL         TCGA-G3-A5SM 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
[1] "hr=" "1.5"
D24V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  12Q GAIN MUTATED         5        2         0          1          2
  12Q GAIN WILD-TYPE      40       23         2         24          1
                    vv
clus                 STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  12Q GAIN MUTATED            1        0         0         0
  12Q GAIN WILD-TYPE          3        1         1         1
D24V3, multiclass
                    vv
clus                 T1 T2 T3 T4
  12Q GAIN MUTATED    6  2  3  0
  12Q GAIN WILD-TYPE 42 26 31  6
D24V4, multiclass
    clus
vv   12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  T1                6                 42
  T2                2                 26
  T3                3                 31
  T4                0                  6
D24V5, binary
                    cls
clus                  0  1
  12Q GAIN MUTATED    8  1
  12Q GAIN WILD-TYPE 66  2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED      8    1
  12Q GAIN WILD-TYPE   66    2
   clus
vv  12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  0                8                 66
  1                1                  2
                    vv
clus                 M0 M1 MX
  12Q GAIN MUTATED   11  0  1
  12Q GAIN WILD-TYPE 79  2 24
D24V6, multiclass
    clus
vv   12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  M0               11                 79
  M1                0                  2
  MX                1                 24
D24V7, binary
                    cls
clus                  0  1
  12Q GAIN MUTATED    7  5
  12Q GAIN WILD-TYPE 37 68
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED      7    5
  12Q GAIN WILD-TYPE   37   68
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  FEMALE                7                 37
  MALE                  5                 68
                    vv
clus                 R0 R1 R2 RX
  12Q GAIN MUTATED   10  0  0  1
  12Q GAIN WILD-TYPE 83 10  1  7
D24V8, multiclass
    clus
vv   12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  R0               10                 83
  R1                0                 10
  R2                0                  1
  RX                1                  7

Clustering(25) Variable = 13Q GAIN MUTATION ANALYSIS
D25V1, survival
                    sevent
clus2                 0  1
  13Q GAIN MUTATED    5  4
  13Q GAIN WILD-TYPE 56 49
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                 9                105 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                 4                 49 
$`13Q GAIN MUTATED`
TCGA-BC-A3KF TCGA-CC-5263 TCGA-DD-A1EJ TCGA-DD-A39Y TCGA-DD-A3A7 TCGA-DD-A4NI 
        0.26         4.24        29.16         5.59        13.78        10.78 
TCGA-EP-A3JL TCGA-FV-A23B TCGA-FV-A496 
        3.19        32.45         0.33 

$`13Q GAIN WILD-TYPE`
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T 
       48.99        27.91        37.32        10.13        46.78        27.52 
TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 
       27.52         2.99        25.32        23.34         1.12        69.57 
TCGA-BC-A112 TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-CC-5258 
        5.03        44.42        13.81        16.37         9.50         0.07 
TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA 
        2.86         3.02         3.39         3.32         0.10         0.07 
TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 
        0.10         0.13        79.73        37.74        83.57        53.29 
TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D 
      112.96         7.33         2.60         0.46        21.76        51.25 
TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE 
       90.67        79.36        66.31        19.76        75.65         6.67 
TCGA-DD-A1EF TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39X 
       12.95        49.15         6.02        13.64        21.14        55.66 
TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 
       19.73        25.81         7.66        70.06        17.59        20.12 
TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A8 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4ND 
      102.74       107.11         0.36        30.58        33.14        73.38 
TCGA-DD-A4NE TCGA-DD-A4NF TCGA-DD-A4NG TCGA-DD-A4NH TCGA-DD-A4NJ TCGA-DD-A4NK 
       21.67        14.07        14.93        14.24        15.06        39.75 
TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-ED-A459 
       56.25        29.56        61.45        93.67        12.26         0.23 
TCGA-ED-A5KG TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC 
        0.20        10.85         7.76        11.74         1.97         0.62 
TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3R2 
        0.43        23.01        14.40        19.07         0.20         6.35 
TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T 
        0.13         0.03        60.36         0.39         1.22        51.02 
TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A25Z 
       53.79        28.27        30.71        58.49        14.86        21.53 
TCGA-G3-A3CG TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SJ 
       22.13        25.64         5.88        19.53        19.23        11.97 
TCGA-G3-A5SK TCGA-G3-A5SL TCGA-G3-A5SM 
        9.93         7.99         4.37 

  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
              0.26               0.03 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
             32.45             112.96 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
              5.59              19.07 
[1] "0.3 - 32.5 (5.6)"   "0.0 - 113.0 (19.1)"
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-BC-A5W4 
  "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-CC-5258         TCGA-CC-5260         TCGA-CC-5261 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-CC-5262         TCGA-CC-5263         TCGA-CC-A1HT 
"13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" 
        TCGA-CC-A3M9         TCGA-CC-A3MA         TCGA-CC-A3MB 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-CC-A3MC         TCGA-DD-A113         TCGA-DD-A114 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DD-A1EA         TCGA-DD-A1EB         TCGA-DD-A1EC 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DD-A1ED         TCGA-DD-A1EE         TCGA-DD-A1EF 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DD-A1EH         TCGA-DD-A1EI         TCGA-DD-A1EJ 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" 
        TCGA-DD-A1EL         TCGA-DD-A39V         TCGA-DD-A39X 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DD-A39Y         TCGA-DD-A39Z         TCGA-DD-A3A0 
  "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DD-A3A1         TCGA-DD-A3A2         TCGA-DD-A3A3 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DD-A3A4         TCGA-DD-A3A5         TCGA-DD-A3A6 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DD-A3A7         TCGA-DD-A3A8         TCGA-DD-A3A9 
  "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DD-A4NA         TCGA-DD-A4ND         TCGA-DD-A4NE 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DD-A4NF         TCGA-DD-A4NG         TCGA-DD-A4NH 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DD-A4NI         TCGA-DD-A4NJ         TCGA-DD-A4NK 
  "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DD-A4NL         TCGA-DD-A4NN         TCGA-DD-A4NO 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DD-A4NP         TCGA-DD-A4NQ         TCGA-ED-A459 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-ED-A5KG         TCGA-EP-A12J         TCGA-EP-A26S 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EP-A2KA         TCGA-EP-A2KB         TCGA-EP-A2KC 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EP-A3JL         TCGA-EP-A3RK         TCGA-ES-A2HS 
  "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-ES-A2HT         TCGA-FV-A23B         TCGA-FV-A2QR 
"13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" 
        TCGA-FV-A3I0         TCGA-FV-A3R2         TCGA-FV-A3R3 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-FV-A495         TCGA-FV-A496         TCGA-FV-A4ZP 
"13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" 
        TCGA-FV-A4ZQ         TCGA-G3-A25S         TCGA-G3-A25T 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-G3-A25U         TCGA-G3-A25V         TCGA-G3-A25W 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-G3-A25X         TCGA-G3-A25Y         TCGA-G3-A25Z 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-G3-A3CG         TCGA-G3-A3CH         TCGA-G3-A3CI 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK         TCGA-G3-A5SJ 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-G3-A5SK         TCGA-G3-A5SL         TCGA-G3-A5SM 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-BC-A5W4 
  "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-CC-5258         TCGA-CC-5260         TCGA-CC-5261 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-CC-5262         TCGA-CC-5263         TCGA-CC-A1HT 
"13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" 
        TCGA-CC-A3M9         TCGA-CC-A3MA         TCGA-CC-A3MB 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-CC-A3MC         TCGA-DD-A113         TCGA-DD-A114 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DD-A1EA         TCGA-DD-A1EB         TCGA-DD-A1EC 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DD-A1ED         TCGA-DD-A1EE         TCGA-DD-A1EF 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DD-A1EH         TCGA-DD-A1EI         TCGA-DD-A1EJ 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" 
        TCGA-DD-A1EL         TCGA-DD-A39V         TCGA-DD-A39X 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DD-A39Y         TCGA-DD-A39Z         TCGA-DD-A3A0 
  "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DD-A3A1         TCGA-DD-A3A2         TCGA-DD-A3A3 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DD-A3A4         TCGA-DD-A3A5         TCGA-DD-A3A6 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DD-A3A7         TCGA-DD-A3A8         TCGA-DD-A3A9 
  "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DD-A4NA         TCGA-DD-A4ND         TCGA-DD-A4NE 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DD-A4NF         TCGA-DD-A4NG         TCGA-DD-A4NH 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DD-A4NI         TCGA-DD-A4NJ         TCGA-DD-A4NK 
  "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DD-A4NL         TCGA-DD-A4NN         TCGA-DD-A4NO 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DD-A4NP         TCGA-DD-A4NQ         TCGA-ED-A459 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-ED-A5KG         TCGA-EP-A12J         TCGA-EP-A26S 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EP-A2KA         TCGA-EP-A2KB         TCGA-EP-A2KC 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EP-A3JL         TCGA-EP-A3RK         TCGA-ES-A2HS 
  "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-ES-A2HT         TCGA-FV-A23B         TCGA-FV-A2QR 
"13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" 
        TCGA-FV-A3I0         TCGA-FV-A3R2         TCGA-FV-A3R3 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-FV-A495         TCGA-FV-A496         TCGA-FV-A4ZP 
"13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" 
        TCGA-FV-A4ZQ         TCGA-G3-A25S         TCGA-G3-A25T 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-G3-A25U         TCGA-G3-A25V         TCGA-G3-A25W 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-G3-A25X         TCGA-G3-A25Y         TCGA-G3-A25Z 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-G3-A3CG         TCGA-G3-A3CH         TCGA-G3-A3CI 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK         TCGA-G3-A5SJ 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-G3-A5SK         TCGA-G3-A5SL         TCGA-G3-A5SM 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-BC-A5W4 
  "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-CC-5258         TCGA-CC-5260         TCGA-CC-5261 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-CC-5262         TCGA-CC-5263         TCGA-CC-A1HT 
"13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" 
        TCGA-CC-A3M9         TCGA-CC-A3MA         TCGA-CC-A3MB 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-CC-A3MC         TCGA-DD-A113         TCGA-DD-A114 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DD-A1EA         TCGA-DD-A1EB         TCGA-DD-A1EC 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DD-A1ED         TCGA-DD-A1EE         TCGA-DD-A1EF 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DD-A1EH         TCGA-DD-A1EI         TCGA-DD-A1EJ 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" 
        TCGA-DD-A1EL         TCGA-DD-A39V         TCGA-DD-A39X 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DD-A39Y         TCGA-DD-A39Z         TCGA-DD-A3A0 
  "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DD-A3A1         TCGA-DD-A3A2         TCGA-DD-A3A3 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DD-A3A4         TCGA-DD-A3A5         TCGA-DD-A3A6 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DD-A3A7         TCGA-DD-A3A8         TCGA-DD-A3A9 
  "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DD-A4NA         TCGA-DD-A4ND         TCGA-DD-A4NE 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DD-A4NF         TCGA-DD-A4NG         TCGA-DD-A4NH 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DD-A4NI         TCGA-DD-A4NJ         TCGA-DD-A4NK 
  "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DD-A4NL         TCGA-DD-A4NN         TCGA-DD-A4NO 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DD-A4NP         TCGA-DD-A4NQ         TCGA-ED-A459 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-ED-A5KG         TCGA-EP-A12J         TCGA-EP-A26S 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EP-A2KA         TCGA-EP-A2KB         TCGA-EP-A2KC 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EP-A3JL         TCGA-EP-A3RK         TCGA-ES-A2HS 
  "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-ES-A2HT         TCGA-FV-A23B         TCGA-FV-A2QR 
"13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" 
        TCGA-FV-A3I0         TCGA-FV-A3R2         TCGA-FV-A3R3 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-FV-A495         TCGA-FV-A496         TCGA-FV-A4ZP 
"13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" 
        TCGA-FV-A4ZQ         TCGA-G3-A25S         TCGA-G3-A25T 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-G3-A25U         TCGA-G3-A25V         TCGA-G3-A25W 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-G3-A25X         TCGA-G3-A25Y         TCGA-G3-A25Z 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-G3-A3CG         TCGA-G3-A3CH         TCGA-G3-A3CI 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK         TCGA-G3-A5SJ 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-G3-A5SK         TCGA-G3-A5SL         TCGA-G3-A5SM 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
[1] "hr=" "2.1"
D25V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  13Q GAIN MUTATED         4        2         0          1          1
  13Q GAIN WILD-TYPE      41       23         2         24          2
                    vv
clus                 STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  13Q GAIN MUTATED            1        0         0         0
  13Q GAIN WILD-TYPE          3        1         1         1
D25V3, multiclass
                    vv
clus                 T1 T2 T3 T4
  13Q GAIN MUTATED    5  2  2  0
  13Q GAIN WILD-TYPE 43 26 32  6
D25V4, multiclass
    clus
vv   13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  T1                5                 43
  T2                2                 26
  T3                2                 32
  T4                0                  6
D25V5, binary
                    cls
clus                  0  1
  13Q GAIN MUTATED    3  1
  13Q GAIN WILD-TYPE 71  2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED      3    1
  13Q GAIN WILD-TYPE   71    2
   clus
vv  13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  0                3                 71
  1                1                  2
                    vv
clus                 M0 M1 MX
  13Q GAIN MUTATED    8  0  1
  13Q GAIN WILD-TYPE 82  2 24
D25V6, multiclass
    clus
vv   13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  M0                8                 82
  M1                0                  2
  MX                1                 24
D25V7, binary
                    cls
clus                  0  1
  13Q GAIN MUTATED    4  5
  13Q GAIN WILD-TYPE 40 68
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED      4    5
  13Q GAIN WILD-TYPE   40   68
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  FEMALE                4                 40
  MALE                  5                 68
                    vv
clus                 R0 R1 R2 RX
  13Q GAIN MUTATED    7  0  0  1
  13Q GAIN WILD-TYPE 86 10  1  7
D25V8, multiclass
    clus
vv   13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  R0                7                 86
  R1                0                 10
  R2                0                  1
  RX                1                  7

Clustering(26) Variable = 14Q GAIN MUTATION ANALYSIS
D26V1, survival
                    sevent
clus2                 0  1
  14Q GAIN MUTATED    5  3
  14Q GAIN WILD-TYPE 56 50
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                 8                106 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                 3                 50 
$`14Q GAIN MUTATED`
TCGA-CC-A3M9 TCGA-DD-A114 TCGA-DD-A119 TCGA-DD-A4ND TCGA-EP-A3JL TCGA-ES-A2HS 
        0.10        37.74         7.33        73.38         3.19        23.01 
TCGA-FV-A3I0 TCGA-G3-A3CG 
        0.20        22.13 

$`14Q GAIN WILD-TYPE`
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T 
       48.99        27.91        37.32        10.13        46.78        27.52 
TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 
       27.52         2.99        25.32        23.34         1.12        69.57 
TCGA-BC-A112 TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 
        5.03        44.42        13.81         0.26        16.37         9.50 
TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A1HT 
        0.07         2.86         3.02         3.39         4.24         3.32 
TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A113 TCGA-DD-A115 TCGA-DD-A116 
        0.07         0.10         0.13        79.73        83.57        53.29 
TCGA-DD-A118 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 
      112.96         2.60         0.46        21.76        51.25        90.67 
TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EF 
       79.36        66.31        19.76        75.65         6.67        12.95 
TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39X 
       49.15         6.02        29.16        13.64        21.14        55.66 
TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 
        5.59        19.73        25.81         7.66        70.06        17.59 
TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A3A9 
       20.12       102.74       107.11        13.78         0.36        30.58 
TCGA-DD-A4NA TCGA-DD-A4NE TCGA-DD-A4NF TCGA-DD-A4NG TCGA-DD-A4NH TCGA-DD-A4NI 
       33.14        21.67        14.07        14.93        14.24        10.78 
TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP 
       15.06        39.75        56.25        29.56        61.45        93.67 
TCGA-DD-A4NQ TCGA-ED-A459 TCGA-ED-A5KG TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA 
       12.26         0.23         0.20        10.85         7.76        11.74 
TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QR 
        1.97         0.62         0.43        14.40        32.45        19.07 
TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZP TCGA-FV-A4ZQ 
        6.35         0.13         0.03         0.33        60.36         0.39 
TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25X 
        1.22        51.02        53.79        28.27        30.71        58.49 
TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK 
       14.86        21.53        25.64         5.88        19.53        19.23 
TCGA-G3-A5SJ TCGA-G3-A5SK TCGA-G3-A5SL TCGA-G3-A5SM 
       11.97         9.93         7.99         4.37 

  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
              0.10               0.03 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
             73.38             112.96 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
            14.730             15.715 
[1] "0.1 - 73.4 (14.7)"  "0.0 - 113.0 (15.7)"
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-BC-A5W4 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CC-5258         TCGA-CC-5260         TCGA-CC-5261 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CC-5262         TCGA-CC-5263         TCGA-CC-A1HT 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CC-A3M9         TCGA-CC-A3MA         TCGA-CC-A3MB 
  "14Q GAIN MUTATED" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CC-A3MC         TCGA-DD-A113         TCGA-DD-A114 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE"   "14Q GAIN MUTATED" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
  "14Q GAIN MUTATED" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DD-A1EA         TCGA-DD-A1EB         TCGA-DD-A1EC 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DD-A1ED         TCGA-DD-A1EE         TCGA-DD-A1EF 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DD-A1EH         TCGA-DD-A1EI         TCGA-DD-A1EJ 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DD-A1EL         TCGA-DD-A39V         TCGA-DD-A39X 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DD-A39Y         TCGA-DD-A39Z         TCGA-DD-A3A0 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DD-A3A1         TCGA-DD-A3A2         TCGA-DD-A3A3 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DD-A3A4         TCGA-DD-A3A5         TCGA-DD-A3A6 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DD-A3A7         TCGA-DD-A3A8         TCGA-DD-A3A9 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DD-A4NA         TCGA-DD-A4ND         TCGA-DD-A4NE 
"14Q GAIN WILD-TYPE"   "14Q GAIN MUTATED" "14Q GAIN WILD-TYPE" 
        TCGA-DD-A4NF         TCGA-DD-A4NG         TCGA-DD-A4NH 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DD-A4NI         TCGA-DD-A4NJ         TCGA-DD-A4NK 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DD-A4NL         TCGA-DD-A4NN         TCGA-DD-A4NO 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DD-A4NP         TCGA-DD-A4NQ         TCGA-ED-A459 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-ED-A5KG         TCGA-EP-A12J         TCGA-EP-A26S 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EP-A2KA         TCGA-EP-A2KB         TCGA-EP-A2KC 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EP-A3JL         TCGA-EP-A3RK         TCGA-ES-A2HS 
  "14Q GAIN MUTATED" "14Q GAIN WILD-TYPE"   "14Q GAIN MUTATED" 
        TCGA-ES-A2HT         TCGA-FV-A23B         TCGA-FV-A2QR 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-FV-A3I0         TCGA-FV-A3R2         TCGA-FV-A3R3 
  "14Q GAIN MUTATED" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-FV-A495         TCGA-FV-A496         TCGA-FV-A4ZP 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-FV-A4ZQ         TCGA-G3-A25S         TCGA-G3-A25T 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-G3-A25U         TCGA-G3-A25V         TCGA-G3-A25W 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-G3-A25X         TCGA-G3-A25Y         TCGA-G3-A25Z 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-G3-A3CG         TCGA-G3-A3CH         TCGA-G3-A3CI 
  "14Q GAIN MUTATED" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK         TCGA-G3-A5SJ 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-G3-A5SK         TCGA-G3-A5SL         TCGA-G3-A5SM 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-BC-A5W4 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CC-5258         TCGA-CC-5260         TCGA-CC-5261 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CC-5262         TCGA-CC-5263         TCGA-CC-A1HT 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CC-A3M9         TCGA-CC-A3MA         TCGA-CC-A3MB 
  "14Q GAIN MUTATED" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CC-A3MC         TCGA-DD-A113         TCGA-DD-A114 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE"   "14Q GAIN MUTATED" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
  "14Q GAIN MUTATED" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DD-A1EA         TCGA-DD-A1EB         TCGA-DD-A1EC 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DD-A1ED         TCGA-DD-A1EE         TCGA-DD-A1EF 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DD-A1EH         TCGA-DD-A1EI         TCGA-DD-A1EJ 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DD-A1EL         TCGA-DD-A39V         TCGA-DD-A39X 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DD-A39Y         TCGA-DD-A39Z         TCGA-DD-A3A0 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DD-A3A1         TCGA-DD-A3A2         TCGA-DD-A3A3 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DD-A3A4         TCGA-DD-A3A5         TCGA-DD-A3A6 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DD-A3A7         TCGA-DD-A3A8         TCGA-DD-A3A9 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DD-A4NA         TCGA-DD-A4ND         TCGA-DD-A4NE 
"14Q GAIN WILD-TYPE"   "14Q GAIN MUTATED" "14Q GAIN WILD-TYPE" 
        TCGA-DD-A4NF         TCGA-DD-A4NG         TCGA-DD-A4NH 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DD-A4NI         TCGA-DD-A4NJ         TCGA-DD-A4NK 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DD-A4NL         TCGA-DD-A4NN         TCGA-DD-A4NO 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DD-A4NP         TCGA-DD-A4NQ         TCGA-ED-A459 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-ED-A5KG         TCGA-EP-A12J         TCGA-EP-A26S 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EP-A2KA         TCGA-EP-A2KB         TCGA-EP-A2KC 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EP-A3JL         TCGA-EP-A3RK         TCGA-ES-A2HS 
  "14Q GAIN MUTATED" "14Q GAIN WILD-TYPE"   "14Q GAIN MUTATED" 
        TCGA-ES-A2HT         TCGA-FV-A23B         TCGA-FV-A2QR 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-FV-A3I0         TCGA-FV-A3R2         TCGA-FV-A3R3 
  "14Q GAIN MUTATED" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-FV-A495         TCGA-FV-A496         TCGA-FV-A4ZP 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-FV-A4ZQ         TCGA-G3-A25S         TCGA-G3-A25T 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-G3-A25U         TCGA-G3-A25V         TCGA-G3-A25W 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-G3-A25X         TCGA-G3-A25Y         TCGA-G3-A25Z 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-G3-A3CG         TCGA-G3-A3CH         TCGA-G3-A3CI 
  "14Q GAIN MUTATED" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK         TCGA-G3-A5SJ 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-G3-A5SK         TCGA-G3-A5SL         TCGA-G3-A5SM 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-BC-A5W4 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CC-5258         TCGA-CC-5260         TCGA-CC-5261 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CC-5262         TCGA-CC-5263         TCGA-CC-A1HT 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CC-A3M9         TCGA-CC-A3MA         TCGA-CC-A3MB 
  "14Q GAIN MUTATED" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CC-A3MC         TCGA-DD-A113         TCGA-DD-A114 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE"   "14Q GAIN MUTATED" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
  "14Q GAIN MUTATED" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DD-A1EA         TCGA-DD-A1EB         TCGA-DD-A1EC 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DD-A1ED         TCGA-DD-A1EE         TCGA-DD-A1EF 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DD-A1EH         TCGA-DD-A1EI         TCGA-DD-A1EJ 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DD-A1EL         TCGA-DD-A39V         TCGA-DD-A39X 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DD-A39Y         TCGA-DD-A39Z         TCGA-DD-A3A0 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DD-A3A1         TCGA-DD-A3A2         TCGA-DD-A3A3 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DD-A3A4         TCGA-DD-A3A5         TCGA-DD-A3A6 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DD-A3A7         TCGA-DD-A3A8         TCGA-DD-A3A9 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DD-A4NA         TCGA-DD-A4ND         TCGA-DD-A4NE 
"14Q GAIN WILD-TYPE"   "14Q GAIN MUTATED" "14Q GAIN WILD-TYPE" 
        TCGA-DD-A4NF         TCGA-DD-A4NG         TCGA-DD-A4NH 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DD-A4NI         TCGA-DD-A4NJ         TCGA-DD-A4NK 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DD-A4NL         TCGA-DD-A4NN         TCGA-DD-A4NO 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DD-A4NP         TCGA-DD-A4NQ         TCGA-ED-A459 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-ED-A5KG         TCGA-EP-A12J         TCGA-EP-A26S 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EP-A2KA         TCGA-EP-A2KB         TCGA-EP-A2KC 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EP-A3JL         TCGA-EP-A3RK         TCGA-ES-A2HS 
  "14Q GAIN MUTATED" "14Q GAIN WILD-TYPE"   "14Q GAIN MUTATED" 
        TCGA-ES-A2HT         TCGA-FV-A23B         TCGA-FV-A2QR 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-FV-A3I0         TCGA-FV-A3R2         TCGA-FV-A3R3 
  "14Q GAIN MUTATED" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-FV-A495         TCGA-FV-A496         TCGA-FV-A4ZP 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-FV-A4ZQ         TCGA-G3-A25S         TCGA-G3-A25T 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-G3-A25U         TCGA-G3-A25V         TCGA-G3-A25W 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-G3-A25X         TCGA-G3-A25Y         TCGA-G3-A25Z 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-G3-A3CG         TCGA-G3-A3CH         TCGA-G3-A3CI 
  "14Q GAIN MUTATED" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK         TCGA-G3-A5SJ 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-G3-A5SK         TCGA-G3-A5SL         TCGA-G3-A5SM 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
[1] "hr=" "1"  
D26V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  14Q GAIN MUTATED         4        2         0          1          0
  14Q GAIN WILD-TYPE      41       23         2         24          3
                    vv
clus                 STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  14Q GAIN MUTATED            0        1         0         0
  14Q GAIN WILD-TYPE          4        0         1         1
D26V3, multiclass
                    vv
clus                 T1 T2 T3 T4
  14Q GAIN MUTATED    4  2  2  0
  14Q GAIN WILD-TYPE 44 26 32  6
D26V4, multiclass
    clus
vv   14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  T1                4                 44
  T2                2                 26
  T3                2                 32
  T4                0                  6
D26V5, binary
                    cls
clus                  0  1
  14Q GAIN MUTATED    4  0
  14Q GAIN WILD-TYPE 70  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED      4    0
  14Q GAIN WILD-TYPE   70    3
   clus
vv  14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  0                4                 70
  1                0                  3
                    vv
clus                 M0 M1 MX
  14Q GAIN MUTATED    5  1  2
  14Q GAIN WILD-TYPE 85  1 23
D26V6, multiclass
    clus
vv   14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  M0                5                 85
  M1                1                  1
  MX                2                 23
D26V7, binary
                    cls
clus                  0  1
  14Q GAIN MUTATED    2  6
  14Q GAIN WILD-TYPE 42 67
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED      2    6
  14Q GAIN WILD-TYPE   42   67
        clus
vv       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  FEMALE                2                 42
  MALE                  6                 67
                    vv
clus                 R0 R1 R2 RX
  14Q GAIN MUTATED    5  1  1  0
  14Q GAIN WILD-TYPE 88  9  0  8
D26V8, multiclass
    clus
vv   14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  R0                5                 88
  R1                1                  9
  R2                1                  0
  RX                0                  8

Clustering(27) Variable = 15Q GAIN MUTATION ANALYSIS
D27V1, survival
                    sevent
clus2                 0  1
  15Q GAIN MUTATED    6  4
  15Q GAIN WILD-TYPE 55 49
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                10                104 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                 4                 49 
$`15Q GAIN MUTATED`
TCGA-BC-A10Q TCGA-BC-A10Y TCGA-BC-A3KG TCGA-CC-A3M9 TCGA-DD-A4NE TCGA-DD-A4NI 
       37.32        23.34        16.37         0.10        21.67        10.78 
TCGA-ES-A2HS TCGA-FV-A4ZQ TCGA-G3-A25T TCGA-G3-A25X 
       23.01         0.39        51.02        58.49 

$`15Q GAIN WILD-TYPE`
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U 
       48.99        27.91        10.13        46.78        27.52        27.52 
TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A216 
        2.99        25.32         1.12        69.57         5.03        44.42 
TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A5W4 TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5261 
       13.81         0.26         9.50         0.07         2.86         3.02 
TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC 
        3.39         4.24         3.32         0.07         0.10         0.13 
TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 
       79.73        37.74        83.57        53.29       112.96         7.33 
TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA 
        2.60         0.46        21.76        51.25        90.67        79.36 
TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EH 
       66.31        19.76        75.65         6.67        12.95        49.15 
TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39X TCGA-DD-A39Y 
        6.02        29.16        13.64        21.14        55.66         5.59 
TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 
       19.73        25.81         7.66        70.06        17.59        20.12 
TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A3A9 TCGA-DD-A4NA 
      102.74       107.11        13.78         0.36        30.58        33.14 
TCGA-DD-A4ND TCGA-DD-A4NF TCGA-DD-A4NG TCGA-DD-A4NH TCGA-DD-A4NJ TCGA-DD-A4NK 
       73.38        14.07        14.93        14.24        15.06        39.75 
TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-ED-A459 
       56.25        29.56        61.45        93.67        12.26         0.23 
TCGA-ED-A5KG TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC 
        0.20        10.85         7.76        11.74         1.97         0.62 
TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-A3I0 
        3.19         0.43        14.40        32.45        19.07         0.20 
TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZP TCGA-G3-A25S 
        6.35         0.13         0.03         0.33        60.36         1.22 
TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG 
       53.79        28.27        30.71        14.86        21.53        22.13 
TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SJ TCGA-G3-A5SK 
       25.64         5.88        19.53        19.23        11.97         9.93 
TCGA-G3-A5SL TCGA-G3-A5SM 
        7.99         4.37 

  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
              0.10               0.03 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
             58.49             112.96 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
            22.340             14.895 
[1] "0.1 - 58.5 (22.3)"  "0.0 - 113.0 (14.9)"
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
  "15Q GAIN MUTATED" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-BC-A5W4 
"15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" "15Q GAIN WILD-TYPE" 
        TCGA-CC-5258         TCGA-CC-5260         TCGA-CC-5261 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-CC-5262         TCGA-CC-5263         TCGA-CC-A1HT 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-CC-A3M9         TCGA-CC-A3MA         TCGA-CC-A3MB 
  "15Q GAIN MUTATED" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-CC-A3MC         TCGA-DD-A113         TCGA-DD-A114 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-DD-A1EA         TCGA-DD-A1EB         TCGA-DD-A1EC 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-DD-A1ED         TCGA-DD-A1EE         TCGA-DD-A1EF 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-DD-A1EH         TCGA-DD-A1EI         TCGA-DD-A1EJ 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-DD-A1EL         TCGA-DD-A39V         TCGA-DD-A39X 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-DD-A39Y         TCGA-DD-A39Z         TCGA-DD-A3A0 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-DD-A3A1         TCGA-DD-A3A2         TCGA-DD-A3A3 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-DD-A3A4         TCGA-DD-A3A5         TCGA-DD-A3A6 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-DD-A3A7         TCGA-DD-A3A8         TCGA-DD-A3A9 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-DD-A4NA         TCGA-DD-A4ND         TCGA-DD-A4NE 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" 
        TCGA-DD-A4NF         TCGA-DD-A4NG         TCGA-DD-A4NH 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-DD-A4NI         TCGA-DD-A4NJ         TCGA-DD-A4NK 
  "15Q GAIN MUTATED" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-DD-A4NL         TCGA-DD-A4NN         TCGA-DD-A4NO 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-DD-A4NP         TCGA-DD-A4NQ         TCGA-ED-A459 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-ED-A5KG         TCGA-EP-A12J         TCGA-EP-A26S 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EP-A2KA         TCGA-EP-A2KB         TCGA-EP-A2KC 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EP-A3JL         TCGA-EP-A3RK         TCGA-ES-A2HS 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" 
        TCGA-ES-A2HT         TCGA-FV-A23B         TCGA-FV-A2QR 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-FV-A3I0         TCGA-FV-A3R2         TCGA-FV-A3R3 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-FV-A495         TCGA-FV-A496         TCGA-FV-A4ZP 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-FV-A4ZQ         TCGA-G3-A25S         TCGA-G3-A25T 
  "15Q GAIN MUTATED" "15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" 
        TCGA-G3-A25U         TCGA-G3-A25V         TCGA-G3-A25W 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-G3-A25X         TCGA-G3-A25Y         TCGA-G3-A25Z 
  "15Q GAIN MUTATED" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-G3-A3CG         TCGA-G3-A3CH         TCGA-G3-A3CI 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK         TCGA-G3-A5SJ 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-G3-A5SK         TCGA-G3-A5SL         TCGA-G3-A5SM 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
  "15Q GAIN MUTATED" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-BC-A5W4 
"15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" "15Q GAIN WILD-TYPE" 
        TCGA-CC-5258         TCGA-CC-5260         TCGA-CC-5261 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-CC-5262         TCGA-CC-5263         TCGA-CC-A1HT 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-CC-A3M9         TCGA-CC-A3MA         TCGA-CC-A3MB 
  "15Q GAIN MUTATED" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-CC-A3MC         TCGA-DD-A113         TCGA-DD-A114 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-DD-A1EA         TCGA-DD-A1EB         TCGA-DD-A1EC 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-DD-A1ED         TCGA-DD-A1EE         TCGA-DD-A1EF 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-DD-A1EH         TCGA-DD-A1EI         TCGA-DD-A1EJ 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-DD-A1EL         TCGA-DD-A39V         TCGA-DD-A39X 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-DD-A39Y         TCGA-DD-A39Z         TCGA-DD-A3A0 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-DD-A3A1         TCGA-DD-A3A2         TCGA-DD-A3A3 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-DD-A3A4         TCGA-DD-A3A5         TCGA-DD-A3A6 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-DD-A3A7         TCGA-DD-A3A8         TCGA-DD-A3A9 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-DD-A4NA         TCGA-DD-A4ND         TCGA-DD-A4NE 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" 
        TCGA-DD-A4NF         TCGA-DD-A4NG         TCGA-DD-A4NH 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-DD-A4NI         TCGA-DD-A4NJ         TCGA-DD-A4NK 
  "15Q GAIN MUTATED" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-DD-A4NL         TCGA-DD-A4NN         TCGA-DD-A4NO 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-DD-A4NP         TCGA-DD-A4NQ         TCGA-ED-A459 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-ED-A5KG         TCGA-EP-A12J         TCGA-EP-A26S 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EP-A2KA         TCGA-EP-A2KB         TCGA-EP-A2KC 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EP-A3JL         TCGA-EP-A3RK         TCGA-ES-A2HS 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" 
        TCGA-ES-A2HT         TCGA-FV-A23B         TCGA-FV-A2QR 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-FV-A3I0         TCGA-FV-A3R2         TCGA-FV-A3R3 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-FV-A495         TCGA-FV-A496         TCGA-FV-A4ZP 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-FV-A4ZQ         TCGA-G3-A25S         TCGA-G3-A25T 
  "15Q GAIN MUTATED" "15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" 
        TCGA-G3-A25U         TCGA-G3-A25V         TCGA-G3-A25W 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-G3-A25X         TCGA-G3-A25Y         TCGA-G3-A25Z 
  "15Q GAIN MUTATED" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-G3-A3CG         TCGA-G3-A3CH         TCGA-G3-A3CI 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK         TCGA-G3-A5SJ 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-G3-A5SK         TCGA-G3-A5SL         TCGA-G3-A5SM 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
  "15Q GAIN MUTATED" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-BC-A5W4 
"15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" "15Q GAIN WILD-TYPE" 
        TCGA-CC-5258         TCGA-CC-5260         TCGA-CC-5261 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-CC-5262         TCGA-CC-5263         TCGA-CC-A1HT 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-CC-A3M9         TCGA-CC-A3MA         TCGA-CC-A3MB 
  "15Q GAIN MUTATED" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-CC-A3MC         TCGA-DD-A113         TCGA-DD-A114 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-DD-A1EA         TCGA-DD-A1EB         TCGA-DD-A1EC 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-DD-A1ED         TCGA-DD-A1EE         TCGA-DD-A1EF 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-DD-A1EH         TCGA-DD-A1EI         TCGA-DD-A1EJ 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-DD-A1EL         TCGA-DD-A39V         TCGA-DD-A39X 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-DD-A39Y         TCGA-DD-A39Z         TCGA-DD-A3A0 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-DD-A3A1         TCGA-DD-A3A2         TCGA-DD-A3A3 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-DD-A3A4         TCGA-DD-A3A5         TCGA-DD-A3A6 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-DD-A3A7         TCGA-DD-A3A8         TCGA-DD-A3A9 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-DD-A4NA         TCGA-DD-A4ND         TCGA-DD-A4NE 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" 
        TCGA-DD-A4NF         TCGA-DD-A4NG         TCGA-DD-A4NH 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-DD-A4NI         TCGA-DD-A4NJ         TCGA-DD-A4NK 
  "15Q GAIN MUTATED" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-DD-A4NL         TCGA-DD-A4NN         TCGA-DD-A4NO 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-DD-A4NP         TCGA-DD-A4NQ         TCGA-ED-A459 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-ED-A5KG         TCGA-EP-A12J         TCGA-EP-A26S 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EP-A2KA         TCGA-EP-A2KB         TCGA-EP-A2KC 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EP-A3JL         TCGA-EP-A3RK         TCGA-ES-A2HS 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" 
        TCGA-ES-A2HT         TCGA-FV-A23B         TCGA-FV-A2QR 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-FV-A3I0         TCGA-FV-A3R2         TCGA-FV-A3R3 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-FV-A495         TCGA-FV-A496         TCGA-FV-A4ZP 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-FV-A4ZQ         TCGA-G3-A25S         TCGA-G3-A25T 
  "15Q GAIN MUTATED" "15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" 
        TCGA-G3-A25U         TCGA-G3-A25V         TCGA-G3-A25W 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-G3-A25X         TCGA-G3-A25Y         TCGA-G3-A25Z 
  "15Q GAIN MUTATED" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-G3-A3CG         TCGA-G3-A3CH         TCGA-G3-A3CI 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK         TCGA-G3-A5SJ 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-G3-A5SK         TCGA-G3-A5SL         TCGA-G3-A5SM 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
[1] "hr=" "1.1"
D27V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  15Q GAIN MUTATED         2        3         0          2          0
  15Q GAIN WILD-TYPE      43       22         2         23          3
                    vv
clus                 STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  15Q GAIN MUTATED            0        0         0         0
  15Q GAIN WILD-TYPE          4        1         1         1
D27V3, multiclass
                    vv
clus                 T1 T2 T3 T4
  15Q GAIN MUTATED    2  4  2  1
  15Q GAIN WILD-TYPE 46 24 32  5
D27V4, multiclass
    clus
vv   15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  T1                2                 46
  T2                4                 24
  T3                2                 32
  T4                1                  5
D27V5, binary
                    cls
clus                  0  1
  15Q GAIN MUTATED    5  0
  15Q GAIN WILD-TYPE 69  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED      5    0
  15Q GAIN WILD-TYPE   69    3
   clus
vv  15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  0                5                 69
  1                0                  3
                    vv
clus                 M0 M1 MX
  15Q GAIN MUTATED    7  0  3
  15Q GAIN WILD-TYPE 83  2 22
D27V6, multiclass
    clus
vv   15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  M0                7                 83
  M1                0                  2
  MX                3                 22
D27V7, binary
                    cls
clus                  0  1
  15Q GAIN MUTATED    4  6
  15Q GAIN WILD-TYPE 40 67
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED      4    6
  15Q GAIN WILD-TYPE   40   67
        clus
vv       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  FEMALE                4                 40
  MALE                  6                 67
                    vv
clus                 R0 R1 R2 RX
  15Q GAIN MUTATED    9  1  0  0
  15Q GAIN WILD-TYPE 84  9  1  8
D27V8, multiclass
    clus
vv   15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  R0                9                 84
  R1                1                  9
  R2                0                  1
  RX                0                  8

Clustering(28) Variable = 16P GAIN MUTATION ANALYSIS
D28V1, survival
                    sevent
clus2                 0  1
  16P GAIN MUTATED    6  5
  16P GAIN WILD-TYPE 55 48
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                11                103 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                 5                 48 
$`16P GAIN MUTATED`
TCGA-BC-A10R TCGA-BC-A112 TCGA-DD-A113 TCGA-DD-A11A TCGA-DD-A1EL TCGA-DD-A3A5 
       10.13         5.03        79.73         2.60        13.64       102.74 
TCGA-ED-A459 TCGA-EP-A3JL TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A5SM 
        0.23         3.19         1.22        51.02         4.37 

$`16P GAIN WILD-TYPE`
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U 
       48.99        27.91        37.32        46.78        27.52        27.52 
TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A216 
        2.99        25.32        23.34         1.12        69.57        44.42 
TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-CC-5258 TCGA-CC-5260 
       13.81         0.26        16.37         9.50         0.07         2.86 
TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA 
        3.02         3.39         4.24         3.32         0.10         0.07 
TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 
        0.10         0.13        37.74        83.57        53.29       112.96 
TCGA-DD-A119 TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA 
        7.33         0.46        21.76        51.25        90.67        79.36 
TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EH 
       66.31        19.76        75.65         6.67        12.95        49.15 
TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A39V TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A39Z 
        6.02        29.16        21.14        55.66         5.59        19.73 
TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A6 
       25.81         7.66        70.06        17.59        20.12       107.11 
TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4ND TCGA-DD-A4NE 
       13.78         0.36        30.58        33.14        73.38        21.67 
TCGA-DD-A4NF TCGA-DD-A4NG TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK 
       14.07        14.93        14.24        10.78        15.06        39.75 
TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-ED-A5KG 
       56.25        29.56        61.45        93.67        12.26         0.20 
TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3RK 
       10.85         7.76        11.74         1.97         0.62         0.43 
TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3R2 
       23.01        14.40        32.45        19.07         0.20         6.35 
TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25U 
        0.13         0.03         0.33        60.36         0.39        53.79 
TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG 
       28.27        30.71        58.49        14.86        21.53        22.13 
TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SJ TCGA-G3-A5SK 
       25.64         5.88        19.53        19.23        11.97         9.93 
TCGA-G3-A5SL 
        7.99 

  16P GAIN MUTATED 16P GAIN WILD-TYPE 
              0.23               0.03 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
            102.74             112.96 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
              5.03              19.07 
[1] "0.2 - 102.7 (5.0)"  "0.0 - 113.0 (19.1)"
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
  "16P GAIN MUTATED" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
  "16P GAIN MUTATED" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-BC-A5W4 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-CC-5258         TCGA-CC-5260         TCGA-CC-5261 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-CC-5262         TCGA-CC-5263         TCGA-CC-A1HT 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-CC-A3M9         TCGA-CC-A3MA         TCGA-CC-A3MB 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-CC-A3MC         TCGA-DD-A113         TCGA-DD-A114 
"16P GAIN WILD-TYPE"   "16P GAIN MUTATED" "16P GAIN WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"16P GAIN WILD-TYPE"   "16P GAIN MUTATED" "16P GAIN WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DD-A1EA         TCGA-DD-A1EB         TCGA-DD-A1EC 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DD-A1ED         TCGA-DD-A1EE         TCGA-DD-A1EF 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DD-A1EH         TCGA-DD-A1EI         TCGA-DD-A1EJ 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DD-A1EL         TCGA-DD-A39V         TCGA-DD-A39X 
  "16P GAIN MUTATED" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DD-A39Y         TCGA-DD-A39Z         TCGA-DD-A3A0 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DD-A3A1         TCGA-DD-A3A2         TCGA-DD-A3A3 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DD-A3A4         TCGA-DD-A3A5         TCGA-DD-A3A6 
"16P GAIN WILD-TYPE"   "16P GAIN MUTATED" "16P GAIN WILD-TYPE" 
        TCGA-DD-A3A7         TCGA-DD-A3A8         TCGA-DD-A3A9 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DD-A4NA         TCGA-DD-A4ND         TCGA-DD-A4NE 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DD-A4NF         TCGA-DD-A4NG         TCGA-DD-A4NH 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DD-A4NI         TCGA-DD-A4NJ         TCGA-DD-A4NK 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DD-A4NL         TCGA-DD-A4NN         TCGA-DD-A4NO 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DD-A4NP         TCGA-DD-A4NQ         TCGA-ED-A459 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE"   "16P GAIN MUTATED" 
        TCGA-ED-A5KG         TCGA-EP-A12J         TCGA-EP-A26S 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-EP-A2KA         TCGA-EP-A2KB         TCGA-EP-A2KC 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-EP-A3JL         TCGA-EP-A3RK         TCGA-ES-A2HS 
  "16P GAIN MUTATED" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-ES-A2HT         TCGA-FV-A23B         TCGA-FV-A2QR 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-FV-A3I0         TCGA-FV-A3R2         TCGA-FV-A3R3 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-FV-A495         TCGA-FV-A496         TCGA-FV-A4ZP 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-FV-A4ZQ         TCGA-G3-A25S         TCGA-G3-A25T 
"16P GAIN WILD-TYPE"   "16P GAIN MUTATED"   "16P GAIN MUTATED" 
        TCGA-G3-A25U         TCGA-G3-A25V         TCGA-G3-A25W 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-G3-A25X         TCGA-G3-A25Y         TCGA-G3-A25Z 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-G3-A3CG         TCGA-G3-A3CH         TCGA-G3-A3CI 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK         TCGA-G3-A5SJ 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-G3-A5SK         TCGA-G3-A5SL         TCGA-G3-A5SM 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE"   "16P GAIN MUTATED" 
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
  "16P GAIN MUTATED" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
  "16P GAIN MUTATED" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-BC-A5W4 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-CC-5258         TCGA-CC-5260         TCGA-CC-5261 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-CC-5262         TCGA-CC-5263         TCGA-CC-A1HT 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-CC-A3M9         TCGA-CC-A3MA         TCGA-CC-A3MB 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-CC-A3MC         TCGA-DD-A113         TCGA-DD-A114 
"16P GAIN WILD-TYPE"   "16P GAIN MUTATED" "16P GAIN WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"16P GAIN WILD-TYPE"   "16P GAIN MUTATED" "16P GAIN WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DD-A1EA         TCGA-DD-A1EB         TCGA-DD-A1EC 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DD-A1ED         TCGA-DD-A1EE         TCGA-DD-A1EF 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DD-A1EH         TCGA-DD-A1EI         TCGA-DD-A1EJ 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DD-A1EL         TCGA-DD-A39V         TCGA-DD-A39X 
  "16P GAIN MUTATED" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DD-A39Y         TCGA-DD-A39Z         TCGA-DD-A3A0 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DD-A3A1         TCGA-DD-A3A2         TCGA-DD-A3A3 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DD-A3A4         TCGA-DD-A3A5         TCGA-DD-A3A6 
"16P GAIN WILD-TYPE"   "16P GAIN MUTATED" "16P GAIN WILD-TYPE" 
        TCGA-DD-A3A7         TCGA-DD-A3A8         TCGA-DD-A3A9 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DD-A4NA         TCGA-DD-A4ND         TCGA-DD-A4NE 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DD-A4NF         TCGA-DD-A4NG         TCGA-DD-A4NH 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DD-A4NI         TCGA-DD-A4NJ         TCGA-DD-A4NK 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DD-A4NL         TCGA-DD-A4NN         TCGA-DD-A4NO 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DD-A4NP         TCGA-DD-A4NQ         TCGA-ED-A459 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE"   "16P GAIN MUTATED" 
        TCGA-ED-A5KG         TCGA-EP-A12J         TCGA-EP-A26S 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-EP-A2KA         TCGA-EP-A2KB         TCGA-EP-A2KC 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-EP-A3JL         TCGA-EP-A3RK         TCGA-ES-A2HS 
  "16P GAIN MUTATED" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-ES-A2HT         TCGA-FV-A23B         TCGA-FV-A2QR 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-FV-A3I0         TCGA-FV-A3R2         TCGA-FV-A3R3 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-FV-A495         TCGA-FV-A496         TCGA-FV-A4ZP 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-FV-A4ZQ         TCGA-G3-A25S         TCGA-G3-A25T 
"16P GAIN WILD-TYPE"   "16P GAIN MUTATED"   "16P GAIN MUTATED" 
        TCGA-G3-A25U         TCGA-G3-A25V         TCGA-G3-A25W 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-G3-A25X         TCGA-G3-A25Y         TCGA-G3-A25Z 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-G3-A3CG         TCGA-G3-A3CH         TCGA-G3-A3CI 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK         TCGA-G3-A5SJ 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-G3-A5SK         TCGA-G3-A5SL         TCGA-G3-A5SM 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE"   "16P GAIN MUTATED" 
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
  "16P GAIN MUTATED" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
  "16P GAIN MUTATED" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-BC-A5W4 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-CC-5258         TCGA-CC-5260         TCGA-CC-5261 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-CC-5262         TCGA-CC-5263         TCGA-CC-A1HT 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-CC-A3M9         TCGA-CC-A3MA         TCGA-CC-A3MB 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-CC-A3MC         TCGA-DD-A113         TCGA-DD-A114 
"16P GAIN WILD-TYPE"   "16P GAIN MUTATED" "16P GAIN WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"16P GAIN WILD-TYPE"   "16P GAIN MUTATED" "16P GAIN WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DD-A1EA         TCGA-DD-A1EB         TCGA-DD-A1EC 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DD-A1ED         TCGA-DD-A1EE         TCGA-DD-A1EF 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DD-A1EH         TCGA-DD-A1EI         TCGA-DD-A1EJ 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DD-A1EL         TCGA-DD-A39V         TCGA-DD-A39X 
  "16P GAIN MUTATED" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DD-A39Y         TCGA-DD-A39Z         TCGA-DD-A3A0 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DD-A3A1         TCGA-DD-A3A2         TCGA-DD-A3A3 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DD-A3A4         TCGA-DD-A3A5         TCGA-DD-A3A6 
"16P GAIN WILD-TYPE"   "16P GAIN MUTATED" "16P GAIN WILD-TYPE" 
        TCGA-DD-A3A7         TCGA-DD-A3A8         TCGA-DD-A3A9 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DD-A4NA         TCGA-DD-A4ND         TCGA-DD-A4NE 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DD-A4NF         TCGA-DD-A4NG         TCGA-DD-A4NH 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DD-A4NI         TCGA-DD-A4NJ         TCGA-DD-A4NK 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DD-A4NL         TCGA-DD-A4NN         TCGA-DD-A4NO 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DD-A4NP         TCGA-DD-A4NQ         TCGA-ED-A459 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE"   "16P GAIN MUTATED" 
        TCGA-ED-A5KG         TCGA-EP-A12J         TCGA-EP-A26S 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-EP-A2KA         TCGA-EP-A2KB         TCGA-EP-A2KC 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-EP-A3JL         TCGA-EP-A3RK         TCGA-ES-A2HS 
  "16P GAIN MUTATED" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-ES-A2HT         TCGA-FV-A23B         TCGA-FV-A2QR 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-FV-A3I0         TCGA-FV-A3R2         TCGA-FV-A3R3 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-FV-A495         TCGA-FV-A496         TCGA-FV-A4ZP 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-FV-A4ZQ         TCGA-G3-A25S         TCGA-G3-A25T 
"16P GAIN WILD-TYPE"   "16P GAIN MUTATED"   "16P GAIN MUTATED" 
        TCGA-G3-A25U         TCGA-G3-A25V         TCGA-G3-A25W 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-G3-A25X         TCGA-G3-A25Y         TCGA-G3-A25Z 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-G3-A3CG         TCGA-G3-A3CH         TCGA-G3-A3CI 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK         TCGA-G3-A5SJ 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-G3-A5SK         TCGA-G3-A5SL         TCGA-G3-A5SM 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE"   "16P GAIN MUTATED" 
[1] "hr=" "1.1"
D28V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  16P GAIN MUTATED         3        4         1          0          0
  16P GAIN WILD-TYPE      42       21         1         25          3
                    vv
clus                 STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  16P GAIN MUTATED            0        0         0         0
  16P GAIN WILD-TYPE          4        1         1         1
D28V3, multiclass
                    vv
clus                 T1 T2 T3 T4
  16P GAIN MUTATED    3  4  3  0
  16P GAIN WILD-TYPE 45 24 31  6
D28V4, multiclass
    clus
vv   16P GAIN MUTATED 16P GAIN WILD-TYPE
  T1                3                 45
  T2                4                 24
  T3                3                 31
  T4                0                  6
D28V5, binary
                    cls
clus                  0  1
  16P GAIN MUTATED    7  0
  16P GAIN WILD-TYPE 67  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED      7    0
  16P GAIN WILD-TYPE   67    3
   clus
vv  16P GAIN MUTATED 16P GAIN WILD-TYPE
  0                7                 67
  1                0                  3
                    vv
clus                 M0 M1 MX
  16P GAIN MUTATED    8  0  3
  16P GAIN WILD-TYPE 82  2 22
D28V6, multiclass
    clus
vv   16P GAIN MUTATED 16P GAIN WILD-TYPE
  M0                8                 82
  M1                0                  2
  MX                3                 22
D28V7, binary
                    cls
clus                  0  1
  16P GAIN MUTATED    4  7
  16P GAIN WILD-TYPE 40 66
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED      4    7
  16P GAIN WILD-TYPE   40   66
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  FEMALE                4                 40
  MALE                  7                 66
                    vv
clus                 R0 R1 R2 RX
  16P GAIN MUTATED    9  1  0  0
  16P GAIN WILD-TYPE 84  9  1  8
D28V8, multiclass
    clus
vv   16P GAIN MUTATED 16P GAIN WILD-TYPE
  R0                9                 84
  R1                1                  9
  R2                0                  1
  RX                0                  8

Clustering(29) Variable = 16Q GAIN MUTATION ANALYSIS
D29V1, survival
                    sevent
clus2                 0  1
  16Q GAIN MUTATED    3  1
  16Q GAIN WILD-TYPE 58 52
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                 4                110 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                 1                 52 
$`16Q GAIN MUTATED`
TCGA-DD-A1EL TCGA-EP-A3JL TCGA-G3-A25T TCGA-G3-A5SM 
       13.64         3.19        51.02         4.37 

$`16Q GAIN WILD-TYPE`
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T 
       48.99        27.91        37.32        10.13        46.78        27.52 
TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 
       27.52         2.99        25.32        23.34         1.12        69.57 
TCGA-BC-A112 TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 
        5.03        44.42        13.81         0.26        16.37         9.50 
TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A1HT 
        0.07         2.86         3.02         3.39         4.24         3.32 
TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A113 TCGA-DD-A114 
        0.10         0.07         0.10         0.13        79.73        37.74 
TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B 
       83.57        53.29       112.96         7.33         2.60         0.46 
TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC 
       21.76        51.25        90.67        79.36        66.31        19.76 
TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ 
       75.65         6.67        12.95        49.15         6.02        29.16 
TCGA-DD-A39V TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 
       21.14        55.66         5.59        19.73        25.81         7.66 
TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 
       70.06        17.59        20.12       102.74       107.11        13.78 
TCGA-DD-A3A8 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4ND TCGA-DD-A4NE TCGA-DD-A4NF 
        0.36        30.58        33.14        73.38        21.67        14.07 
TCGA-DD-A4NG TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL 
       14.93        14.24        10.78        15.06        39.75        56.25 
TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-ED-A459 TCGA-ED-A5KG 
       29.56        61.45        93.67        12.26         0.23         0.20 
TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3RK 
       10.85         7.76        11.74         1.97         0.62         0.43 
TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3R2 
       23.01        14.40        32.45        19.07         0.20         6.35 
TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25S 
        0.13         0.03         0.33        60.36         0.39         1.22 
TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A25Z 
       53.79        28.27        30.71        58.49        14.86        21.53 
TCGA-G3-A3CG TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SJ 
       22.13        25.64         5.88        19.53        19.23        11.97 
TCGA-G3-A5SK TCGA-G3-A5SL 
        9.93         7.99 

  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
              3.19               0.03 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
             51.02             112.96 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
             9.005             16.980 
[1] "3.2 - 51.0 (9.0)"   "0.0 - 113.0 (17.0)"
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-BC-A5W4 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-CC-5258         TCGA-CC-5260         TCGA-CC-5261 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-CC-5262         TCGA-CC-5263         TCGA-CC-A1HT 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-CC-A3M9         TCGA-CC-A3MA         TCGA-CC-A3MB 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-CC-A3MC         TCGA-DD-A113         TCGA-DD-A114 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-DD-A1EA         TCGA-DD-A1EB         TCGA-DD-A1EC 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-DD-A1ED         TCGA-DD-A1EE         TCGA-DD-A1EF 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-DD-A1EH         TCGA-DD-A1EI         TCGA-DD-A1EJ 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-DD-A1EL         TCGA-DD-A39V         TCGA-DD-A39X 
  "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-DD-A39Y         TCGA-DD-A39Z         TCGA-DD-A3A0 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-DD-A3A1         TCGA-DD-A3A2         TCGA-DD-A3A3 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-DD-A3A4         TCGA-DD-A3A5         TCGA-DD-A3A6 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-DD-A3A7         TCGA-DD-A3A8         TCGA-DD-A3A9 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-DD-A4NA         TCGA-DD-A4ND         TCGA-DD-A4NE 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-DD-A4NF         TCGA-DD-A4NG         TCGA-DD-A4NH 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-DD-A4NI         TCGA-DD-A4NJ         TCGA-DD-A4NK 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-DD-A4NL         TCGA-DD-A4NN         TCGA-DD-A4NO 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-DD-A4NP         TCGA-DD-A4NQ         TCGA-ED-A459 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-ED-A5KG         TCGA-EP-A12J         TCGA-EP-A26S 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EP-A2KA         TCGA-EP-A2KB         TCGA-EP-A2KC 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EP-A3JL         TCGA-EP-A3RK         TCGA-ES-A2HS 
  "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-ES-A2HT         TCGA-FV-A23B         TCGA-FV-A2QR 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-FV-A3I0         TCGA-FV-A3R2         TCGA-FV-A3R3 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-FV-A495         TCGA-FV-A496         TCGA-FV-A4ZP 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-FV-A4ZQ         TCGA-G3-A25S         TCGA-G3-A25T 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" 
        TCGA-G3-A25U         TCGA-G3-A25V         TCGA-G3-A25W 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-G3-A25X         TCGA-G3-A25Y         TCGA-G3-A25Z 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-G3-A3CG         TCGA-G3-A3CH         TCGA-G3-A3CI 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK         TCGA-G3-A5SJ 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-G3-A5SK         TCGA-G3-A5SL         TCGA-G3-A5SM 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" 
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-BC-A5W4 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-CC-5258         TCGA-CC-5260         TCGA-CC-5261 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-CC-5262         TCGA-CC-5263         TCGA-CC-A1HT 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-CC-A3M9         TCGA-CC-A3MA         TCGA-CC-A3MB 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-CC-A3MC         TCGA-DD-A113         TCGA-DD-A114 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-DD-A1EA         TCGA-DD-A1EB         TCGA-DD-A1EC 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-DD-A1ED         TCGA-DD-A1EE         TCGA-DD-A1EF 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-DD-A1EH         TCGA-DD-A1EI         TCGA-DD-A1EJ 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-DD-A1EL         TCGA-DD-A39V         TCGA-DD-A39X 
  "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-DD-A39Y         TCGA-DD-A39Z         TCGA-DD-A3A0 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-DD-A3A1         TCGA-DD-A3A2         TCGA-DD-A3A3 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-DD-A3A4         TCGA-DD-A3A5         TCGA-DD-A3A6 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-DD-A3A7         TCGA-DD-A3A8         TCGA-DD-A3A9 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-DD-A4NA         TCGA-DD-A4ND         TCGA-DD-A4NE 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-DD-A4NF         TCGA-DD-A4NG         TCGA-DD-A4NH 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-DD-A4NI         TCGA-DD-A4NJ         TCGA-DD-A4NK 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-DD-A4NL         TCGA-DD-A4NN         TCGA-DD-A4NO 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-DD-A4NP         TCGA-DD-A4NQ         TCGA-ED-A459 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-ED-A5KG         TCGA-EP-A12J         TCGA-EP-A26S 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EP-A2KA         TCGA-EP-A2KB         TCGA-EP-A2KC 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EP-A3JL         TCGA-EP-A3RK         TCGA-ES-A2HS 
  "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-ES-A2HT         TCGA-FV-A23B         TCGA-FV-A2QR 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-FV-A3I0         TCGA-FV-A3R2         TCGA-FV-A3R3 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-FV-A495         TCGA-FV-A496         TCGA-FV-A4ZP 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-FV-A4ZQ         TCGA-G3-A25S         TCGA-G3-A25T 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" 
        TCGA-G3-A25U         TCGA-G3-A25V         TCGA-G3-A25W 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-G3-A25X         TCGA-G3-A25Y         TCGA-G3-A25Z 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-G3-A3CG         TCGA-G3-A3CH         TCGA-G3-A3CI 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK         TCGA-G3-A5SJ 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-G3-A5SK         TCGA-G3-A5SL         TCGA-G3-A5SM 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" 
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-BC-A5W4 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-CC-5258         TCGA-CC-5260         TCGA-CC-5261 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-CC-5262         TCGA-CC-5263         TCGA-CC-A1HT 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-CC-A3M9         TCGA-CC-A3MA         TCGA-CC-A3MB 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-CC-A3MC         TCGA-DD-A113         TCGA-DD-A114 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-DD-A1EA         TCGA-DD-A1EB         TCGA-DD-A1EC 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-DD-A1ED         TCGA-DD-A1EE         TCGA-DD-A1EF 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-DD-A1EH         TCGA-DD-A1EI         TCGA-DD-A1EJ 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-DD-A1EL         TCGA-DD-A39V         TCGA-DD-A39X 
  "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-DD-A39Y         TCGA-DD-A39Z         TCGA-DD-A3A0 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-DD-A3A1         TCGA-DD-A3A2         TCGA-DD-A3A3 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-DD-A3A4         TCGA-DD-A3A5         TCGA-DD-A3A6 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-DD-A3A7         TCGA-DD-A3A8         TCGA-DD-A3A9 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-DD-A4NA         TCGA-DD-A4ND         TCGA-DD-A4NE 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-DD-A4NF         TCGA-DD-A4NG         TCGA-DD-A4NH 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-DD-A4NI         TCGA-DD-A4NJ         TCGA-DD-A4NK 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-DD-A4NL         TCGA-DD-A4NN         TCGA-DD-A4NO 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-DD-A4NP         TCGA-DD-A4NQ         TCGA-ED-A459 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-ED-A5KG         TCGA-EP-A12J         TCGA-EP-A26S 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EP-A2KA         TCGA-EP-A2KB         TCGA-EP-A2KC 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EP-A3JL         TCGA-EP-A3RK         TCGA-ES-A2HS 
  "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-ES-A2HT         TCGA-FV-A23B         TCGA-FV-A2QR 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-FV-A3I0         TCGA-FV-A3R2         TCGA-FV-A3R3 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-FV-A495         TCGA-FV-A496         TCGA-FV-A4ZP 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-FV-A4ZQ         TCGA-G3-A25S         TCGA-G3-A25T 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" 
        TCGA-G3-A25U         TCGA-G3-A25V         TCGA-G3-A25W 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-G3-A25X         TCGA-G3-A25Y         TCGA-G3-A25Z 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-G3-A3CG         TCGA-G3-A3CH         TCGA-G3-A3CI 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK         TCGA-G3-A5SJ 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-G3-A5SK         TCGA-G3-A5SL         TCGA-G3-A5SM 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" 
[1] "hr=" "1.3"
D29V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  16Q GAIN MUTATED         1        2         0          0          0
  16Q GAIN WILD-TYPE      44       23         2         25          3
                    vv
clus                 STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  16Q GAIN MUTATED            0        0         0         0
  16Q GAIN WILD-TYPE          4        1         1         1
D29V3, multiclass
                    vv
clus                 T1 T2 T3 T4
  16Q GAIN MUTATED    1  2  0  0
  16Q GAIN WILD-TYPE 47 26 34  6
D29V4, multiclass
    clus
vv   16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  T1                1                 47
  T2                2                 26
  T3                0                 34
  T4                0                  6
D29V5, binary
                    cls
clus                  0  1
  16Q GAIN MUTATED    2  0
  16Q GAIN WILD-TYPE 72  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED      2    0
  16Q GAIN WILD-TYPE   72    3
   clus
vv  16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  0                2                 72
  1                0                  3
                    vv
clus                 M0 M1 MX
  16Q GAIN MUTATED    3  0  1
  16Q GAIN WILD-TYPE 87  2 24
D29V6, multiclass
    clus
vv   16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  M0                3                 87
  M1                0                  2
  MX                1                 24
D29V7, binary
                    cls
clus                  0  1
  16Q GAIN MUTATED    1  3
  16Q GAIN WILD-TYPE 43 70
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED      1    3
  16Q GAIN WILD-TYPE   43   70
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  FEMALE                1                 43
  MALE                  3                 70
                    vv
clus                 R0 R1 R2 RX
  16Q GAIN MUTATED    3  0  0  0
  16Q GAIN WILD-TYPE 90 10  1  8
D29V8, multiclass
    clus
vv   16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  R0                3                 90
  R1                0                 10
  R2                0                  1
  RX                0                  8

Clustering(30) Variable = 17P GAIN MUTATION ANALYSIS
D30V1, survival
                    sevent
clus2                 0  1
  17P GAIN MUTATED    6  4
  17P GAIN WILD-TYPE 55 49
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                10                104 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                 4                 49 
$`17P GAIN MUTATED`
TCGA-BC-A10Q TCGA-CC-A3M9 TCGA-DD-A114 TCGA-DD-A3A7 TCGA-DD-A4NO TCGA-DD-A4NP 
       37.32         0.10        37.74        13.78        61.45        93.67 
TCGA-EP-A2KB TCGA-ES-A2HS TCGA-FV-A4ZP TCGA-G3-A25W 
        1.97        23.01        60.36        30.71 

$`17P GAIN WILD-TYPE`
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U 
       48.99        27.91        10.13        46.78        27.52        27.52 
TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 
        2.99        25.32        23.34         1.12        69.57         5.03 
TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-CC-5258 
       44.42        13.81         0.26        16.37         9.50         0.07 
TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3MA 
        2.86         3.02         3.39         4.24         3.32         0.07 
TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A113 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 
        0.10         0.13        79.73        83.57        53.29       112.96 
TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 
        7.33         2.60         0.46        21.76        51.25        90.67 
TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EF 
       79.36        66.31        19.76        75.65         6.67        12.95 
TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39X 
       49.15         6.02        29.16        13.64        21.14        55.66 
TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 
        5.59        19.73        25.81         7.66        70.06        17.59 
TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A8 TCGA-DD-A3A9 TCGA-DD-A4NA 
       20.12       102.74       107.11         0.36        30.58        33.14 
TCGA-DD-A4ND TCGA-DD-A4NE TCGA-DD-A4NF TCGA-DD-A4NG TCGA-DD-A4NH TCGA-DD-A4NI 
       73.38        21.67        14.07        14.93        14.24        10.78 
TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NQ TCGA-ED-A459 
       15.06        39.75        56.25        29.56        12.26         0.23 
TCGA-ED-A5KG TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KC TCGA-EP-A3JL 
        0.20        10.85         7.76        11.74         0.62         3.19 
TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3R2 
        0.43        14.40        32.45        19.07         0.20         6.35 
TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T 
        0.13         0.03         0.33         0.39         1.22        51.02 
TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG 
       53.79        28.27        58.49        14.86        21.53        22.13 
TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SJ TCGA-G3-A5SK 
       25.64         5.88        19.53        19.23        11.97         9.93 
TCGA-G3-A5SL TCGA-G3-A5SM 
        7.99         4.37 

  17P GAIN MUTATED 17P GAIN WILD-TYPE 
              0.10               0.03 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
             93.67             112.96 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
            34.015             14.895 
[1] "0.1 - 93.7 (34.0)"  "0.0 - 113.0 (14.9)"
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE"   "17P GAIN MUTATED" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-BC-A5W4 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-CC-5258         TCGA-CC-5260         TCGA-CC-5261 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-CC-5262         TCGA-CC-5263         TCGA-CC-A1HT 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-CC-A3M9         TCGA-CC-A3MA         TCGA-CC-A3MB 
  "17P GAIN MUTATED" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-CC-A3MC         TCGA-DD-A113         TCGA-DD-A114 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE"   "17P GAIN MUTATED" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DD-A1EA         TCGA-DD-A1EB         TCGA-DD-A1EC 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DD-A1ED         TCGA-DD-A1EE         TCGA-DD-A1EF 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DD-A1EH         TCGA-DD-A1EI         TCGA-DD-A1EJ 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DD-A1EL         TCGA-DD-A39V         TCGA-DD-A39X 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DD-A39Y         TCGA-DD-A39Z         TCGA-DD-A3A0 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DD-A3A1         TCGA-DD-A3A2         TCGA-DD-A3A3 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DD-A3A4         TCGA-DD-A3A5         TCGA-DD-A3A6 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DD-A3A7         TCGA-DD-A3A8         TCGA-DD-A3A9 
  "17P GAIN MUTATED" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DD-A4NA         TCGA-DD-A4ND         TCGA-DD-A4NE 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DD-A4NF         TCGA-DD-A4NG         TCGA-DD-A4NH 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DD-A4NI         TCGA-DD-A4NJ         TCGA-DD-A4NK 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DD-A4NL         TCGA-DD-A4NN         TCGA-DD-A4NO 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE"   "17P GAIN MUTATED" 
        TCGA-DD-A4NP         TCGA-DD-A4NQ         TCGA-ED-A459 
  "17P GAIN MUTATED" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-ED-A5KG         TCGA-EP-A12J         TCGA-EP-A26S 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EP-A2KA         TCGA-EP-A2KB         TCGA-EP-A2KC 
"17P GAIN WILD-TYPE"   "17P GAIN MUTATED" "17P GAIN WILD-TYPE" 
        TCGA-EP-A3JL         TCGA-EP-A3RK         TCGA-ES-A2HS 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE"   "17P GAIN MUTATED" 
        TCGA-ES-A2HT         TCGA-FV-A23B         TCGA-FV-A2QR 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-FV-A3I0         TCGA-FV-A3R2         TCGA-FV-A3R3 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-FV-A495         TCGA-FV-A496         TCGA-FV-A4ZP 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE"   "17P GAIN MUTATED" 
        TCGA-FV-A4ZQ         TCGA-G3-A25S         TCGA-G3-A25T 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-G3-A25U         TCGA-G3-A25V         TCGA-G3-A25W 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE"   "17P GAIN MUTATED" 
        TCGA-G3-A25X         TCGA-G3-A25Y         TCGA-G3-A25Z 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-G3-A3CG         TCGA-G3-A3CH         TCGA-G3-A3CI 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK         TCGA-G3-A5SJ 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-G3-A5SK         TCGA-G3-A5SL         TCGA-G3-A5SM 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE"   "17P GAIN MUTATED" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-BC-A5W4 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-CC-5258         TCGA-CC-5260         TCGA-CC-5261 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-CC-5262         TCGA-CC-5263         TCGA-CC-A1HT 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-CC-A3M9         TCGA-CC-A3MA         TCGA-CC-A3MB 
  "17P GAIN MUTATED" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-CC-A3MC         TCGA-DD-A113         TCGA-DD-A114 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE"   "17P GAIN MUTATED" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DD-A1EA         TCGA-DD-A1EB         TCGA-DD-A1EC 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DD-A1ED         TCGA-DD-A1EE         TCGA-DD-A1EF 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DD-A1EH         TCGA-DD-A1EI         TCGA-DD-A1EJ 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DD-A1EL         TCGA-DD-A39V         TCGA-DD-A39X 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DD-A39Y         TCGA-DD-A39Z         TCGA-DD-A3A0 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DD-A3A1         TCGA-DD-A3A2         TCGA-DD-A3A3 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DD-A3A4         TCGA-DD-A3A5         TCGA-DD-A3A6 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DD-A3A7         TCGA-DD-A3A8         TCGA-DD-A3A9 
  "17P GAIN MUTATED" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DD-A4NA         TCGA-DD-A4ND         TCGA-DD-A4NE 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DD-A4NF         TCGA-DD-A4NG         TCGA-DD-A4NH 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DD-A4NI         TCGA-DD-A4NJ         TCGA-DD-A4NK 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DD-A4NL         TCGA-DD-A4NN         TCGA-DD-A4NO 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE"   "17P GAIN MUTATED" 
        TCGA-DD-A4NP         TCGA-DD-A4NQ         TCGA-ED-A459 
  "17P GAIN MUTATED" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-ED-A5KG         TCGA-EP-A12J         TCGA-EP-A26S 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EP-A2KA         TCGA-EP-A2KB         TCGA-EP-A2KC 
"17P GAIN WILD-TYPE"   "17P GAIN MUTATED" "17P GAIN WILD-TYPE" 
        TCGA-EP-A3JL         TCGA-EP-A3RK         TCGA-ES-A2HS 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE"   "17P GAIN MUTATED" 
        TCGA-ES-A2HT         TCGA-FV-A23B         TCGA-FV-A2QR 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-FV-A3I0         TCGA-FV-A3R2         TCGA-FV-A3R3 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-FV-A495         TCGA-FV-A496         TCGA-FV-A4ZP 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE"   "17P GAIN MUTATED" 
        TCGA-FV-A4ZQ         TCGA-G3-A25S         TCGA-G3-A25T 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-G3-A25U         TCGA-G3-A25V         TCGA-G3-A25W 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE"   "17P GAIN MUTATED" 
        TCGA-G3-A25X         TCGA-G3-A25Y         TCGA-G3-A25Z 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-G3-A3CG         TCGA-G3-A3CH         TCGA-G3-A3CI 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK         TCGA-G3-A5SJ 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-G3-A5SK         TCGA-G3-A5SL         TCGA-G3-A5SM 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE"   "17P GAIN MUTATED" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-BC-A5W4 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-CC-5258         TCGA-CC-5260         TCGA-CC-5261 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-CC-5262         TCGA-CC-5263         TCGA-CC-A1HT 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-CC-A3M9         TCGA-CC-A3MA         TCGA-CC-A3MB 
  "17P GAIN MUTATED" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-CC-A3MC         TCGA-DD-A113         TCGA-DD-A114 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE"   "17P GAIN MUTATED" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DD-A1EA         TCGA-DD-A1EB         TCGA-DD-A1EC 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DD-A1ED         TCGA-DD-A1EE         TCGA-DD-A1EF 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DD-A1EH         TCGA-DD-A1EI         TCGA-DD-A1EJ 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DD-A1EL         TCGA-DD-A39V         TCGA-DD-A39X 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DD-A39Y         TCGA-DD-A39Z         TCGA-DD-A3A0 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DD-A3A1         TCGA-DD-A3A2         TCGA-DD-A3A3 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DD-A3A4         TCGA-DD-A3A5         TCGA-DD-A3A6 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DD-A3A7         TCGA-DD-A3A8         TCGA-DD-A3A9 
  "17P GAIN MUTATED" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DD-A4NA         TCGA-DD-A4ND         TCGA-DD-A4NE 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DD-A4NF         TCGA-DD-A4NG         TCGA-DD-A4NH 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DD-A4NI         TCGA-DD-A4NJ         TCGA-DD-A4NK 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DD-A4NL         TCGA-DD-A4NN         TCGA-DD-A4NO 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE"   "17P GAIN MUTATED" 
        TCGA-DD-A4NP         TCGA-DD-A4NQ         TCGA-ED-A459 
  "17P GAIN MUTATED" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-ED-A5KG         TCGA-EP-A12J         TCGA-EP-A26S 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EP-A2KA         TCGA-EP-A2KB         TCGA-EP-A2KC 
"17P GAIN WILD-TYPE"   "17P GAIN MUTATED" "17P GAIN WILD-TYPE" 
        TCGA-EP-A3JL         TCGA-EP-A3RK         TCGA-ES-A2HS 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE"   "17P GAIN MUTATED" 
        TCGA-ES-A2HT         TCGA-FV-A23B         TCGA-FV-A2QR 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-FV-A3I0         TCGA-FV-A3R2         TCGA-FV-A3R3 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-FV-A495         TCGA-FV-A496         TCGA-FV-A4ZP 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE"   "17P GAIN MUTATED" 
        TCGA-FV-A4ZQ         TCGA-G3-A25S         TCGA-G3-A25T 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-G3-A25U         TCGA-G3-A25V         TCGA-G3-A25W 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE"   "17P GAIN MUTATED" 
        TCGA-G3-A25X         TCGA-G3-A25Y         TCGA-G3-A25Z 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-G3-A3CG         TCGA-G3-A3CH         TCGA-G3-A3CI 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK         TCGA-G3-A5SJ 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-G3-A5SK         TCGA-G3-A5SL         TCGA-G3-A5SM 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
[1] "hr=" "1.7"
D30V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  17P GAIN MUTATED         4        1         0          2          2
  17P GAIN WILD-TYPE      41       24         2         23          1
                    vv
clus                 STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  17P GAIN MUTATED            0        0         0         0
  17P GAIN WILD-TYPE          4        1         1         1
D30V3, multiclass
                    vv
clus                 T1 T2 T3 T4
  17P GAIN MUTATED    4  2  4  0
  17P GAIN WILD-TYPE 44 26 30  6
D30V4, multiclass
    clus
vv   17P GAIN MUTATED 17P GAIN WILD-TYPE
  T1                4                 44
  T2                2                 26
  T3                4                 30
  T4                0                  6
D30V5, binary
                    cls
clus                  0  1
  17P GAIN MUTATED    5  0
  17P GAIN WILD-TYPE 69  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED      5    0
  17P GAIN WILD-TYPE   69    3
   clus
vv  17P GAIN MUTATED 17P GAIN WILD-TYPE
  0                5                 69
  1                0                  3
                    vv
clus                 M0 M1 MX
  17P GAIN MUTATED    7  0  3
  17P GAIN WILD-TYPE 83  2 22
D30V6, multiclass
    clus
vv   17P GAIN MUTATED 17P GAIN WILD-TYPE
  M0                7                 83
  M1                0                  2
  MX                3                 22
D30V7, binary
                    cls
clus                  0  1
  17P GAIN MUTATED    3  7
  17P GAIN WILD-TYPE 41 66
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED      3    7
  17P GAIN WILD-TYPE   41   66
        clus
vv       17P GAIN MUTATED 17P GAIN WILD-TYPE
  FEMALE                3                 41
  MALE                  7                 66
                    vv
clus                 R0 R1 R2 RX
  17P GAIN MUTATED    8  2  0  0
  17P GAIN WILD-TYPE 85  8  1  8
D30V8, multiclass
    clus
vv   17P GAIN MUTATED 17P GAIN WILD-TYPE
  R0                8                 85
  R1                2                  8
  R2                0                  1
  RX                0                  8

Clustering(31) Variable = 17Q GAIN MUTATION ANALYSIS
D31V1, survival
                    sevent
clus2                 0  1
  17Q GAIN MUTATED   17 18
  17Q GAIN WILD-TYPE 44 35
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                35                 79 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                18                 35 
$`17Q GAIN MUTATED`
TCGA-BC-4072 TCGA-BC-A10Q TCGA-BC-A10W TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A112 
       48.99        37.32         2.99        23.34         1.12         5.03 
TCGA-BC-A217 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5263 TCGA-CC-A3M9 TCGA-CC-A3MC 
       13.81         2.86         3.02         4.24         0.10         0.13 
TCGA-DD-A114 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A1EA TCGA-DD-A1EI TCGA-DD-A1EJ 
       37.74         7.33         2.60        79.36         6.02        29.16 
TCGA-DD-A39Y TCGA-DD-A3A3 TCGA-DD-A3A7 TCGA-DD-A3A9 TCGA-DD-A4NH TCGA-DD-A4NO 
        5.59        17.59        13.78        30.58        14.24        61.45 
TCGA-DD-A4NP TCGA-EP-A2KB TCGA-EP-A2KC TCGA-ES-A2HS TCGA-FV-A495 TCGA-FV-A4ZP 
       93.67         1.97         0.62        23.01         0.03        60.36 
TCGA-G3-A25U TCGA-G3-A25W TCGA-G3-A25Z TCGA-G3-A3CK TCGA-G3-A5SJ 
       53.79        30.71        21.53        19.23        11.97 

$`17Q GAIN WILD-TYPE`
TCGA-BC-4073 TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10X 
       27.91        10.13        46.78        27.52        27.52        25.32 
TCGA-BC-A110 TCGA-BC-A216 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-CC-5258 
       69.57        44.42         0.26        16.37         9.50         0.07 
TCGA-CC-5262 TCGA-CC-A1HT TCGA-CC-A3MA TCGA-CC-A3MB TCGA-DD-A113 TCGA-DD-A115 
        3.39         3.32         0.07         0.10        79.73        83.57 
TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 
       53.29       112.96         0.46        21.76        51.25        90.67 
TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EH 
       66.31        19.76        75.65         6.67        12.95        49.15 
TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39X TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 
       13.64        21.14        55.66        19.73        25.81         7.66 
TCGA-DD-A3A2 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A8 TCGA-DD-A4NA 
       70.06        20.12       102.74       107.11         0.36        33.14 
TCGA-DD-A4ND TCGA-DD-A4NE TCGA-DD-A4NF TCGA-DD-A4NG TCGA-DD-A4NI TCGA-DD-A4NJ 
       73.38        21.67        14.07        14.93        10.78        15.06 
TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NQ TCGA-ED-A459 TCGA-ED-A5KG 
       39.75        56.25        29.56        12.26         0.23         0.20 
TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HT 
       10.85         7.76        11.74         3.19         0.43        14.40 
TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A496 
       32.45        19.07         0.20         6.35         0.13         0.33 
TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25V TCGA-G3-A25X TCGA-G3-A25Y 
        0.39         1.22        51.02        28.27        58.49        14.86 
TCGA-G3-A3CG TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A5SK TCGA-G3-A5SL 
       22.13        25.64         5.88        19.53         9.93         7.99 
TCGA-G3-A5SM 
        4.37 

  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
              0.03               0.07 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
             93.67             112.96 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
             13.81              19.07 
[1] "0.0 - 93.7 (13.8)"  "0.1 - 113.0 (19.1)"
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
  "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
  "17Q GAIN MUTATED"   "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
  "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-BC-A5W4 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-CC-5258         TCGA-CC-5260         TCGA-CC-5261 
"17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED"   "17Q GAIN MUTATED" 
        TCGA-CC-5262         TCGA-CC-5263         TCGA-CC-A1HT 
"17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" 
        TCGA-CC-A3M9         TCGA-CC-A3MA         TCGA-CC-A3MB 
  "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-CC-A3MC         TCGA-DD-A113         TCGA-DD-A114 
  "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
  "17Q GAIN MUTATED"   "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-DD-A1EA         TCGA-DD-A1EB         TCGA-DD-A1EC 
  "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-DD-A1ED         TCGA-DD-A1EE         TCGA-DD-A1EF 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-DD-A1EH         TCGA-DD-A1EI         TCGA-DD-A1EJ 
"17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED"   "17Q GAIN MUTATED" 
        TCGA-DD-A1EL         TCGA-DD-A39V         TCGA-DD-A39X 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-DD-A39Y         TCGA-DD-A39Z         TCGA-DD-A3A0 
  "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-DD-A3A1         TCGA-DD-A3A2         TCGA-DD-A3A3 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
        TCGA-DD-A3A4         TCGA-DD-A3A5         TCGA-DD-A3A6 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-DD-A3A7         TCGA-DD-A3A8         TCGA-DD-A3A9 
  "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
        TCGA-DD-A4NA         TCGA-DD-A4ND         TCGA-DD-A4NE 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-DD-A4NF         TCGA-DD-A4NG         TCGA-DD-A4NH 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
        TCGA-DD-A4NI         TCGA-DD-A4NJ         TCGA-DD-A4NK 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-DD-A4NL         TCGA-DD-A4NN         TCGA-DD-A4NO 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
        TCGA-DD-A4NP         TCGA-DD-A4NQ         TCGA-ED-A459 
  "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-ED-A5KG         TCGA-EP-A12J         TCGA-EP-A26S 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-EP-A2KA         TCGA-EP-A2KB         TCGA-EP-A2KC 
"17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED"   "17Q GAIN MUTATED" 
        TCGA-EP-A3JL         TCGA-EP-A3RK         TCGA-ES-A2HS 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
        TCGA-ES-A2HT         TCGA-FV-A23B         TCGA-FV-A2QR 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-FV-A3I0         TCGA-FV-A3R2         TCGA-FV-A3R3 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-FV-A495         TCGA-FV-A496         TCGA-FV-A4ZP 
  "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
        TCGA-FV-A4ZQ         TCGA-G3-A25S         TCGA-G3-A25T 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-G3-A25U         TCGA-G3-A25V         TCGA-G3-A25W 
  "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
        TCGA-G3-A25X         TCGA-G3-A25Y         TCGA-G3-A25Z 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
        TCGA-G3-A3CG         TCGA-G3-A3CH         TCGA-G3-A3CI 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK         TCGA-G3-A5SJ 
"17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED"   "17Q GAIN MUTATED" 
        TCGA-G3-A5SK         TCGA-G3-A5SL         TCGA-G3-A5SM 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
  "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
  "17Q GAIN MUTATED"   "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
  "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-BC-A5W4 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-CC-5258         TCGA-CC-5260         TCGA-CC-5261 
"17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED"   "17Q GAIN MUTATED" 
        TCGA-CC-5262         TCGA-CC-5263         TCGA-CC-A1HT 
"17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" 
        TCGA-CC-A3M9         TCGA-CC-A3MA         TCGA-CC-A3MB 
  "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-CC-A3MC         TCGA-DD-A113         TCGA-DD-A114 
  "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
  "17Q GAIN MUTATED"   "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-DD-A1EA         TCGA-DD-A1EB         TCGA-DD-A1EC 
  "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-DD-A1ED         TCGA-DD-A1EE         TCGA-DD-A1EF 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-DD-A1EH         TCGA-DD-A1EI         TCGA-DD-A1EJ 
"17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED"   "17Q GAIN MUTATED" 
        TCGA-DD-A1EL         TCGA-DD-A39V         TCGA-DD-A39X 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-DD-A39Y         TCGA-DD-A39Z         TCGA-DD-A3A0 
  "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-DD-A3A1         TCGA-DD-A3A2         TCGA-DD-A3A3 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
        TCGA-DD-A3A4         TCGA-DD-A3A5         TCGA-DD-A3A6 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-DD-A3A7         TCGA-DD-A3A8         TCGA-DD-A3A9 
  "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
        TCGA-DD-A4NA         TCGA-DD-A4ND         TCGA-DD-A4NE 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-DD-A4NF         TCGA-DD-A4NG         TCGA-DD-A4NH 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
        TCGA-DD-A4NI         TCGA-DD-A4NJ         TCGA-DD-A4NK 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-DD-A4NL         TCGA-DD-A4NN         TCGA-DD-A4NO 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
        TCGA-DD-A4NP         TCGA-DD-A4NQ         TCGA-ED-A459 
  "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-ED-A5KG         TCGA-EP-A12J         TCGA-EP-A26S 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-EP-A2KA         TCGA-EP-A2KB         TCGA-EP-A2KC 
"17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED"   "17Q GAIN MUTATED" 
        TCGA-EP-A3JL         TCGA-EP-A3RK         TCGA-ES-A2HS 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
        TCGA-ES-A2HT         TCGA-FV-A23B         TCGA-FV-A2QR 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-FV-A3I0         TCGA-FV-A3R2         TCGA-FV-A3R3 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-FV-A495         TCGA-FV-A496         TCGA-FV-A4ZP 
  "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
        TCGA-FV-A4ZQ         TCGA-G3-A25S         TCGA-G3-A25T 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-G3-A25U         TCGA-G3-A25V         TCGA-G3-A25W 
  "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
        TCGA-G3-A25X         TCGA-G3-A25Y         TCGA-G3-A25Z 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
        TCGA-G3-A3CG         TCGA-G3-A3CH         TCGA-G3-A3CI 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK         TCGA-G3-A5SJ 
"17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED"   "17Q GAIN MUTATED" 
        TCGA-G3-A5SK         TCGA-G3-A5SL         TCGA-G3-A5SM 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
  "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
  "17Q GAIN MUTATED"   "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
  "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-BC-A5W4 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-CC-5258         TCGA-CC-5260         TCGA-CC-5261 
"17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED"   "17Q GAIN MUTATED" 
        TCGA-CC-5262         TCGA-CC-5263         TCGA-CC-A1HT 
"17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" 
        TCGA-CC-A3M9         TCGA-CC-A3MA         TCGA-CC-A3MB 
  "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-CC-A3MC         TCGA-DD-A113         TCGA-DD-A114 
  "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
  "17Q GAIN MUTATED"   "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-DD-A1EA         TCGA-DD-A1EB         TCGA-DD-A1EC 
  "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-DD-A1ED         TCGA-DD-A1EE         TCGA-DD-A1EF 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-DD-A1EH         TCGA-DD-A1EI         TCGA-DD-A1EJ 
"17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED"   "17Q GAIN MUTATED" 
        TCGA-DD-A1EL         TCGA-DD-A39V         TCGA-DD-A39X 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-DD-A39Y         TCGA-DD-A39Z         TCGA-DD-A3A0 
  "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-DD-A3A1         TCGA-DD-A3A2         TCGA-DD-A3A3 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
        TCGA-DD-A3A4         TCGA-DD-A3A5         TCGA-DD-A3A6 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-DD-A3A7         TCGA-DD-A3A8         TCGA-DD-A3A9 
  "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
        TCGA-DD-A4NA         TCGA-DD-A4ND         TCGA-DD-A4NE 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-DD-A4NF         TCGA-DD-A4NG         TCGA-DD-A4NH 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
        TCGA-DD-A4NI         TCGA-DD-A4NJ         TCGA-DD-A4NK 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-DD-A4NL         TCGA-DD-A4NN         TCGA-DD-A4NO 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
        TCGA-DD-A4NP         TCGA-DD-A4NQ         TCGA-ED-A459 
  "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-ED-A5KG         TCGA-EP-A12J         TCGA-EP-A26S 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-EP-A2KA         TCGA-EP-A2KB         TCGA-EP-A2KC 
"17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED"   "17Q GAIN MUTATED" 
        TCGA-EP-A3JL         TCGA-EP-A3RK         TCGA-ES-A2HS 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
        TCGA-ES-A2HT         TCGA-FV-A23B         TCGA-FV-A2QR 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-FV-A3I0         TCGA-FV-A3R2         TCGA-FV-A3R3 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-FV-A495         TCGA-FV-A496         TCGA-FV-A4ZP 
  "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
        TCGA-FV-A4ZQ         TCGA-G3-A25S         TCGA-G3-A25T 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-G3-A25U         TCGA-G3-A25V         TCGA-G3-A25W 
  "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
        TCGA-G3-A25X         TCGA-G3-A25Y         TCGA-G3-A25Z 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
        TCGA-G3-A3CG         TCGA-G3-A3CH         TCGA-G3-A3CI 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK         TCGA-G3-A5SJ 
"17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED"   "17Q GAIN MUTATED" 
        TCGA-G3-A5SK         TCGA-G3-A5SL         TCGA-G3-A5SM 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
[1] "hr=" "1.5"
D31V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  17Q GAIN MUTATED        14        5         0          6          3
  17Q GAIN WILD-TYPE      31       20         2         19          0
                    vv
clus                 STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  17Q GAIN MUTATED            2        1         0         1
  17Q GAIN WILD-TYPE          2        0         1         0
D31V3, multiclass
                    vv
clus                 T1 T2 T3 T4
  17Q GAIN MUTATED   15  6 11  4
  17Q GAIN WILD-TYPE 33 22 23  2
D31V4, multiclass
    clus
vv   17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  T1               15                 33
  T2                6                 22
  T3               11                 23
  T4                4                  2
D31V5, binary
                    cls
clus                  0  1
  17Q GAIN MUTATED   22  1
  17Q GAIN WILD-TYPE 52  2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED     22    1
  17Q GAIN WILD-TYPE   52    2
   clus
vv  17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  0               22                 52
  1                1                  2
                    vv
clus                 M0 M1 MX
  17Q GAIN MUTATED   26  2  8
  17Q GAIN WILD-TYPE 64  0 17
D31V6, multiclass
    clus
vv   17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  M0               26                 64
  M1                2                  0
  MX                8                 17
D31V7, binary
                    cls
clus                  0  1
  17Q GAIN MUTATED   12 24
  17Q GAIN WILD-TYPE 32 49
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED     12   24
  17Q GAIN WILD-TYPE   32   49
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  FEMALE               12                 32
  MALE                 24                 49
                    vv
clus                 R0 R1 R2 RX
  17Q GAIN MUTATED   27  4  1  4
  17Q GAIN WILD-TYPE 66  6  0  4
D31V8, multiclass
    clus
vv   17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  R0               27                 66
  R1                4                  6
  R2                1                  0
  RX                4                  4

Clustering(32) Variable = 18P GAIN MUTATION ANALYSIS
D32V1, survival
                    sevent
clus2                 0  1
  18P GAIN MUTATED    6  3
  18P GAIN WILD-TYPE 55 50
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                 9                105 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                 3                 50 
$`18P GAIN MUTATED`
TCGA-CC-5263 TCGA-CC-A3MC TCGA-DD-A113 TCGA-DD-A119 TCGA-DD-A4NN TCGA-EP-A3JL 
        4.24         0.13        79.73         7.33        29.56         3.19 
TCGA-FV-A4ZP TCGA-G3-A25T TCGA-G3-A25X 
       60.36        51.02        58.49 

$`18P GAIN WILD-TYPE`
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T 
       48.99        27.91        37.32        10.13        46.78        27.52 
TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 
       27.52         2.99        25.32        23.34         1.12        69.57 
TCGA-BC-A112 TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 
        5.03        44.42        13.81         0.26        16.37         9.50 
TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-A1HT TCGA-CC-A3M9 
        0.07         2.86         3.02         3.39         3.32         0.10 
TCGA-CC-A3MA TCGA-CC-A3MB TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 
        0.07         0.10        37.74        83.57        53.29       112.96 
TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA 
        2.60         0.46        21.76        51.25        90.67        79.36 
TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EH 
       66.31        19.76        75.65         6.67        12.95        49.15 
TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39X TCGA-DD-A39Y 
        6.02        29.16        13.64        21.14        55.66         5.59 
TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 
       19.73        25.81         7.66        70.06        17.59        20.12 
TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A3A9 TCGA-DD-A4NA 
      102.74       107.11        13.78         0.36        30.58        33.14 
TCGA-DD-A4ND TCGA-DD-A4NE TCGA-DD-A4NF TCGA-DD-A4NG TCGA-DD-A4NH TCGA-DD-A4NI 
       73.38        21.67        14.07        14.93        14.24        10.78 
TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ 
       15.06        39.75        56.25        61.45        93.67        12.26 
TCGA-ED-A459 TCGA-ED-A5KG TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB 
        0.23         0.20        10.85         7.76        11.74         1.97 
TCGA-EP-A2KC TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QR 
        0.62         0.43        23.01        14.40        32.45        19.07 
TCGA-FV-A3I0 TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZQ 
        0.20         6.35         0.13         0.03         0.33         0.39 
TCGA-G3-A25S TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25Y TCGA-G3-A25Z 
        1.22        53.79        28.27        30.71        14.86        21.53 
TCGA-G3-A3CG TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SJ 
       22.13        25.64         5.88        19.53        19.23        11.97 
TCGA-G3-A5SK TCGA-G3-A5SL TCGA-G3-A5SM 
        9.93         7.99         4.37 

  18P GAIN MUTATED 18P GAIN WILD-TYPE 
              0.13               0.03 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
             79.73             112.96 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
             29.56              15.06 
[1] "0.1 - 79.7 (29.6)"  "0.0 - 113.0 (15.1)"
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-BC-A5W4 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-CC-5258         TCGA-CC-5260         TCGA-CC-5261 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-CC-5262         TCGA-CC-5263         TCGA-CC-A1HT 
"18P GAIN WILD-TYPE"   "18P GAIN MUTATED" "18P GAIN WILD-TYPE" 
        TCGA-CC-A3M9         TCGA-CC-A3MA         TCGA-CC-A3MB 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-CC-A3MC         TCGA-DD-A113         TCGA-DD-A114 
  "18P GAIN MUTATED"   "18P GAIN MUTATED" "18P GAIN WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
  "18P GAIN MUTATED" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DD-A1EA         TCGA-DD-A1EB         TCGA-DD-A1EC 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DD-A1ED         TCGA-DD-A1EE         TCGA-DD-A1EF 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DD-A1EH         TCGA-DD-A1EI         TCGA-DD-A1EJ 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DD-A1EL         TCGA-DD-A39V         TCGA-DD-A39X 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DD-A39Y         TCGA-DD-A39Z         TCGA-DD-A3A0 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DD-A3A1         TCGA-DD-A3A2         TCGA-DD-A3A3 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DD-A3A4         TCGA-DD-A3A5         TCGA-DD-A3A6 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DD-A3A7         TCGA-DD-A3A8         TCGA-DD-A3A9 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DD-A4NA         TCGA-DD-A4ND         TCGA-DD-A4NE 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DD-A4NF         TCGA-DD-A4NG         TCGA-DD-A4NH 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DD-A4NI         TCGA-DD-A4NJ         TCGA-DD-A4NK 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DD-A4NL         TCGA-DD-A4NN         TCGA-DD-A4NO 
"18P GAIN WILD-TYPE"   "18P GAIN MUTATED" "18P GAIN WILD-TYPE" 
        TCGA-DD-A4NP         TCGA-DD-A4NQ         TCGA-ED-A459 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-ED-A5KG         TCGA-EP-A12J         TCGA-EP-A26S 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EP-A2KA         TCGA-EP-A2KB         TCGA-EP-A2KC 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EP-A3JL         TCGA-EP-A3RK         TCGA-ES-A2HS 
  "18P GAIN MUTATED" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-ES-A2HT         TCGA-FV-A23B         TCGA-FV-A2QR 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-FV-A3I0         TCGA-FV-A3R2         TCGA-FV-A3R3 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-FV-A495         TCGA-FV-A496         TCGA-FV-A4ZP 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE"   "18P GAIN MUTATED" 
        TCGA-FV-A4ZQ         TCGA-G3-A25S         TCGA-G3-A25T 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE"   "18P GAIN MUTATED" 
        TCGA-G3-A25U         TCGA-G3-A25V         TCGA-G3-A25W 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-G3-A25X         TCGA-G3-A25Y         TCGA-G3-A25Z 
  "18P GAIN MUTATED" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-G3-A3CG         TCGA-G3-A3CH         TCGA-G3-A3CI 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK         TCGA-G3-A5SJ 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-G3-A5SK         TCGA-G3-A5SL         TCGA-G3-A5SM 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-BC-A5W4 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-CC-5258         TCGA-CC-5260         TCGA-CC-5261 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-CC-5262         TCGA-CC-5263         TCGA-CC-A1HT 
"18P GAIN WILD-TYPE"   "18P GAIN MUTATED" "18P GAIN WILD-TYPE" 
        TCGA-CC-A3M9         TCGA-CC-A3MA         TCGA-CC-A3MB 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-CC-A3MC         TCGA-DD-A113         TCGA-DD-A114 
  "18P GAIN MUTATED"   "18P GAIN MUTATED" "18P GAIN WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
  "18P GAIN MUTATED" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DD-A1EA         TCGA-DD-A1EB         TCGA-DD-A1EC 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DD-A1ED         TCGA-DD-A1EE         TCGA-DD-A1EF 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DD-A1EH         TCGA-DD-A1EI         TCGA-DD-A1EJ 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DD-A1EL         TCGA-DD-A39V         TCGA-DD-A39X 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DD-A39Y         TCGA-DD-A39Z         TCGA-DD-A3A0 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DD-A3A1         TCGA-DD-A3A2         TCGA-DD-A3A3 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DD-A3A4         TCGA-DD-A3A5         TCGA-DD-A3A6 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DD-A3A7         TCGA-DD-A3A8         TCGA-DD-A3A9 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DD-A4NA         TCGA-DD-A4ND         TCGA-DD-A4NE 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DD-A4NF         TCGA-DD-A4NG         TCGA-DD-A4NH 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DD-A4NI         TCGA-DD-A4NJ         TCGA-DD-A4NK 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DD-A4NL         TCGA-DD-A4NN         TCGA-DD-A4NO 
"18P GAIN WILD-TYPE"   "18P GAIN MUTATED" "18P GAIN WILD-TYPE" 
        TCGA-DD-A4NP         TCGA-DD-A4NQ         TCGA-ED-A459 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-ED-A5KG         TCGA-EP-A12J         TCGA-EP-A26S 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EP-A2KA         TCGA-EP-A2KB         TCGA-EP-A2KC 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EP-A3JL         TCGA-EP-A3RK         TCGA-ES-A2HS 
  "18P GAIN MUTATED" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-ES-A2HT         TCGA-FV-A23B         TCGA-FV-A2QR 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-FV-A3I0         TCGA-FV-A3R2         TCGA-FV-A3R3 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-FV-A495         TCGA-FV-A496         TCGA-FV-A4ZP 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE"   "18P GAIN MUTATED" 
        TCGA-FV-A4ZQ         TCGA-G3-A25S         TCGA-G3-A25T 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE"   "18P GAIN MUTATED" 
        TCGA-G3-A25U         TCGA-G3-A25V         TCGA-G3-A25W 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-G3-A25X         TCGA-G3-A25Y         TCGA-G3-A25Z 
  "18P GAIN MUTATED" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-G3-A3CG         TCGA-G3-A3CH         TCGA-G3-A3CI 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK         TCGA-G3-A5SJ 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-G3-A5SK         TCGA-G3-A5SL         TCGA-G3-A5SM 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-BC-A5W4 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-CC-5258         TCGA-CC-5260         TCGA-CC-5261 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-CC-5262         TCGA-CC-5263         TCGA-CC-A1HT 
"18P GAIN WILD-TYPE"   "18P GAIN MUTATED" "18P GAIN WILD-TYPE" 
        TCGA-CC-A3M9         TCGA-CC-A3MA         TCGA-CC-A3MB 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-CC-A3MC         TCGA-DD-A113         TCGA-DD-A114 
  "18P GAIN MUTATED"   "18P GAIN MUTATED" "18P GAIN WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
  "18P GAIN MUTATED" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DD-A1EA         TCGA-DD-A1EB         TCGA-DD-A1EC 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DD-A1ED         TCGA-DD-A1EE         TCGA-DD-A1EF 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DD-A1EH         TCGA-DD-A1EI         TCGA-DD-A1EJ 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DD-A1EL         TCGA-DD-A39V         TCGA-DD-A39X 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DD-A39Y         TCGA-DD-A39Z         TCGA-DD-A3A0 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DD-A3A1         TCGA-DD-A3A2         TCGA-DD-A3A3 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DD-A3A4         TCGA-DD-A3A5         TCGA-DD-A3A6 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DD-A3A7         TCGA-DD-A3A8         TCGA-DD-A3A9 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DD-A4NA         TCGA-DD-A4ND         TCGA-DD-A4NE 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DD-A4NF         TCGA-DD-A4NG         TCGA-DD-A4NH 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DD-A4NI         TCGA-DD-A4NJ         TCGA-DD-A4NK 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DD-A4NL         TCGA-DD-A4NN         TCGA-DD-A4NO 
"18P GAIN WILD-TYPE"   "18P GAIN MUTATED" "18P GAIN WILD-TYPE" 
        TCGA-DD-A4NP         TCGA-DD-A4NQ         TCGA-ED-A459 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-ED-A5KG         TCGA-EP-A12J         TCGA-EP-A26S 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EP-A2KA         TCGA-EP-A2KB         TCGA-EP-A2KC 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EP-A3JL         TCGA-EP-A3RK         TCGA-ES-A2HS 
  "18P GAIN MUTATED" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-ES-A2HT         TCGA-FV-A23B         TCGA-FV-A2QR 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-FV-A3I0         TCGA-FV-A3R2         TCGA-FV-A3R3 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-FV-A495         TCGA-FV-A496         TCGA-FV-A4ZP 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE"   "18P GAIN MUTATED" 
        TCGA-FV-A4ZQ         TCGA-G3-A25S         TCGA-G3-A25T 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE"   "18P GAIN MUTATED" 
        TCGA-G3-A25U         TCGA-G3-A25V         TCGA-G3-A25W 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-G3-A25X         TCGA-G3-A25Y         TCGA-G3-A25Z 
  "18P GAIN MUTATED" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-G3-A3CG         TCGA-G3-A3CH         TCGA-G3-A3CI 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK         TCGA-G3-A5SJ 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-G3-A5SK         TCGA-G3-A5SL         TCGA-G3-A5SM 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
[1] "hr=" "1.7"
D32V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  18P GAIN MUTATED         2        2         0          3          0
  18P GAIN WILD-TYPE      43       23         2         22          3
                    vv
clus                 STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  18P GAIN MUTATED            0        1         0         0
  18P GAIN WILD-TYPE          4        0         1         1
D32V3, multiclass
                    vv
clus                 T1 T2 T3 T4
  18P GAIN MUTATED    2  2  4  0
  18P GAIN WILD-TYPE 46 26 30  6
D32V4, multiclass
    clus
vv   18P GAIN MUTATED 18P GAIN WILD-TYPE
  T1                2                 46
  T2                2                 26
  T3                4                 30
  T4                0                  6
D32V5, binary
                    cls
clus                  0  1
  18P GAIN MUTATED    7  0
  18P GAIN WILD-TYPE 67  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED      7    0
  18P GAIN WILD-TYPE   67    3
   clus
vv  18P GAIN MUTATED 18P GAIN WILD-TYPE
  0                7                 67
  1                0                  3
                    vv
clus                 M0 M1 MX
  18P GAIN MUTATED    7  1  1
  18P GAIN WILD-TYPE 83  1 24
D32V6, multiclass
    clus
vv   18P GAIN MUTATED 18P GAIN WILD-TYPE
  M0                7                 83
  M1                1                  1
  MX                1                 24
D32V7, binary
                    cls
clus                  0  1
  18P GAIN MUTATED    3  6
  18P GAIN WILD-TYPE 41 67
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED      3    6
  18P GAIN WILD-TYPE   41   67
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  FEMALE                3                 41
  MALE                  6                 67
                    vv
clus                 R0 R1 R2 RX
  18P GAIN MUTATED    5  1  1  1
  18P GAIN WILD-TYPE 88  9  0  7
D32V8, multiclass
    clus
vv   18P GAIN MUTATED 18P GAIN WILD-TYPE
  R0                5                 88
  R1                1                  9
  R2                1                  0
  RX                1                  7

Clustering(33) Variable = 18Q GAIN MUTATION ANALYSIS
D33V1, survival
                    sevent
clus2                 0  1
  18Q GAIN MUTATED    6  3
  18Q GAIN WILD-TYPE 55 50
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 9                105 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 3                 50 
$`18Q GAIN MUTATED`
TCGA-CC-5263 TCGA-CC-A3MC TCGA-DD-A113 TCGA-DD-A119 TCGA-DD-A4NN TCGA-EP-A3JL 
        4.24         0.13        79.73         7.33        29.56         3.19 
TCGA-FV-A4ZP TCGA-G3-A25T TCGA-G3-A25X 
       60.36        51.02        58.49 

$`18Q GAIN WILD-TYPE`
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T 
       48.99        27.91        37.32        10.13        46.78        27.52 
TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 
       27.52         2.99        25.32        23.34         1.12        69.57 
TCGA-BC-A112 TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 
        5.03        44.42        13.81         0.26        16.37         9.50 
TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-A1HT TCGA-CC-A3M9 
        0.07         2.86         3.02         3.39         3.32         0.10 
TCGA-CC-A3MA TCGA-CC-A3MB TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 
        0.07         0.10        37.74        83.57        53.29       112.96 
TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA 
        2.60         0.46        21.76        51.25        90.67        79.36 
TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EH 
       66.31        19.76        75.65         6.67        12.95        49.15 
TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39X TCGA-DD-A39Y 
        6.02        29.16        13.64        21.14        55.66         5.59 
TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 
       19.73        25.81         7.66        70.06        17.59        20.12 
TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A3A9 TCGA-DD-A4NA 
      102.74       107.11        13.78         0.36        30.58        33.14 
TCGA-DD-A4ND TCGA-DD-A4NE TCGA-DD-A4NF TCGA-DD-A4NG TCGA-DD-A4NH TCGA-DD-A4NI 
       73.38        21.67        14.07        14.93        14.24        10.78 
TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ 
       15.06        39.75        56.25        61.45        93.67        12.26 
TCGA-ED-A459 TCGA-ED-A5KG TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB 
        0.23         0.20        10.85         7.76        11.74         1.97 
TCGA-EP-A2KC TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QR 
        0.62         0.43        23.01        14.40        32.45        19.07 
TCGA-FV-A3I0 TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZQ 
        0.20         6.35         0.13         0.03         0.33         0.39 
TCGA-G3-A25S TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25Y TCGA-G3-A25Z 
        1.22        53.79        28.27        30.71        14.86        21.53 
TCGA-G3-A3CG TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SJ 
       22.13        25.64         5.88        19.53        19.23        11.97 
TCGA-G3-A5SK TCGA-G3-A5SL TCGA-G3-A5SM 
        9.93         7.99         4.37 

  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
              0.13               0.03 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
             79.73             112.96 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
             29.56              15.06 
[1] "0.1 - 79.7 (29.6)"  "0.0 - 113.0 (15.1)"
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-BC-A5W4 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-CC-5258         TCGA-CC-5260         TCGA-CC-5261 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-CC-5262         TCGA-CC-5263         TCGA-CC-A1HT 
"18Q GAIN WILD-TYPE"   "18Q GAIN MUTATED" "18Q GAIN WILD-TYPE" 
        TCGA-CC-A3M9         TCGA-CC-A3MA         TCGA-CC-A3MB 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-CC-A3MC         TCGA-DD-A113         TCGA-DD-A114 
  "18Q GAIN MUTATED"   "18Q GAIN MUTATED" "18Q GAIN WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
  "18Q GAIN MUTATED" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DD-A1EA         TCGA-DD-A1EB         TCGA-DD-A1EC 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DD-A1ED         TCGA-DD-A1EE         TCGA-DD-A1EF 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DD-A1EH         TCGA-DD-A1EI         TCGA-DD-A1EJ 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DD-A1EL         TCGA-DD-A39V         TCGA-DD-A39X 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DD-A39Y         TCGA-DD-A39Z         TCGA-DD-A3A0 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DD-A3A1         TCGA-DD-A3A2         TCGA-DD-A3A3 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DD-A3A4         TCGA-DD-A3A5         TCGA-DD-A3A6 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DD-A3A7         TCGA-DD-A3A8         TCGA-DD-A3A9 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DD-A4NA         TCGA-DD-A4ND         TCGA-DD-A4NE 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DD-A4NF         TCGA-DD-A4NG         TCGA-DD-A4NH 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DD-A4NI         TCGA-DD-A4NJ         TCGA-DD-A4NK 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DD-A4NL         TCGA-DD-A4NN         TCGA-DD-A4NO 
"18Q GAIN WILD-TYPE"   "18Q GAIN MUTATED" "18Q GAIN WILD-TYPE" 
        TCGA-DD-A4NP         TCGA-DD-A4NQ         TCGA-ED-A459 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-ED-A5KG         TCGA-EP-A12J         TCGA-EP-A26S 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EP-A2KA         TCGA-EP-A2KB         TCGA-EP-A2KC 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EP-A3JL         TCGA-EP-A3RK         TCGA-ES-A2HS 
  "18Q GAIN MUTATED" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-ES-A2HT         TCGA-FV-A23B         TCGA-FV-A2QR 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-FV-A3I0         TCGA-FV-A3R2         TCGA-FV-A3R3 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-FV-A495         TCGA-FV-A496         TCGA-FV-A4ZP 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE"   "18Q GAIN MUTATED" 
        TCGA-FV-A4ZQ         TCGA-G3-A25S         TCGA-G3-A25T 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE"   "18Q GAIN MUTATED" 
        TCGA-G3-A25U         TCGA-G3-A25V         TCGA-G3-A25W 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-G3-A25X         TCGA-G3-A25Y         TCGA-G3-A25Z 
  "18Q GAIN MUTATED" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-G3-A3CG         TCGA-G3-A3CH         TCGA-G3-A3CI 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK         TCGA-G3-A5SJ 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-G3-A5SK         TCGA-G3-A5SL         TCGA-G3-A5SM 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-BC-A5W4 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-CC-5258         TCGA-CC-5260         TCGA-CC-5261 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-CC-5262         TCGA-CC-5263         TCGA-CC-A1HT 
"18Q GAIN WILD-TYPE"   "18Q GAIN MUTATED" "18Q GAIN WILD-TYPE" 
        TCGA-CC-A3M9         TCGA-CC-A3MA         TCGA-CC-A3MB 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-CC-A3MC         TCGA-DD-A113         TCGA-DD-A114 
  "18Q GAIN MUTATED"   "18Q GAIN MUTATED" "18Q GAIN WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
  "18Q GAIN MUTATED" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DD-A1EA         TCGA-DD-A1EB         TCGA-DD-A1EC 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DD-A1ED         TCGA-DD-A1EE         TCGA-DD-A1EF 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DD-A1EH         TCGA-DD-A1EI         TCGA-DD-A1EJ 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DD-A1EL         TCGA-DD-A39V         TCGA-DD-A39X 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DD-A39Y         TCGA-DD-A39Z         TCGA-DD-A3A0 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DD-A3A1         TCGA-DD-A3A2         TCGA-DD-A3A3 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DD-A3A4         TCGA-DD-A3A5         TCGA-DD-A3A6 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DD-A3A7         TCGA-DD-A3A8         TCGA-DD-A3A9 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DD-A4NA         TCGA-DD-A4ND         TCGA-DD-A4NE 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DD-A4NF         TCGA-DD-A4NG         TCGA-DD-A4NH 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DD-A4NI         TCGA-DD-A4NJ         TCGA-DD-A4NK 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DD-A4NL         TCGA-DD-A4NN         TCGA-DD-A4NO 
"18Q GAIN WILD-TYPE"   "18Q GAIN MUTATED" "18Q GAIN WILD-TYPE" 
        TCGA-DD-A4NP         TCGA-DD-A4NQ         TCGA-ED-A459 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-ED-A5KG         TCGA-EP-A12J         TCGA-EP-A26S 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EP-A2KA         TCGA-EP-A2KB         TCGA-EP-A2KC 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EP-A3JL         TCGA-EP-A3RK         TCGA-ES-A2HS 
  "18Q GAIN MUTATED" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-ES-A2HT         TCGA-FV-A23B         TCGA-FV-A2QR 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-FV-A3I0         TCGA-FV-A3R2         TCGA-FV-A3R3 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-FV-A495         TCGA-FV-A496         TCGA-FV-A4ZP 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE"   "18Q GAIN MUTATED" 
        TCGA-FV-A4ZQ         TCGA-G3-A25S         TCGA-G3-A25T 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE"   "18Q GAIN MUTATED" 
        TCGA-G3-A25U         TCGA-G3-A25V         TCGA-G3-A25W 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-G3-A25X         TCGA-G3-A25Y         TCGA-G3-A25Z 
  "18Q GAIN MUTATED" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-G3-A3CG         TCGA-G3-A3CH         TCGA-G3-A3CI 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK         TCGA-G3-A5SJ 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-G3-A5SK         TCGA-G3-A5SL         TCGA-G3-A5SM 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-BC-A5W4 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-CC-5258         TCGA-CC-5260         TCGA-CC-5261 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-CC-5262         TCGA-CC-5263         TCGA-CC-A1HT 
"18Q GAIN WILD-TYPE"   "18Q GAIN MUTATED" "18Q GAIN WILD-TYPE" 
        TCGA-CC-A3M9         TCGA-CC-A3MA         TCGA-CC-A3MB 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-CC-A3MC         TCGA-DD-A113         TCGA-DD-A114 
  "18Q GAIN MUTATED"   "18Q GAIN MUTATED" "18Q GAIN WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
  "18Q GAIN MUTATED" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DD-A1EA         TCGA-DD-A1EB         TCGA-DD-A1EC 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DD-A1ED         TCGA-DD-A1EE         TCGA-DD-A1EF 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DD-A1EH         TCGA-DD-A1EI         TCGA-DD-A1EJ 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DD-A1EL         TCGA-DD-A39V         TCGA-DD-A39X 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DD-A39Y         TCGA-DD-A39Z         TCGA-DD-A3A0 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DD-A3A1         TCGA-DD-A3A2         TCGA-DD-A3A3 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DD-A3A4         TCGA-DD-A3A5         TCGA-DD-A3A6 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DD-A3A7         TCGA-DD-A3A8         TCGA-DD-A3A9 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DD-A4NA         TCGA-DD-A4ND         TCGA-DD-A4NE 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DD-A4NF         TCGA-DD-A4NG         TCGA-DD-A4NH 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DD-A4NI         TCGA-DD-A4NJ         TCGA-DD-A4NK 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DD-A4NL         TCGA-DD-A4NN         TCGA-DD-A4NO 
"18Q GAIN WILD-TYPE"   "18Q GAIN MUTATED" "18Q GAIN WILD-TYPE" 
        TCGA-DD-A4NP         TCGA-DD-A4NQ         TCGA-ED-A459 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-ED-A5KG         TCGA-EP-A12J         TCGA-EP-A26S 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EP-A2KA         TCGA-EP-A2KB         TCGA-EP-A2KC 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EP-A3JL         TCGA-EP-A3RK         TCGA-ES-A2HS 
  "18Q GAIN MUTATED" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-ES-A2HT         TCGA-FV-A23B         TCGA-FV-A2QR 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-FV-A3I0         TCGA-FV-A3R2         TCGA-FV-A3R3 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-FV-A495         TCGA-FV-A496         TCGA-FV-A4ZP 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE"   "18Q GAIN MUTATED" 
        TCGA-FV-A4ZQ         TCGA-G3-A25S         TCGA-G3-A25T 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE"   "18Q GAIN MUTATED" 
        TCGA-G3-A25U         TCGA-G3-A25V         TCGA-G3-A25W 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-G3-A25X         TCGA-G3-A25Y         TCGA-G3-A25Z 
  "18Q GAIN MUTATED" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-G3-A3CG         TCGA-G3-A3CH         TCGA-G3-A3CI 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK         TCGA-G3-A5SJ 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-G3-A5SK         TCGA-G3-A5SL         TCGA-G3-A5SM 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
[1] "hr=" "1.7"
D33V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  18Q GAIN MUTATED         2        2         0          3          0
  18Q GAIN WILD-TYPE      43       23         2         22          3
                    vv
clus                 STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  18Q GAIN MUTATED            0        1         0         0
  18Q GAIN WILD-TYPE          4        0         1         1
D33V3, multiclass
                    vv
clus                 T1 T2 T3 T4
  18Q GAIN MUTATED    2  2  4  0
  18Q GAIN WILD-TYPE 46 26 30  6
D33V4, multiclass
    clus
vv   18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  T1                2                 46
  T2                2                 26
  T3                4                 30
  T4                0                  6
D33V5, binary
                    cls
clus                  0  1
  18Q GAIN MUTATED    7  0
  18Q GAIN WILD-TYPE 67  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      7    0
  18Q GAIN WILD-TYPE   67    3
   clus
vv  18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  0                7                 67
  1                0                  3
                    vv
clus                 M0 M1 MX
  18Q GAIN MUTATED    7  1  1
  18Q GAIN WILD-TYPE 83  1 24
D33V6, multiclass
    clus
vv   18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  M0                7                 83
  M1                1                  1
  MX                1                 24
D33V7, binary
                    cls
clus                  0  1
  18Q GAIN MUTATED    3  6
  18Q GAIN WILD-TYPE 41 67
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      3    6
  18Q GAIN WILD-TYPE   41   67
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  FEMALE                3                 41
  MALE                  6                 67
                    vv
clus                 R0 R1 R2 RX
  18Q GAIN MUTATED    5  1  1  1
  18Q GAIN WILD-TYPE 88  9  0  7
D33V8, multiclass
    clus
vv   18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  R0                5                 88
  R1                1                  9
  R2                1                  0
  RX                1                  7

Clustering(34) Variable = 19P GAIN MUTATION ANALYSIS
D34V1, survival
                    sevent
clus2                 0  1
  19P GAIN MUTATED   13 13
  19P GAIN WILD-TYPE 48 40
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                26                 88 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                13                 40 
$`19P GAIN MUTATED`
TCGA-BC-A10Q TCGA-CC-5261 TCGA-DD-A113 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A1E9 
       37.32         3.02        79.73       112.96         7.33        90.67 
TCGA-DD-A1EC TCGA-DD-A1EF TCGA-DD-A39V TCGA-DD-A39X TCGA-DD-A3A7 TCGA-DD-A3A9 
       19.76        12.95        21.14        55.66        13.78        30.58 
TCGA-DD-A4ND TCGA-DD-A4NI TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NQ TCGA-EP-A2KB 
       73.38        10.78        29.56        61.45        12.26         1.97 
TCGA-EP-A2KC TCGA-EP-A3JL TCGA-ES-A2HS TCGA-FV-A23B TCGA-FV-A3I0 TCGA-G3-A25T 
        0.62         3.19        23.01        32.45         0.20        51.02 
TCGA-G3-A25X TCGA-G3-A5SM 
       58.49         4.37 

$`19P GAIN WILD-TYPE`
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U 
       48.99        27.91        10.13        46.78        27.52        27.52 
TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 
        2.99        25.32        23.34         1.12        69.57         5.03 
TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-CC-5258 
       44.42        13.81         0.26        16.37         9.50         0.07 
TCGA-CC-5260 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA 
        2.86         3.39         4.24         3.32         0.10         0.07 
TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A11A 
        0.10         0.13        37.74        83.57        53.29         2.60 
TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1ED 
        0.46        21.76        51.25        79.36        66.31        75.65 
TCGA-DD-A1EE TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EL TCGA-DD-A39Y 
        6.67        49.15         6.02        29.16        13.64         5.59 
TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 
       19.73        25.81         7.66        70.06        17.59        20.12 
TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A8 TCGA-DD-A4NA TCGA-DD-A4NE TCGA-DD-A4NF 
      102.74       107.11         0.36        33.14        21.67        14.07 
TCGA-DD-A4NG TCGA-DD-A4NH TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NP 
       14.93        14.24        15.06        39.75        56.25        93.67 
TCGA-ED-A459 TCGA-ED-A5KG TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A3RK 
        0.23         0.20        10.85         7.76        11.74         0.43 
TCGA-ES-A2HT TCGA-FV-A2QR TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 
       14.40        19.07         6.35         0.13         0.03         0.33 
TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W 
       60.36         0.39         1.22        53.79        28.27        30.71 
TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ 
       14.86        21.53        22.13        25.64         5.88        19.53 
TCGA-G3-A3CK TCGA-G3-A5SJ TCGA-G3-A5SK TCGA-G3-A5SL 
       19.23        11.97         9.93         7.99 

  19P GAIN MUTATED 19P GAIN WILD-TYPE 
              0.20               0.03 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
            112.96             107.11 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
            22.075             14.895 
[1] "0.2 - 113.0 (22.1)" "0.0 - 107.1 (14.9)"
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE"   "19P GAIN MUTATED" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-BC-A5W4 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-CC-5258         TCGA-CC-5260         TCGA-CC-5261 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE"   "19P GAIN MUTATED" 
        TCGA-CC-5262         TCGA-CC-5263         TCGA-CC-A1HT 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-CC-A3M9         TCGA-CC-A3MA         TCGA-CC-A3MB 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-CC-A3MC         TCGA-DD-A113         TCGA-DD-A114 
"19P GAIN WILD-TYPE"   "19P GAIN MUTATED" "19P GAIN WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE"   "19P GAIN MUTATED" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
  "19P GAIN MUTATED" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE"   "19P GAIN MUTATED" 
        TCGA-DD-A1EA         TCGA-DD-A1EB         TCGA-DD-A1EC 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE"   "19P GAIN MUTATED" 
        TCGA-DD-A1ED         TCGA-DD-A1EE         TCGA-DD-A1EF 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE"   "19P GAIN MUTATED" 
        TCGA-DD-A1EH         TCGA-DD-A1EI         TCGA-DD-A1EJ 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-DD-A1EL         TCGA-DD-A39V         TCGA-DD-A39X 
"19P GAIN WILD-TYPE"   "19P GAIN MUTATED"   "19P GAIN MUTATED" 
        TCGA-DD-A39Y         TCGA-DD-A39Z         TCGA-DD-A3A0 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-DD-A3A1         TCGA-DD-A3A2         TCGA-DD-A3A3 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-DD-A3A4         TCGA-DD-A3A5         TCGA-DD-A3A6 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-DD-A3A7         TCGA-DD-A3A8         TCGA-DD-A3A9 
  "19P GAIN MUTATED" "19P GAIN WILD-TYPE"   "19P GAIN MUTATED" 
        TCGA-DD-A4NA         TCGA-DD-A4ND         TCGA-DD-A4NE 
"19P GAIN WILD-TYPE"   "19P GAIN MUTATED" "19P GAIN WILD-TYPE" 
        TCGA-DD-A4NF         TCGA-DD-A4NG         TCGA-DD-A4NH 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-DD-A4NI         TCGA-DD-A4NJ         TCGA-DD-A4NK 
  "19P GAIN MUTATED" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-DD-A4NL         TCGA-DD-A4NN         TCGA-DD-A4NO 
"19P GAIN WILD-TYPE"   "19P GAIN MUTATED"   "19P GAIN MUTATED" 
        TCGA-DD-A4NP         TCGA-DD-A4NQ         TCGA-ED-A459 
"19P GAIN WILD-TYPE"   "19P GAIN MUTATED" "19P GAIN WILD-TYPE" 
        TCGA-ED-A5KG         TCGA-EP-A12J         TCGA-EP-A26S 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EP-A2KA         TCGA-EP-A2KB         TCGA-EP-A2KC 
"19P GAIN WILD-TYPE"   "19P GAIN MUTATED"   "19P GAIN MUTATED" 
        TCGA-EP-A3JL         TCGA-EP-A3RK         TCGA-ES-A2HS 
  "19P GAIN MUTATED" "19P GAIN WILD-TYPE"   "19P GAIN MUTATED" 
        TCGA-ES-A2HT         TCGA-FV-A23B         TCGA-FV-A2QR 
"19P GAIN WILD-TYPE"   "19P GAIN MUTATED" "19P GAIN WILD-TYPE" 
        TCGA-FV-A3I0         TCGA-FV-A3R2         TCGA-FV-A3R3 
  "19P GAIN MUTATED" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-FV-A495         TCGA-FV-A496         TCGA-FV-A4ZP 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-FV-A4ZQ         TCGA-G3-A25S         TCGA-G3-A25T 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE"   "19P GAIN MUTATED" 
        TCGA-G3-A25U         TCGA-G3-A25V         TCGA-G3-A25W 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-G3-A25X         TCGA-G3-A25Y         TCGA-G3-A25Z 
  "19P GAIN MUTATED" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-G3-A3CG         TCGA-G3-A3CH         TCGA-G3-A3CI 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK         TCGA-G3-A5SJ 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-G3-A5SK         TCGA-G3-A5SL         TCGA-G3-A5SM 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE"   "19P GAIN MUTATED" 
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE"   "19P GAIN MUTATED" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-BC-A5W4 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-CC-5258         TCGA-CC-5260         TCGA-CC-5261 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE"   "19P GAIN MUTATED" 
        TCGA-CC-5262         TCGA-CC-5263         TCGA-CC-A1HT 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-CC-A3M9         TCGA-CC-A3MA         TCGA-CC-A3MB 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-CC-A3MC         TCGA-DD-A113         TCGA-DD-A114 
"19P GAIN WILD-TYPE"   "19P GAIN MUTATED" "19P GAIN WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE"   "19P GAIN MUTATED" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
  "19P GAIN MUTATED" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE"   "19P GAIN MUTATED" 
        TCGA-DD-A1EA         TCGA-DD-A1EB         TCGA-DD-A1EC 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE"   "19P GAIN MUTATED" 
        TCGA-DD-A1ED         TCGA-DD-A1EE         TCGA-DD-A1EF 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE"   "19P GAIN MUTATED" 
        TCGA-DD-A1EH         TCGA-DD-A1EI         TCGA-DD-A1EJ 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-DD-A1EL         TCGA-DD-A39V         TCGA-DD-A39X 
"19P GAIN WILD-TYPE"   "19P GAIN MUTATED"   "19P GAIN MUTATED" 
        TCGA-DD-A39Y         TCGA-DD-A39Z         TCGA-DD-A3A0 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-DD-A3A1         TCGA-DD-A3A2         TCGA-DD-A3A3 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-DD-A3A4         TCGA-DD-A3A5         TCGA-DD-A3A6 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-DD-A3A7         TCGA-DD-A3A8         TCGA-DD-A3A9 
  "19P GAIN MUTATED" "19P GAIN WILD-TYPE"   "19P GAIN MUTATED" 
        TCGA-DD-A4NA         TCGA-DD-A4ND         TCGA-DD-A4NE 
"19P GAIN WILD-TYPE"   "19P GAIN MUTATED" "19P GAIN WILD-TYPE" 
        TCGA-DD-A4NF         TCGA-DD-A4NG         TCGA-DD-A4NH 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-DD-A4NI         TCGA-DD-A4NJ         TCGA-DD-A4NK 
  "19P GAIN MUTATED" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-DD-A4NL         TCGA-DD-A4NN         TCGA-DD-A4NO 
"19P GAIN WILD-TYPE"   "19P GAIN MUTATED"   "19P GAIN MUTATED" 
        TCGA-DD-A4NP         TCGA-DD-A4NQ         TCGA-ED-A459 
"19P GAIN WILD-TYPE"   "19P GAIN MUTATED" "19P GAIN WILD-TYPE" 
        TCGA-ED-A5KG         TCGA-EP-A12J         TCGA-EP-A26S 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EP-A2KA         TCGA-EP-A2KB         TCGA-EP-A2KC 
"19P GAIN WILD-TYPE"   "19P GAIN MUTATED"   "19P GAIN MUTATED" 
        TCGA-EP-A3JL         TCGA-EP-A3RK         TCGA-ES-A2HS 
  "19P GAIN MUTATED" "19P GAIN WILD-TYPE"   "19P GAIN MUTATED" 
        TCGA-ES-A2HT         TCGA-FV-A23B         TCGA-FV-A2QR 
"19P GAIN WILD-TYPE"   "19P GAIN MUTATED" "19P GAIN WILD-TYPE" 
        TCGA-FV-A3I0         TCGA-FV-A3R2         TCGA-FV-A3R3 
  "19P GAIN MUTATED" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-FV-A495         TCGA-FV-A496         TCGA-FV-A4ZP 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-FV-A4ZQ         TCGA-G3-A25S         TCGA-G3-A25T 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE"   "19P GAIN MUTATED" 
        TCGA-G3-A25U         TCGA-G3-A25V         TCGA-G3-A25W 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-G3-A25X         TCGA-G3-A25Y         TCGA-G3-A25Z 
  "19P GAIN MUTATED" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-G3-A3CG         TCGA-G3-A3CH         TCGA-G3-A3CI 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK         TCGA-G3-A5SJ 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-G3-A5SK         TCGA-G3-A5SL         TCGA-G3-A5SM 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE"   "19P GAIN MUTATED" 
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE"   "19P GAIN MUTATED" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-BC-A5W4 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-CC-5258         TCGA-CC-5260         TCGA-CC-5261 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE"   "19P GAIN MUTATED" 
        TCGA-CC-5262         TCGA-CC-5263         TCGA-CC-A1HT 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-CC-A3M9         TCGA-CC-A3MA         TCGA-CC-A3MB 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-CC-A3MC         TCGA-DD-A113         TCGA-DD-A114 
"19P GAIN WILD-TYPE"   "19P GAIN MUTATED" "19P GAIN WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE"   "19P GAIN MUTATED" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
  "19P GAIN MUTATED" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE"   "19P GAIN MUTATED" 
        TCGA-DD-A1EA         TCGA-DD-A1EB         TCGA-DD-A1EC 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE"   "19P GAIN MUTATED" 
        TCGA-DD-A1ED         TCGA-DD-A1EE         TCGA-DD-A1EF 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE"   "19P GAIN MUTATED" 
        TCGA-DD-A1EH         TCGA-DD-A1EI         TCGA-DD-A1EJ 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-DD-A1EL         TCGA-DD-A39V         TCGA-DD-A39X 
"19P GAIN WILD-TYPE"   "19P GAIN MUTATED"   "19P GAIN MUTATED" 
        TCGA-DD-A39Y         TCGA-DD-A39Z         TCGA-DD-A3A0 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-DD-A3A1         TCGA-DD-A3A2         TCGA-DD-A3A3 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-DD-A3A4         TCGA-DD-A3A5         TCGA-DD-A3A6 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-DD-A3A7         TCGA-DD-A3A8         TCGA-DD-A3A9 
  "19P GAIN MUTATED" "19P GAIN WILD-TYPE"   "19P GAIN MUTATED" 
        TCGA-DD-A4NA         TCGA-DD-A4ND         TCGA-DD-A4NE 
"19P GAIN WILD-TYPE"   "19P GAIN MUTATED" "19P GAIN WILD-TYPE" 
        TCGA-DD-A4NF         TCGA-DD-A4NG         TCGA-DD-A4NH 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-DD-A4NI         TCGA-DD-A4NJ         TCGA-DD-A4NK 
  "19P GAIN MUTATED" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-DD-A4NL         TCGA-DD-A4NN         TCGA-DD-A4NO 
"19P GAIN WILD-TYPE"   "19P GAIN MUTATED"   "19P GAIN MUTATED" 
        TCGA-DD-A4NP         TCGA-DD-A4NQ         TCGA-ED-A459 
"19P GAIN WILD-TYPE"   "19P GAIN MUTATED" "19P GAIN WILD-TYPE" 
        TCGA-ED-A5KG         TCGA-EP-A12J         TCGA-EP-A26S 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EP-A2KA         TCGA-EP-A2KB         TCGA-EP-A2KC 
"19P GAIN WILD-TYPE"   "19P GAIN MUTATED"   "19P GAIN MUTATED" 
        TCGA-EP-A3JL         TCGA-EP-A3RK         TCGA-ES-A2HS 
  "19P GAIN MUTATED" "19P GAIN WILD-TYPE"   "19P GAIN MUTATED" 
        TCGA-ES-A2HT         TCGA-FV-A23B         TCGA-FV-A2QR 
"19P GAIN WILD-TYPE"   "19P GAIN MUTATED" "19P GAIN WILD-TYPE" 
        TCGA-FV-A3I0         TCGA-FV-A3R2         TCGA-FV-A3R3 
  "19P GAIN MUTATED" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-FV-A495         TCGA-FV-A496         TCGA-FV-A4ZP 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-FV-A4ZQ         TCGA-G3-A25S         TCGA-G3-A25T 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE"   "19P GAIN MUTATED" 
        TCGA-G3-A25U         TCGA-G3-A25V         TCGA-G3-A25W 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-G3-A25X         TCGA-G3-A25Y         TCGA-G3-A25Z 
  "19P GAIN MUTATED" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-G3-A3CG         TCGA-G3-A3CH         TCGA-G3-A3CI 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK         TCGA-G3-A5SJ 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-G3-A5SK         TCGA-G3-A5SL         TCGA-G3-A5SM 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE"   "19P GAIN MUTATED" 
[1] "hr=" "1.3"
D34V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  19P GAIN MUTATED        11       10         0          0          1
  19P GAIN WILD-TYPE      34       15         2         25          2
                    vv
clus                 STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  19P GAIN MUTATED            0        1         1         1
  19P GAIN WILD-TYPE          4        0         0         0
D34V3, multiclass
                    vv
clus                 T1 T2 T3 T4
  19P GAIN MUTATED   12 11  2  1
  19P GAIN WILD-TYPE 36 17 32  5
D34V4, multiclass
    clus
vv   19P GAIN MUTATED 19P GAIN WILD-TYPE
  T1               12                 36
  T2               11                 17
  T3                2                 32
  T4                1                  5
D34V5, binary
                    cls
clus                  0  1
  19P GAIN MUTATED   16  1
  19P GAIN WILD-TYPE 58  2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED     16    1
  19P GAIN WILD-TYPE   58    2
   clus
vv  19P GAIN MUTATED 19P GAIN WILD-TYPE
  0               16                 58
  1                1                  2
                    vv
clus                 M0 M1 MX
  19P GAIN MUTATED   19  2  6
  19P GAIN WILD-TYPE 71  0 19
D34V6, multiclass
    clus
vv   19P GAIN MUTATED 19P GAIN WILD-TYPE
  M0               19                 71
  M1                2                  0
  MX                6                 19
D34V7, binary
                    cls
clus                  0  1
  19P GAIN MUTATED   13 14
  19P GAIN WILD-TYPE 31 59
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED     13   14
  19P GAIN WILD-TYPE   31   59
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  FEMALE               13                 31
  MALE                 14                 59
                    vv
clus                 R0 R1 R2 RX
  19P GAIN MUTATED   23  1  1  1
  19P GAIN WILD-TYPE 70  9  0  7
D34V8, multiclass
    clus
vv   19P GAIN MUTATED 19P GAIN WILD-TYPE
  R0               23                 70
  R1                1                  9
  R2                1                  0
  RX                1                  7

Clustering(35) Variable = 19Q GAIN MUTATION ANALYSIS
D35V1, survival
                    sevent
clus2                 0  1
  19Q GAIN MUTATED   15 13
  19Q GAIN WILD-TYPE 46 40
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                28                 86 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                13                 40 
$`19Q GAIN MUTATED`
TCGA-BC-A10Q TCGA-BC-A10R TCGA-CC-5261 TCGA-CC-A3M9 TCGA-DD-A113 TCGA-DD-A118 
       37.32        10.13         3.02         0.10        79.73       112.96 
TCGA-DD-A119 TCGA-DD-A1E9 TCGA-DD-A1EC TCGA-DD-A1EF TCGA-DD-A39V TCGA-DD-A39X 
        7.33        90.67        19.76        12.95        21.14        55.66 
TCGA-DD-A3A9 TCGA-DD-A4ND TCGA-DD-A4NI TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NQ 
       30.58        73.38        10.78        29.56        61.45        12.26 
TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL TCGA-ES-A2HS TCGA-FV-A23B TCGA-FV-A3I0 
        1.97         0.62         3.19        23.01        32.45         0.20 
TCGA-FV-A4ZQ TCGA-G3-A25T TCGA-G3-A25X TCGA-G3-A5SM 
        0.39        51.02        58.49         4.37 

$`19Q GAIN WILD-TYPE`
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W 
       48.99        27.91        46.78        27.52        27.52         2.99 
TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A216 
       25.32        23.34         1.12        69.57         5.03        44.42 
TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-CC-5258 TCGA-CC-5260 
       13.81         0.26        16.37         9.50         0.07         2.86 
TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC 
        3.39         4.24         3.32         0.07         0.10         0.13 
TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C 
       37.74        83.57        53.29         2.60         0.46        21.76 
TCGA-DD-A11D TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EH 
       51.25        79.36        66.31        75.65         6.67        49.15 
TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EL TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A0 
        6.02        29.16        13.64         5.59        19.73        25.81 
TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 
        7.66        70.06        17.59        20.12       102.74       107.11 
TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A4NA TCGA-DD-A4NE TCGA-DD-A4NF TCGA-DD-A4NG 
       13.78         0.36        33.14        21.67        14.07        14.93 
TCGA-DD-A4NH TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NP TCGA-ED-A459 
       14.24        15.06        39.75        56.25        93.67         0.23 
TCGA-ED-A5KG TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A3RK TCGA-ES-A2HT 
        0.20        10.85         7.76        11.74         0.43        14.40 
TCGA-FV-A2QR TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZP 
       19.07         6.35         0.13         0.03         0.33        60.36 
TCGA-G3-A25S TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25Y TCGA-G3-A25Z 
        1.22        53.79        28.27        30.71        14.86        21.53 
TCGA-G3-A3CG TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SJ 
       22.13        25.64         5.88        19.53        19.23        11.97 
TCGA-G3-A5SK TCGA-G3-A5SL 
        9.93         7.99 

  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
              0.10               0.03 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
            112.96             107.11 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
            20.450             14.995 
[1] "0.1 - 113.0 (20.5)" "0.0 - 107.1 (15.0)"
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
  "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-BC-A5W4 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-CC-5258         TCGA-CC-5260         TCGA-CC-5261 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" 
        TCGA-CC-5262         TCGA-CC-5263         TCGA-CC-A1HT 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-CC-A3M9         TCGA-CC-A3MA         TCGA-CC-A3MB 
  "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-CC-A3MC         TCGA-DD-A113         TCGA-DD-A114 
"19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
  "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" 
        TCGA-DD-A1EA         TCGA-DD-A1EB         TCGA-DD-A1EC 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" 
        TCGA-DD-A1ED         TCGA-DD-A1EE         TCGA-DD-A1EF 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" 
        TCGA-DD-A1EH         TCGA-DD-A1EI         TCGA-DD-A1EJ 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-DD-A1EL         TCGA-DD-A39V         TCGA-DD-A39X 
"19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED"   "19Q GAIN MUTATED" 
        TCGA-DD-A39Y         TCGA-DD-A39Z         TCGA-DD-A3A0 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-DD-A3A1         TCGA-DD-A3A2         TCGA-DD-A3A3 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-DD-A3A4         TCGA-DD-A3A5         TCGA-DD-A3A6 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-DD-A3A7         TCGA-DD-A3A8         TCGA-DD-A3A9 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" 
        TCGA-DD-A4NA         TCGA-DD-A4ND         TCGA-DD-A4NE 
"19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" 
        TCGA-DD-A4NF         TCGA-DD-A4NG         TCGA-DD-A4NH 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-DD-A4NI         TCGA-DD-A4NJ         TCGA-DD-A4NK 
  "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-DD-A4NL         TCGA-DD-A4NN         TCGA-DD-A4NO 
"19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED"   "19Q GAIN MUTATED" 
        TCGA-DD-A4NP         TCGA-DD-A4NQ         TCGA-ED-A459 
"19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" 
        TCGA-ED-A5KG         TCGA-EP-A12J         TCGA-EP-A26S 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-EP-A2KA         TCGA-EP-A2KB         TCGA-EP-A2KC 
"19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED"   "19Q GAIN MUTATED" 
        TCGA-EP-A3JL         TCGA-EP-A3RK         TCGA-ES-A2HS 
  "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" 
        TCGA-ES-A2HT         TCGA-FV-A23B         TCGA-FV-A2QR 
"19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" 
        TCGA-FV-A3I0         TCGA-FV-A3R2         TCGA-FV-A3R3 
  "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-FV-A495         TCGA-FV-A496         TCGA-FV-A4ZP 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-FV-A4ZQ         TCGA-G3-A25S         TCGA-G3-A25T 
  "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" 
        TCGA-G3-A25U         TCGA-G3-A25V         TCGA-G3-A25W 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-G3-A25X         TCGA-G3-A25Y         TCGA-G3-A25Z 
  "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-G3-A3CG         TCGA-G3-A3CH         TCGA-G3-A3CI 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK         TCGA-G3-A5SJ 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-G3-A5SK         TCGA-G3-A5SL         TCGA-G3-A5SM 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" 
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
  "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-BC-A5W4 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-CC-5258         TCGA-CC-5260         TCGA-CC-5261 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" 
        TCGA-CC-5262         TCGA-CC-5263         TCGA-CC-A1HT 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-CC-A3M9         TCGA-CC-A3MA         TCGA-CC-A3MB 
  "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-CC-A3MC         TCGA-DD-A113         TCGA-DD-A114 
"19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
  "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" 
        TCGA-DD-A1EA         TCGA-DD-A1EB         TCGA-DD-A1EC 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" 
        TCGA-DD-A1ED         TCGA-DD-A1EE         TCGA-DD-A1EF 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" 
        TCGA-DD-A1EH         TCGA-DD-A1EI         TCGA-DD-A1EJ 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-DD-A1EL         TCGA-DD-A39V         TCGA-DD-A39X 
"19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED"   "19Q GAIN MUTATED" 
        TCGA-DD-A39Y         TCGA-DD-A39Z         TCGA-DD-A3A0 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-DD-A3A1         TCGA-DD-A3A2         TCGA-DD-A3A3 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-DD-A3A4         TCGA-DD-A3A5         TCGA-DD-A3A6 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-DD-A3A7         TCGA-DD-A3A8         TCGA-DD-A3A9 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" 
        TCGA-DD-A4NA         TCGA-DD-A4ND         TCGA-DD-A4NE 
"19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" 
        TCGA-DD-A4NF         TCGA-DD-A4NG         TCGA-DD-A4NH 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-DD-A4NI         TCGA-DD-A4NJ         TCGA-DD-A4NK 
  "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-DD-A4NL         TCGA-DD-A4NN         TCGA-DD-A4NO 
"19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED"   "19Q GAIN MUTATED" 
        TCGA-DD-A4NP         TCGA-DD-A4NQ         TCGA-ED-A459 
"19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" 
        TCGA-ED-A5KG         TCGA-EP-A12J         TCGA-EP-A26S 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-EP-A2KA         TCGA-EP-A2KB         TCGA-EP-A2KC 
"19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED"   "19Q GAIN MUTATED" 
        TCGA-EP-A3JL         TCGA-EP-A3RK         TCGA-ES-A2HS 
  "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" 
        TCGA-ES-A2HT         TCGA-FV-A23B         TCGA-FV-A2QR 
"19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" 
        TCGA-FV-A3I0         TCGA-FV-A3R2         TCGA-FV-A3R3 
  "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-FV-A495         TCGA-FV-A496         TCGA-FV-A4ZP 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-FV-A4ZQ         TCGA-G3-A25S         TCGA-G3-A25T 
  "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" 
        TCGA-G3-A25U         TCGA-G3-A25V         TCGA-G3-A25W 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-G3-A25X         TCGA-G3-A25Y         TCGA-G3-A25Z 
  "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-G3-A3CG         TCGA-G3-A3CH         TCGA-G3-A3CI 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK         TCGA-G3-A5SJ 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-G3-A5SK         TCGA-G3-A5SL         TCGA-G3-A5SM 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" 
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
  "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-BC-A5W4 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-CC-5258         TCGA-CC-5260         TCGA-CC-5261 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" 
        TCGA-CC-5262         TCGA-CC-5263         TCGA-CC-A1HT 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-CC-A3M9         TCGA-CC-A3MA         TCGA-CC-A3MB 
  "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-CC-A3MC         TCGA-DD-A113         TCGA-DD-A114 
"19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
  "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" 
        TCGA-DD-A1EA         TCGA-DD-A1EB         TCGA-DD-A1EC 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" 
        TCGA-DD-A1ED         TCGA-DD-A1EE         TCGA-DD-A1EF 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" 
        TCGA-DD-A1EH         TCGA-DD-A1EI         TCGA-DD-A1EJ 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-DD-A1EL         TCGA-DD-A39V         TCGA-DD-A39X 
"19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED"   "19Q GAIN MUTATED" 
        TCGA-DD-A39Y         TCGA-DD-A39Z         TCGA-DD-A3A0 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-DD-A3A1         TCGA-DD-A3A2         TCGA-DD-A3A3 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-DD-A3A4         TCGA-DD-A3A5         TCGA-DD-A3A6 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-DD-A3A7         TCGA-DD-A3A8         TCGA-DD-A3A9 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" 
        TCGA-DD-A4NA         TCGA-DD-A4ND         TCGA-DD-A4NE 
"19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" 
        TCGA-DD-A4NF         TCGA-DD-A4NG         TCGA-DD-A4NH 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-DD-A4NI         TCGA-DD-A4NJ         TCGA-DD-A4NK 
  "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-DD-A4NL         TCGA-DD-A4NN         TCGA-DD-A4NO 
"19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED"   "19Q GAIN MUTATED" 
        TCGA-DD-A4NP         TCGA-DD-A4NQ         TCGA-ED-A459 
"19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" 
        TCGA-ED-A5KG         TCGA-EP-A12J         TCGA-EP-A26S 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-EP-A2KA         TCGA-EP-A2KB         TCGA-EP-A2KC 
"19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED"   "19Q GAIN MUTATED" 
        TCGA-EP-A3JL         TCGA-EP-A3RK         TCGA-ES-A2HS 
  "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" 
        TCGA-ES-A2HT         TCGA-FV-A23B         TCGA-FV-A2QR 
"19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" 
        TCGA-FV-A3I0         TCGA-FV-A3R2         TCGA-FV-A3R3 
  "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-FV-A495         TCGA-FV-A496         TCGA-FV-A4ZP 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-FV-A4ZQ         TCGA-G3-A25S         TCGA-G3-A25T 
  "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" 
        TCGA-G3-A25U         TCGA-G3-A25V         TCGA-G3-A25W 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-G3-A25X         TCGA-G3-A25Y         TCGA-G3-A25Z 
  "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-G3-A3CG         TCGA-G3-A3CH         TCGA-G3-A3CI 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK         TCGA-G3-A5SJ 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-G3-A5SK         TCGA-G3-A5SL         TCGA-G3-A5SM 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" 
[1] "hr=" "1.2"
D35V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  19Q GAIN MUTATED        12       10         0          1          0
  19Q GAIN WILD-TYPE      33       15         2         24          3
                    vv
clus                 STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  19Q GAIN MUTATED            0        1         1         1
  19Q GAIN WILD-TYPE          4        0         0         0
D35V3, multiclass
                    vv
clus                 T1 T2 T3 T4
  19Q GAIN MUTATED   13 11  3  1
  19Q GAIN WILD-TYPE 35 17 31  5
D35V4, multiclass
    clus
vv   19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  T1               13                 35
  T2               11                 17
  T3                3                 31
  T4                1                  5
D35V5, binary
                    cls
clus                  0  1
  19Q GAIN MUTATED   16  1
  19Q GAIN WILD-TYPE 58  2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED     16    1
  19Q GAIN WILD-TYPE   58    2
   clus
vv  19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  0               16                 58
  1                1                  2
                    vv
clus                 M0 M1 MX
  19Q GAIN MUTATED   20  2  7
  19Q GAIN WILD-TYPE 70  0 18
D35V6, multiclass
    clus
vv   19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  M0               20                 70
  M1                2                  0
  MX                7                 18
D35V7, binary
                    cls
clus                  0  1
  19Q GAIN MUTATED   14 15
  19Q GAIN WILD-TYPE 30 58
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED     14   15
  19Q GAIN WILD-TYPE   30   58
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  FEMALE               14                 30
  MALE                 15                 58
                    vv
clus                 R0 R1 R2 RX
  19Q GAIN MUTATED   25  1  1  1
  19Q GAIN WILD-TYPE 68  9  0  7
D35V8, multiclass
    clus
vv   19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  R0               25                 68
  R1                1                  9
  R2                1                  0
  RX                1                  7

Clustering(36) Variable = 20P GAIN MUTATION ANALYSIS
D36V1, survival
                    sevent
clus2                 0  1
  20P GAIN MUTATED   16 17
  20P GAIN WILD-TYPE 45 36
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                33                 81 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                17                 36 
$`20P GAIN MUTATED`
TCGA-BC-4072 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A217 TCGA-BC-A3KF TCGA-CC-5261 
       48.99        37.32        10.13        13.81         0.26         3.02 
TCGA-CC-A3M9 TCGA-CC-A3MB TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B 
        0.10         0.10       112.96         7.33         2.60         0.46 
TCGA-DD-A1EF TCGA-DD-A1EH TCGA-DD-A1EJ TCGA-DD-A39V TCGA-DD-A3A7 TCGA-DD-A3A9 
       12.95        49.15        29.16        21.14        13.78        30.58 
TCGA-DD-A4ND TCGA-DD-A4NE TCGA-DD-A4NG TCGA-DD-A4NI TCGA-DD-A4NN TCGA-EP-A2KB 
       73.38        21.67        14.93        10.78        29.56         1.97 
TCGA-EP-A3JL TCGA-ES-A2HS TCGA-FV-A23B TCGA-FV-A3R2 TCGA-FV-A4ZQ TCGA-G3-A25S 
        3.19        23.01        32.45         6.35         0.39         1.22 
TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A5SM 
       58.49        14.86         4.37 

$`20P GAIN WILD-TYPE`
TCGA-BC-4073 TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X 
       27.91        46.78        27.52        27.52         2.99        25.32 
TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A216 TCGA-BC-A3KG 
       23.34         1.12        69.57         5.03        44.42        16.37 
TCGA-BC-A5W4 TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A1HT 
        9.50         0.07         2.86         3.39         4.24         3.32 
TCGA-CC-A3MA TCGA-CC-A3MC TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 
        0.07         0.13        79.73        37.74        83.57        53.29 
TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC 
       21.76        51.25        90.67        79.36        66.31        19.76 
TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EI TCGA-DD-A1EL TCGA-DD-A39X TCGA-DD-A39Y 
       75.65         6.67         6.02        13.64        55.66         5.59 
TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 
       19.73        25.81         7.66        70.06        17.59        20.12 
TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A8 TCGA-DD-A4NA TCGA-DD-A4NF TCGA-DD-A4NH 
      102.74       107.11         0.36        33.14        14.07        14.24 
TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ 
       15.06        39.75        56.25        61.45        93.67        12.26 
TCGA-ED-A459 TCGA-ED-A5KG TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KC 
        0.23         0.20        10.85         7.76        11.74         0.62 
TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3R3 TCGA-FV-A495 
        0.43        14.40        19.07         0.20         0.13         0.03 
TCGA-FV-A496 TCGA-FV-A4ZP TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W 
        0.33        60.36        51.02        53.79        28.27        30.71 
TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK 
       21.53        22.13        25.64         5.88        19.53        19.23 
TCGA-G3-A5SJ TCGA-G3-A5SK TCGA-G3-A5SL 
       11.97         9.93         7.99 

  20P GAIN MUTATED 20P GAIN WILD-TYPE 
              0.10               0.03 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
            112.96             107.11 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
             13.78              19.23 
[1] "0.1 - 113.0 (13.8)" "0.0 - 107.1 (19.2)"
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-BC-A5W4 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-CC-5258         TCGA-CC-5260         TCGA-CC-5261 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-CC-5262         TCGA-CC-5263         TCGA-CC-A1HT 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-CC-A3M9         TCGA-CC-A3MA         TCGA-CC-A3MB 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-CC-A3MC         TCGA-DD-A113         TCGA-DD-A114 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
  "20P GAIN MUTATED"   "20P GAIN MUTATED"   "20P GAIN MUTATED" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-DD-A1EA         TCGA-DD-A1EB         TCGA-DD-A1EC 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-DD-A1ED         TCGA-DD-A1EE         TCGA-DD-A1EF 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-DD-A1EH         TCGA-DD-A1EI         TCGA-DD-A1EJ 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-DD-A1EL         TCGA-DD-A39V         TCGA-DD-A39X 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-DD-A39Y         TCGA-DD-A39Z         TCGA-DD-A3A0 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-DD-A3A1         TCGA-DD-A3A2         TCGA-DD-A3A3 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-DD-A3A4         TCGA-DD-A3A5         TCGA-DD-A3A6 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-DD-A3A7         TCGA-DD-A3A8         TCGA-DD-A3A9 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-DD-A4NA         TCGA-DD-A4ND         TCGA-DD-A4NE 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED"   "20P GAIN MUTATED" 
        TCGA-DD-A4NF         TCGA-DD-A4NG         TCGA-DD-A4NH 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-DD-A4NI         TCGA-DD-A4NJ         TCGA-DD-A4NK 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-DD-A4NL         TCGA-DD-A4NN         TCGA-DD-A4NO 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-DD-A4NP         TCGA-DD-A4NQ         TCGA-ED-A459 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-ED-A5KG         TCGA-EP-A12J         TCGA-EP-A26S 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-EP-A2KA         TCGA-EP-A2KB         TCGA-EP-A2KC 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-EP-A3JL         TCGA-EP-A3RK         TCGA-ES-A2HS 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-ES-A2HT         TCGA-FV-A23B         TCGA-FV-A2QR 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-FV-A3I0         TCGA-FV-A3R2         TCGA-FV-A3R3 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-FV-A495         TCGA-FV-A496         TCGA-FV-A4ZP 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-FV-A4ZQ         TCGA-G3-A25S         TCGA-G3-A25T 
  "20P GAIN MUTATED"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-G3-A25U         TCGA-G3-A25V         TCGA-G3-A25W 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-G3-A25X         TCGA-G3-A25Y         TCGA-G3-A25Z 
  "20P GAIN MUTATED"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-G3-A3CG         TCGA-G3-A3CH         TCGA-G3-A3CI 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK         TCGA-G3-A5SJ 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-G3-A5SK         TCGA-G3-A5SL         TCGA-G3-A5SM 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-BC-A5W4 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-CC-5258         TCGA-CC-5260         TCGA-CC-5261 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-CC-5262         TCGA-CC-5263         TCGA-CC-A1HT 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-CC-A3M9         TCGA-CC-A3MA         TCGA-CC-A3MB 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-CC-A3MC         TCGA-DD-A113         TCGA-DD-A114 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
  "20P GAIN MUTATED"   "20P GAIN MUTATED"   "20P GAIN MUTATED" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-DD-A1EA         TCGA-DD-A1EB         TCGA-DD-A1EC 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-DD-A1ED         TCGA-DD-A1EE         TCGA-DD-A1EF 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-DD-A1EH         TCGA-DD-A1EI         TCGA-DD-A1EJ 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-DD-A1EL         TCGA-DD-A39V         TCGA-DD-A39X 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-DD-A39Y         TCGA-DD-A39Z         TCGA-DD-A3A0 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-DD-A3A1         TCGA-DD-A3A2         TCGA-DD-A3A3 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-DD-A3A4         TCGA-DD-A3A5         TCGA-DD-A3A6 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-DD-A3A7         TCGA-DD-A3A8         TCGA-DD-A3A9 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-DD-A4NA         TCGA-DD-A4ND         TCGA-DD-A4NE 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED"   "20P GAIN MUTATED" 
        TCGA-DD-A4NF         TCGA-DD-A4NG         TCGA-DD-A4NH 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-DD-A4NI         TCGA-DD-A4NJ         TCGA-DD-A4NK 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-DD-A4NL         TCGA-DD-A4NN         TCGA-DD-A4NO 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-DD-A4NP         TCGA-DD-A4NQ         TCGA-ED-A459 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-ED-A5KG         TCGA-EP-A12J         TCGA-EP-A26S 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-EP-A2KA         TCGA-EP-A2KB         TCGA-EP-A2KC 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-EP-A3JL         TCGA-EP-A3RK         TCGA-ES-A2HS 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-ES-A2HT         TCGA-FV-A23B         TCGA-FV-A2QR 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-FV-A3I0         TCGA-FV-A3R2         TCGA-FV-A3R3 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-FV-A495         TCGA-FV-A496         TCGA-FV-A4ZP 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-FV-A4ZQ         TCGA-G3-A25S         TCGA-G3-A25T 
  "20P GAIN MUTATED"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-G3-A25U         TCGA-G3-A25V         TCGA-G3-A25W 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-G3-A25X         TCGA-G3-A25Y         TCGA-G3-A25Z 
  "20P GAIN MUTATED"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-G3-A3CG         TCGA-G3-A3CH         TCGA-G3-A3CI 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK         TCGA-G3-A5SJ 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-G3-A5SK         TCGA-G3-A5SL         TCGA-G3-A5SM 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-BC-A5W4 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-CC-5258         TCGA-CC-5260         TCGA-CC-5261 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-CC-5262         TCGA-CC-5263         TCGA-CC-A1HT 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-CC-A3M9         TCGA-CC-A3MA         TCGA-CC-A3MB 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-CC-A3MC         TCGA-DD-A113         TCGA-DD-A114 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
  "20P GAIN MUTATED"   "20P GAIN MUTATED"   "20P GAIN MUTATED" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-DD-A1EA         TCGA-DD-A1EB         TCGA-DD-A1EC 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-DD-A1ED         TCGA-DD-A1EE         TCGA-DD-A1EF 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-DD-A1EH         TCGA-DD-A1EI         TCGA-DD-A1EJ 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-DD-A1EL         TCGA-DD-A39V         TCGA-DD-A39X 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-DD-A39Y         TCGA-DD-A39Z         TCGA-DD-A3A0 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-DD-A3A1         TCGA-DD-A3A2         TCGA-DD-A3A3 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-DD-A3A4         TCGA-DD-A3A5         TCGA-DD-A3A6 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-DD-A3A7         TCGA-DD-A3A8         TCGA-DD-A3A9 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-DD-A4NA         TCGA-DD-A4ND         TCGA-DD-A4NE 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED"   "20P GAIN MUTATED" 
        TCGA-DD-A4NF         TCGA-DD-A4NG         TCGA-DD-A4NH 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-DD-A4NI         TCGA-DD-A4NJ         TCGA-DD-A4NK 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-DD-A4NL         TCGA-DD-A4NN         TCGA-DD-A4NO 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-DD-A4NP         TCGA-DD-A4NQ         TCGA-ED-A459 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-ED-A5KG         TCGA-EP-A12J         TCGA-EP-A26S 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-EP-A2KA         TCGA-EP-A2KB         TCGA-EP-A2KC 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-EP-A3JL         TCGA-EP-A3RK         TCGA-ES-A2HS 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-ES-A2HT         TCGA-FV-A23B         TCGA-FV-A2QR 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-FV-A3I0         TCGA-FV-A3R2         TCGA-FV-A3R3 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-FV-A495         TCGA-FV-A496         TCGA-FV-A4ZP 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-FV-A4ZQ         TCGA-G3-A25S         TCGA-G3-A25T 
  "20P GAIN MUTATED"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-G3-A25U         TCGA-G3-A25V         TCGA-G3-A25W 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-G3-A25X         TCGA-G3-A25Y         TCGA-G3-A25Z 
  "20P GAIN MUTATED"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-G3-A3CG         TCGA-G3-A3CH         TCGA-G3-A3CI 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK         TCGA-G3-A5SJ 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-G3-A5SK         TCGA-G3-A5SL         TCGA-G3-A5SM 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
[1] "hr=" "1.4"
D36V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  20P GAIN MUTATED        13        8         1          6          1
  20P GAIN WILD-TYPE      32       17         1         19          2
                    vv
clus                 STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  20P GAIN MUTATED            1        1         0         1
  20P GAIN WILD-TYPE          3        0         1         0
D36V3, multiclass
                    vv
clus                 T1 T2 T3 T4
  20P GAIN MUTATED   14  9 10  1
  20P GAIN WILD-TYPE 34 19 24  5
D36V4, multiclass
    clus
vv   20P GAIN MUTATED 20P GAIN WILD-TYPE
  T1               14                 34
  T2                9                 19
  T3               10                 24
  T4                1                  5
D36V5, binary
                    cls
clus                  0  1
  20P GAIN MUTATED   20  1
  20P GAIN WILD-TYPE 54  2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED     20    1
  20P GAIN WILD-TYPE   54    2
   clus
vv  20P GAIN MUTATED 20P GAIN WILD-TYPE
  0               20                 54
  1                1                  2
                    vv
clus                 M0 M1 MX
  20P GAIN MUTATED   26  2  6
  20P GAIN WILD-TYPE 64  0 19
D36V6, multiclass
    clus
vv   20P GAIN MUTATED 20P GAIN WILD-TYPE
  M0               26                 64
  M1                2                  0
  MX                6                 19
D36V7, binary
                    cls
clus                  0  1
  20P GAIN MUTATED   15 19
  20P GAIN WILD-TYPE 29 54
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED     15   19
  20P GAIN WILD-TYPE   29   54
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  FEMALE               15                 29
  MALE                 19                 54
                    vv
clus                 R0 R1 R2 RX
  20P GAIN MUTATED   26  3  1  3
  20P GAIN WILD-TYPE 67  7  0  5
D36V8, multiclass
    clus
vv   20P GAIN MUTATED 20P GAIN WILD-TYPE
  R0               26                 67
  R1                3                  7
  R2                1                  0
  RX                3                  5

Clustering(37) Variable = 20Q GAIN MUTATION ANALYSIS
D37V1, survival
                    sevent
clus2                 0  1
  20Q GAIN MUTATED   18 17
  20Q GAIN WILD-TYPE 43 36
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                35                 79 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                17                 36 
$`20Q GAIN MUTATED`
TCGA-BC-4072 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A217 TCGA-BC-A3KF TCGA-CC-5261 
       48.99        37.32        10.13        13.81         0.26         3.02 
TCGA-CC-A3M9 TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A 
        0.10         0.10         0.13       112.96         7.33         2.60 
TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A1EF TCGA-DD-A1EH TCGA-DD-A1EJ TCGA-DD-A39V 
        0.46        21.76        12.95        49.15        29.16        21.14 
TCGA-DD-A3A7 TCGA-DD-A3A9 TCGA-DD-A4ND TCGA-DD-A4NE TCGA-DD-A4NG TCGA-DD-A4NI 
       13.78        30.58        73.38        21.67        14.93        10.78 
TCGA-DD-A4NN TCGA-EP-A2KB TCGA-EP-A3JL TCGA-ES-A2HS TCGA-FV-A23B TCGA-FV-A3R2 
       29.56         1.97         3.19        23.01        32.45         6.35 
TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A5SM 
        0.39         1.22        58.49        14.86         4.37 

$`20Q GAIN WILD-TYPE`
TCGA-BC-4073 TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X 
       27.91        46.78        27.52        27.52         2.99        25.32 
TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A216 TCGA-BC-A3KG 
       23.34         1.12        69.57         5.03        44.42        16.37 
TCGA-BC-A5W4 TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A1HT 
        9.50         0.07         2.86         3.39         4.24         3.32 
TCGA-CC-A3MA TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A11D 
        0.07        79.73        37.74        83.57        53.29        51.25 
TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE 
       90.67        79.36        66.31        19.76        75.65         6.67 
TCGA-DD-A1EI TCGA-DD-A1EL TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A0 
        6.02        13.64        55.66         5.59        19.73        25.81 
TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 
        7.66        70.06        17.59        20.12       102.74       107.11 
TCGA-DD-A3A8 TCGA-DD-A4NA TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NJ TCGA-DD-A4NK 
        0.36        33.14        14.07        14.24        15.06        39.75 
TCGA-DD-A4NL TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-ED-A459 TCGA-ED-A5KG 
       56.25        61.45        93.67        12.26         0.23         0.20 
TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KC TCGA-EP-A3RK TCGA-ES-A2HT 
       10.85         7.76        11.74         0.62         0.43        14.40 
TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZP 
       19.07         0.20         0.13         0.03         0.33        60.36 
TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25Z TCGA-G3-A3CG 
       51.02        53.79        28.27        30.71        21.53        22.13 
TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SJ TCGA-G3-A5SK 
       25.64         5.88        19.53        19.23        11.97         9.93 
TCGA-G3-A5SL 
        7.99 

  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
              0.10               0.03 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
            112.96             107.11 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
             13.78              19.23 
[1] "0.1 - 113.0 (13.8)" "0.0 - 107.1 (19.2)"
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-BC-A5W4 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-CC-5258         TCGA-CC-5260         TCGA-CC-5261 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-CC-5262         TCGA-CC-5263         TCGA-CC-A1HT 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-CC-A3M9         TCGA-CC-A3MA         TCGA-CC-A3MB 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-CC-A3MC         TCGA-DD-A113         TCGA-DD-A114 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-DD-A1EA         TCGA-DD-A1EB         TCGA-DD-A1EC 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-DD-A1ED         TCGA-DD-A1EE         TCGA-DD-A1EF 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-DD-A1EH         TCGA-DD-A1EI         TCGA-DD-A1EJ 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-DD-A1EL         TCGA-DD-A39V         TCGA-DD-A39X 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-DD-A39Y         TCGA-DD-A39Z         TCGA-DD-A3A0 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-DD-A3A1         TCGA-DD-A3A2         TCGA-DD-A3A3 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-DD-A3A4         TCGA-DD-A3A5         TCGA-DD-A3A6 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-DD-A3A7         TCGA-DD-A3A8         TCGA-DD-A3A9 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-DD-A4NA         TCGA-DD-A4ND         TCGA-DD-A4NE 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-DD-A4NF         TCGA-DD-A4NG         TCGA-DD-A4NH 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-DD-A4NI         TCGA-DD-A4NJ         TCGA-DD-A4NK 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-DD-A4NL         TCGA-DD-A4NN         TCGA-DD-A4NO 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-DD-A4NP         TCGA-DD-A4NQ         TCGA-ED-A459 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-ED-A5KG         TCGA-EP-A12J         TCGA-EP-A26S 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-EP-A2KA         TCGA-EP-A2KB         TCGA-EP-A2KC 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-EP-A3JL         TCGA-EP-A3RK         TCGA-ES-A2HS 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-ES-A2HT         TCGA-FV-A23B         TCGA-FV-A2QR 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-FV-A3I0         TCGA-FV-A3R2         TCGA-FV-A3R3 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-FV-A495         TCGA-FV-A496         TCGA-FV-A4ZP 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-FV-A4ZQ         TCGA-G3-A25S         TCGA-G3-A25T 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-G3-A25U         TCGA-G3-A25V         TCGA-G3-A25W 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-G3-A25X         TCGA-G3-A25Y         TCGA-G3-A25Z 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-G3-A3CG         TCGA-G3-A3CH         TCGA-G3-A3CI 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK         TCGA-G3-A5SJ 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-G3-A5SK         TCGA-G3-A5SL         TCGA-G3-A5SM 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-BC-A5W4 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-CC-5258         TCGA-CC-5260         TCGA-CC-5261 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-CC-5262         TCGA-CC-5263         TCGA-CC-A1HT 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-CC-A3M9         TCGA-CC-A3MA         TCGA-CC-A3MB 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-CC-A3MC         TCGA-DD-A113         TCGA-DD-A114 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-DD-A1EA         TCGA-DD-A1EB         TCGA-DD-A1EC 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-DD-A1ED         TCGA-DD-A1EE         TCGA-DD-A1EF 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-DD-A1EH         TCGA-DD-A1EI         TCGA-DD-A1EJ 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-DD-A1EL         TCGA-DD-A39V         TCGA-DD-A39X 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-DD-A39Y         TCGA-DD-A39Z         TCGA-DD-A3A0 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-DD-A3A1         TCGA-DD-A3A2         TCGA-DD-A3A3 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-DD-A3A4         TCGA-DD-A3A5         TCGA-DD-A3A6 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-DD-A3A7         TCGA-DD-A3A8         TCGA-DD-A3A9 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-DD-A4NA         TCGA-DD-A4ND         TCGA-DD-A4NE 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-DD-A4NF         TCGA-DD-A4NG         TCGA-DD-A4NH 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-DD-A4NI         TCGA-DD-A4NJ         TCGA-DD-A4NK 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-DD-A4NL         TCGA-DD-A4NN         TCGA-DD-A4NO 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-DD-A4NP         TCGA-DD-A4NQ         TCGA-ED-A459 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-ED-A5KG         TCGA-EP-A12J         TCGA-EP-A26S 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-EP-A2KA         TCGA-EP-A2KB         TCGA-EP-A2KC 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-EP-A3JL         TCGA-EP-A3RK         TCGA-ES-A2HS 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-ES-A2HT         TCGA-FV-A23B         TCGA-FV-A2QR 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-FV-A3I0         TCGA-FV-A3R2         TCGA-FV-A3R3 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-FV-A495         TCGA-FV-A496         TCGA-FV-A4ZP 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-FV-A4ZQ         TCGA-G3-A25S         TCGA-G3-A25T 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-G3-A25U         TCGA-G3-A25V         TCGA-G3-A25W 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-G3-A25X         TCGA-G3-A25Y         TCGA-G3-A25Z 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-G3-A3CG         TCGA-G3-A3CH         TCGA-G3-A3CI 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK         TCGA-G3-A5SJ 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-G3-A5SK         TCGA-G3-A5SL         TCGA-G3-A5SM 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-BC-A5W4 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-CC-5258         TCGA-CC-5260         TCGA-CC-5261 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-CC-5262         TCGA-CC-5263         TCGA-CC-A1HT 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-CC-A3M9         TCGA-CC-A3MA         TCGA-CC-A3MB 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-CC-A3MC         TCGA-DD-A113         TCGA-DD-A114 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-DD-A1EA         TCGA-DD-A1EB         TCGA-DD-A1EC 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-DD-A1ED         TCGA-DD-A1EE         TCGA-DD-A1EF 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-DD-A1EH         TCGA-DD-A1EI         TCGA-DD-A1EJ 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-DD-A1EL         TCGA-DD-A39V         TCGA-DD-A39X 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-DD-A39Y         TCGA-DD-A39Z         TCGA-DD-A3A0 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-DD-A3A1         TCGA-DD-A3A2         TCGA-DD-A3A3 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-DD-A3A4         TCGA-DD-A3A5         TCGA-DD-A3A6 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-DD-A3A7         TCGA-DD-A3A8         TCGA-DD-A3A9 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-DD-A4NA         TCGA-DD-A4ND         TCGA-DD-A4NE 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-DD-A4NF         TCGA-DD-A4NG         TCGA-DD-A4NH 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-DD-A4NI         TCGA-DD-A4NJ         TCGA-DD-A4NK 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-DD-A4NL         TCGA-DD-A4NN         TCGA-DD-A4NO 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-DD-A4NP         TCGA-DD-A4NQ         TCGA-ED-A459 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-ED-A5KG         TCGA-EP-A12J         TCGA-EP-A26S 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-EP-A2KA         TCGA-EP-A2KB         TCGA-EP-A2KC 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-EP-A3JL         TCGA-EP-A3RK         TCGA-ES-A2HS 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-ES-A2HT         TCGA-FV-A23B         TCGA-FV-A2QR 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-FV-A3I0         TCGA-FV-A3R2         TCGA-FV-A3R3 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-FV-A495         TCGA-FV-A496         TCGA-FV-A4ZP 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-FV-A4ZQ         TCGA-G3-A25S         TCGA-G3-A25T 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-G3-A25U         TCGA-G3-A25V         TCGA-G3-A25W 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-G3-A25X         TCGA-G3-A25Y         TCGA-G3-A25Z 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-G3-A3CG         TCGA-G3-A3CH         TCGA-G3-A3CI 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK         TCGA-G3-A5SJ 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-G3-A5SK         TCGA-G3-A5SL         TCGA-G3-A5SM 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
[1] "hr=" "1.4"
D37V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  20Q GAIN MUTATED        14        8         1          7          1
  20Q GAIN WILD-TYPE      31       17         1         18          2
                    vv
clus                 STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  20Q GAIN MUTATED            1        1         0         1
  20Q GAIN WILD-TYPE          3        0         1         0
D37V3, multiclass
                    vv
clus                 T1 T2 T3 T4
  20Q GAIN MUTATED   15  9 11  1
  20Q GAIN WILD-TYPE 33 19 23  5
D37V4, multiclass
    clus
vv   20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  T1               15                 33
  T2                9                 19
  T3               11                 23
  T4                1                  5
D37V5, binary
                    cls
clus                  0  1
  20Q GAIN MUTATED   22  1
  20Q GAIN WILD-TYPE 52  2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED     22    1
  20Q GAIN WILD-TYPE   52    2
   clus
vv  20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  0               22                 52
  1                1                  2
                    vv
clus                 M0 M1 MX
  20Q GAIN MUTATED   28  2  6
  20Q GAIN WILD-TYPE 62  0 19
D37V6, multiclass
    clus
vv   20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  M0               28                 62
  M1                2                  0
  MX                6                 19
D37V7, binary
                    cls
clus                  0  1
  20Q GAIN MUTATED   15 21
  20Q GAIN WILD-TYPE 29 52
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED     15   21
  20Q GAIN WILD-TYPE   29   52
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  FEMALE               15                 29
  MALE                 21                 52
                    vv
clus                 R0 R1 R2 RX
  20Q GAIN MUTATED   27  3  1  4
  20Q GAIN WILD-TYPE 66  7  0  4
D37V8, multiclass
    clus
vv   20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  R0               27                 66
  R1                3                  7
  R2                1                  0
  RX                4                  4

Clustering(38) Variable = 21Q GAIN MUTATION ANALYSIS
D38V1, survival
                    sevent
clus2                 0  1
  21Q GAIN MUTATED    6  4
  21Q GAIN WILD-TYPE 55 49
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                10                104 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                 4                 49 
$`21Q GAIN MUTATED`
TCGA-BC-A217 TCGA-CC-5261 TCGA-CC-5263 TCGA-DD-A113 TCGA-DD-A3A5 TCGA-EP-A2KB 
       13.81         3.02         4.24        79.73       102.74         1.97 
TCGA-ES-A2HS TCGA-FV-A3I0 TCGA-G3-A25T TCGA-G3-A3CG 
       23.01         0.20        51.02        22.13 

$`21Q GAIN WILD-TYPE`
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T 
       48.99        27.91        37.32        10.13        46.78        27.52 
TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 
       27.52         2.99        25.32        23.34         1.12        69.57 
TCGA-BC-A112 TCGA-BC-A216 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-CC-5258 
        5.03        44.42         0.26        16.37         9.50         0.07 
TCGA-CC-5260 TCGA-CC-5262 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB 
        2.86         3.39         3.32         0.10         0.07         0.10 
TCGA-CC-A3MC TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 
        0.13        37.74        83.57        53.29       112.96         7.33 
TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA 
        2.60         0.46        21.76        51.25        90.67        79.36 
TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EH 
       66.31        19.76        75.65         6.67        12.95        49.15 
TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39X TCGA-DD-A39Y 
        6.02        29.16        13.64        21.14        55.66         5.59 
TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 
       19.73        25.81         7.66        70.06        17.59        20.12 
TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4ND 
      107.11        13.78         0.36        30.58        33.14        73.38 
TCGA-DD-A4NE TCGA-DD-A4NF TCGA-DD-A4NG TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ 
       21.67        14.07        14.93        14.24        10.78        15.06 
TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ 
       39.75        56.25        29.56        61.45        93.67        12.26 
TCGA-ED-A459 TCGA-ED-A5KG TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KC 
        0.23         0.20        10.85         7.76        11.74         0.62 
TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-A3R2 
        3.19         0.43        14.40        32.45        19.07         6.35 
TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25S 
        0.13         0.03         0.33        60.36         0.39         1.22 
TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A25Z 
       53.79        28.27        30.71        58.49        14.86        21.53 
TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SJ TCGA-G3-A5SK 
       25.64         5.88        19.53        19.23        11.97         9.93 
TCGA-G3-A5SL TCGA-G3-A5SM 
        7.99         4.37 

  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
              0.20               0.03 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
            102.74             112.96 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
            17.970             15.715 
[1] "0.2 - 102.7 (18.0)" "0.0 - 113.0 (15.7)"
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE"   "21Q GAIN MUTATED" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-BC-A5W4 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-CC-5258         TCGA-CC-5260         TCGA-CC-5261 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE"   "21Q GAIN MUTATED" 
        TCGA-CC-5262         TCGA-CC-5263         TCGA-CC-A1HT 
"21Q GAIN WILD-TYPE"   "21Q GAIN MUTATED" "21Q GAIN WILD-TYPE" 
        TCGA-CC-A3M9         TCGA-CC-A3MA         TCGA-CC-A3MB 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-CC-A3MC         TCGA-DD-A113         TCGA-DD-A114 
"21Q GAIN WILD-TYPE"   "21Q GAIN MUTATED" "21Q GAIN WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DD-A1EA         TCGA-DD-A1EB         TCGA-DD-A1EC 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DD-A1ED         TCGA-DD-A1EE         TCGA-DD-A1EF 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DD-A1EH         TCGA-DD-A1EI         TCGA-DD-A1EJ 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DD-A1EL         TCGA-DD-A39V         TCGA-DD-A39X 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DD-A39Y         TCGA-DD-A39Z         TCGA-DD-A3A0 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DD-A3A1         TCGA-DD-A3A2         TCGA-DD-A3A3 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DD-A3A4         TCGA-DD-A3A5         TCGA-DD-A3A6 
"21Q GAIN WILD-TYPE"   "21Q GAIN MUTATED" "21Q GAIN WILD-TYPE" 
        TCGA-DD-A3A7         TCGA-DD-A3A8         TCGA-DD-A3A9 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DD-A4NA         TCGA-DD-A4ND         TCGA-DD-A4NE 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DD-A4NF         TCGA-DD-A4NG         TCGA-DD-A4NH 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DD-A4NI         TCGA-DD-A4NJ         TCGA-DD-A4NK 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DD-A4NL         TCGA-DD-A4NN         TCGA-DD-A4NO 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DD-A4NP         TCGA-DD-A4NQ         TCGA-ED-A459 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-ED-A5KG         TCGA-EP-A12J         TCGA-EP-A26S 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EP-A2KA         TCGA-EP-A2KB         TCGA-EP-A2KC 
"21Q GAIN WILD-TYPE"   "21Q GAIN MUTATED" "21Q GAIN WILD-TYPE" 
        TCGA-EP-A3JL         TCGA-EP-A3RK         TCGA-ES-A2HS 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE"   "21Q GAIN MUTATED" 
        TCGA-ES-A2HT         TCGA-FV-A23B         TCGA-FV-A2QR 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-FV-A3I0         TCGA-FV-A3R2         TCGA-FV-A3R3 
  "21Q GAIN MUTATED" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-FV-A495         TCGA-FV-A496         TCGA-FV-A4ZP 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-FV-A4ZQ         TCGA-G3-A25S         TCGA-G3-A25T 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE"   "21Q GAIN MUTATED" 
        TCGA-G3-A25U         TCGA-G3-A25V         TCGA-G3-A25W 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-G3-A25X         TCGA-G3-A25Y         TCGA-G3-A25Z 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-G3-A3CG         TCGA-G3-A3CH         TCGA-G3-A3CI 
  "21Q GAIN MUTATED" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK         TCGA-G3-A5SJ 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-G3-A5SK         TCGA-G3-A5SL         TCGA-G3-A5SM 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE"   "21Q GAIN MUTATED" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-BC-A5W4 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-CC-5258         TCGA-CC-5260         TCGA-CC-5261 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE"   "21Q GAIN MUTATED" 
        TCGA-CC-5262         TCGA-CC-5263         TCGA-CC-A1HT 
"21Q GAIN WILD-TYPE"   "21Q GAIN MUTATED" "21Q GAIN WILD-TYPE" 
        TCGA-CC-A3M9         TCGA-CC-A3MA         TCGA-CC-A3MB 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-CC-A3MC         TCGA-DD-A113         TCGA-DD-A114 
"21Q GAIN WILD-TYPE"   "21Q GAIN MUTATED" "21Q GAIN WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DD-A1EA         TCGA-DD-A1EB         TCGA-DD-A1EC 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DD-A1ED         TCGA-DD-A1EE         TCGA-DD-A1EF 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DD-A1EH         TCGA-DD-A1EI         TCGA-DD-A1EJ 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DD-A1EL         TCGA-DD-A39V         TCGA-DD-A39X 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DD-A39Y         TCGA-DD-A39Z         TCGA-DD-A3A0 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DD-A3A1         TCGA-DD-A3A2         TCGA-DD-A3A3 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DD-A3A4         TCGA-DD-A3A5         TCGA-DD-A3A6 
"21Q GAIN WILD-TYPE"   "21Q GAIN MUTATED" "21Q GAIN WILD-TYPE" 
        TCGA-DD-A3A7         TCGA-DD-A3A8         TCGA-DD-A3A9 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DD-A4NA         TCGA-DD-A4ND         TCGA-DD-A4NE 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DD-A4NF         TCGA-DD-A4NG         TCGA-DD-A4NH 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DD-A4NI         TCGA-DD-A4NJ         TCGA-DD-A4NK 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DD-A4NL         TCGA-DD-A4NN         TCGA-DD-A4NO 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DD-A4NP         TCGA-DD-A4NQ         TCGA-ED-A459 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-ED-A5KG         TCGA-EP-A12J         TCGA-EP-A26S 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EP-A2KA         TCGA-EP-A2KB         TCGA-EP-A2KC 
"21Q GAIN WILD-TYPE"   "21Q GAIN MUTATED" "21Q GAIN WILD-TYPE" 
        TCGA-EP-A3JL         TCGA-EP-A3RK         TCGA-ES-A2HS 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE"   "21Q GAIN MUTATED" 
        TCGA-ES-A2HT         TCGA-FV-A23B         TCGA-FV-A2QR 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-FV-A3I0         TCGA-FV-A3R2         TCGA-FV-A3R3 
  "21Q GAIN MUTATED" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-FV-A495         TCGA-FV-A496         TCGA-FV-A4ZP 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-FV-A4ZQ         TCGA-G3-A25S         TCGA-G3-A25T 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE"   "21Q GAIN MUTATED" 
        TCGA-G3-A25U         TCGA-G3-A25V         TCGA-G3-A25W 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-G3-A25X         TCGA-G3-A25Y         TCGA-G3-A25Z 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-G3-A3CG         TCGA-G3-A3CH         TCGA-G3-A3CI 
  "21Q GAIN MUTATED" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK         TCGA-G3-A5SJ 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-G3-A5SK         TCGA-G3-A5SL         TCGA-G3-A5SM 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE"   "21Q GAIN MUTATED" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-BC-A5W4 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-CC-5258         TCGA-CC-5260         TCGA-CC-5261 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE"   "21Q GAIN MUTATED" 
        TCGA-CC-5262         TCGA-CC-5263         TCGA-CC-A1HT 
"21Q GAIN WILD-TYPE"   "21Q GAIN MUTATED" "21Q GAIN WILD-TYPE" 
        TCGA-CC-A3M9         TCGA-CC-A3MA         TCGA-CC-A3MB 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-CC-A3MC         TCGA-DD-A113         TCGA-DD-A114 
"21Q GAIN WILD-TYPE"   "21Q GAIN MUTATED" "21Q GAIN WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DD-A1EA         TCGA-DD-A1EB         TCGA-DD-A1EC 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DD-A1ED         TCGA-DD-A1EE         TCGA-DD-A1EF 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DD-A1EH         TCGA-DD-A1EI         TCGA-DD-A1EJ 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DD-A1EL         TCGA-DD-A39V         TCGA-DD-A39X 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DD-A39Y         TCGA-DD-A39Z         TCGA-DD-A3A0 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DD-A3A1         TCGA-DD-A3A2         TCGA-DD-A3A3 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DD-A3A4         TCGA-DD-A3A5         TCGA-DD-A3A6 
"21Q GAIN WILD-TYPE"   "21Q GAIN MUTATED" "21Q GAIN WILD-TYPE" 
        TCGA-DD-A3A7         TCGA-DD-A3A8         TCGA-DD-A3A9 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DD-A4NA         TCGA-DD-A4ND         TCGA-DD-A4NE 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DD-A4NF         TCGA-DD-A4NG         TCGA-DD-A4NH 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DD-A4NI         TCGA-DD-A4NJ         TCGA-DD-A4NK 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DD-A4NL         TCGA-DD-A4NN         TCGA-DD-A4NO 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DD-A4NP         TCGA-DD-A4NQ         TCGA-ED-A459 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-ED-A5KG         TCGA-EP-A12J         TCGA-EP-A26S 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EP-A2KA         TCGA-EP-A2KB         TCGA-EP-A2KC 
"21Q GAIN WILD-TYPE"   "21Q GAIN MUTATED" "21Q GAIN WILD-TYPE" 
        TCGA-EP-A3JL         TCGA-EP-A3RK         TCGA-ES-A2HS 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE"   "21Q GAIN MUTATED" 
        TCGA-ES-A2HT         TCGA-FV-A23B         TCGA-FV-A2QR 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-FV-A3I0         TCGA-FV-A3R2         TCGA-FV-A3R3 
  "21Q GAIN MUTATED" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-FV-A495         TCGA-FV-A496         TCGA-FV-A4ZP 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-FV-A4ZQ         TCGA-G3-A25S         TCGA-G3-A25T 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE"   "21Q GAIN MUTATED" 
        TCGA-G3-A25U         TCGA-G3-A25V         TCGA-G3-A25W 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-G3-A25X         TCGA-G3-A25Y         TCGA-G3-A25Z 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-G3-A3CG         TCGA-G3-A3CH         TCGA-G3-A3CI 
  "21Q GAIN MUTATED" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK         TCGA-G3-A5SJ 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-G3-A5SK         TCGA-G3-A5SL         TCGA-G3-A5SM 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
[1] "hr=" "1.4"
D38V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  21Q GAIN MUTATED         3        4         1          1          0
  21Q GAIN WILD-TYPE      42       21         1         24          3
                    vv
clus                 STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  21Q GAIN MUTATED            0        0         0         0
  21Q GAIN WILD-TYPE          4        1         1         1
D38V3, multiclass
                    vv
clus                 T1 T2 T3 T4
  21Q GAIN MUTATED    3  4  2  0
  21Q GAIN WILD-TYPE 45 24 32  6
D38V4, multiclass
    clus
vv   21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  T1                3                 45
  T2                4                 24
  T3                2                 32
  T4                0                  6
D38V5, binary
                    cls
clus                  0  1
  21Q GAIN MUTATED    6  0
  21Q GAIN WILD-TYPE 68  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED      6    0
  21Q GAIN WILD-TYPE   68    3
   clus
vv  21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  0                6                 68
  1                0                  3
                    vv
clus                 M0 M1 MX
  21Q GAIN MUTATED    8  0  2
  21Q GAIN WILD-TYPE 82  2 23
D38V6, multiclass
    clus
vv   21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  M0                8                 82
  M1                0                  2
  MX                2                 23
D38V7, binary
                    cls
clus                  0  1
  21Q GAIN MUTATED    6  4
  21Q GAIN WILD-TYPE 38 69
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED      6    4
  21Q GAIN WILD-TYPE   38   69
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  FEMALE                6                 38
  MALE                  4                 69
                    vv
clus                 R0 R1 R2 RX
  21Q GAIN MUTATED    7  1  0  2
  21Q GAIN WILD-TYPE 86  9  1  6
D38V8, multiclass
    clus
vv   21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  R0                7                 86
  R1                1                  9
  R2                0                  1
  RX                2                  6

Clustering(39) Variable = 22Q GAIN MUTATION ANALYSIS
D39V1, survival
                    sevent
clus2                 0  1
  22Q GAIN MUTATED    8  8
  22Q GAIN WILD-TYPE 53 45
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                16                 98 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                 8                 45 
$`22Q GAIN MUTATED`
TCGA-BC-A10R TCGA-BC-A10W TCGA-BC-A112 TCGA-CC-5258 TCGA-CC-5261 TCGA-CC-A3MB 
       10.13         2.99         5.03         0.07         3.02         0.10 
TCGA-DD-A118 TCGA-DD-A11A TCGA-DD-A11D TCGA-DD-A1EJ TCGA-DD-A4ND TCGA-ES-A2HS 
      112.96         2.60        51.25        29.16        73.38        23.01 
TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-G3-A25X TCGA-G3-A3CG 
       19.07         0.20        58.49        22.13 

$`22Q GAIN WILD-TYPE`
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U 
       48.99        27.91        37.32        46.78        27.52        27.52 
TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A216 TCGA-BC-A217 
       25.32        23.34         1.12        69.57        44.42        13.81 
TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-CC-5260 TCGA-CC-5262 TCGA-CC-5263 
        0.26        16.37         9.50         2.86         3.39         4.24 
TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MC TCGA-DD-A113 TCGA-DD-A114 
        3.32         0.10         0.07         0.13        79.73        37.74 
TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A119 TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A1E9 
       83.57        53.29         7.33         0.46        21.76        90.67 
TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EF 
       79.36        66.31        19.76        75.65         6.67        12.95 
TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39X TCGA-DD-A39Y 
       49.15         6.02        13.64        21.14        55.66         5.59 
TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 
       19.73        25.81         7.66        70.06        17.59        20.12 
TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A3A9 TCGA-DD-A4NA 
      102.74       107.11        13.78         0.36        30.58        33.14 
TCGA-DD-A4NE TCGA-DD-A4NF TCGA-DD-A4NG TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ 
       21.67        14.07        14.93        14.24        10.78        15.06 
TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ 
       39.75        56.25        29.56        61.45        93.67        12.26 
TCGA-ED-A459 TCGA-ED-A5KG TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB 
        0.23         0.20        10.85         7.76        11.74         1.97 
TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A3R2 
        0.62         3.19         0.43        14.40        32.45         6.35 
TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25S 
        0.13         0.03         0.33        60.36         0.39         1.22 
TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25Y TCGA-G3-A25Z 
       51.02        53.79        28.27        30.71        14.86        21.53 
TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SJ TCGA-G3-A5SK 
       25.64         5.88        19.53        19.23        11.97         9.93 
TCGA-G3-A5SL TCGA-G3-A5SM 
        7.99         4.37 

  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
              0.07               0.03 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
            112.96             107.11 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
            14.600             15.715 
[1] "0.1 - 113.0 (14.6)" "0.0 - 107.1 (15.7)"
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
  "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
  "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-BC-A5W4 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-CC-5258         TCGA-CC-5260         TCGA-CC-5261 
  "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" 
        TCGA-CC-5262         TCGA-CC-5263         TCGA-CC-A1HT 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-CC-A3M9         TCGA-CC-A3MA         TCGA-CC-A3MB 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" 
        TCGA-CC-A3MC         TCGA-DD-A113         TCGA-DD-A114 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" 
        TCGA-DD-A1EA         TCGA-DD-A1EB         TCGA-DD-A1EC 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-DD-A1ED         TCGA-DD-A1EE         TCGA-DD-A1EF 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-DD-A1EH         TCGA-DD-A1EI         TCGA-DD-A1EJ 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" 
        TCGA-DD-A1EL         TCGA-DD-A39V         TCGA-DD-A39X 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-DD-A39Y         TCGA-DD-A39Z         TCGA-DD-A3A0 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-DD-A3A1         TCGA-DD-A3A2         TCGA-DD-A3A3 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-DD-A3A4         TCGA-DD-A3A5         TCGA-DD-A3A6 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-DD-A3A7         TCGA-DD-A3A8         TCGA-DD-A3A9 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-DD-A4NA         TCGA-DD-A4ND         TCGA-DD-A4NE 
"22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" 
        TCGA-DD-A4NF         TCGA-DD-A4NG         TCGA-DD-A4NH 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-DD-A4NI         TCGA-DD-A4NJ         TCGA-DD-A4NK 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-DD-A4NL         TCGA-DD-A4NN         TCGA-DD-A4NO 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-DD-A4NP         TCGA-DD-A4NQ         TCGA-ED-A459 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-ED-A5KG         TCGA-EP-A12J         TCGA-EP-A26S 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EP-A2KA         TCGA-EP-A2KB         TCGA-EP-A2KC 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EP-A3JL         TCGA-EP-A3RK         TCGA-ES-A2HS 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" 
        TCGA-ES-A2HT         TCGA-FV-A23B         TCGA-FV-A2QR 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" 
        TCGA-FV-A3I0         TCGA-FV-A3R2         TCGA-FV-A3R3 
  "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-FV-A495         TCGA-FV-A496         TCGA-FV-A4ZP 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-FV-A4ZQ         TCGA-G3-A25S         TCGA-G3-A25T 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-G3-A25U         TCGA-G3-A25V         TCGA-G3-A25W 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-G3-A25X         TCGA-G3-A25Y         TCGA-G3-A25Z 
  "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-G3-A3CG         TCGA-G3-A3CH         TCGA-G3-A3CI 
  "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK         TCGA-G3-A5SJ 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-G3-A5SK         TCGA-G3-A5SL         TCGA-G3-A5SM 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
  "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
  "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-BC-A5W4 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-CC-5258         TCGA-CC-5260         TCGA-CC-5261 
  "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" 
        TCGA-CC-5262         TCGA-CC-5263         TCGA-CC-A1HT 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-CC-A3M9         TCGA-CC-A3MA         TCGA-CC-A3MB 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" 
        TCGA-CC-A3MC         TCGA-DD-A113         TCGA-DD-A114 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" 
        TCGA-DD-A1EA         TCGA-DD-A1EB         TCGA-DD-A1EC 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-DD-A1ED         TCGA-DD-A1EE         TCGA-DD-A1EF 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-DD-A1EH         TCGA-DD-A1EI         TCGA-DD-A1EJ 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" 
        TCGA-DD-A1EL         TCGA-DD-A39V         TCGA-DD-A39X 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-DD-A39Y         TCGA-DD-A39Z         TCGA-DD-A3A0 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-DD-A3A1         TCGA-DD-A3A2         TCGA-DD-A3A3 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-DD-A3A4         TCGA-DD-A3A5         TCGA-DD-A3A6 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-DD-A3A7         TCGA-DD-A3A8         TCGA-DD-A3A9 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-DD-A4NA         TCGA-DD-A4ND         TCGA-DD-A4NE 
"22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" 
        TCGA-DD-A4NF         TCGA-DD-A4NG         TCGA-DD-A4NH 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-DD-A4NI         TCGA-DD-A4NJ         TCGA-DD-A4NK 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-DD-A4NL         TCGA-DD-A4NN         TCGA-DD-A4NO 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-DD-A4NP         TCGA-DD-A4NQ         TCGA-ED-A459 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-ED-A5KG         TCGA-EP-A12J         TCGA-EP-A26S 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EP-A2KA         TCGA-EP-A2KB         TCGA-EP-A2KC 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EP-A3JL         TCGA-EP-A3RK         TCGA-ES-A2HS 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" 
        TCGA-ES-A2HT         TCGA-FV-A23B         TCGA-FV-A2QR 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" 
        TCGA-FV-A3I0         TCGA-FV-A3R2         TCGA-FV-A3R3 
  "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-FV-A495         TCGA-FV-A496         TCGA-FV-A4ZP 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-FV-A4ZQ         TCGA-G3-A25S         TCGA-G3-A25T 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-G3-A25U         TCGA-G3-A25V         TCGA-G3-A25W 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-G3-A25X         TCGA-G3-A25Y         TCGA-G3-A25Z 
  "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-G3-A3CG         TCGA-G3-A3CH         TCGA-G3-A3CI 
  "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK         TCGA-G3-A5SJ 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-G3-A5SK         TCGA-G3-A5SL         TCGA-G3-A5SM 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
  "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
  "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-BC-A5W4 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-CC-5258         TCGA-CC-5260         TCGA-CC-5261 
  "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" 
        TCGA-CC-5262         TCGA-CC-5263         TCGA-CC-A1HT 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-CC-A3M9         TCGA-CC-A3MA         TCGA-CC-A3MB 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" 
        TCGA-CC-A3MC         TCGA-DD-A113         TCGA-DD-A114 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" 
        TCGA-DD-A1EA         TCGA-DD-A1EB         TCGA-DD-A1EC 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-DD-A1ED         TCGA-DD-A1EE         TCGA-DD-A1EF 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-DD-A1EH         TCGA-DD-A1EI         TCGA-DD-A1EJ 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" 
        TCGA-DD-A1EL         TCGA-DD-A39V         TCGA-DD-A39X 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-DD-A39Y         TCGA-DD-A39Z         TCGA-DD-A3A0 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-DD-A3A1         TCGA-DD-A3A2         TCGA-DD-A3A3 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-DD-A3A4         TCGA-DD-A3A5         TCGA-DD-A3A6 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-DD-A3A7         TCGA-DD-A3A8         TCGA-DD-A3A9 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-DD-A4NA         TCGA-DD-A4ND         TCGA-DD-A4NE 
"22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" 
        TCGA-DD-A4NF         TCGA-DD-A4NG         TCGA-DD-A4NH 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-DD-A4NI         TCGA-DD-A4NJ         TCGA-DD-A4NK 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-DD-A4NL         TCGA-DD-A4NN         TCGA-DD-A4NO 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-DD-A4NP         TCGA-DD-A4NQ         TCGA-ED-A459 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-ED-A5KG         TCGA-EP-A12J         TCGA-EP-A26S 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EP-A2KA         TCGA-EP-A2KB         TCGA-EP-A2KC 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EP-A3JL         TCGA-EP-A3RK         TCGA-ES-A2HS 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" 
        TCGA-ES-A2HT         TCGA-FV-A23B         TCGA-FV-A2QR 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" 
        TCGA-FV-A3I0         TCGA-FV-A3R2         TCGA-FV-A3R3 
  "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-FV-A495         TCGA-FV-A496         TCGA-FV-A4ZP 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-FV-A4ZQ         TCGA-G3-A25S         TCGA-G3-A25T 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-G3-A25U         TCGA-G3-A25V         TCGA-G3-A25W 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-G3-A25X         TCGA-G3-A25Y         TCGA-G3-A25Z 
  "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-G3-A3CG         TCGA-G3-A3CH         TCGA-G3-A3CI 
  "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK         TCGA-G3-A5SJ 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-G3-A5SK         TCGA-G3-A5SL         TCGA-G3-A5SM 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
[1] "hr=" "1"  
D39V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  22Q GAIN MUTATED         6        5         0          1          0
  22Q GAIN WILD-TYPE      39       20         2         24          3
                    vv
clus                 STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  22Q GAIN MUTATED            1        0         0         0
  22Q GAIN WILD-TYPE          3        1         1         1
D39V3, multiclass
                    vv
clus                 T1 T2 T3 T4
  22Q GAIN MUTATED    7  5  3  1
  22Q GAIN WILD-TYPE 41 23 31  5
D39V4, multiclass
    clus
vv   22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  T1                7                 41
  T2                5                 23
  T3                3                 31
  T4                1                  5
D39V5, binary
                    cls
clus                  0  1
  22Q GAIN MUTATED   10  1
  22Q GAIN WILD-TYPE 64  2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED     10    1
  22Q GAIN WILD-TYPE   64    2
   clus
vv  22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  0               10                 64
  1                1                  2
                    vv
clus                 M0 M1 MX
  22Q GAIN MUTATED   12  0  4
  22Q GAIN WILD-TYPE 78  2 21
D39V6, multiclass
    clus
vv   22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  M0               12                 78
  M1                0                  2
  MX                4                 21
D39V7, binary
                    cls
clus                  0  1
  22Q GAIN MUTATED    6 10
  22Q GAIN WILD-TYPE 38 63
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED      6   10
  22Q GAIN WILD-TYPE   38   63
        clus
vv       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  FEMALE                6                 38
  MALE                 10                 63
                    vv
clus                 R0 R1 R2 RX
  22Q GAIN MUTATED   11  2  0  3
  22Q GAIN WILD-TYPE 82  8  1  5
D39V8, multiclass
    clus
vv   22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  R0               11                 82
  R1                2                  8
  R2                0                  1
  RX                3                  5

Clustering(40) Variable = XQ GAIN MUTATION ANALYSIS
D40V1, survival
                   sevent
clus2                0  1
  XQ GAIN MUTATED   14  9
  XQ GAIN WILD-TYPE 47 44
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               23                91 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
                9                44 
$`XQ GAIN MUTATED`
TCGA-BC-A10U TCGA-BC-A10Z TCGA-BC-A3KF TCGA-CC-5260 TCGA-DD-A11A TCGA-DD-A39V 
       27.52         1.12         0.26         2.86         2.60        21.14 
TCGA-DD-A39Y TCGA-DD-A3A3 TCGA-DD-A3A7 TCGA-DD-A4NF TCGA-DD-A4NI TCGA-DD-A4NK 
        5.59        17.59        13.78        14.07        10.78        39.75 
TCGA-EP-A12J TCGA-EP-A2KA TCGA-EP-A3JL TCGA-ES-A2HS TCGA-FV-A496 TCGA-FV-A4ZQ 
       10.85        11.74         3.19        23.01         0.33         0.39 
TCGA-G3-A25U TCGA-G3-A3CG TCGA-G3-A3CJ TCGA-G3-A5SK TCGA-G3-A5SL 
       53.79        22.13        19.53         9.93         7.99 

$`XQ GAIN WILD-TYPE`
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T 
       48.99        27.91        37.32        10.13        46.78        27.52 
TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A216 
        2.99        25.32        23.34        69.57         5.03        44.42 
TCGA-BC-A217 TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-CC-5258 TCGA-CC-5261 TCGA-CC-5262 
       13.81        16.37         9.50         0.07         3.02         3.39 
TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC 
        4.24         3.32         0.10         0.07         0.10         0.13 
TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 
       79.73        37.74        83.57        53.29       112.96         7.33 
TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB 
        0.46        21.76        51.25        90.67        79.36        66.31 
TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EH TCGA-DD-A1EI 
       19.76        75.65         6.67        12.95        49.15         6.02 
TCGA-DD-A1EJ TCGA-DD-A1EL TCGA-DD-A39X TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 
       29.16        13.64        55.66        19.73        25.81         7.66 
TCGA-DD-A3A2 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A8 TCGA-DD-A3A9 
       70.06        20.12       102.74       107.11         0.36        30.58 
TCGA-DD-A4NA TCGA-DD-A4ND TCGA-DD-A4NE TCGA-DD-A4NG TCGA-DD-A4NH TCGA-DD-A4NJ 
       33.14        73.38        21.67        14.93        14.24        15.06 
TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-ED-A459 
       56.25        29.56        61.45        93.67        12.26         0.23 
TCGA-ED-A5KG TCGA-EP-A26S TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3RK TCGA-ES-A2HT 
        0.20         7.76         1.97         0.62         0.43        14.40 
TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 
       32.45        19.07         0.20         6.35         0.13         0.03 
TCGA-FV-A4ZP TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25X 
       60.36         1.22        51.02        28.27        30.71        58.49 
TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CK TCGA-G3-A5SJ 
       14.86        21.53        25.64         5.88        19.23        11.97 
TCGA-G3-A5SM 
        4.37 

  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
             0.26              0.03 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
            53.79            112.96 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
            10.85             19.73 
[1] "0.3 - 53.8 (10.8)"  "0.0 - 113.0 (19.7)"
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED" "XQ GAIN WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED" "XQ GAIN WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED" 
       TCGA-BC-A3KG        TCGA-BC-A5W4        TCGA-CC-5258        TCGA-CC-5260 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED" 
       TCGA-CC-5261        TCGA-CC-5262        TCGA-CC-5263        TCGA-CC-A1HT 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-CC-A3M9        TCGA-CC-A3MA        TCGA-CC-A3MB        TCGA-CC-A3MC 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-DD-A113        TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-DD-A118        TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED" "XQ GAIN WILD-TYPE" 
       TCGA-DD-A11C        TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EA 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-DD-A1EB        TCGA-DD-A1EC        TCGA-DD-A1ED        TCGA-DD-A1EE 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-DD-A1EF        TCGA-DD-A1EH        TCGA-DD-A1EI        TCGA-DD-A1EJ 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-DD-A1EL        TCGA-DD-A39V        TCGA-DD-A39X        TCGA-DD-A39Y 
"XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED" "XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED" 
       TCGA-DD-A39Z        TCGA-DD-A3A0        TCGA-DD-A3A1        TCGA-DD-A3A2 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-DD-A3A3        TCGA-DD-A3A4        TCGA-DD-A3A5        TCGA-DD-A3A6 
  "XQ GAIN MUTATED" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-DD-A3A7        TCGA-DD-A3A8        TCGA-DD-A3A9        TCGA-DD-A4NA 
  "XQ GAIN MUTATED" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-DD-A4ND        TCGA-DD-A4NE        TCGA-DD-A4NF        TCGA-DD-A4NG 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED" "XQ GAIN WILD-TYPE" 
       TCGA-DD-A4NH        TCGA-DD-A4NI        TCGA-DD-A4NJ        TCGA-DD-A4NK 
"XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED" "XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED" 
       TCGA-DD-A4NL        TCGA-DD-A4NN        TCGA-DD-A4NO        TCGA-DD-A4NP 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-DD-A4NQ        TCGA-ED-A459        TCGA-ED-A5KG        TCGA-EP-A12J 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED" 
       TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC 
"XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-EP-A3JL        TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT 
  "XQ GAIN MUTATED" "XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED" "XQ GAIN WILD-TYPE" 
       TCGA-FV-A23B        TCGA-FV-A2QR        TCGA-FV-A3I0        TCGA-FV-A3R2 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-FV-A3R3        TCGA-FV-A495        TCGA-FV-A496        TCGA-FV-A4ZP 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED" "XQ GAIN WILD-TYPE" 
       TCGA-FV-A4ZQ        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
  "XQ GAIN MUTATED" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI 
"XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-G3-A3CJ        TCGA-G3-A3CK        TCGA-G3-A5SJ        TCGA-G3-A5SK 
  "XQ GAIN MUTATED" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED" 
       TCGA-G3-A5SL        TCGA-G3-A5SM 
  "XQ GAIN MUTATED" "XQ GAIN WILD-TYPE" 
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED" "XQ GAIN WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED" "XQ GAIN WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED" 
       TCGA-BC-A3KG        TCGA-BC-A5W4        TCGA-CC-5258        TCGA-CC-5260 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED" 
       TCGA-CC-5261        TCGA-CC-5262        TCGA-CC-5263        TCGA-CC-A1HT 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-CC-A3M9        TCGA-CC-A3MA        TCGA-CC-A3MB        TCGA-CC-A3MC 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-DD-A113        TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-DD-A118        TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED" "XQ GAIN WILD-TYPE" 
       TCGA-DD-A11C        TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EA 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-DD-A1EB        TCGA-DD-A1EC        TCGA-DD-A1ED        TCGA-DD-A1EE 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-DD-A1EF        TCGA-DD-A1EH        TCGA-DD-A1EI        TCGA-DD-A1EJ 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-DD-A1EL        TCGA-DD-A39V        TCGA-DD-A39X        TCGA-DD-A39Y 
"XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED" "XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED" 
       TCGA-DD-A39Z        TCGA-DD-A3A0        TCGA-DD-A3A1        TCGA-DD-A3A2 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-DD-A3A3        TCGA-DD-A3A4        TCGA-DD-A3A5        TCGA-DD-A3A6 
  "XQ GAIN MUTATED" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-DD-A3A7        TCGA-DD-A3A8        TCGA-DD-A3A9        TCGA-DD-A4NA 
  "XQ GAIN MUTATED" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-DD-A4ND        TCGA-DD-A4NE        TCGA-DD-A4NF        TCGA-DD-A4NG 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED" "XQ GAIN WILD-TYPE" 
       TCGA-DD-A4NH        TCGA-DD-A4NI        TCGA-DD-A4NJ        TCGA-DD-A4NK 
"XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED" "XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED" 
       TCGA-DD-A4NL        TCGA-DD-A4NN        TCGA-DD-A4NO        TCGA-DD-A4NP 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-DD-A4NQ        TCGA-ED-A459        TCGA-ED-A5KG        TCGA-EP-A12J 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED" 
       TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC 
"XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-EP-A3JL        TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT 
  "XQ GAIN MUTATED" "XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED" "XQ GAIN WILD-TYPE" 
       TCGA-FV-A23B        TCGA-FV-A2QR        TCGA-FV-A3I0        TCGA-FV-A3R2 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-FV-A3R3        TCGA-FV-A495        TCGA-FV-A496        TCGA-FV-A4ZP 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED" "XQ GAIN WILD-TYPE" 
       TCGA-FV-A4ZQ        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
  "XQ GAIN MUTATED" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI 
"XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-G3-A3CJ        TCGA-G3-A3CK        TCGA-G3-A5SJ        TCGA-G3-A5SK 
  "XQ GAIN MUTATED" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED" 
       TCGA-G3-A5SL        TCGA-G3-A5SM 
  "XQ GAIN MUTATED" "XQ GAIN WILD-TYPE" 
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED" "XQ GAIN WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED" "XQ GAIN WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED" 
       TCGA-BC-A3KG        TCGA-BC-A5W4        TCGA-CC-5258        TCGA-CC-5260 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED" 
       TCGA-CC-5261        TCGA-CC-5262        TCGA-CC-5263        TCGA-CC-A1HT 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-CC-A3M9        TCGA-CC-A3MA        TCGA-CC-A3MB        TCGA-CC-A3MC 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-DD-A113        TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-DD-A118        TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED" "XQ GAIN WILD-TYPE" 
       TCGA-DD-A11C        TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EA 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-DD-A1EB        TCGA-DD-A1EC        TCGA-DD-A1ED        TCGA-DD-A1EE 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-DD-A1EF        TCGA-DD-A1EH        TCGA-DD-A1EI        TCGA-DD-A1EJ 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-DD-A1EL        TCGA-DD-A39V        TCGA-DD-A39X        TCGA-DD-A39Y 
"XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED" "XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED" 
       TCGA-DD-A39Z        TCGA-DD-A3A0        TCGA-DD-A3A1        TCGA-DD-A3A2 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-DD-A3A3        TCGA-DD-A3A4        TCGA-DD-A3A5        TCGA-DD-A3A6 
  "XQ GAIN MUTATED" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-DD-A3A7        TCGA-DD-A3A8        TCGA-DD-A3A9        TCGA-DD-A4NA 
  "XQ GAIN MUTATED" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-DD-A4ND        TCGA-DD-A4NE        TCGA-DD-A4NF        TCGA-DD-A4NG 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED" "XQ GAIN WILD-TYPE" 
       TCGA-DD-A4NH        TCGA-DD-A4NI        TCGA-DD-A4NJ        TCGA-DD-A4NK 
"XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED" "XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED" 
       TCGA-DD-A4NL        TCGA-DD-A4NN        TCGA-DD-A4NO        TCGA-DD-A4NP 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-DD-A4NQ        TCGA-ED-A459        TCGA-ED-A5KG        TCGA-EP-A12J 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED" 
       TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC 
"XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-EP-A3JL        TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT 
  "XQ GAIN MUTATED" "XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED" "XQ GAIN WILD-TYPE" 
       TCGA-FV-A23B        TCGA-FV-A2QR        TCGA-FV-A3I0        TCGA-FV-A3R2 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-FV-A3R3        TCGA-FV-A495        TCGA-FV-A496        TCGA-FV-A4ZP 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED" "XQ GAIN WILD-TYPE" 
       TCGA-FV-A4ZQ        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
  "XQ GAIN MUTATED" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI 
"XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-G3-A3CJ        TCGA-G3-A3CK        TCGA-G3-A5SJ        TCGA-G3-A5SK 
  "XQ GAIN MUTATED" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED" 
       TCGA-G3-A5SL        TCGA-G3-A5SM 
  "XQ GAIN MUTATED" "XQ GAIN WILD-TYPE" 
[1] "hr=" "1.6"
D40V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  XQ GAIN MUTATED        14        3         0          4          1          1
  XQ GAIN WILD-TYPE      31       22         2         21          2          3
                   vv
clus                STAGE IV STAGE IVA STAGE IVB
  XQ GAIN MUTATED          0         0         0
  XQ GAIN WILD-TYPE        1         1         1
D40V3, multiclass
                   vv
clus                T1 T2 T3 T4
  XQ GAIN MUTATED   14  4  5  1
  XQ GAIN WILD-TYPE 34 24 29  5
D40V4, multiclass
    clus
vv   XQ GAIN MUTATED XQ GAIN WILD-TYPE
  T1              14                34
  T2               4                24
  T3               5                29
  T4               1                 5
D40V5, binary
                   cls
clus                 0  1
  XQ GAIN MUTATED   11  0
  XQ GAIN WILD-TYPE 63  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED     11    0
  XQ GAIN WILD-TYPE   63    3
   clus
vv  XQ GAIN MUTATED XQ GAIN WILD-TYPE
  0              11                63
  1               0                 3
                   vv
clus                M0 M1 MX
  XQ GAIN MUTATED   18  0  6
  XQ GAIN WILD-TYPE 72  2 19
D40V6, multiclass
    clus
vv   XQ GAIN MUTATED XQ GAIN WILD-TYPE
  M0              18                72
  M1               0                 2
  MX               6                19
D40V7, binary
                   cls
clus                 0  1
  XQ GAIN MUTATED    7 17
  XQ GAIN WILD-TYPE 37 56
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED      7   17
  XQ GAIN WILD-TYPE   37   56
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  FEMALE               7                37
  MALE                17                56
                   vv
clus                R0 R1 R2 RX
  XQ GAIN MUTATED   19  2  0  2
  XQ GAIN WILD-TYPE 74  8  1  6
D40V8, multiclass
    clus
vv   XQ GAIN MUTATED XQ GAIN WILD-TYPE
  R0              19                74
  R1               2                 8
  R2               0                 1
  RX               2                 6

Clustering(41) Variable = 1P LOSS MUTATION ANALYSIS
D41V1, survival
                   sevent
clus2                0  1
  1P LOSS MUTATED   15 12
  1P LOSS WILD-TYPE 46 41
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               27                87 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               12                41 
$`1P LOSS MUTATED`
TCGA-BC-A10S TCGA-BC-A217 TCGA-CC-5258 TCGA-CC-5261 TCGA-CC-A3MB TCGA-CC-A3MC 
       46.78        13.81         0.07         3.02         0.10         0.13 
TCGA-DD-A113 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11B TCGA-DD-A11D TCGA-DD-A1E9 
       79.73       112.96         7.33         0.46        51.25        90.67 
TCGA-DD-A1EH TCGA-DD-A1EJ TCGA-DD-A3A1 TCGA-DD-A3A9 TCGA-DD-A4NG TCGA-DD-A4NH 
       49.15        29.16         7.66        30.58        14.93        14.24 
TCGA-EP-A2KB TCGA-EP-A2KC TCGA-ES-A2HS TCGA-FV-A3I0 TCGA-FV-A496 TCGA-G3-A25U 
        1.97         0.62        23.01         0.20         0.33        53.79 
TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A5SM 
       58.49        14.86         4.37 

$`1P LOSS WILD-TYPE`
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A10U 
       48.99        27.91        37.32        10.13        27.52        27.52 
TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 
        2.99        25.32        23.34         1.12        69.57         5.03 
TCGA-BC-A216 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-CC-5260 TCGA-CC-5262 
       44.42         0.26        16.37         9.50         2.86         3.39 
TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-DD-A114 TCGA-DD-A115 
        4.24         3.32         0.10         0.07        37.74        83.57 
TCGA-DD-A116 TCGA-DD-A11A TCGA-DD-A11C TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC 
       53.29         2.60        21.76        79.36        66.31        19.76 
TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EI TCGA-DD-A1EL TCGA-DD-A39V 
       75.65         6.67        12.95         6.02        13.64        21.14 
TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A2 TCGA-DD-A3A3 
       55.66         5.59        19.73        25.81        70.06        17.59 
TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A4NA 
       20.12       102.74       107.11        13.78         0.36        33.14 
TCGA-DD-A4ND TCGA-DD-A4NE TCGA-DD-A4NF TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK 
       73.38        21.67        14.07        10.78        15.06        39.75 
TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-ED-A459 
       56.25        29.56        61.45        93.67        12.26         0.23 
TCGA-ED-A5KG TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A3JL TCGA-EP-A3RK 
        0.20        10.85         7.76        11.74         3.19         0.43 
TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 
       14.40        32.45        19.07         6.35         0.13         0.03 
TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25V TCGA-G3-A25W 
       60.36         0.39         1.22        51.02        28.27        30.71 
TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK 
       21.53        22.13        25.64         5.88        19.53        19.23 
TCGA-G3-A5SJ TCGA-G3-A5SK TCGA-G3-A5SL 
       11.97         9.93         7.99 

  1P LOSS MUTATED 1P LOSS WILD-TYPE 
             0.07              0.03 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
           112.96            107.11 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
            14.24             19.07 
[1] "0.1 - 113.0 (14.2)" "0.0 - 107.1 (19.1)"
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
  "1P LOSS MUTATED" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-BC-A5W4        TCGA-CC-5258        TCGA-CC-5260 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE" 
       TCGA-CC-5261        TCGA-CC-5262        TCGA-CC-5263        TCGA-CC-A1HT 
  "1P LOSS MUTATED" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-CC-A3M9        TCGA-CC-A3MA        TCGA-CC-A3MB        TCGA-CC-A3MC 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED"   "1P LOSS MUTATED" 
       TCGA-DD-A113        TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116 
  "1P LOSS MUTATED" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DD-A118        TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B 
  "1P LOSS MUTATED"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" 
       TCGA-DD-A11C        TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EA 
"1P LOSS WILD-TYPE"   "1P LOSS MUTATED"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE" 
       TCGA-DD-A1EB        TCGA-DD-A1EC        TCGA-DD-A1ED        TCGA-DD-A1EE 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DD-A1EF        TCGA-DD-A1EH        TCGA-DD-A1EI        TCGA-DD-A1EJ 
"1P LOSS WILD-TYPE"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" 
       TCGA-DD-A1EL        TCGA-DD-A39V        TCGA-DD-A39X        TCGA-DD-A39Y 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DD-A39Z        TCGA-DD-A3A0        TCGA-DD-A3A1        TCGA-DD-A3A2 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE" 
       TCGA-DD-A3A3        TCGA-DD-A3A4        TCGA-DD-A3A5        TCGA-DD-A3A6 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DD-A3A7        TCGA-DD-A3A8        TCGA-DD-A3A9        TCGA-DD-A4NA 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE" 
       TCGA-DD-A4ND        TCGA-DD-A4NE        TCGA-DD-A4NF        TCGA-DD-A4NG 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" 
       TCGA-DD-A4NH        TCGA-DD-A4NI        TCGA-DD-A4NJ        TCGA-DD-A4NK 
  "1P LOSS MUTATED" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DD-A4NL        TCGA-DD-A4NN        TCGA-DD-A4NO        TCGA-DD-A4NP 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DD-A4NQ        TCGA-ED-A459        TCGA-ED-A5KG        TCGA-EP-A12J 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED"   "1P LOSS MUTATED" 
       TCGA-EP-A3JL        TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE" 
       TCGA-FV-A23B        TCGA-FV-A2QR        TCGA-FV-A3I0        TCGA-FV-A3R2 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE" 
       TCGA-FV-A3R3        TCGA-FV-A495        TCGA-FV-A496        TCGA-FV-A4ZP 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE" 
       TCGA-FV-A4ZQ        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED"   "1P LOSS MUTATED" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-G3-A3CJ        TCGA-G3-A3CK        TCGA-G3-A5SJ        TCGA-G3-A5SK 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-G3-A5SL        TCGA-G3-A5SM 
"1P LOSS WILD-TYPE"   "1P LOSS MUTATED" 
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
  "1P LOSS MUTATED" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-BC-A5W4        TCGA-CC-5258        TCGA-CC-5260 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE" 
       TCGA-CC-5261        TCGA-CC-5262        TCGA-CC-5263        TCGA-CC-A1HT 
  "1P LOSS MUTATED" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-CC-A3M9        TCGA-CC-A3MA        TCGA-CC-A3MB        TCGA-CC-A3MC 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED"   "1P LOSS MUTATED" 
       TCGA-DD-A113        TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116 
  "1P LOSS MUTATED" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DD-A118        TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B 
  "1P LOSS MUTATED"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" 
       TCGA-DD-A11C        TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EA 
"1P LOSS WILD-TYPE"   "1P LOSS MUTATED"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE" 
       TCGA-DD-A1EB        TCGA-DD-A1EC        TCGA-DD-A1ED        TCGA-DD-A1EE 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DD-A1EF        TCGA-DD-A1EH        TCGA-DD-A1EI        TCGA-DD-A1EJ 
"1P LOSS WILD-TYPE"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" 
       TCGA-DD-A1EL        TCGA-DD-A39V        TCGA-DD-A39X        TCGA-DD-A39Y 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DD-A39Z        TCGA-DD-A3A0        TCGA-DD-A3A1        TCGA-DD-A3A2 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE" 
       TCGA-DD-A3A3        TCGA-DD-A3A4        TCGA-DD-A3A5        TCGA-DD-A3A6 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DD-A3A7        TCGA-DD-A3A8        TCGA-DD-A3A9        TCGA-DD-A4NA 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE" 
       TCGA-DD-A4ND        TCGA-DD-A4NE        TCGA-DD-A4NF        TCGA-DD-A4NG 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" 
       TCGA-DD-A4NH        TCGA-DD-A4NI        TCGA-DD-A4NJ        TCGA-DD-A4NK 
  "1P LOSS MUTATED" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DD-A4NL        TCGA-DD-A4NN        TCGA-DD-A4NO        TCGA-DD-A4NP 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DD-A4NQ        TCGA-ED-A459        TCGA-ED-A5KG        TCGA-EP-A12J 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED"   "1P LOSS MUTATED" 
       TCGA-EP-A3JL        TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE" 
       TCGA-FV-A23B        TCGA-FV-A2QR        TCGA-FV-A3I0        TCGA-FV-A3R2 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE" 
       TCGA-FV-A3R3        TCGA-FV-A495        TCGA-FV-A496        TCGA-FV-A4ZP 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE" 
       TCGA-FV-A4ZQ        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED"   "1P LOSS MUTATED" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-G3-A3CJ        TCGA-G3-A3CK        TCGA-G3-A5SJ        TCGA-G3-A5SK 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-G3-A5SL        TCGA-G3-A5SM 
"1P LOSS WILD-TYPE"   "1P LOSS MUTATED" 
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
  "1P LOSS MUTATED" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-BC-A5W4        TCGA-CC-5258        TCGA-CC-5260 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE" 
       TCGA-CC-5261        TCGA-CC-5262        TCGA-CC-5263        TCGA-CC-A1HT 
  "1P LOSS MUTATED" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-CC-A3M9        TCGA-CC-A3MA        TCGA-CC-A3MB        TCGA-CC-A3MC 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED"   "1P LOSS MUTATED" 
       TCGA-DD-A113        TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116 
  "1P LOSS MUTATED" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DD-A118        TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B 
  "1P LOSS MUTATED"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" 
       TCGA-DD-A11C        TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EA 
"1P LOSS WILD-TYPE"   "1P LOSS MUTATED"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE" 
       TCGA-DD-A1EB        TCGA-DD-A1EC        TCGA-DD-A1ED        TCGA-DD-A1EE 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DD-A1EF        TCGA-DD-A1EH        TCGA-DD-A1EI        TCGA-DD-A1EJ 
"1P LOSS WILD-TYPE"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" 
       TCGA-DD-A1EL        TCGA-DD-A39V        TCGA-DD-A39X        TCGA-DD-A39Y 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DD-A39Z        TCGA-DD-A3A0        TCGA-DD-A3A1        TCGA-DD-A3A2 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE" 
       TCGA-DD-A3A3        TCGA-DD-A3A4        TCGA-DD-A3A5        TCGA-DD-A3A6 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DD-A3A7        TCGA-DD-A3A8        TCGA-DD-A3A9        TCGA-DD-A4NA 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE" 
       TCGA-DD-A4ND        TCGA-DD-A4NE        TCGA-DD-A4NF        TCGA-DD-A4NG 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" 
       TCGA-DD-A4NH        TCGA-DD-A4NI        TCGA-DD-A4NJ        TCGA-DD-A4NK 
  "1P LOSS MUTATED" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DD-A4NL        TCGA-DD-A4NN        TCGA-DD-A4NO        TCGA-DD-A4NP 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DD-A4NQ        TCGA-ED-A459        TCGA-ED-A5KG        TCGA-EP-A12J 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED"   "1P LOSS MUTATED" 
       TCGA-EP-A3JL        TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE" 
       TCGA-FV-A23B        TCGA-FV-A2QR        TCGA-FV-A3I0        TCGA-FV-A3R2 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE" 
       TCGA-FV-A3R3        TCGA-FV-A495        TCGA-FV-A496        TCGA-FV-A4ZP 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE" 
       TCGA-FV-A4ZQ        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED"   "1P LOSS MUTATED" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-G3-A3CJ        TCGA-G3-A3CK        TCGA-G3-A5SJ        TCGA-G3-A5SK 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-G3-A5SL        TCGA-G3-A5SM 
"1P LOSS WILD-TYPE"   "1P LOSS MUTATED" 
[1] "hr=" "1.1"
D41V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  1P LOSS MUTATED         9        8         1          4          1          1
  1P LOSS WILD-TYPE      36       17         1         21          2          3
                   vv
clus                STAGE IV STAGE IVA STAGE IVB
  1P LOSS MUTATED          1         1         1
  1P LOSS WILD-TYPE        0         0         0
D41V3, multiclass
                   vv
clus                T1 T2 T3 T4
  1P LOSS MUTATED   11  8  8  1
  1P LOSS WILD-TYPE 37 20 26  5
D41V4, multiclass
    clus
vv   1P LOSS MUTATED 1P LOSS WILD-TYPE
  T1              11                37
  T2               8                20
  T3               8                26
  T4               1                 5
D41V5, binary
                   cls
clus                 0  1
  1P LOSS MUTATED   17  2
  1P LOSS WILD-TYPE 57  1
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED     17    2
  1P LOSS WILD-TYPE   57    1
   clus
vv  1P LOSS MUTATED 1P LOSS WILD-TYPE
  0              17                57
  1               2                 1
                   vv
clus                M0 M1 MX
  1P LOSS MUTATED   21  2  5
  1P LOSS WILD-TYPE 69  0 20
D41V6, multiclass
    clus
vv   1P LOSS MUTATED 1P LOSS WILD-TYPE
  M0              21                69
  M1               2                 0
  MX               5                20
D41V7, binary
                   cls
clus                 0  1
  1P LOSS MUTATED   12 16
  1P LOSS WILD-TYPE 32 57
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED     12   16
  1P LOSS WILD-TYPE   32   57
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  FEMALE              12                32
  MALE                16                57
                   vv
clus                R0 R1 R2 RX
  1P LOSS MUTATED   24  0  1  3
  1P LOSS WILD-TYPE 69 10  0  5
D41V8, multiclass
    clus
vv   1P LOSS MUTATED 1P LOSS WILD-TYPE
  R0              24                69
  R1               0                10
  R2               1                 0
  RX               3                 5

Clustering(42) Variable = 1Q LOSS MUTATION ANALYSIS
D42V1, survival
                   sevent
clus2                0  1
  1Q LOSS MUTATED    5  6
  1Q LOSS WILD-TYPE 56 47
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               11               103 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
                6                47 
$`1Q LOSS MUTATED`
TCGA-BC-A10S TCGA-BC-A217 TCGA-CC-5258 TCGA-CC-A3MB TCGA-DD-A11B TCGA-DD-A11D 
       46.78        13.81         0.07         0.10         0.46        51.25 
TCGA-DD-A1EJ TCGA-DD-A3A1 TCGA-ES-A2HS TCGA-FV-A496 TCGA-G3-A25U 
       29.16         7.66        23.01         0.33        53.79 

$`1Q LOSS WILD-TYPE`
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A10U 
       48.99        27.91        37.32        10.13        27.52        27.52 
TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 
        2.99        25.32        23.34         1.12        69.57         5.03 
TCGA-BC-A216 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-CC-5260 TCGA-CC-5261 
       44.42         0.26        16.37         9.50         2.86         3.02 
TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MC 
        3.39         4.24         3.32         0.10         0.07         0.13 
TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 
       79.73        37.74        83.57        53.29       112.96         7.33 
TCGA-DD-A11A TCGA-DD-A11C TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC 
        2.60        21.76        90.67        79.36        66.31        19.76 
TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EL 
       75.65         6.67        12.95        49.15         6.02        13.64 
TCGA-DD-A39V TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A2 
       21.14        55.66         5.59        19.73        25.81        70.06 
TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A8 
       17.59        20.12       102.74       107.11        13.78         0.36 
TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4ND TCGA-DD-A4NE TCGA-DD-A4NF TCGA-DD-A4NG 
       30.58        33.14        73.38        21.67        14.07        14.93 
TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN 
       14.24        10.78        15.06        39.75        56.25        29.56 
TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-ED-A459 TCGA-ED-A5KG TCGA-EP-A12J 
       61.45        93.67        12.26         0.23         0.20        10.85 
TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK 
        7.76        11.74         1.97         0.62         3.19         0.43 
TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3R2 TCGA-FV-A3R3 
       14.40        32.45        19.07         0.20         6.35         0.13 
TCGA-FV-A495 TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25V 
        0.03        60.36         0.39         1.22        51.02        28.27 
TCGA-G3-A25W TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CH 
       30.71        58.49        14.86        21.53        22.13        25.64 
TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SJ TCGA-G3-A5SK TCGA-G3-A5SL 
        5.88        19.53        19.23        11.97         9.93         7.99 
TCGA-G3-A5SM 
        4.37 

  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
             0.07              0.03 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
            53.79            112.96 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
            13.81             16.37 
[1] "0.1 - 53.8 (13.8)"  "0.0 - 113.0 (16.4)"
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
  "1Q LOSS MUTATED" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE"   "1Q LOSS MUTATED" "1Q LOSS WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-BC-A5W4        TCGA-CC-5258        TCGA-CC-5260 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE"   "1Q LOSS MUTATED" "1Q LOSS WILD-TYPE" 
       TCGA-CC-5261        TCGA-CC-5262        TCGA-CC-5263        TCGA-CC-A1HT 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-CC-A3M9        TCGA-CC-A3MA        TCGA-CC-A3MB        TCGA-CC-A3MC 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE"   "1Q LOSS MUTATED" "1Q LOSS WILD-TYPE" 
       TCGA-DD-A113        TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DD-A118        TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE"   "1Q LOSS MUTATED" 
       TCGA-DD-A11C        TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EA 
"1Q LOSS WILD-TYPE"   "1Q LOSS MUTATED" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DD-A1EB        TCGA-DD-A1EC        TCGA-DD-A1ED        TCGA-DD-A1EE 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DD-A1EF        TCGA-DD-A1EH        TCGA-DD-A1EI        TCGA-DD-A1EJ 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE"   "1Q LOSS MUTATED" 
       TCGA-DD-A1EL        TCGA-DD-A39V        TCGA-DD-A39X        TCGA-DD-A39Y 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DD-A39Z        TCGA-DD-A3A0        TCGA-DD-A3A1        TCGA-DD-A3A2 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE"   "1Q LOSS MUTATED" "1Q LOSS WILD-TYPE" 
       TCGA-DD-A3A3        TCGA-DD-A3A4        TCGA-DD-A3A5        TCGA-DD-A3A6 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DD-A3A7        TCGA-DD-A3A8        TCGA-DD-A3A9        TCGA-DD-A4NA 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DD-A4ND        TCGA-DD-A4NE        TCGA-DD-A4NF        TCGA-DD-A4NG 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DD-A4NH        TCGA-DD-A4NI        TCGA-DD-A4NJ        TCGA-DD-A4NK 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DD-A4NL        TCGA-DD-A4NN        TCGA-DD-A4NO        TCGA-DD-A4NP 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DD-A4NQ        TCGA-ED-A459        TCGA-ED-A5KG        TCGA-EP-A12J 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EP-A3JL        TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE"   "1Q LOSS MUTATED" "1Q LOSS WILD-TYPE" 
       TCGA-FV-A23B        TCGA-FV-A2QR        TCGA-FV-A3I0        TCGA-FV-A3R2 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-FV-A3R3        TCGA-FV-A495        TCGA-FV-A496        TCGA-FV-A4ZP 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE"   "1Q LOSS MUTATED" "1Q LOSS WILD-TYPE" 
       TCGA-FV-A4ZQ        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE"   "1Q LOSS MUTATED" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-G3-A3CJ        TCGA-G3-A3CK        TCGA-G3-A5SJ        TCGA-G3-A5SK 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-G3-A5SL        TCGA-G3-A5SM 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
  "1Q LOSS MUTATED" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE"   "1Q LOSS MUTATED" "1Q LOSS WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-BC-A5W4        TCGA-CC-5258        TCGA-CC-5260 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE"   "1Q LOSS MUTATED" "1Q LOSS WILD-TYPE" 
       TCGA-CC-5261        TCGA-CC-5262        TCGA-CC-5263        TCGA-CC-A1HT 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-CC-A3M9        TCGA-CC-A3MA        TCGA-CC-A3MB        TCGA-CC-A3MC 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE"   "1Q LOSS MUTATED" "1Q LOSS WILD-TYPE" 
       TCGA-DD-A113        TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DD-A118        TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE"   "1Q LOSS MUTATED" 
       TCGA-DD-A11C        TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EA 
"1Q LOSS WILD-TYPE"   "1Q LOSS MUTATED" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DD-A1EB        TCGA-DD-A1EC        TCGA-DD-A1ED        TCGA-DD-A1EE 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DD-A1EF        TCGA-DD-A1EH        TCGA-DD-A1EI        TCGA-DD-A1EJ 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE"   "1Q LOSS MUTATED" 
       TCGA-DD-A1EL        TCGA-DD-A39V        TCGA-DD-A39X        TCGA-DD-A39Y 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DD-A39Z        TCGA-DD-A3A0        TCGA-DD-A3A1        TCGA-DD-A3A2 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE"   "1Q LOSS MUTATED" "1Q LOSS WILD-TYPE" 
       TCGA-DD-A3A3        TCGA-DD-A3A4        TCGA-DD-A3A5        TCGA-DD-A3A6 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DD-A3A7        TCGA-DD-A3A8        TCGA-DD-A3A9        TCGA-DD-A4NA 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DD-A4ND        TCGA-DD-A4NE        TCGA-DD-A4NF        TCGA-DD-A4NG 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DD-A4NH        TCGA-DD-A4NI        TCGA-DD-A4NJ        TCGA-DD-A4NK 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DD-A4NL        TCGA-DD-A4NN        TCGA-DD-A4NO        TCGA-DD-A4NP 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DD-A4NQ        TCGA-ED-A459        TCGA-ED-A5KG        TCGA-EP-A12J 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EP-A3JL        TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE"   "1Q LOSS MUTATED" "1Q LOSS WILD-TYPE" 
       TCGA-FV-A23B        TCGA-FV-A2QR        TCGA-FV-A3I0        TCGA-FV-A3R2 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-FV-A3R3        TCGA-FV-A495        TCGA-FV-A496        TCGA-FV-A4ZP 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE"   "1Q LOSS MUTATED" "1Q LOSS WILD-TYPE" 
       TCGA-FV-A4ZQ        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE"   "1Q LOSS MUTATED" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-G3-A3CJ        TCGA-G3-A3CK        TCGA-G3-A5SJ        TCGA-G3-A5SK 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-G3-A5SL        TCGA-G3-A5SM 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
  "1Q LOSS MUTATED" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE"   "1Q LOSS MUTATED" "1Q LOSS WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-BC-A5W4        TCGA-CC-5258        TCGA-CC-5260 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE"   "1Q LOSS MUTATED" "1Q LOSS WILD-TYPE" 
       TCGA-CC-5261        TCGA-CC-5262        TCGA-CC-5263        TCGA-CC-A1HT 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-CC-A3M9        TCGA-CC-A3MA        TCGA-CC-A3MB        TCGA-CC-A3MC 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE"   "1Q LOSS MUTATED" "1Q LOSS WILD-TYPE" 
       TCGA-DD-A113        TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DD-A118        TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE"   "1Q LOSS MUTATED" 
       TCGA-DD-A11C        TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EA 
"1Q LOSS WILD-TYPE"   "1Q LOSS MUTATED" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DD-A1EB        TCGA-DD-A1EC        TCGA-DD-A1ED        TCGA-DD-A1EE 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DD-A1EF        TCGA-DD-A1EH        TCGA-DD-A1EI        TCGA-DD-A1EJ 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE"   "1Q LOSS MUTATED" 
       TCGA-DD-A1EL        TCGA-DD-A39V        TCGA-DD-A39X        TCGA-DD-A39Y 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DD-A39Z        TCGA-DD-A3A0        TCGA-DD-A3A1        TCGA-DD-A3A2 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE"   "1Q LOSS MUTATED" "1Q LOSS WILD-TYPE" 
       TCGA-DD-A3A3        TCGA-DD-A3A4        TCGA-DD-A3A5        TCGA-DD-A3A6 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DD-A3A7        TCGA-DD-A3A8        TCGA-DD-A3A9        TCGA-DD-A4NA 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DD-A4ND        TCGA-DD-A4NE        TCGA-DD-A4NF        TCGA-DD-A4NG 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DD-A4NH        TCGA-DD-A4NI        TCGA-DD-A4NJ        TCGA-DD-A4NK 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DD-A4NL        TCGA-DD-A4NN        TCGA-DD-A4NO        TCGA-DD-A4NP 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DD-A4NQ        TCGA-ED-A459        TCGA-ED-A5KG        TCGA-EP-A12J 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EP-A3JL        TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE"   "1Q LOSS MUTATED" "1Q LOSS WILD-TYPE" 
       TCGA-FV-A23B        TCGA-FV-A2QR        TCGA-FV-A3I0        TCGA-FV-A3R2 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-FV-A3R3        TCGA-FV-A495        TCGA-FV-A496        TCGA-FV-A4ZP 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE"   "1Q LOSS MUTATED" "1Q LOSS WILD-TYPE" 
       TCGA-FV-A4ZQ        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE"   "1Q LOSS MUTATED" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-G3-A3CJ        TCGA-G3-A3CK        TCGA-G3-A5SJ        TCGA-G3-A5SK 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-G3-A5SL        TCGA-G3-A5SM 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
[1] "hr=" "1.5"
D42V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  1Q LOSS MUTATED         5        2         0          2          0          1
  1Q LOSS WILD-TYPE      40       23         2         23          3          3
                   vv
clus                STAGE IV STAGE IVA STAGE IVB
  1Q LOSS MUTATED          0         1         0
  1Q LOSS WILD-TYPE        1         0         1
D42V3, multiclass
                   vv
clus                T1 T2 T3 T4
  1Q LOSS MUTATED    7  2  3  0
  1Q LOSS WILD-TYPE 41 26 31  6
D42V4, multiclass
    clus
vv   1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  T1               7                41
  T2               2                26
  T3               3                31
  T4               0                 6
D42V5, binary
                   cls
clus                 0  1
  1Q LOSS MUTATED    6  2
  1Q LOSS WILD-TYPE 68  1
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED      6    2
  1Q LOSS WILD-TYPE   68    1
   clus
vv  1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  0               6                68
  1               2                 1
                   vv
clus                M0 M1 MX
  1Q LOSS MUTATED    9  0  3
  1Q LOSS WILD-TYPE 81  2 22
D42V6, multiclass
    clus
vv   1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  M0               9                81
  M1               0                 2
  MX               3                22
D42V7, binary
                   cls
clus                 0  1
  1Q LOSS MUTATED    5  7
  1Q LOSS WILD-TYPE 39 66
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED      5    7
  1Q LOSS WILD-TYPE   39   66
        clus
vv       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  FEMALE               5                39
  MALE                 7                66
                   vv
clus                R0 R1 R2 RX
  1Q LOSS MUTATED   10  0  0  2
  1Q LOSS WILD-TYPE 83 10  1  6
D42V8, multiclass
    clus
vv   1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  R0              10                83
  R1               0                10
  R2               0                 1
  RX               2                 6

Clustering(43) Variable = 2P LOSS MUTATION ANALYSIS
D43V1, survival
                   sevent
clus2                0  1
  2P LOSS MUTATED    4  3
  2P LOSS WILD-TYPE 57 50
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
                7               107 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
                3                50 
$`2P LOSS MUTATED`
TCGA-BC-A10Y TCGA-BC-A3KF TCGA-DD-A11C TCGA-DD-A4NN TCGA-ED-A459 TCGA-G3-A25S 
       23.34         0.26        21.76        29.56         0.23         1.22 
TCGA-G3-A5SM 
        4.37 

$`2P LOSS WILD-TYPE`
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T 
       48.99        27.91        37.32        10.13        46.78        27.52 
TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 
       27.52         2.99        25.32         1.12        69.57         5.03 
TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-CC-5258 TCGA-CC-5260 
       44.42        13.81        16.37         9.50         0.07         2.86 
TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA 
        3.02         3.39         4.24         3.32         0.10         0.07 
TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 
        0.10         0.13        79.73        37.74        83.57        53.29 
TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11D TCGA-DD-A1E9 
      112.96         7.33         2.60         0.46        51.25        90.67 
TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EF 
       79.36        66.31        19.76        75.65         6.67        12.95 
TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39X 
       49.15         6.02        29.16        13.64        21.14        55.66 
TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 
        5.59        19.73        25.81         7.66        70.06        17.59 
TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A3A9 
       20.12       102.74       107.11        13.78         0.36        30.58 
TCGA-DD-A4NA TCGA-DD-A4ND TCGA-DD-A4NE TCGA-DD-A4NF TCGA-DD-A4NG TCGA-DD-A4NH 
       33.14        73.38        21.67        14.07        14.93        14.24 
TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NO TCGA-DD-A4NP 
       10.78        15.06        39.75        56.25        61.45        93.67 
TCGA-DD-A4NQ TCGA-ED-A5KG TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB 
       12.26         0.20        10.85         7.76        11.74         1.97 
TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A23B 
        0.62         3.19         0.43        23.01        14.40        32.45 
TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 
       19.07         0.20         6.35         0.13         0.03         0.33 
TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W 
       60.36         0.39        51.02        53.79        28.27        30.71 
TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CH TCGA-G3-A3CI 
       58.49        14.86        21.53        22.13        25.64         5.88 
TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SJ TCGA-G3-A5SK TCGA-G3-A5SL 
       19.53        19.23        11.97         9.93         7.99 

  2P LOSS MUTATED 2P LOSS WILD-TYPE 
             0.23              0.03 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
            29.56            112.96 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
             4.37             16.37 
[1] "0.2 - 29.6 (4.4)"   "0.0 - 113.0 (16.4)"
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"2P LOSS WILD-TYPE"   "2P LOSS MUTATED" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE"   "2P LOSS MUTATED" 
       TCGA-BC-A3KG        TCGA-BC-A5W4        TCGA-CC-5258        TCGA-CC-5260 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CC-5261        TCGA-CC-5262        TCGA-CC-5263        TCGA-CC-A1HT 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CC-A3M9        TCGA-CC-A3MA        TCGA-CC-A3MB        TCGA-CC-A3MC 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-DD-A113        TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-DD-A118        TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-DD-A11C        TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EA 
  "2P LOSS MUTATED" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-DD-A1EB        TCGA-DD-A1EC        TCGA-DD-A1ED        TCGA-DD-A1EE 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-DD-A1EF        TCGA-DD-A1EH        TCGA-DD-A1EI        TCGA-DD-A1EJ 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-DD-A1EL        TCGA-DD-A39V        TCGA-DD-A39X        TCGA-DD-A39Y 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-DD-A39Z        TCGA-DD-A3A0        TCGA-DD-A3A1        TCGA-DD-A3A2 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-DD-A3A3        TCGA-DD-A3A4        TCGA-DD-A3A5        TCGA-DD-A3A6 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-DD-A3A7        TCGA-DD-A3A8        TCGA-DD-A3A9        TCGA-DD-A4NA 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-DD-A4ND        TCGA-DD-A4NE        TCGA-DD-A4NF        TCGA-DD-A4NG 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-DD-A4NH        TCGA-DD-A4NI        TCGA-DD-A4NJ        TCGA-DD-A4NK 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-DD-A4NL        TCGA-DD-A4NN        TCGA-DD-A4NO        TCGA-DD-A4NP 
"2P LOSS WILD-TYPE"   "2P LOSS MUTATED" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-DD-A4NQ        TCGA-ED-A459        TCGA-ED-A5KG        TCGA-EP-A12J 
"2P LOSS WILD-TYPE"   "2P LOSS MUTATED" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-EP-A3JL        TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-FV-A23B        TCGA-FV-A2QR        TCGA-FV-A3I0        TCGA-FV-A3R2 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-FV-A3R3        TCGA-FV-A495        TCGA-FV-A496        TCGA-FV-A4ZP 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-FV-A4ZQ        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"2P LOSS WILD-TYPE"   "2P LOSS MUTATED" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-G3-A3CJ        TCGA-G3-A3CK        TCGA-G3-A5SJ        TCGA-G3-A5SK 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-G3-A5SL        TCGA-G3-A5SM 
"2P LOSS WILD-TYPE"   "2P LOSS MUTATED" 
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"2P LOSS WILD-TYPE"   "2P LOSS MUTATED" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE"   "2P LOSS MUTATED" 
       TCGA-BC-A3KG        TCGA-BC-A5W4        TCGA-CC-5258        TCGA-CC-5260 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CC-5261        TCGA-CC-5262        TCGA-CC-5263        TCGA-CC-A1HT 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CC-A3M9        TCGA-CC-A3MA        TCGA-CC-A3MB        TCGA-CC-A3MC 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-DD-A113        TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-DD-A118        TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-DD-A11C        TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EA 
  "2P LOSS MUTATED" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-DD-A1EB        TCGA-DD-A1EC        TCGA-DD-A1ED        TCGA-DD-A1EE 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-DD-A1EF        TCGA-DD-A1EH        TCGA-DD-A1EI        TCGA-DD-A1EJ 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-DD-A1EL        TCGA-DD-A39V        TCGA-DD-A39X        TCGA-DD-A39Y 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-DD-A39Z        TCGA-DD-A3A0        TCGA-DD-A3A1        TCGA-DD-A3A2 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-DD-A3A3        TCGA-DD-A3A4        TCGA-DD-A3A5        TCGA-DD-A3A6 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-DD-A3A7        TCGA-DD-A3A8        TCGA-DD-A3A9        TCGA-DD-A4NA 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-DD-A4ND        TCGA-DD-A4NE        TCGA-DD-A4NF        TCGA-DD-A4NG 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-DD-A4NH        TCGA-DD-A4NI        TCGA-DD-A4NJ        TCGA-DD-A4NK 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-DD-A4NL        TCGA-DD-A4NN        TCGA-DD-A4NO        TCGA-DD-A4NP 
"2P LOSS WILD-TYPE"   "2P LOSS MUTATED" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-DD-A4NQ        TCGA-ED-A459        TCGA-ED-A5KG        TCGA-EP-A12J 
"2P LOSS WILD-TYPE"   "2P LOSS MUTATED" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-EP-A3JL        TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-FV-A23B        TCGA-FV-A2QR        TCGA-FV-A3I0        TCGA-FV-A3R2 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-FV-A3R3        TCGA-FV-A495        TCGA-FV-A496        TCGA-FV-A4ZP 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-FV-A4ZQ        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"2P LOSS WILD-TYPE"   "2P LOSS MUTATED" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-G3-A3CJ        TCGA-G3-A3CK        TCGA-G3-A5SJ        TCGA-G3-A5SK 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-G3-A5SL        TCGA-G3-A5SM 
"2P LOSS WILD-TYPE"   "2P LOSS MUTATED" 
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"2P LOSS WILD-TYPE"   "2P LOSS MUTATED" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE"   "2P LOSS MUTATED" 
       TCGA-BC-A3KG        TCGA-BC-A5W4        TCGA-CC-5258        TCGA-CC-5260 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CC-5261        TCGA-CC-5262        TCGA-CC-5263        TCGA-CC-A1HT 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CC-A3M9        TCGA-CC-A3MA        TCGA-CC-A3MB        TCGA-CC-A3MC 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-DD-A113        TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-DD-A118        TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-DD-A11C        TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EA 
  "2P LOSS MUTATED" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-DD-A1EB        TCGA-DD-A1EC        TCGA-DD-A1ED        TCGA-DD-A1EE 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-DD-A1EF        TCGA-DD-A1EH        TCGA-DD-A1EI        TCGA-DD-A1EJ 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-DD-A1EL        TCGA-DD-A39V        TCGA-DD-A39X        TCGA-DD-A39Y 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-DD-A39Z        TCGA-DD-A3A0        TCGA-DD-A3A1        TCGA-DD-A3A2 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-DD-A3A3        TCGA-DD-A3A4        TCGA-DD-A3A5        TCGA-DD-A3A6 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-DD-A3A7        TCGA-DD-A3A8        TCGA-DD-A3A9        TCGA-DD-A4NA 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-DD-A4ND        TCGA-DD-A4NE        TCGA-DD-A4NF        TCGA-DD-A4NG 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-DD-A4NH        TCGA-DD-A4NI        TCGA-DD-A4NJ        TCGA-DD-A4NK 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-DD-A4NL        TCGA-DD-A4NN        TCGA-DD-A4NO        TCGA-DD-A4NP 
"2P LOSS WILD-TYPE"   "2P LOSS MUTATED" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-DD-A4NQ        TCGA-ED-A459        TCGA-ED-A5KG        TCGA-EP-A12J 
"2P LOSS WILD-TYPE"   "2P LOSS MUTATED" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-EP-A3JL        TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-FV-A23B        TCGA-FV-A2QR        TCGA-FV-A3I0        TCGA-FV-A3R2 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-FV-A3R3        TCGA-FV-A495        TCGA-FV-A496        TCGA-FV-A4ZP 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-FV-A4ZQ        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"2P LOSS WILD-TYPE"   "2P LOSS MUTATED" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-G3-A3CJ        TCGA-G3-A3CK        TCGA-G3-A5SJ        TCGA-G3-A5SK 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-G3-A5SL        TCGA-G3-A5SM 
"2P LOSS WILD-TYPE"   "2P LOSS MUTATED" 
[1] "hr=" "1.9"
D43V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  2P LOSS MUTATED         4        3         0          0          0          0
  2P LOSS WILD-TYPE      41       22         2         25          3          4
                   vv
clus                STAGE IV STAGE IVA STAGE IVB
  2P LOSS MUTATED          0         0         0
  2P LOSS WILD-TYPE        1         1         1
D43V3, multiclass
                   vv
clus                T1 T2 T3 T4
  2P LOSS MUTATED    4  3  0  1
  2P LOSS WILD-TYPE 44 25 34  5
D43V4, multiclass
    clus
vv   2P LOSS MUTATED 2P LOSS WILD-TYPE
  T1               4                44
  T2               3                25
  T3               0                34
  T4               1                 5
D43V5, binary
                   cls
clus                 0  1
  2P LOSS MUTATED    5  0
  2P LOSS WILD-TYPE 69  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED      5    0
  2P LOSS WILD-TYPE   69    3
   clus
vv  2P LOSS MUTATED 2P LOSS WILD-TYPE
  0               5                69
  1               0                 3
                   vv
clus                M0 M1 MX
  2P LOSS MUTATED    6  0  2
  2P LOSS WILD-TYPE 84  2 23
D43V6, multiclass
    clus
vv   2P LOSS MUTATED 2P LOSS WILD-TYPE
  M0               6                84
  M1               0                 2
  MX               2                23
D43V7, binary
                   cls
clus                 0  1
  2P LOSS MUTATED    3  5
  2P LOSS WILD-TYPE 41 68
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED      3    5
  2P LOSS WILD-TYPE   41   68
        clus
vv       2P LOSS MUTATED 2P LOSS WILD-TYPE
  FEMALE               3                41
  MALE                 5                68
                   vv
clus                R0 R1 R2 RX
  2P LOSS MUTATED    6  1  0  1
  2P LOSS WILD-TYPE 87  9  1  7
D43V8, multiclass
    clus
vv   2P LOSS MUTATED 2P LOSS WILD-TYPE
  R0               6                87
  R1               1                 9
  R2               0                 1
  RX               1                 7

Clustering(44) Variable = 2Q LOSS MUTATION ANALYSIS
D44V1, survival
                   sevent
clus2                0  1
  2Q LOSS MUTATED    5  3
  2Q LOSS WILD-TYPE 56 50
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
                8               106 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
                3                50 
$`2Q LOSS MUTATED`
TCGA-BC-A10Y TCGA-BC-A3KF TCGA-DD-A115 TCGA-DD-A11C TCGA-DD-A4NJ TCGA-DD-A4NN 
       23.34         0.26        83.57        21.76        15.06        29.56 
TCGA-ED-A459 TCGA-G3-A5SM 
        0.23         4.37 

$`2Q LOSS WILD-TYPE`
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T 
       48.99        27.91        37.32        10.13        46.78        27.52 
TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 
       27.52         2.99        25.32         1.12        69.57         5.03 
TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-CC-5258 TCGA-CC-5260 
       44.42        13.81        16.37         9.50         0.07         2.86 
TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA 
        3.02         3.39         4.24         3.32         0.10         0.07 
TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A116 TCGA-DD-A118 
        0.10         0.13        79.73        37.74        53.29       112.96 
TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA 
        7.33         2.60         0.46        51.25        90.67        79.36 
TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EH 
       66.31        19.76        75.65         6.67        12.95        49.15 
TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39X TCGA-DD-A39Y 
        6.02        29.16        13.64        21.14        55.66         5.59 
TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 
       19.73        25.81         7.66        70.06        17.59        20.12 
TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A3A9 TCGA-DD-A4NA 
      102.74       107.11        13.78         0.36        30.58        33.14 
TCGA-DD-A4ND TCGA-DD-A4NE TCGA-DD-A4NF TCGA-DD-A4NG TCGA-DD-A4NH TCGA-DD-A4NI 
       73.38        21.67        14.07        14.93        14.24        10.78 
TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-ED-A5KG 
       39.75        56.25        61.45        93.67        12.26         0.20 
TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL 
       10.85         7.76        11.74         1.97         0.62         3.19 
TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-A3I0 
        0.43        23.01        14.40        32.45        19.07         0.20 
TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZP TCGA-FV-A4ZQ 
        6.35         0.13         0.03         0.33        60.36         0.39 
TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25X 
        1.22        51.02        53.79        28.27        30.71        58.49 
TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ 
       14.86        21.53        22.13        25.64         5.88        19.53 
TCGA-G3-A3CK TCGA-G3-A5SJ TCGA-G3-A5SK TCGA-G3-A5SL 
       19.23        11.97         9.93         7.99 

  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
             0.23              0.03 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
            83.57            112.96 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
            18.41             15.65 
[1] "0.2 - 83.6 (18.4)"  "0.0 - 113.0 (15.7)"
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"2Q LOSS WILD-TYPE"   "2Q LOSS MUTATED" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE"   "2Q LOSS MUTATED" 
       TCGA-BC-A3KG        TCGA-BC-A5W4        TCGA-CC-5258        TCGA-CC-5260 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-CC-5261        TCGA-CC-5262        TCGA-CC-5263        TCGA-CC-A1HT 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-CC-A3M9        TCGA-CC-A3MA        TCGA-CC-A3MB        TCGA-CC-A3MC 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-DD-A113        TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE"   "2Q LOSS MUTATED" "2Q LOSS WILD-TYPE" 
       TCGA-DD-A118        TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-DD-A11C        TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EA 
  "2Q LOSS MUTATED" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-DD-A1EB        TCGA-DD-A1EC        TCGA-DD-A1ED        TCGA-DD-A1EE 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-DD-A1EF        TCGA-DD-A1EH        TCGA-DD-A1EI        TCGA-DD-A1EJ 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-DD-A1EL        TCGA-DD-A39V        TCGA-DD-A39X        TCGA-DD-A39Y 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-DD-A39Z        TCGA-DD-A3A0        TCGA-DD-A3A1        TCGA-DD-A3A2 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-DD-A3A3        TCGA-DD-A3A4        TCGA-DD-A3A5        TCGA-DD-A3A6 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-DD-A3A7        TCGA-DD-A3A8        TCGA-DD-A3A9        TCGA-DD-A4NA 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-DD-A4ND        TCGA-DD-A4NE        TCGA-DD-A4NF        TCGA-DD-A4NG 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-DD-A4NH        TCGA-DD-A4NI        TCGA-DD-A4NJ        TCGA-DD-A4NK 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE"   "2Q LOSS MUTATED" "2Q LOSS WILD-TYPE" 
       TCGA-DD-A4NL        TCGA-DD-A4NN        TCGA-DD-A4NO        TCGA-DD-A4NP 
"2Q LOSS WILD-TYPE"   "2Q LOSS MUTATED" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-DD-A4NQ        TCGA-ED-A459        TCGA-ED-A5KG        TCGA-EP-A12J 
"2Q LOSS WILD-TYPE"   "2Q LOSS MUTATED" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-EP-A3JL        TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-FV-A23B        TCGA-FV-A2QR        TCGA-FV-A3I0        TCGA-FV-A3R2 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-FV-A3R3        TCGA-FV-A495        TCGA-FV-A496        TCGA-FV-A4ZP 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-FV-A4ZQ        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-G3-A3CJ        TCGA-G3-A3CK        TCGA-G3-A5SJ        TCGA-G3-A5SK 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-G3-A5SL        TCGA-G3-A5SM 
"2Q LOSS WILD-TYPE"   "2Q LOSS MUTATED" 
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"2Q LOSS WILD-TYPE"   "2Q LOSS MUTATED" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE"   "2Q LOSS MUTATED" 
       TCGA-BC-A3KG        TCGA-BC-A5W4        TCGA-CC-5258        TCGA-CC-5260 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-CC-5261        TCGA-CC-5262        TCGA-CC-5263        TCGA-CC-A1HT 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-CC-A3M9        TCGA-CC-A3MA        TCGA-CC-A3MB        TCGA-CC-A3MC 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-DD-A113        TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE"   "2Q LOSS MUTATED" "2Q LOSS WILD-TYPE" 
       TCGA-DD-A118        TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-DD-A11C        TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EA 
  "2Q LOSS MUTATED" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-DD-A1EB        TCGA-DD-A1EC        TCGA-DD-A1ED        TCGA-DD-A1EE 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-DD-A1EF        TCGA-DD-A1EH        TCGA-DD-A1EI        TCGA-DD-A1EJ 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-DD-A1EL        TCGA-DD-A39V        TCGA-DD-A39X        TCGA-DD-A39Y 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-DD-A39Z        TCGA-DD-A3A0        TCGA-DD-A3A1        TCGA-DD-A3A2 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-DD-A3A3        TCGA-DD-A3A4        TCGA-DD-A3A5        TCGA-DD-A3A6 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-DD-A3A7        TCGA-DD-A3A8        TCGA-DD-A3A9        TCGA-DD-A4NA 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-DD-A4ND        TCGA-DD-A4NE        TCGA-DD-A4NF        TCGA-DD-A4NG 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-DD-A4NH        TCGA-DD-A4NI        TCGA-DD-A4NJ        TCGA-DD-A4NK 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE"   "2Q LOSS MUTATED" "2Q LOSS WILD-TYPE" 
       TCGA-DD-A4NL        TCGA-DD-A4NN        TCGA-DD-A4NO        TCGA-DD-A4NP 
"2Q LOSS WILD-TYPE"   "2Q LOSS MUTATED" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-DD-A4NQ        TCGA-ED-A459        TCGA-ED-A5KG        TCGA-EP-A12J 
"2Q LOSS WILD-TYPE"   "2Q LOSS MUTATED" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-EP-A3JL        TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-FV-A23B        TCGA-FV-A2QR        TCGA-FV-A3I0        TCGA-FV-A3R2 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-FV-A3R3        TCGA-FV-A495        TCGA-FV-A496        TCGA-FV-A4ZP 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-FV-A4ZQ        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-G3-A3CJ        TCGA-G3-A3CK        TCGA-G3-A5SJ        TCGA-G3-A5SK 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-G3-A5SL        TCGA-G3-A5SM 
"2Q LOSS WILD-TYPE"   "2Q LOSS MUTATED" 
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"2Q LOSS WILD-TYPE"   "2Q LOSS MUTATED" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE"   "2Q LOSS MUTATED" 
       TCGA-BC-A3KG        TCGA-BC-A5W4        TCGA-CC-5258        TCGA-CC-5260 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-CC-5261        TCGA-CC-5262        TCGA-CC-5263        TCGA-CC-A1HT 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-CC-A3M9        TCGA-CC-A3MA        TCGA-CC-A3MB        TCGA-CC-A3MC 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-DD-A113        TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE"   "2Q LOSS MUTATED" "2Q LOSS WILD-TYPE" 
       TCGA-DD-A118        TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-DD-A11C        TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EA 
  "2Q LOSS MUTATED" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-DD-A1EB        TCGA-DD-A1EC        TCGA-DD-A1ED        TCGA-DD-A1EE 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-DD-A1EF        TCGA-DD-A1EH        TCGA-DD-A1EI        TCGA-DD-A1EJ 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-DD-A1EL        TCGA-DD-A39V        TCGA-DD-A39X        TCGA-DD-A39Y 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-DD-A39Z        TCGA-DD-A3A0        TCGA-DD-A3A1        TCGA-DD-A3A2 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-DD-A3A3        TCGA-DD-A3A4        TCGA-DD-A3A5        TCGA-DD-A3A6 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-DD-A3A7        TCGA-DD-A3A8        TCGA-DD-A3A9        TCGA-DD-A4NA 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-DD-A4ND        TCGA-DD-A4NE        TCGA-DD-A4NF        TCGA-DD-A4NG 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-DD-A4NH        TCGA-DD-A4NI        TCGA-DD-A4NJ        TCGA-DD-A4NK 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE"   "2Q LOSS MUTATED" "2Q LOSS WILD-TYPE" 
       TCGA-DD-A4NL        TCGA-DD-A4NN        TCGA-DD-A4NO        TCGA-DD-A4NP 
"2Q LOSS WILD-TYPE"   "2Q LOSS MUTATED" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-DD-A4NQ        TCGA-ED-A459        TCGA-ED-A5KG        TCGA-EP-A12J 
"2Q LOSS WILD-TYPE"   "2Q LOSS MUTATED" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-EP-A3JL        TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-FV-A23B        TCGA-FV-A2QR        TCGA-FV-A3I0        TCGA-FV-A3R2 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-FV-A3R3        TCGA-FV-A495        TCGA-FV-A496        TCGA-FV-A4ZP 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-FV-A4ZQ        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-G3-A3CJ        TCGA-G3-A3CK        TCGA-G3-A5SJ        TCGA-G3-A5SK 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-G3-A5SL        TCGA-G3-A5SM 
"2Q LOSS WILD-TYPE"   "2Q LOSS MUTATED" 
[1] "hr=" "1.1"
D44V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  2Q LOSS MUTATED         3        4         0          2          0          0
  2Q LOSS WILD-TYPE      42       21         2         23          3          4
                   vv
clus                STAGE IV STAGE IVA STAGE IVB
  2Q LOSS MUTATED          0         0         0
  2Q LOSS WILD-TYPE        1         1         1
D44V3, multiclass
                   vv
clus                T1 T2 T3 T4
  2Q LOSS MUTATED    3  4  2  1
  2Q LOSS WILD-TYPE 45 24 32  5
D44V4, multiclass
    clus
vv   2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  T1               3                45
  T2               4                24
  T3               2                32
  T4               1                 5
D44V5, binary
                   cls
clus                 0  1
  2Q LOSS MUTATED    7  0
  2Q LOSS WILD-TYPE 67  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED      7    0
  2Q LOSS WILD-TYPE   67    3
   clus
vv  2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  0               7                67
  1               0                 3
                   vv
clus                M0 M1 MX
  2Q LOSS MUTATED    8  0  2
  2Q LOSS WILD-TYPE 82  2 23
D44V6, multiclass
    clus
vv   2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  M0               8                82
  M1               0                 2
  MX               2                23
D44V7, binary
                   cls
clus                 0  1
  2Q LOSS MUTATED    4  6
  2Q LOSS WILD-TYPE 40 67
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED      4    6
  2Q LOSS WILD-TYPE   40   67
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  FEMALE               4                40
  MALE                 6                67
                   vv
clus                R0 R1 R2 RX
  2Q LOSS MUTATED    8  0  0  2
  2Q LOSS WILD-TYPE 85 10  1  6
D44V8, multiclass
    clus
vv   2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  R0               8                85
  R1               0                10
  R2               0                 1
  RX               2                 6

Clustering(45) Variable = 3P LOSS MUTATION ANALYSIS
D45V1, survival
                   sevent
clus2                0  1
  3P LOSS MUTATED    9  5
  3P LOSS WILD-TYPE 52 48
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               14               100 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
                5                48 
$`3P LOSS MUTATED`
TCGA-BC-A10R TCGA-BC-A112 TCGA-CC-5263 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-DD-A113 
       10.13         5.03         4.24         0.07         0.10        79.73 
TCGA-DD-A118 TCGA-DD-A1E9 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NO TCGA-FV-A3I0 
      112.96        90.67        30.58        33.14        61.45         0.20 
TCGA-G3-A25T TCGA-G3-A25X 
       51.02        58.49 

$`3P LOSS WILD-TYPE`
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U 
       48.99        27.91        37.32        46.78        27.52        27.52 
TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A216 
        2.99        25.32        23.34         1.12        69.57        44.42 
TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-CC-5258 TCGA-CC-5260 
       13.81         0.26        16.37         9.50         0.07         2.86 
TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MC TCGA-DD-A114 
        3.02         3.39         3.32         0.10         0.13        37.74 
TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C 
       83.57        53.29         7.33         2.60         0.46        21.76 
TCGA-DD-A11D TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE 
       51.25        79.36        66.31        19.76        75.65         6.67 
TCGA-DD-A1EF TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EL TCGA-DD-A39V 
       12.95        49.15         6.02        29.16        13.64        21.14 
TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 
       55.66         5.59        19.73        25.81         7.66        70.06 
TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A8 
       17.59        20.12       102.74       107.11        13.78         0.36 
TCGA-DD-A4ND TCGA-DD-A4NE TCGA-DD-A4NF TCGA-DD-A4NG TCGA-DD-A4NH TCGA-DD-A4NI 
       73.38        21.67        14.07        14.93        14.24        10.78 
TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NP TCGA-DD-A4NQ 
       15.06        39.75        56.25        29.56        93.67        12.26 
TCGA-ED-A459 TCGA-ED-A5KG TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB 
        0.23         0.20        10.85         7.76        11.74         1.97 
TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A23B 
        0.62         3.19         0.43        23.01        14.40        32.45 
TCGA-FV-A2QR TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZP 
       19.07         6.35         0.13         0.03         0.33        60.36 
TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25Y 
        0.39         1.22        53.79        28.27        30.71        14.86 
TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK 
       21.53        22.13        25.64         5.88        19.53        19.23 
TCGA-G3-A5SJ TCGA-G3-A5SK TCGA-G3-A5SL TCGA-G3-A5SM 
       11.97         9.93         7.99         4.37 

  3P LOSS MUTATED 3P LOSS WILD-TYPE 
             0.07              0.03 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
           112.96            107.11 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
           31.860            14.995 
[1] "0.1 - 113.0 (31.9)" "0.0 - 107.1 (15.0)"
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE"   "3P LOSS MUTATED" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
  "3P LOSS MUTATED" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-BC-A5W4        TCGA-CC-5258        TCGA-CC-5260 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-CC-5261        TCGA-CC-5262        TCGA-CC-5263        TCGA-CC-A1HT 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE"   "3P LOSS MUTATED" "3P LOSS WILD-TYPE" 
       TCGA-CC-A3M9        TCGA-CC-A3MA        TCGA-CC-A3MB        TCGA-CC-A3MC 
"3P LOSS WILD-TYPE"   "3P LOSS MUTATED"   "3P LOSS MUTATED" "3P LOSS WILD-TYPE" 
       TCGA-DD-A113        TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116 
  "3P LOSS MUTATED" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DD-A118        TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B 
  "3P LOSS MUTATED" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DD-A11C        TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EA 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE"   "3P LOSS MUTATED" "3P LOSS WILD-TYPE" 
       TCGA-DD-A1EB        TCGA-DD-A1EC        TCGA-DD-A1ED        TCGA-DD-A1EE 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DD-A1EF        TCGA-DD-A1EH        TCGA-DD-A1EI        TCGA-DD-A1EJ 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DD-A1EL        TCGA-DD-A39V        TCGA-DD-A39X        TCGA-DD-A39Y 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DD-A39Z        TCGA-DD-A3A0        TCGA-DD-A3A1        TCGA-DD-A3A2 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DD-A3A3        TCGA-DD-A3A4        TCGA-DD-A3A5        TCGA-DD-A3A6 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DD-A3A7        TCGA-DD-A3A8        TCGA-DD-A3A9        TCGA-DD-A4NA 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE"   "3P LOSS MUTATED"   "3P LOSS MUTATED" 
       TCGA-DD-A4ND        TCGA-DD-A4NE        TCGA-DD-A4NF        TCGA-DD-A4NG 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DD-A4NH        TCGA-DD-A4NI        TCGA-DD-A4NJ        TCGA-DD-A4NK 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DD-A4NL        TCGA-DD-A4NN        TCGA-DD-A4NO        TCGA-DD-A4NP 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE"   "3P LOSS MUTATED" "3P LOSS WILD-TYPE" 
       TCGA-DD-A4NQ        TCGA-ED-A459        TCGA-ED-A5KG        TCGA-EP-A12J 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EP-A3JL        TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-FV-A23B        TCGA-FV-A2QR        TCGA-FV-A3I0        TCGA-FV-A3R2 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE"   "3P LOSS MUTATED" "3P LOSS WILD-TYPE" 
       TCGA-FV-A3R3        TCGA-FV-A495        TCGA-FV-A496        TCGA-FV-A4ZP 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-FV-A4ZQ        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE"   "3P LOSS MUTATED" "3P LOSS WILD-TYPE" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE"   "3P LOSS MUTATED" "3P LOSS WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-G3-A3CJ        TCGA-G3-A3CK        TCGA-G3-A5SJ        TCGA-G3-A5SK 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-G3-A5SL        TCGA-G3-A5SM 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE"   "3P LOSS MUTATED" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
  "3P LOSS MUTATED" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-BC-A5W4        TCGA-CC-5258        TCGA-CC-5260 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-CC-5261        TCGA-CC-5262        TCGA-CC-5263        TCGA-CC-A1HT 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE"   "3P LOSS MUTATED" "3P LOSS WILD-TYPE" 
       TCGA-CC-A3M9        TCGA-CC-A3MA        TCGA-CC-A3MB        TCGA-CC-A3MC 
"3P LOSS WILD-TYPE"   "3P LOSS MUTATED"   "3P LOSS MUTATED" "3P LOSS WILD-TYPE" 
       TCGA-DD-A113        TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116 
  "3P LOSS MUTATED" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DD-A118        TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B 
  "3P LOSS MUTATED" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DD-A11C        TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EA 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE"   "3P LOSS MUTATED" "3P LOSS WILD-TYPE" 
       TCGA-DD-A1EB        TCGA-DD-A1EC        TCGA-DD-A1ED        TCGA-DD-A1EE 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DD-A1EF        TCGA-DD-A1EH        TCGA-DD-A1EI        TCGA-DD-A1EJ 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DD-A1EL        TCGA-DD-A39V        TCGA-DD-A39X        TCGA-DD-A39Y 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DD-A39Z        TCGA-DD-A3A0        TCGA-DD-A3A1        TCGA-DD-A3A2 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DD-A3A3        TCGA-DD-A3A4        TCGA-DD-A3A5        TCGA-DD-A3A6 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DD-A3A7        TCGA-DD-A3A8        TCGA-DD-A3A9        TCGA-DD-A4NA 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE"   "3P LOSS MUTATED"   "3P LOSS MUTATED" 
       TCGA-DD-A4ND        TCGA-DD-A4NE        TCGA-DD-A4NF        TCGA-DD-A4NG 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DD-A4NH        TCGA-DD-A4NI        TCGA-DD-A4NJ        TCGA-DD-A4NK 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DD-A4NL        TCGA-DD-A4NN        TCGA-DD-A4NO        TCGA-DD-A4NP 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE"   "3P LOSS MUTATED" "3P LOSS WILD-TYPE" 
       TCGA-DD-A4NQ        TCGA-ED-A459        TCGA-ED-A5KG        TCGA-EP-A12J 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EP-A3JL        TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-FV-A23B        TCGA-FV-A2QR        TCGA-FV-A3I0        TCGA-FV-A3R2 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE"   "3P LOSS MUTATED" "3P LOSS WILD-TYPE" 
       TCGA-FV-A3R3        TCGA-FV-A495        TCGA-FV-A496        TCGA-FV-A4ZP 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-FV-A4ZQ        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE"   "3P LOSS MUTATED" "3P LOSS WILD-TYPE" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE"   "3P LOSS MUTATED" "3P LOSS WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-G3-A3CJ        TCGA-G3-A3CK        TCGA-G3-A5SJ        TCGA-G3-A5SK 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-G3-A5SL        TCGA-G3-A5SM 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE"   "3P LOSS MUTATED" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
  "3P LOSS MUTATED" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-BC-A5W4        TCGA-CC-5258        TCGA-CC-5260 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-CC-5261        TCGA-CC-5262        TCGA-CC-5263        TCGA-CC-A1HT 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE"   "3P LOSS MUTATED" "3P LOSS WILD-TYPE" 
       TCGA-CC-A3M9        TCGA-CC-A3MA        TCGA-CC-A3MB        TCGA-CC-A3MC 
"3P LOSS WILD-TYPE"   "3P LOSS MUTATED"   "3P LOSS MUTATED" "3P LOSS WILD-TYPE" 
       TCGA-DD-A113        TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116 
  "3P LOSS MUTATED" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DD-A118        TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B 
  "3P LOSS MUTATED" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DD-A11C        TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EA 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE"   "3P LOSS MUTATED" "3P LOSS WILD-TYPE" 
       TCGA-DD-A1EB        TCGA-DD-A1EC        TCGA-DD-A1ED        TCGA-DD-A1EE 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DD-A1EF        TCGA-DD-A1EH        TCGA-DD-A1EI        TCGA-DD-A1EJ 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DD-A1EL        TCGA-DD-A39V        TCGA-DD-A39X        TCGA-DD-A39Y 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DD-A39Z        TCGA-DD-A3A0        TCGA-DD-A3A1        TCGA-DD-A3A2 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DD-A3A3        TCGA-DD-A3A4        TCGA-DD-A3A5        TCGA-DD-A3A6 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DD-A3A7        TCGA-DD-A3A8        TCGA-DD-A3A9        TCGA-DD-A4NA 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE"   "3P LOSS MUTATED"   "3P LOSS MUTATED" 
       TCGA-DD-A4ND        TCGA-DD-A4NE        TCGA-DD-A4NF        TCGA-DD-A4NG 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DD-A4NH        TCGA-DD-A4NI        TCGA-DD-A4NJ        TCGA-DD-A4NK 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DD-A4NL        TCGA-DD-A4NN        TCGA-DD-A4NO        TCGA-DD-A4NP 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE"   "3P LOSS MUTATED" "3P LOSS WILD-TYPE" 
       TCGA-DD-A4NQ        TCGA-ED-A459        TCGA-ED-A5KG        TCGA-EP-A12J 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EP-A3JL        TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-FV-A23B        TCGA-FV-A2QR        TCGA-FV-A3I0        TCGA-FV-A3R2 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE"   "3P LOSS MUTATED" "3P LOSS WILD-TYPE" 
       TCGA-FV-A3R3        TCGA-FV-A495        TCGA-FV-A496        TCGA-FV-A4ZP 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-FV-A4ZQ        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE"   "3P LOSS MUTATED" "3P LOSS WILD-TYPE" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE"   "3P LOSS MUTATED" "3P LOSS WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-G3-A3CJ        TCGA-G3-A3CK        TCGA-G3-A5SJ        TCGA-G3-A5SK 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-G3-A5SL        TCGA-G3-A5SM 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
[1] "hr=" "2.2"
D45V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  3P LOSS MUTATED         2        4         0          3          0          1
  3P LOSS WILD-TYPE      43       21         2         22          3          3
                   vv
clus                STAGE IV STAGE IVA STAGE IVB
  3P LOSS MUTATED          0         0         1
  3P LOSS WILD-TYPE        1         1         0
D45V3, multiclass
                   vv
clus                T1 T2 T3 T4
  3P LOSS MUTATED    2  5  5  1
  3P LOSS WILD-TYPE 46 23 29  5
D45V4, multiclass
    clus
vv   3P LOSS MUTATED 3P LOSS WILD-TYPE
  T1               2                46
  T2               5                23
  T3               5                29
  T4               1                 5
D45V5, binary
                   cls
clus                 0  1
  3P LOSS MUTATED   10  1
  3P LOSS WILD-TYPE 64  2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED     10    1
  3P LOSS WILD-TYPE   64    2
   clus
vv  3P LOSS MUTATED 3P LOSS WILD-TYPE
  0              10                64
  1               1                 2
                   vv
clus                M0 M1 MX
  3P LOSS MUTATED   11  1  2
  3P LOSS WILD-TYPE 79  1 23
D45V6, multiclass
    clus
vv   3P LOSS MUTATED 3P LOSS WILD-TYPE
  M0              11                79
  M1               1                 1
  MX               2                23
D45V7, binary
                   cls
clus                 0  1
  3P LOSS MUTATED    7  7
  3P LOSS WILD-TYPE 37 66
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED      7    7
  3P LOSS WILD-TYPE   37   66
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  FEMALE               7                37
  MALE                 7                66
                   vv
clus                R0 R1 R2 RX
  3P LOSS MUTATED   13  0  0  1
  3P LOSS WILD-TYPE 80 10  1  7
D45V8, multiclass
    clus
vv   3P LOSS MUTATED 3P LOSS WILD-TYPE
  R0              13                80
  R1               0                10
  R2               0                 1
  RX               1                 7

Clustering(46) Variable = 3Q LOSS MUTATION ANALYSIS
D46V1, survival
                   sevent
clus2                0  1
  3Q LOSS MUTATED    4  2
  3Q LOSS WILD-TYPE 57 51
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
                6               108 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
                2                51 
$`3Q LOSS MUTATED`
TCGA-BC-A112 TCGA-DD-A113 TCGA-DD-A118 TCGA-DD-A1E9 TCGA-DD-A4NA TCGA-DD-A4NO 
        5.03        79.73       112.96        90.67        33.14        61.45 

$`3Q LOSS WILD-TYPE`
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T 
       48.99        27.91        37.32        10.13        46.78        27.52 
TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 
       27.52         2.99        25.32        23.34         1.12        69.57 
TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-CC-5258 
       44.42        13.81         0.26        16.37         9.50         0.07 
TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3M9 
        2.86         3.02         3.39         4.24         3.32         0.10 
TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 
        0.07         0.10         0.13        37.74        83.57        53.29 
TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1EA 
        7.33         2.60         0.46        21.76        51.25        79.36 
TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EH 
       66.31        19.76        75.65         6.67        12.95        49.15 
TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39X TCGA-DD-A39Y 
        6.02        29.16        13.64        21.14        55.66         5.59 
TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 
       19.73        25.81         7.66        70.06        17.59        20.12 
TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A3A9 TCGA-DD-A4ND 
      102.74       107.11        13.78         0.36        30.58        73.38 
TCGA-DD-A4NE TCGA-DD-A4NF TCGA-DD-A4NG TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ 
       21.67        14.07        14.93        14.24        10.78        15.06 
TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-ED-A459 
       39.75        56.25        29.56        93.67        12.26         0.23 
TCGA-ED-A5KG TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC 
        0.20        10.85         7.76        11.74         1.97         0.62 
TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QR 
        3.19         0.43        23.01        14.40        32.45        19.07 
TCGA-FV-A3I0 TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZP 
        0.20         6.35         0.13         0.03         0.33        60.36 
TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W 
        0.39         1.22        51.02        53.79        28.27        30.71 
TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CH TCGA-G3-A3CI 
       58.49        14.86        21.53        22.13        25.64         5.88 
TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SJ TCGA-G3-A5SK TCGA-G3-A5SL TCGA-G3-A5SM 
       19.53        19.23        11.97         9.93         7.99         4.37 

  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
             5.03              0.03 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
           112.96            107.11 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
           70.590            14.895 
[1] "5.0 - 113.0 (70.6)" "0.0 - 107.1 (14.9)"
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
  "3Q LOSS MUTATED" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-BC-A5W4        TCGA-CC-5258        TCGA-CC-5260 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-CC-5261        TCGA-CC-5262        TCGA-CC-5263        TCGA-CC-A1HT 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-CC-A3M9        TCGA-CC-A3MA        TCGA-CC-A3MB        TCGA-CC-A3MC 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-DD-A113        TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116 
  "3Q LOSS MUTATED" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-DD-A118        TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B 
  "3Q LOSS MUTATED" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-DD-A11C        TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EA 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE"   "3Q LOSS MUTATED" "3Q LOSS WILD-TYPE" 
       TCGA-DD-A1EB        TCGA-DD-A1EC        TCGA-DD-A1ED        TCGA-DD-A1EE 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-DD-A1EF        TCGA-DD-A1EH        TCGA-DD-A1EI        TCGA-DD-A1EJ 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-DD-A1EL        TCGA-DD-A39V        TCGA-DD-A39X        TCGA-DD-A39Y 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-DD-A39Z        TCGA-DD-A3A0        TCGA-DD-A3A1        TCGA-DD-A3A2 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-DD-A3A3        TCGA-DD-A3A4        TCGA-DD-A3A5        TCGA-DD-A3A6 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-DD-A3A7        TCGA-DD-A3A8        TCGA-DD-A3A9        TCGA-DD-A4NA 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE"   "3Q LOSS MUTATED" 
       TCGA-DD-A4ND        TCGA-DD-A4NE        TCGA-DD-A4NF        TCGA-DD-A4NG 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-DD-A4NH        TCGA-DD-A4NI        TCGA-DD-A4NJ        TCGA-DD-A4NK 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-DD-A4NL        TCGA-DD-A4NN        TCGA-DD-A4NO        TCGA-DD-A4NP 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE"   "3Q LOSS MUTATED" "3Q LOSS WILD-TYPE" 
       TCGA-DD-A4NQ        TCGA-ED-A459        TCGA-ED-A5KG        TCGA-EP-A12J 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-EP-A3JL        TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-FV-A23B        TCGA-FV-A2QR        TCGA-FV-A3I0        TCGA-FV-A3R2 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-FV-A3R3        TCGA-FV-A495        TCGA-FV-A496        TCGA-FV-A4ZP 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-FV-A4ZQ        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-G3-A3CJ        TCGA-G3-A3CK        TCGA-G3-A5SJ        TCGA-G3-A5SK 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-G3-A5SL        TCGA-G3-A5SM 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
  "3Q LOSS MUTATED" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-BC-A5W4        TCGA-CC-5258        TCGA-CC-5260 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-CC-5261        TCGA-CC-5262        TCGA-CC-5263        TCGA-CC-A1HT 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-CC-A3M9        TCGA-CC-A3MA        TCGA-CC-A3MB        TCGA-CC-A3MC 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-DD-A113        TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116 
  "3Q LOSS MUTATED" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-DD-A118        TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B 
  "3Q LOSS MUTATED" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-DD-A11C        TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EA 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE"   "3Q LOSS MUTATED" "3Q LOSS WILD-TYPE" 
       TCGA-DD-A1EB        TCGA-DD-A1EC        TCGA-DD-A1ED        TCGA-DD-A1EE 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-DD-A1EF        TCGA-DD-A1EH        TCGA-DD-A1EI        TCGA-DD-A1EJ 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-DD-A1EL        TCGA-DD-A39V        TCGA-DD-A39X        TCGA-DD-A39Y 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-DD-A39Z        TCGA-DD-A3A0        TCGA-DD-A3A1        TCGA-DD-A3A2 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-DD-A3A3        TCGA-DD-A3A4        TCGA-DD-A3A5        TCGA-DD-A3A6 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-DD-A3A7        TCGA-DD-A3A8        TCGA-DD-A3A9        TCGA-DD-A4NA 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE"   "3Q LOSS MUTATED" 
       TCGA-DD-A4ND        TCGA-DD-A4NE        TCGA-DD-A4NF        TCGA-DD-A4NG 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-DD-A4NH        TCGA-DD-A4NI        TCGA-DD-A4NJ        TCGA-DD-A4NK 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-DD-A4NL        TCGA-DD-A4NN        TCGA-DD-A4NO        TCGA-DD-A4NP 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE"   "3Q LOSS MUTATED" "3Q LOSS WILD-TYPE" 
       TCGA-DD-A4NQ        TCGA-ED-A459        TCGA-ED-A5KG        TCGA-EP-A12J 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-EP-A3JL        TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-FV-A23B        TCGA-FV-A2QR        TCGA-FV-A3I0        TCGA-FV-A3R2 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-FV-A3R3        TCGA-FV-A495        TCGA-FV-A496        TCGA-FV-A4ZP 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-FV-A4ZQ        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-G3-A3CJ        TCGA-G3-A3CK        TCGA-G3-A5SJ        TCGA-G3-A5SK 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-G3-A5SL        TCGA-G3-A5SM 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
  "3Q LOSS MUTATED" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-BC-A5W4        TCGA-CC-5258        TCGA-CC-5260 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-CC-5261        TCGA-CC-5262        TCGA-CC-5263        TCGA-CC-A1HT 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-CC-A3M9        TCGA-CC-A3MA        TCGA-CC-A3MB        TCGA-CC-A3MC 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-DD-A113        TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116 
  "3Q LOSS MUTATED" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-DD-A118        TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B 
  "3Q LOSS MUTATED" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-DD-A11C        TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EA 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE"   "3Q LOSS MUTATED" "3Q LOSS WILD-TYPE" 
       TCGA-DD-A1EB        TCGA-DD-A1EC        TCGA-DD-A1ED        TCGA-DD-A1EE 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-DD-A1EF        TCGA-DD-A1EH        TCGA-DD-A1EI        TCGA-DD-A1EJ 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-DD-A1EL        TCGA-DD-A39V        TCGA-DD-A39X        TCGA-DD-A39Y 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-DD-A39Z        TCGA-DD-A3A0        TCGA-DD-A3A1        TCGA-DD-A3A2 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-DD-A3A3        TCGA-DD-A3A4        TCGA-DD-A3A5        TCGA-DD-A3A6 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-DD-A3A7        TCGA-DD-A3A8        TCGA-DD-A3A9        TCGA-DD-A4NA 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE"   "3Q LOSS MUTATED" 
       TCGA-DD-A4ND        TCGA-DD-A4NE        TCGA-DD-A4NF        TCGA-DD-A4NG 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-DD-A4NH        TCGA-DD-A4NI        TCGA-DD-A4NJ        TCGA-DD-A4NK 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-DD-A4NL        TCGA-DD-A4NN        TCGA-DD-A4NO        TCGA-DD-A4NP 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE"   "3Q LOSS MUTATED" "3Q LOSS WILD-TYPE" 
       TCGA-DD-A4NQ        TCGA-ED-A459        TCGA-ED-A5KG        TCGA-EP-A12J 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-EP-A3JL        TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-FV-A23B        TCGA-FV-A2QR        TCGA-FV-A3I0        TCGA-FV-A3R2 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-FV-A3R3        TCGA-FV-A495        TCGA-FV-A496        TCGA-FV-A4ZP 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-FV-A4ZQ        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-G3-A3CJ        TCGA-G3-A3CK        TCGA-G3-A5SJ        TCGA-G3-A5SK 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-G3-A5SL        TCGA-G3-A5SM 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
[1] "hr=" "4.1"
D46V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  3Q LOSS MUTATED         2        2         0          0          0          1
  3Q LOSS WILD-TYPE      43       23         2         25          3          3
                   vv
clus                STAGE IV STAGE IVA STAGE IVB
  3Q LOSS MUTATED          0         0         0
  3Q LOSS WILD-TYPE        1         1         1
D46V3, multiclass
                   vv
clus                T1 T2 T3 T4
  3Q LOSS MUTATED    2  3  1  0
  3Q LOSS WILD-TYPE 46 25 33  6
D46V4, multiclass
    clus
vv   3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  T1               2                46
  T2               3                25
  T3               1                33
  T4               0                 6
D46V5, binary
                   cls
clus                 0  1
  3Q LOSS MUTATED    4  1
  3Q LOSS WILD-TYPE 70  2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED      4    1
  3Q LOSS WILD-TYPE   70    2
   clus
vv  3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  0               4                70
  1               1                 2
                   vv
clus                M0 M1 MX
  3Q LOSS MUTATED    5  0  1
  3Q LOSS WILD-TYPE 85  2 24
D46V6, multiclass
    clus
vv   3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  M0               5                85
  M1               0                 2
  MX               1                24
D46V7, binary
                   cls
clus                 0  1
  3Q LOSS MUTATED    3  3
  3Q LOSS WILD-TYPE 41 70
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED      3    3
  3Q LOSS WILD-TYPE   41   70
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  FEMALE               3                41
  MALE                 3                70
                   vv
clus                R0 R1 R2 RX
  3Q LOSS MUTATED    6  0  0  0
  3Q LOSS WILD-TYPE 87 10  1  8
D46V8, multiclass
    clus
vv   3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  R0               6                87
  R1               0                10
  R2               0                 1
  RX               0                 8

Clustering(47) Variable = 4P LOSS MUTATION ANALYSIS
D47V1, survival
                   sevent
clus2                0  1
  4P LOSS MUTATED   15 11
  4P LOSS WILD-TYPE 46 42
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               26                88 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               11                42 
$`4P LOSS MUTATED`
TCGA-BC-A10Y TCGA-BC-A112 TCGA-BC-A217 TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-CC-A3MC 
       23.34         5.03        13.81        16.37         9.50         0.13 
TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A119 TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ 
       79.73        37.74         7.33        49.15         6.02        29.16 
TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A3A9 TCGA-DD-A4NH TCGA-DD-A4NJ TCGA-DD-A4NN 
       55.66         5.59        30.58        14.24        15.06        29.56 
TCGA-ED-A459 TCGA-EP-A2KB TCGA-EP-A2KC TCGA-FV-A496 TCGA-FV-A4ZP TCGA-G3-A25S 
        0.23         1.97         0.62         0.33        60.36         1.22 
TCGA-G3-A25U TCGA-G3-A25X 
       53.79        58.49 

$`4P LOSS WILD-TYPE`
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T 
       48.99        27.91        37.32        10.13        46.78        27.52 
TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A216 
       27.52         2.99        25.32         1.12        69.57        44.42 
TCGA-BC-A3KF TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 
        0.26         0.07         2.86         3.02         3.39         4.24 
TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-DD-A115 TCGA-DD-A116 
        3.32         0.10         0.07         0.10        83.57        53.29 
TCGA-DD-A118 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 
      112.96         2.60         0.46        21.76        51.25        90.67 
TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EF 
       79.36        66.31        19.76        75.65         6.67        12.95 
TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 
       13.64        21.14        19.73        25.81         7.66        70.06 
TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A8 
       17.59        20.12       102.74       107.11        13.78         0.36 
TCGA-DD-A4NA TCGA-DD-A4ND TCGA-DD-A4NE TCGA-DD-A4NF TCGA-DD-A4NG TCGA-DD-A4NI 
       33.14        73.38        21.67        14.07        14.93        10.78 
TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-ED-A5KG 
       39.75        56.25        61.45        93.67        12.26         0.20 
TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS 
       10.85         7.76        11.74         3.19         0.43        23.01 
TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3R2 TCGA-FV-A3R3 
       14.40        32.45        19.07         0.20         6.35         0.13 
TCGA-FV-A495 TCGA-FV-A4ZQ TCGA-G3-A25T TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25Y 
        0.03         0.39        51.02        28.27        30.71        14.86 
TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK 
       21.53        22.13        25.64         5.88        19.53        19.23 
TCGA-G3-A5SJ TCGA-G3-A5SK TCGA-G3-A5SL TCGA-G3-A5SM 
       11.97         9.93         7.99         4.37 

  4P LOSS MUTATED 4P LOSS WILD-TYPE 
             0.13              0.03 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
            79.73            112.96 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
            14.65             18.33 
[1] "0.1 - 79.7 (14.7)"  "0.0 - 113.0 (18.3)"
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"4P LOSS WILD-TYPE"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
  "4P LOSS MUTATED" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-BC-A5W4        TCGA-CC-5258        TCGA-CC-5260 
  "4P LOSS MUTATED"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-CC-5261        TCGA-CC-5262        TCGA-CC-5263        TCGA-CC-A1HT 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-CC-A3M9        TCGA-CC-A3MA        TCGA-CC-A3MB        TCGA-CC-A3MC 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" 
       TCGA-DD-A113        TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116 
  "4P LOSS MUTATED"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-DD-A118        TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B 
"4P LOSS WILD-TYPE"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-DD-A11C        TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EA 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-DD-A1EB        TCGA-DD-A1EC        TCGA-DD-A1ED        TCGA-DD-A1EE 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-DD-A1EF        TCGA-DD-A1EH        TCGA-DD-A1EI        TCGA-DD-A1EJ 
"4P LOSS WILD-TYPE"   "4P LOSS MUTATED"   "4P LOSS MUTATED"   "4P LOSS MUTATED" 
       TCGA-DD-A1EL        TCGA-DD-A39V        TCGA-DD-A39X        TCGA-DD-A39Y 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED"   "4P LOSS MUTATED" 
       TCGA-DD-A39Z        TCGA-DD-A3A0        TCGA-DD-A3A1        TCGA-DD-A3A2 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-DD-A3A3        TCGA-DD-A3A4        TCGA-DD-A3A5        TCGA-DD-A3A6 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-DD-A3A7        TCGA-DD-A3A8        TCGA-DD-A3A9        TCGA-DD-A4NA 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" 
       TCGA-DD-A4ND        TCGA-DD-A4NE        TCGA-DD-A4NF        TCGA-DD-A4NG 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-DD-A4NH        TCGA-DD-A4NI        TCGA-DD-A4NJ        TCGA-DD-A4NK 
  "4P LOSS MUTATED" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" 
       TCGA-DD-A4NL        TCGA-DD-A4NN        TCGA-DD-A4NO        TCGA-DD-A4NP 
"4P LOSS WILD-TYPE"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-DD-A4NQ        TCGA-ED-A459        TCGA-ED-A5KG        TCGA-EP-A12J 
"4P LOSS WILD-TYPE"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED"   "4P LOSS MUTATED" 
       TCGA-EP-A3JL        TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-FV-A23B        TCGA-FV-A2QR        TCGA-FV-A3I0        TCGA-FV-A3R2 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-FV-A3R3        TCGA-FV-A495        TCGA-FV-A496        TCGA-FV-A4ZP 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED"   "4P LOSS MUTATED" 
       TCGA-FV-A4ZQ        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"4P LOSS WILD-TYPE"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-G3-A3CJ        TCGA-G3-A3CK        TCGA-G3-A5SJ        TCGA-G3-A5SK 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-G3-A5SL        TCGA-G3-A5SM 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"4P LOSS WILD-TYPE"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
  "4P LOSS MUTATED" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-BC-A5W4        TCGA-CC-5258        TCGA-CC-5260 
  "4P LOSS MUTATED"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-CC-5261        TCGA-CC-5262        TCGA-CC-5263        TCGA-CC-A1HT 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-CC-A3M9        TCGA-CC-A3MA        TCGA-CC-A3MB        TCGA-CC-A3MC 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" 
       TCGA-DD-A113        TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116 
  "4P LOSS MUTATED"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-DD-A118        TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B 
"4P LOSS WILD-TYPE"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-DD-A11C        TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EA 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-DD-A1EB        TCGA-DD-A1EC        TCGA-DD-A1ED        TCGA-DD-A1EE 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-DD-A1EF        TCGA-DD-A1EH        TCGA-DD-A1EI        TCGA-DD-A1EJ 
"4P LOSS WILD-TYPE"   "4P LOSS MUTATED"   "4P LOSS MUTATED"   "4P LOSS MUTATED" 
       TCGA-DD-A1EL        TCGA-DD-A39V        TCGA-DD-A39X        TCGA-DD-A39Y 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED"   "4P LOSS MUTATED" 
       TCGA-DD-A39Z        TCGA-DD-A3A0        TCGA-DD-A3A1        TCGA-DD-A3A2 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-DD-A3A3        TCGA-DD-A3A4        TCGA-DD-A3A5        TCGA-DD-A3A6 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-DD-A3A7        TCGA-DD-A3A8        TCGA-DD-A3A9        TCGA-DD-A4NA 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" 
       TCGA-DD-A4ND        TCGA-DD-A4NE        TCGA-DD-A4NF        TCGA-DD-A4NG 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-DD-A4NH        TCGA-DD-A4NI        TCGA-DD-A4NJ        TCGA-DD-A4NK 
  "4P LOSS MUTATED" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" 
       TCGA-DD-A4NL        TCGA-DD-A4NN        TCGA-DD-A4NO        TCGA-DD-A4NP 
"4P LOSS WILD-TYPE"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-DD-A4NQ        TCGA-ED-A459        TCGA-ED-A5KG        TCGA-EP-A12J 
"4P LOSS WILD-TYPE"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED"   "4P LOSS MUTATED" 
       TCGA-EP-A3JL        TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-FV-A23B        TCGA-FV-A2QR        TCGA-FV-A3I0        TCGA-FV-A3R2 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-FV-A3R3        TCGA-FV-A495        TCGA-FV-A496        TCGA-FV-A4ZP 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED"   "4P LOSS MUTATED" 
       TCGA-FV-A4ZQ        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"4P LOSS WILD-TYPE"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-G3-A3CJ        TCGA-G3-A3CK        TCGA-G3-A5SJ        TCGA-G3-A5SK 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-G3-A5SL        TCGA-G3-A5SM 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"4P LOSS WILD-TYPE"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
  "4P LOSS MUTATED" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-BC-A5W4        TCGA-CC-5258        TCGA-CC-5260 
  "4P LOSS MUTATED"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-CC-5261        TCGA-CC-5262        TCGA-CC-5263        TCGA-CC-A1HT 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-CC-A3M9        TCGA-CC-A3MA        TCGA-CC-A3MB        TCGA-CC-A3MC 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" 
       TCGA-DD-A113        TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116 
  "4P LOSS MUTATED"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-DD-A118        TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B 
"4P LOSS WILD-TYPE"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-DD-A11C        TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EA 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-DD-A1EB        TCGA-DD-A1EC        TCGA-DD-A1ED        TCGA-DD-A1EE 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-DD-A1EF        TCGA-DD-A1EH        TCGA-DD-A1EI        TCGA-DD-A1EJ 
"4P LOSS WILD-TYPE"   "4P LOSS MUTATED"   "4P LOSS MUTATED"   "4P LOSS MUTATED" 
       TCGA-DD-A1EL        TCGA-DD-A39V        TCGA-DD-A39X        TCGA-DD-A39Y 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED"   "4P LOSS MUTATED" 
       TCGA-DD-A39Z        TCGA-DD-A3A0        TCGA-DD-A3A1        TCGA-DD-A3A2 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-DD-A3A3        TCGA-DD-A3A4        TCGA-DD-A3A5        TCGA-DD-A3A6 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-DD-A3A7        TCGA-DD-A3A8        TCGA-DD-A3A9        TCGA-DD-A4NA 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" 
       TCGA-DD-A4ND        TCGA-DD-A4NE        TCGA-DD-A4NF        TCGA-DD-A4NG 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-DD-A4NH        TCGA-DD-A4NI        TCGA-DD-A4NJ        TCGA-DD-A4NK 
  "4P LOSS MUTATED" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" 
       TCGA-DD-A4NL        TCGA-DD-A4NN        TCGA-DD-A4NO        TCGA-DD-A4NP 
"4P LOSS WILD-TYPE"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-DD-A4NQ        TCGA-ED-A459        TCGA-ED-A5KG        TCGA-EP-A12J 
"4P LOSS WILD-TYPE"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED"   "4P LOSS MUTATED" 
       TCGA-EP-A3JL        TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-FV-A23B        TCGA-FV-A2QR        TCGA-FV-A3I0        TCGA-FV-A3R2 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-FV-A3R3        TCGA-FV-A495        TCGA-FV-A496        TCGA-FV-A4ZP 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED"   "4P LOSS MUTATED" 
       TCGA-FV-A4ZQ        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"4P LOSS WILD-TYPE"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-G3-A3CJ        TCGA-G3-A3CK        TCGA-G3-A5SJ        TCGA-G3-A5SK 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-G3-A5SL        TCGA-G3-A5SM 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
[1] "hr=" "1"  
D47V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  4P LOSS MUTATED         9        7         1          4          1          1
  4P LOSS WILD-TYPE      36       18         1         21          2          3
                   vv
clus                STAGE IV STAGE IVA STAGE IVB
  4P LOSS MUTATED          1         1         1
  4P LOSS WILD-TYPE        0         0         0
D47V3, multiclass
                   vv
clus                T1 T2 T3 T4
  4P LOSS MUTATED   11  7  8  2
  4P LOSS WILD-TYPE 37 21 26  4
D47V4, multiclass
    clus
vv   4P LOSS MUTATED 4P LOSS WILD-TYPE
  T1              11                37
  T2               7                21
  T3               8                26
  T4               2                 4
D47V5, binary
                   cls
clus                 0  1
  4P LOSS MUTATED   15  2
  4P LOSS WILD-TYPE 59  1
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED     15    2
  4P LOSS WILD-TYPE   59    1
   clus
vv  4P LOSS MUTATED 4P LOSS WILD-TYPE
  0              15                59
  1               2                 1
                   vv
clus                M0 M1 MX
  4P LOSS MUTATED   21  2  5
  4P LOSS WILD-TYPE 69  0 20
D47V6, multiclass
    clus
vv   4P LOSS MUTATED 4P LOSS WILD-TYPE
  M0              21                69
  M1               2                 0
  MX               5                20
D47V7, binary
                   cls
clus                 0  1
  4P LOSS MUTATED   12 16
  4P LOSS WILD-TYPE 32 57
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED     12   16
  4P LOSS WILD-TYPE   32   57
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  FEMALE              12                32
  MALE                16                57
                   vv
clus                R0 R1 R2 RX
  4P LOSS MUTATED   23  3  1  1
  4P LOSS WILD-TYPE 70  7  0  7
D47V8, multiclass
    clus
vv   4P LOSS MUTATED 4P LOSS WILD-TYPE
  R0              23                70
  R1               3                 7
  R2               1                 0
  RX               1                 7

Clustering(48) Variable = 4Q LOSS MUTATION ANALYSIS
D48V1, survival
                   sevent
clus2                0  1
  4Q LOSS MUTATED   20 14
  4Q LOSS WILD-TYPE 41 39
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               34                80 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               14                39 
$`4Q LOSS MUTATED`
TCGA-BC-A10T TCGA-BC-A10Y TCGA-BC-A112 TCGA-BC-A217 TCGA-BC-A3KG TCGA-BC-A5W4 
       27.52        23.34         5.03        13.81        16.37         9.50 
TCGA-CC-A3M9 TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A116 
        0.10         0.10         0.13        79.73        37.74        53.29 
TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A39X 
        7.33         2.60        49.15         6.02        29.16        55.66 
TCGA-DD-A39Y TCGA-DD-A3A9 TCGA-DD-A4NH TCGA-DD-A4NJ TCGA-DD-A4NN TCGA-DD-A4NO 
        5.59        30.58        14.24        15.06        29.56        61.45 
TCGA-ED-A459 TCGA-EP-A2KB TCGA-EP-A2KC TCGA-FV-A496 TCGA-FV-A4ZP TCGA-G3-A25S 
        0.23         1.97         0.62         0.33        60.36         1.22 
TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A5SM 
       58.49        14.86        21.53         4.37 

$`4Q LOSS WILD-TYPE`
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10U 
       48.99        27.91        37.32        10.13        46.78        27.52 
TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A216 TCGA-BC-A3KF 
        2.99        25.32         1.12        69.57        44.42         0.26 
TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A1HT 
        0.07         2.86         3.02         3.39         4.24         3.32 
TCGA-CC-A3MA TCGA-DD-A115 TCGA-DD-A118 TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D 
        0.07        83.57       112.96         0.46        21.76        51.25 
TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE 
       90.67        79.36        66.31        19.76        75.65         6.67 
TCGA-DD-A1EF TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 
       12.95        13.64        21.14        19.73        25.81         7.66 
TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 
       70.06        17.59        20.12       102.74       107.11        13.78 
TCGA-DD-A3A8 TCGA-DD-A4NA TCGA-DD-A4ND TCGA-DD-A4NE TCGA-DD-A4NF TCGA-DD-A4NG 
        0.36        33.14        73.38        21.67        14.07        14.93 
TCGA-DD-A4NI TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-ED-A5KG 
       10.78        39.75        56.25        93.67        12.26         0.20 
TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS 
       10.85         7.76        11.74         3.19         0.43        23.01 
TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3R2 TCGA-FV-A3R3 
       14.40        32.45        19.07         0.20         6.35         0.13 
TCGA-FV-A495 TCGA-FV-A4ZQ TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W 
        0.03         0.39        51.02        53.79        28.27        30.71 
TCGA-G3-A3CG TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SJ 
       22.13        25.64         5.88        19.53        19.23        11.97 
TCGA-G3-A5SK TCGA-G3-A5SL 
        9.93         7.99 

  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
             0.10              0.03 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
            79.73            112.96 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
            14.55             19.15 
[1] "0.1 - 79.7 (14.6)"  "0.0 - 113.0 (19.1)"
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
  "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-BC-A5W4        TCGA-CC-5258        TCGA-CC-5260 
  "4Q LOSS MUTATED"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-CC-5261        TCGA-CC-5262        TCGA-CC-5263        TCGA-CC-A1HT 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-CC-A3M9        TCGA-CC-A3MA        TCGA-CC-A3MB        TCGA-CC-A3MC 
  "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED"   "4Q LOSS MUTATED" 
       TCGA-DD-A113        TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116 
  "4Q LOSS MUTATED"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" 
       TCGA-DD-A118        TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B 
"4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" 
       TCGA-DD-A11C        TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EA 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-DD-A1EB        TCGA-DD-A1EC        TCGA-DD-A1ED        TCGA-DD-A1EE 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-DD-A1EF        TCGA-DD-A1EH        TCGA-DD-A1EI        TCGA-DD-A1EJ 
"4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED"   "4Q LOSS MUTATED"   "4Q LOSS MUTATED" 
       TCGA-DD-A1EL        TCGA-DD-A39V        TCGA-DD-A39X        TCGA-DD-A39Y 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED"   "4Q LOSS MUTATED" 
       TCGA-DD-A39Z        TCGA-DD-A3A0        TCGA-DD-A3A1        TCGA-DD-A3A2 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-DD-A3A3        TCGA-DD-A3A4        TCGA-DD-A3A5        TCGA-DD-A3A6 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-DD-A3A7        TCGA-DD-A3A8        TCGA-DD-A3A9        TCGA-DD-A4NA 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" 
       TCGA-DD-A4ND        TCGA-DD-A4NE        TCGA-DD-A4NF        TCGA-DD-A4NG 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-DD-A4NH        TCGA-DD-A4NI        TCGA-DD-A4NJ        TCGA-DD-A4NK 
  "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" 
       TCGA-DD-A4NL        TCGA-DD-A4NN        TCGA-DD-A4NO        TCGA-DD-A4NP 
"4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" 
       TCGA-DD-A4NQ        TCGA-ED-A459        TCGA-ED-A5KG        TCGA-EP-A12J 
"4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED"   "4Q LOSS MUTATED" 
       TCGA-EP-A3JL        TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-FV-A23B        TCGA-FV-A2QR        TCGA-FV-A3I0        TCGA-FV-A3R2 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-FV-A3R3        TCGA-FV-A495        TCGA-FV-A496        TCGA-FV-A4ZP 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED"   "4Q LOSS MUTATED" 
       TCGA-FV-A4ZQ        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED"   "4Q LOSS MUTATED" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI 
  "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-G3-A3CJ        TCGA-G3-A3CK        TCGA-G3-A5SJ        TCGA-G3-A5SK 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-G3-A5SL        TCGA-G3-A5SM 
"4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" 
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
  "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-BC-A5W4        TCGA-CC-5258        TCGA-CC-5260 
  "4Q LOSS MUTATED"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-CC-5261        TCGA-CC-5262        TCGA-CC-5263        TCGA-CC-A1HT 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-CC-A3M9        TCGA-CC-A3MA        TCGA-CC-A3MB        TCGA-CC-A3MC 
  "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED"   "4Q LOSS MUTATED" 
       TCGA-DD-A113        TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116 
  "4Q LOSS MUTATED"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" 
       TCGA-DD-A118        TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B 
"4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" 
       TCGA-DD-A11C        TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EA 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-DD-A1EB        TCGA-DD-A1EC        TCGA-DD-A1ED        TCGA-DD-A1EE 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-DD-A1EF        TCGA-DD-A1EH        TCGA-DD-A1EI        TCGA-DD-A1EJ 
"4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED"   "4Q LOSS MUTATED"   "4Q LOSS MUTATED" 
       TCGA-DD-A1EL        TCGA-DD-A39V        TCGA-DD-A39X        TCGA-DD-A39Y 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED"   "4Q LOSS MUTATED" 
       TCGA-DD-A39Z        TCGA-DD-A3A0        TCGA-DD-A3A1        TCGA-DD-A3A2 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-DD-A3A3        TCGA-DD-A3A4        TCGA-DD-A3A5        TCGA-DD-A3A6 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-DD-A3A7        TCGA-DD-A3A8        TCGA-DD-A3A9        TCGA-DD-A4NA 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" 
       TCGA-DD-A4ND        TCGA-DD-A4NE        TCGA-DD-A4NF        TCGA-DD-A4NG 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-DD-A4NH        TCGA-DD-A4NI        TCGA-DD-A4NJ        TCGA-DD-A4NK 
  "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" 
       TCGA-DD-A4NL        TCGA-DD-A4NN        TCGA-DD-A4NO        TCGA-DD-A4NP 
"4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" 
       TCGA-DD-A4NQ        TCGA-ED-A459        TCGA-ED-A5KG        TCGA-EP-A12J 
"4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED"   "4Q LOSS MUTATED" 
       TCGA-EP-A3JL        TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-FV-A23B        TCGA-FV-A2QR        TCGA-FV-A3I0        TCGA-FV-A3R2 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-FV-A3R3        TCGA-FV-A495        TCGA-FV-A496        TCGA-FV-A4ZP 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED"   "4Q LOSS MUTATED" 
       TCGA-FV-A4ZQ        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED"   "4Q LOSS MUTATED" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI 
  "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-G3-A3CJ        TCGA-G3-A3CK        TCGA-G3-A5SJ        TCGA-G3-A5SK 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-G3-A5SL        TCGA-G3-A5SM 
"4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" 
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
  "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-BC-A5W4        TCGA-CC-5258        TCGA-CC-5260 
  "4Q LOSS MUTATED"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-CC-5261        TCGA-CC-5262        TCGA-CC-5263        TCGA-CC-A1HT 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-CC-A3M9        TCGA-CC-A3MA        TCGA-CC-A3MB        TCGA-CC-A3MC 
  "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED"   "4Q LOSS MUTATED" 
       TCGA-DD-A113        TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116 
  "4Q LOSS MUTATED"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" 
       TCGA-DD-A118        TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B 
"4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" 
       TCGA-DD-A11C        TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EA 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-DD-A1EB        TCGA-DD-A1EC        TCGA-DD-A1ED        TCGA-DD-A1EE 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-DD-A1EF        TCGA-DD-A1EH        TCGA-DD-A1EI        TCGA-DD-A1EJ 
"4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED"   "4Q LOSS MUTATED"   "4Q LOSS MUTATED" 
       TCGA-DD-A1EL        TCGA-DD-A39V        TCGA-DD-A39X        TCGA-DD-A39Y 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED"   "4Q LOSS MUTATED" 
       TCGA-DD-A39Z        TCGA-DD-A3A0        TCGA-DD-A3A1        TCGA-DD-A3A2 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-DD-A3A3        TCGA-DD-A3A4        TCGA-DD-A3A5        TCGA-DD-A3A6 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-DD-A3A7        TCGA-DD-A3A8        TCGA-DD-A3A9        TCGA-DD-A4NA 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" 
       TCGA-DD-A4ND        TCGA-DD-A4NE        TCGA-DD-A4NF        TCGA-DD-A4NG 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-DD-A4NH        TCGA-DD-A4NI        TCGA-DD-A4NJ        TCGA-DD-A4NK 
  "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" 
       TCGA-DD-A4NL        TCGA-DD-A4NN        TCGA-DD-A4NO        TCGA-DD-A4NP 
"4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" 
       TCGA-DD-A4NQ        TCGA-ED-A459        TCGA-ED-A5KG        TCGA-EP-A12J 
"4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED"   "4Q LOSS MUTATED" 
       TCGA-EP-A3JL        TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-FV-A23B        TCGA-FV-A2QR        TCGA-FV-A3I0        TCGA-FV-A3R2 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-FV-A3R3        TCGA-FV-A495        TCGA-FV-A496        TCGA-FV-A4ZP 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED"   "4Q LOSS MUTATED" 
       TCGA-FV-A4ZQ        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED"   "4Q LOSS MUTATED" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI 
  "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-G3-A3CJ        TCGA-G3-A3CK        TCGA-G3-A5SJ        TCGA-G3-A5SK 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-G3-A5SL        TCGA-G3-A5SM 
"4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" 
[1] "hr=" "1.1"
D48V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  4Q LOSS MUTATED        12        9         1          7          1          1
  4Q LOSS WILD-TYPE      33       16         1         18          2          3
                   vv
clus                STAGE IV STAGE IVA STAGE IVB
  4Q LOSS MUTATED          1         1         1
  4Q LOSS WILD-TYPE        0         0         0
D48V3, multiclass
                   vv
clus                T1 T2 T3 T4
  4Q LOSS MUTATED   14  9 11  3
  4Q LOSS WILD-TYPE 34 19 23  3
D48V4, multiclass
    clus
vv   4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  T1              14                34
  T2               9                19
  T3              11                23
  T4               3                 3
D48V5, binary
                   cls
clus                 0  1
  4Q LOSS MUTATED   22  2
  4Q LOSS WILD-TYPE 52  1
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED     22    2
  4Q LOSS WILD-TYPE   52    1
   clus
vv  4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  0              22                52
  1               2                 1
                   vv
clus                M0 M1 MX
  4Q LOSS MUTATED   28  2  7
  4Q LOSS WILD-TYPE 62  0 18
D48V6, multiclass
    clus
vv   4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  M0              28                62
  M1               2                 0
  MX               7                18
D48V7, binary
                   cls
clus                 0  1
  4Q LOSS MUTATED   13 24
  4Q LOSS WILD-TYPE 31 49
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED     13   24
  4Q LOSS WILD-TYPE   31   49
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  FEMALE              13                31
  MALE                24                49
                   vv
clus                R0 R1 R2 RX
  4Q LOSS MUTATED   31  4  1  1
  4Q LOSS WILD-TYPE 62  6  0  7
D48V8, multiclass
    clus
vv   4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  R0              31                62
  R1               4                 6
  R2               1                 0
  RX               1                 7

Clustering(49) Variable = 5P LOSS MUTATION ANALYSIS
D49V1, survival
                   sevent
clus2                0  1
  5P LOSS MUTATED    5  4
  5P LOSS WILD-TYPE 56 49
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
                9               105 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
                4                49 
$`5P LOSS MUTATED`
TCGA-BC-A10S TCGA-CC-5258 TCGA-CC-A3M9 TCGA-DD-A11A TCGA-DD-A1EH TCGA-DD-A1EJ 
       46.78         0.07         0.10         2.60        49.15        29.16 
TCGA-ES-A2HS TCGA-FV-A496 TCGA-G3-A25S 
       23.01         0.33         1.22 

$`5P LOSS WILD-TYPE`
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A10U 
       48.99        27.91        37.32        10.13        27.52        27.52 
TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 
        2.99        25.32        23.34         1.12        69.57         5.03 
TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-CC-5260 
       44.42        13.81         0.26        16.37         9.50         2.86 
TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3MA TCGA-CC-A3MB 
        3.02         3.39         4.24         3.32         0.07         0.10 
TCGA-CC-A3MC TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 
        0.13        79.73        37.74        83.57        53.29       112.96 
TCGA-DD-A119 TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA 
        7.33         0.46        21.76        51.25        90.67        79.36 
TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EI 
       66.31        19.76        75.65         6.67        12.95         6.02 
TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A0 
       13.64        21.14        55.66         5.59        19.73        25.81 
TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 
        7.66        70.06        17.59        20.12       102.74       107.11 
TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4ND TCGA-DD-A4NE 
       13.78         0.36        30.58        33.14        73.38        21.67 
TCGA-DD-A4NF TCGA-DD-A4NG TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK 
       14.07        14.93        14.24        10.78        15.06        39.75 
TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-ED-A459 
       56.25        29.56        61.45        93.67        12.26         0.23 
TCGA-ED-A5KG TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC 
        0.20        10.85         7.76        11.74         1.97         0.62 
TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-A3I0 
        3.19         0.43        14.40        32.45        19.07         0.20 
TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25T 
        6.35         0.13         0.03        60.36         0.39        51.02 
TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A25Z 
       53.79        28.27        30.71        58.49        14.86        21.53 
TCGA-G3-A3CG TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SJ 
       22.13        25.64         5.88        19.53        19.23        11.97 
TCGA-G3-A5SK TCGA-G3-A5SL TCGA-G3-A5SM 
        9.93         7.99         4.37 

  5P LOSS MUTATED 5P LOSS WILD-TYPE 
             0.07              0.03 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
            49.15            112.96 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
             2.60             16.37 
[1] "0.1 - 49.1 (2.6)"   "0.0 - 113.0 (16.4)"
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
  "5P LOSS MUTATED" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-BC-A5W4        TCGA-CC-5258        TCGA-CC-5260 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE"   "5P LOSS MUTATED" "5P LOSS WILD-TYPE" 
       TCGA-CC-5261        TCGA-CC-5262        TCGA-CC-5263        TCGA-CC-A1HT 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-CC-A3M9        TCGA-CC-A3MA        TCGA-CC-A3MB        TCGA-CC-A3MC 
  "5P LOSS MUTATED" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-DD-A113        TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-DD-A118        TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE"   "5P LOSS MUTATED" "5P LOSS WILD-TYPE" 
       TCGA-DD-A11C        TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EA 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-DD-A1EB        TCGA-DD-A1EC        TCGA-DD-A1ED        TCGA-DD-A1EE 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-DD-A1EF        TCGA-DD-A1EH        TCGA-DD-A1EI        TCGA-DD-A1EJ 
"5P LOSS WILD-TYPE"   "5P LOSS MUTATED" "5P LOSS WILD-TYPE"   "5P LOSS MUTATED" 
       TCGA-DD-A1EL        TCGA-DD-A39V        TCGA-DD-A39X        TCGA-DD-A39Y 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-DD-A39Z        TCGA-DD-A3A0        TCGA-DD-A3A1        TCGA-DD-A3A2 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-DD-A3A3        TCGA-DD-A3A4        TCGA-DD-A3A5        TCGA-DD-A3A6 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-DD-A3A7        TCGA-DD-A3A8        TCGA-DD-A3A9        TCGA-DD-A4NA 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-DD-A4ND        TCGA-DD-A4NE        TCGA-DD-A4NF        TCGA-DD-A4NG 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-DD-A4NH        TCGA-DD-A4NI        TCGA-DD-A4NJ        TCGA-DD-A4NK 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-DD-A4NL        TCGA-DD-A4NN        TCGA-DD-A4NO        TCGA-DD-A4NP 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-DD-A4NQ        TCGA-ED-A459        TCGA-ED-A5KG        TCGA-EP-A12J 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-EP-A3JL        TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE"   "5P LOSS MUTATED" "5P LOSS WILD-TYPE" 
       TCGA-FV-A23B        TCGA-FV-A2QR        TCGA-FV-A3I0        TCGA-FV-A3R2 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-FV-A3R3        TCGA-FV-A495        TCGA-FV-A496        TCGA-FV-A4ZP 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE"   "5P LOSS MUTATED" "5P LOSS WILD-TYPE" 
       TCGA-FV-A4ZQ        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"5P LOSS WILD-TYPE"   "5P LOSS MUTATED" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-G3-A3CJ        TCGA-G3-A3CK        TCGA-G3-A5SJ        TCGA-G3-A5SK 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-G3-A5SL        TCGA-G3-A5SM 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
  "5P LOSS MUTATED" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-BC-A5W4        TCGA-CC-5258        TCGA-CC-5260 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE"   "5P LOSS MUTATED" "5P LOSS WILD-TYPE" 
       TCGA-CC-5261        TCGA-CC-5262        TCGA-CC-5263        TCGA-CC-A1HT 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-CC-A3M9        TCGA-CC-A3MA        TCGA-CC-A3MB        TCGA-CC-A3MC 
  "5P LOSS MUTATED" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-DD-A113        TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-DD-A118        TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE"   "5P LOSS MUTATED" "5P LOSS WILD-TYPE" 
       TCGA-DD-A11C        TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EA 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-DD-A1EB        TCGA-DD-A1EC        TCGA-DD-A1ED        TCGA-DD-A1EE 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-DD-A1EF        TCGA-DD-A1EH        TCGA-DD-A1EI        TCGA-DD-A1EJ 
"5P LOSS WILD-TYPE"   "5P LOSS MUTATED" "5P LOSS WILD-TYPE"   "5P LOSS MUTATED" 
       TCGA-DD-A1EL        TCGA-DD-A39V        TCGA-DD-A39X        TCGA-DD-A39Y 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-DD-A39Z        TCGA-DD-A3A0        TCGA-DD-A3A1        TCGA-DD-A3A2 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-DD-A3A3        TCGA-DD-A3A4        TCGA-DD-A3A5        TCGA-DD-A3A6 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-DD-A3A7        TCGA-DD-A3A8        TCGA-DD-A3A9        TCGA-DD-A4NA 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-DD-A4ND        TCGA-DD-A4NE        TCGA-DD-A4NF        TCGA-DD-A4NG 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-DD-A4NH        TCGA-DD-A4NI        TCGA-DD-A4NJ        TCGA-DD-A4NK 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-DD-A4NL        TCGA-DD-A4NN        TCGA-DD-A4NO        TCGA-DD-A4NP 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-DD-A4NQ        TCGA-ED-A459        TCGA-ED-A5KG        TCGA-EP-A12J 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-EP-A3JL        TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE"   "5P LOSS MUTATED" "5P LOSS WILD-TYPE" 
       TCGA-FV-A23B        TCGA-FV-A2QR        TCGA-FV-A3I0        TCGA-FV-A3R2 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-FV-A3R3        TCGA-FV-A495        TCGA-FV-A496        TCGA-FV-A4ZP 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE"   "5P LOSS MUTATED" "5P LOSS WILD-TYPE" 
       TCGA-FV-A4ZQ        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"5P LOSS WILD-TYPE"   "5P LOSS MUTATED" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-G3-A3CJ        TCGA-G3-A3CK        TCGA-G3-A5SJ        TCGA-G3-A5SK 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-G3-A5SL        TCGA-G3-A5SM 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
  "5P LOSS MUTATED" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-BC-A5W4        TCGA-CC-5258        TCGA-CC-5260 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE"   "5P LOSS MUTATED" "5P LOSS WILD-TYPE" 
       TCGA-CC-5261        TCGA-CC-5262        TCGA-CC-5263        TCGA-CC-A1HT 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-CC-A3M9        TCGA-CC-A3MA        TCGA-CC-A3MB        TCGA-CC-A3MC 
  "5P LOSS MUTATED" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-DD-A113        TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-DD-A118        TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE"   "5P LOSS MUTATED" "5P LOSS WILD-TYPE" 
       TCGA-DD-A11C        TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EA 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-DD-A1EB        TCGA-DD-A1EC        TCGA-DD-A1ED        TCGA-DD-A1EE 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-DD-A1EF        TCGA-DD-A1EH        TCGA-DD-A1EI        TCGA-DD-A1EJ 
"5P LOSS WILD-TYPE"   "5P LOSS MUTATED" "5P LOSS WILD-TYPE"   "5P LOSS MUTATED" 
       TCGA-DD-A1EL        TCGA-DD-A39V        TCGA-DD-A39X        TCGA-DD-A39Y 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-DD-A39Z        TCGA-DD-A3A0        TCGA-DD-A3A1        TCGA-DD-A3A2 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-DD-A3A3        TCGA-DD-A3A4        TCGA-DD-A3A5        TCGA-DD-A3A6 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-DD-A3A7        TCGA-DD-A3A8        TCGA-DD-A3A9        TCGA-DD-A4NA 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-DD-A4ND        TCGA-DD-A4NE        TCGA-DD-A4NF        TCGA-DD-A4NG 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-DD-A4NH        TCGA-DD-A4NI        TCGA-DD-A4NJ        TCGA-DD-A4NK 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-DD-A4NL        TCGA-DD-A4NN        TCGA-DD-A4NO        TCGA-DD-A4NP 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-DD-A4NQ        TCGA-ED-A459        TCGA-ED-A5KG        TCGA-EP-A12J 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-EP-A3JL        TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE"   "5P LOSS MUTATED" "5P LOSS WILD-TYPE" 
       TCGA-FV-A23B        TCGA-FV-A2QR        TCGA-FV-A3I0        TCGA-FV-A3R2 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-FV-A3R3        TCGA-FV-A495        TCGA-FV-A496        TCGA-FV-A4ZP 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE"   "5P LOSS MUTATED" "5P LOSS WILD-TYPE" 
       TCGA-FV-A4ZQ        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"5P LOSS WILD-TYPE"   "5P LOSS MUTATED" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-G3-A3CJ        TCGA-G3-A3CK        TCGA-G3-A5SJ        TCGA-G3-A5SK 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-G3-A5SL        TCGA-G3-A5SM 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
[1] "hr=" "1.5"
D49V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  5P LOSS MUTATED         4        1         1          1          0          1
  5P LOSS WILD-TYPE      41       24         1         24          3          3
                   vv
clus                STAGE IV STAGE IVA STAGE IVB
  5P LOSS MUTATED          0         0         0
  5P LOSS WILD-TYPE        1         1         1
D49V3, multiclass
                   vv
clus                T1 T2 T3 T4
  5P LOSS MUTATED    5  1  3  0
  5P LOSS WILD-TYPE 43 27 31  6
D49V4, multiclass
    clus
vv   5P LOSS MUTATED 5P LOSS WILD-TYPE
  T1               5                43
  T2               1                27
  T3               3                31
  T4               0                 6
D49V5, binary
                   cls
clus                 0  1
  5P LOSS MUTATED    5  1
  5P LOSS WILD-TYPE 69  2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED      5    1
  5P LOSS WILD-TYPE   69    2
   clus
vv  5P LOSS MUTATED 5P LOSS WILD-TYPE
  0               5                69
  1               1                 2
                   vv
clus                M0 M1 MX
  5P LOSS MUTATED    7  0  2
  5P LOSS WILD-TYPE 83  2 23
D49V6, multiclass
    clus
vv   5P LOSS MUTATED 5P LOSS WILD-TYPE
  M0               7                83
  M1               0                 2
  MX               2                23
D49V7, binary
                   cls
clus                 0  1
  5P LOSS MUTATED    2  7
  5P LOSS WILD-TYPE 42 66
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED      2    7
  5P LOSS WILD-TYPE   42   66
        clus
vv       5P LOSS MUTATED 5P LOSS WILD-TYPE
  FEMALE               2                42
  MALE                 7                66
                   vv
clus                R0 R1 R2 RX
  5P LOSS MUTATED    7  1  0  1
  5P LOSS WILD-TYPE 86  9  1  7
D49V8, multiclass
    clus
vv   5P LOSS MUTATED 5P LOSS WILD-TYPE
  R0               7                86
  R1               1                 9
  R2               0                 1
  RX               1                 7

Clustering(50) Variable = 5Q LOSS MUTATION ANALYSIS
D50V1, survival
                   sevent
clus2                0  1
  5Q LOSS MUTATED    6  7
  5Q LOSS WILD-TYPE 55 46
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               13               101 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
                7                46 
$`5Q LOSS MUTATED`
TCGA-BC-A10R TCGA-BC-A10S TCGA-CC-5263 TCGA-CC-A3M9 TCGA-DD-A11A TCGA-DD-A1EF 
       10.13        46.78         4.24         0.10         2.60        12.95 
TCGA-DD-A1EH TCGA-DD-A1EJ TCGA-ES-A2HS TCGA-FV-A3I0 TCGA-FV-A496 TCGA-FV-A4ZP 
       49.15        29.16        23.01         0.20         0.33        60.36 
TCGA-G3-A25S 
        1.22 

$`5Q LOSS WILD-TYPE`
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W 
       48.99        27.91        37.32        27.52        27.52         2.99 
TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A216 
       25.32        23.34         1.12        69.57         5.03        44.42 
TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-CC-5258 TCGA-CC-5260 
       13.81         0.26        16.37         9.50         0.07         2.86 
TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-A1HT TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC 
        3.02         3.39         3.32         0.07         0.10         0.13 
TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 
       79.73        37.74        83.57        53.29       112.96         7.33 
TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB 
        0.46        21.76        51.25        90.67        79.36        66.31 
TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EI TCGA-DD-A1EL TCGA-DD-A39V 
       19.76        75.65         6.67         6.02        13.64        21.14 
TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 
       55.66         5.59        19.73        25.81         7.66        70.06 
TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A8 
       17.59        20.12       102.74       107.11        13.78         0.36 
TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4ND TCGA-DD-A4NE TCGA-DD-A4NF TCGA-DD-A4NG 
       30.58        33.14        73.38        21.67        14.07        14.93 
TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN 
       14.24        10.78        15.06        39.75        56.25        29.56 
TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-ED-A459 TCGA-ED-A5KG TCGA-EP-A12J 
       61.45        93.67        12.26         0.23         0.20        10.85 
TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK 
        7.76        11.74         1.97         0.62         3.19         0.43 
TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 
       14.40        32.45        19.07         6.35         0.13         0.03 
TCGA-FV-A4ZQ TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25X 
        0.39        51.02        53.79        28.27        30.71        58.49 
TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ 
       14.86        21.53        22.13        25.64         5.88        19.53 
TCGA-G3-A3CK TCGA-G3-A5SJ TCGA-G3-A5SK TCGA-G3-A5SL TCGA-G3-A5SM 
       19.23        11.97         9.93         7.99         4.37 

  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
             0.10              0.03 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
            60.36            112.96 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
            10.13             17.59 
[1] "0.1 - 60.4 (10.1)"  "0.0 - 113.0 (17.6)"
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
  "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-BC-A5W4        TCGA-CC-5258        TCGA-CC-5260 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-CC-5261        TCGA-CC-5262        TCGA-CC-5263        TCGA-CC-A1HT 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" 
       TCGA-CC-A3M9        TCGA-CC-A3MA        TCGA-CC-A3MB        TCGA-CC-A3MC 
  "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-DD-A113        TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-DD-A118        TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" 
       TCGA-DD-A11C        TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EA 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-DD-A1EB        TCGA-DD-A1EC        TCGA-DD-A1ED        TCGA-DD-A1EE 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-DD-A1EF        TCGA-DD-A1EH        TCGA-DD-A1EI        TCGA-DD-A1EJ 
  "5Q LOSS MUTATED"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" 
       TCGA-DD-A1EL        TCGA-DD-A39V        TCGA-DD-A39X        TCGA-DD-A39Y 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-DD-A39Z        TCGA-DD-A3A0        TCGA-DD-A3A1        TCGA-DD-A3A2 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-DD-A3A3        TCGA-DD-A3A4        TCGA-DD-A3A5        TCGA-DD-A3A6 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-DD-A3A7        TCGA-DD-A3A8        TCGA-DD-A3A9        TCGA-DD-A4NA 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-DD-A4ND        TCGA-DD-A4NE        TCGA-DD-A4NF        TCGA-DD-A4NG 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-DD-A4NH        TCGA-DD-A4NI        TCGA-DD-A4NJ        TCGA-DD-A4NK 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-DD-A4NL        TCGA-DD-A4NN        TCGA-DD-A4NO        TCGA-DD-A4NP 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-DD-A4NQ        TCGA-ED-A459        TCGA-ED-A5KG        TCGA-EP-A12J 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-EP-A3JL        TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" 
       TCGA-FV-A23B        TCGA-FV-A2QR        TCGA-FV-A3I0        TCGA-FV-A3R2 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" 
       TCGA-FV-A3R3        TCGA-FV-A495        TCGA-FV-A496        TCGA-FV-A4ZP 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED"   "5Q LOSS MUTATED" 
       TCGA-FV-A4ZQ        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-G3-A3CJ        TCGA-G3-A3CK        TCGA-G3-A5SJ        TCGA-G3-A5SK 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-G3-A5SL        TCGA-G3-A5SM 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
  "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-BC-A5W4        TCGA-CC-5258        TCGA-CC-5260 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-CC-5261        TCGA-CC-5262        TCGA-CC-5263        TCGA-CC-A1HT 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" 
       TCGA-CC-A3M9        TCGA-CC-A3MA        TCGA-CC-A3MB        TCGA-CC-A3MC 
  "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-DD-A113        TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-DD-A118        TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" 
       TCGA-DD-A11C        TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EA 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-DD-A1EB        TCGA-DD-A1EC        TCGA-DD-A1ED        TCGA-DD-A1EE 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-DD-A1EF        TCGA-DD-A1EH        TCGA-DD-A1EI        TCGA-DD-A1EJ 
  "5Q LOSS MUTATED"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" 
       TCGA-DD-A1EL        TCGA-DD-A39V        TCGA-DD-A39X        TCGA-DD-A39Y 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-DD-A39Z        TCGA-DD-A3A0        TCGA-DD-A3A1        TCGA-DD-A3A2 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-DD-A3A3        TCGA-DD-A3A4        TCGA-DD-A3A5        TCGA-DD-A3A6 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-DD-A3A7        TCGA-DD-A3A8        TCGA-DD-A3A9        TCGA-DD-A4NA 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-DD-A4ND        TCGA-DD-A4NE        TCGA-DD-A4NF        TCGA-DD-A4NG 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-DD-A4NH        TCGA-DD-A4NI        TCGA-DD-A4NJ        TCGA-DD-A4NK 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-DD-A4NL        TCGA-DD-A4NN        TCGA-DD-A4NO        TCGA-DD-A4NP 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-DD-A4NQ        TCGA-ED-A459        TCGA-ED-A5KG        TCGA-EP-A12J 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-EP-A3JL        TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" 
       TCGA-FV-A23B        TCGA-FV-A2QR        TCGA-FV-A3I0        TCGA-FV-A3R2 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" 
       TCGA-FV-A3R3        TCGA-FV-A495        TCGA-FV-A496        TCGA-FV-A4ZP 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED"   "5Q LOSS MUTATED" 
       TCGA-FV-A4ZQ        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-G3-A3CJ        TCGA-G3-A3CK        TCGA-G3-A5SJ        TCGA-G3-A5SK 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-G3-A5SL        TCGA-G3-A5SM 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
  "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-BC-A5W4        TCGA-CC-5258        TCGA-CC-5260 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-CC-5261        TCGA-CC-5262        TCGA-CC-5263        TCGA-CC-A1HT 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" 
       TCGA-CC-A3M9        TCGA-CC-A3MA        TCGA-CC-A3MB        TCGA-CC-A3MC 
  "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-DD-A113        TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-DD-A118        TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" 
       TCGA-DD-A11C        TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EA 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-DD-A1EB        TCGA-DD-A1EC        TCGA-DD-A1ED        TCGA-DD-A1EE 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-DD-A1EF        TCGA-DD-A1EH        TCGA-DD-A1EI        TCGA-DD-A1EJ 
  "5Q LOSS MUTATED"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" 
       TCGA-DD-A1EL        TCGA-DD-A39V        TCGA-DD-A39X        TCGA-DD-A39Y 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-DD-A39Z        TCGA-DD-A3A0        TCGA-DD-A3A1        TCGA-DD-A3A2 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-DD-A3A3        TCGA-DD-A3A4        TCGA-DD-A3A5        TCGA-DD-A3A6 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-DD-A3A7        TCGA-DD-A3A8        TCGA-DD-A3A9        TCGA-DD-A4NA 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-DD-A4ND        TCGA-DD-A4NE        TCGA-DD-A4NF        TCGA-DD-A4NG 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-DD-A4NH        TCGA-DD-A4NI        TCGA-DD-A4NJ        TCGA-DD-A4NK 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-DD-A4NL        TCGA-DD-A4NN        TCGA-DD-A4NO        TCGA-DD-A4NP 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-DD-A4NQ        TCGA-ED-A459        TCGA-ED-A5KG        TCGA-EP-A12J 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-EP-A3JL        TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" 
       TCGA-FV-A23B        TCGA-FV-A2QR        TCGA-FV-A3I0        TCGA-FV-A3R2 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" 
       TCGA-FV-A3R3        TCGA-FV-A495        TCGA-FV-A496        TCGA-FV-A4ZP 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED"   "5Q LOSS MUTATED" 
       TCGA-FV-A4ZQ        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-G3-A3CJ        TCGA-G3-A3CK        TCGA-G3-A5SJ        TCGA-G3-A5SK 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-G3-A5SL        TCGA-G3-A5SM 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
[1] "hr=" "1.7"
D50V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  5Q LOSS MUTATED         5        1         1          3          0          1
  5Q LOSS WILD-TYPE      40       24         1         22          3          3
                   vv
clus                STAGE IV STAGE IVA STAGE IVB
  5Q LOSS MUTATED          0         0         0
  5Q LOSS WILD-TYPE        1         1         1
D50V3, multiclass
                   vv
clus                T1 T2 T3 T4
  5Q LOSS MUTATED    6  1  6  0
  5Q LOSS WILD-TYPE 42 27 28  6
D50V4, multiclass
    clus
vv   5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  T1               6                42
  T2               1                27
  T3               6                28
  T4               0                 6
D50V5, binary
                   cls
clus                 0  1
  5Q LOSS MUTATED    6  1
  5Q LOSS WILD-TYPE 68  2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED      6    1
  5Q LOSS WILD-TYPE   68    2
   clus
vv  5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  0               6                68
  1               1                 2
                   vv
clus                M0 M1 MX
  5Q LOSS MUTATED   10  0  3
  5Q LOSS WILD-TYPE 80  2 22
D50V6, multiclass
    clus
vv   5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  M0              10                80
  M1               0                 2
  MX               3                22
D50V7, binary
                   cls
clus                 0  1
  5Q LOSS MUTATED    5  8
  5Q LOSS WILD-TYPE 39 65
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED      5    8
  5Q LOSS WILD-TYPE   39   65
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  FEMALE               5                39
  MALE                 8                65
                   vv
clus                R0 R1 R2 RX
  5Q LOSS MUTATED   10  2  0  1
  5Q LOSS WILD-TYPE 83  8  1  7
D50V8, multiclass
    clus
vv   5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  R0              10                83
  R1               2                 8
  R2               0                 1
  RX               1                 7

Clustering(51) Variable = 6P LOSS MUTATION ANALYSIS
D51V1, survival
                   sevent
clus2                0  1
  6P LOSS MUTATED    7  6
  6P LOSS WILD-TYPE 54 47
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               13               101 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
                6                47 
$`6P LOSS MUTATED`
TCGA-BC-A5W4 TCGA-CC-A3M9 TCGA-DD-A118 TCGA-DD-A11A TCGA-DD-A11C TCGA-DD-A1E9 
        9.50         0.10       112.96         2.60        21.76        90.67 
TCGA-DD-A1EC TCGA-DD-A1EE TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A39Z TCGA-DD-A3A8 
       19.76         6.67         6.02        29.16        19.73         0.36 
TCGA-DD-A4NK 
       39.75 

$`6P LOSS WILD-TYPE`
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T 
       48.99        27.91        37.32        10.13        46.78        27.52 
TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 
       27.52         2.99        25.32        23.34         1.12        69.57 
TCGA-BC-A112 TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-CC-5258 
        5.03        44.42        13.81         0.26        16.37         0.07 
TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3MA 
        2.86         3.02         3.39         4.24         3.32         0.07 
TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 
        0.10         0.13        79.73        37.74        83.57        53.29 
TCGA-DD-A119 TCGA-DD-A11B TCGA-DD-A11D TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1ED 
        7.33         0.46        51.25        79.36        66.31        75.65 
TCGA-DD-A1EF TCGA-DD-A1EH TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39X TCGA-DD-A39Y 
       12.95        49.15        13.64        21.14        55.66         5.59 
TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 
       25.81         7.66        70.06        17.59        20.12       102.74 
TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4ND TCGA-DD-A4NE 
      107.11        13.78        30.58        33.14        73.38        21.67 
TCGA-DD-A4NF TCGA-DD-A4NG TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NL 
       14.07        14.93        14.24        10.78        15.06        56.25 
TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-ED-A459 TCGA-ED-A5KG 
       29.56        61.45        93.67        12.26         0.23         0.20 
TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL 
       10.85         7.76        11.74         1.97         0.62         3.19 
TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-A3I0 
        0.43        23.01        14.40        32.45        19.07         0.20 
TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZP TCGA-FV-A4ZQ 
        6.35         0.13         0.03         0.33        60.36         0.39 
TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25X 
        1.22        51.02        53.79        28.27        30.71        58.49 
TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ 
       14.86        21.53        22.13        25.64         5.88        19.53 
TCGA-G3-A3CK TCGA-G3-A5SJ TCGA-G3-A5SK TCGA-G3-A5SL TCGA-G3-A5SM 
       19.23        11.97         9.93         7.99         4.37 

  6P LOSS MUTATED 6P LOSS WILD-TYPE 
             0.10              0.03 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
           112.96            107.11 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
            19.73             15.06 
[1] "0.1 - 113.0 (19.7)" "0.0 - 107.1 (15.1)"
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-BC-A5W4        TCGA-CC-5258        TCGA-CC-5260 
"6P LOSS WILD-TYPE"   "6P LOSS MUTATED" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-CC-5261        TCGA-CC-5262        TCGA-CC-5263        TCGA-CC-A1HT 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-CC-A3M9        TCGA-CC-A3MA        TCGA-CC-A3MB        TCGA-CC-A3MC 
  "6P LOSS MUTATED" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-DD-A113        TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-DD-A118        TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B 
  "6P LOSS MUTATED" "6P LOSS WILD-TYPE"   "6P LOSS MUTATED" "6P LOSS WILD-TYPE" 
       TCGA-DD-A11C        TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EA 
  "6P LOSS MUTATED" "6P LOSS WILD-TYPE"   "6P LOSS MUTATED" "6P LOSS WILD-TYPE" 
       TCGA-DD-A1EB        TCGA-DD-A1EC        TCGA-DD-A1ED        TCGA-DD-A1EE 
"6P LOSS WILD-TYPE"   "6P LOSS MUTATED" "6P LOSS WILD-TYPE"   "6P LOSS MUTATED" 
       TCGA-DD-A1EF        TCGA-DD-A1EH        TCGA-DD-A1EI        TCGA-DD-A1EJ 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE"   "6P LOSS MUTATED"   "6P LOSS MUTATED" 
       TCGA-DD-A1EL        TCGA-DD-A39V        TCGA-DD-A39X        TCGA-DD-A39Y 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-DD-A39Z        TCGA-DD-A3A0        TCGA-DD-A3A1        TCGA-DD-A3A2 
  "6P LOSS MUTATED" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-DD-A3A3        TCGA-DD-A3A4        TCGA-DD-A3A5        TCGA-DD-A3A6 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-DD-A3A7        TCGA-DD-A3A8        TCGA-DD-A3A9        TCGA-DD-A4NA 
"6P LOSS WILD-TYPE"   "6P LOSS MUTATED" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-DD-A4ND        TCGA-DD-A4NE        TCGA-DD-A4NF        TCGA-DD-A4NG 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-DD-A4NH        TCGA-DD-A4NI        TCGA-DD-A4NJ        TCGA-DD-A4NK 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE"   "6P LOSS MUTATED" 
       TCGA-DD-A4NL        TCGA-DD-A4NN        TCGA-DD-A4NO        TCGA-DD-A4NP 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-DD-A4NQ        TCGA-ED-A459        TCGA-ED-A5KG        TCGA-EP-A12J 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EP-A3JL        TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-FV-A23B        TCGA-FV-A2QR        TCGA-FV-A3I0        TCGA-FV-A3R2 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-FV-A3R3        TCGA-FV-A495        TCGA-FV-A496        TCGA-FV-A4ZP 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-FV-A4ZQ        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-G3-A3CJ        TCGA-G3-A3CK        TCGA-G3-A5SJ        TCGA-G3-A5SK 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-G3-A5SL        TCGA-G3-A5SM 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-BC-A5W4        TCGA-CC-5258        TCGA-CC-5260 
"6P LOSS WILD-TYPE"   "6P LOSS MUTATED" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-CC-5261        TCGA-CC-5262        TCGA-CC-5263        TCGA-CC-A1HT 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-CC-A3M9        TCGA-CC-A3MA        TCGA-CC-A3MB        TCGA-CC-A3MC 
  "6P LOSS MUTATED" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-DD-A113        TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-DD-A118        TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B 
  "6P LOSS MUTATED" "6P LOSS WILD-TYPE"   "6P LOSS MUTATED" "6P LOSS WILD-TYPE" 
       TCGA-DD-A11C        TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EA 
  "6P LOSS MUTATED" "6P LOSS WILD-TYPE"   "6P LOSS MUTATED" "6P LOSS WILD-TYPE" 
       TCGA-DD-A1EB        TCGA-DD-A1EC        TCGA-DD-A1ED        TCGA-DD-A1EE 
"6P LOSS WILD-TYPE"   "6P LOSS MUTATED" "6P LOSS WILD-TYPE"   "6P LOSS MUTATED" 
       TCGA-DD-A1EF        TCGA-DD-A1EH        TCGA-DD-A1EI        TCGA-DD-A1EJ 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE"   "6P LOSS MUTATED"   "6P LOSS MUTATED" 
       TCGA-DD-A1EL        TCGA-DD-A39V        TCGA-DD-A39X        TCGA-DD-A39Y 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-DD-A39Z        TCGA-DD-A3A0        TCGA-DD-A3A1        TCGA-DD-A3A2 
  "6P LOSS MUTATED" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-DD-A3A3        TCGA-DD-A3A4        TCGA-DD-A3A5        TCGA-DD-A3A6 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-DD-A3A7        TCGA-DD-A3A8        TCGA-DD-A3A9        TCGA-DD-A4NA 
"6P LOSS WILD-TYPE"   "6P LOSS MUTATED" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-DD-A4ND        TCGA-DD-A4NE        TCGA-DD-A4NF        TCGA-DD-A4NG 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-DD-A4NH        TCGA-DD-A4NI        TCGA-DD-A4NJ        TCGA-DD-A4NK 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE"   "6P LOSS MUTATED" 
       TCGA-DD-A4NL        TCGA-DD-A4NN        TCGA-DD-A4NO        TCGA-DD-A4NP 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-DD-A4NQ        TCGA-ED-A459        TCGA-ED-A5KG        TCGA-EP-A12J 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EP-A3JL        TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-FV-A23B        TCGA-FV-A2QR        TCGA-FV-A3I0        TCGA-FV-A3R2 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-FV-A3R3        TCGA-FV-A495        TCGA-FV-A496        TCGA-FV-A4ZP 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-FV-A4ZQ        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-G3-A3CJ        TCGA-G3-A3CK        TCGA-G3-A5SJ        TCGA-G3-A5SK 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-G3-A5SL        TCGA-G3-A5SM 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-BC-A5W4        TCGA-CC-5258        TCGA-CC-5260 
"6P LOSS WILD-TYPE"   "6P LOSS MUTATED" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-CC-5261        TCGA-CC-5262        TCGA-CC-5263        TCGA-CC-A1HT 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-CC-A3M9        TCGA-CC-A3MA        TCGA-CC-A3MB        TCGA-CC-A3MC 
  "6P LOSS MUTATED" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-DD-A113        TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-DD-A118        TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B 
  "6P LOSS MUTATED" "6P LOSS WILD-TYPE"   "6P LOSS MUTATED" "6P LOSS WILD-TYPE" 
       TCGA-DD-A11C        TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EA 
  "6P LOSS MUTATED" "6P LOSS WILD-TYPE"   "6P LOSS MUTATED" "6P LOSS WILD-TYPE" 
       TCGA-DD-A1EB        TCGA-DD-A1EC        TCGA-DD-A1ED        TCGA-DD-A1EE 
"6P LOSS WILD-TYPE"   "6P LOSS MUTATED" "6P LOSS WILD-TYPE"   "6P LOSS MUTATED" 
       TCGA-DD-A1EF        TCGA-DD-A1EH        TCGA-DD-A1EI        TCGA-DD-A1EJ 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE"   "6P LOSS MUTATED"   "6P LOSS MUTATED" 
       TCGA-DD-A1EL        TCGA-DD-A39V        TCGA-DD-A39X        TCGA-DD-A39Y 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-DD-A39Z        TCGA-DD-A3A0        TCGA-DD-A3A1        TCGA-DD-A3A2 
  "6P LOSS MUTATED" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-DD-A3A3        TCGA-DD-A3A4        TCGA-DD-A3A5        TCGA-DD-A3A6 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-DD-A3A7        TCGA-DD-A3A8        TCGA-DD-A3A9        TCGA-DD-A4NA 
"6P LOSS WILD-TYPE"   "6P LOSS MUTATED" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-DD-A4ND        TCGA-DD-A4NE        TCGA-DD-A4NF        TCGA-DD-A4NG 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-DD-A4NH        TCGA-DD-A4NI        TCGA-DD-A4NJ        TCGA-DD-A4NK 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE"   "6P LOSS MUTATED" 
       TCGA-DD-A4NL        TCGA-DD-A4NN        TCGA-DD-A4NO        TCGA-DD-A4NP 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-DD-A4NQ        TCGA-ED-A459        TCGA-ED-A5KG        TCGA-EP-A12J 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EP-A3JL        TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-FV-A23B        TCGA-FV-A2QR        TCGA-FV-A3I0        TCGA-FV-A3R2 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-FV-A3R3        TCGA-FV-A495        TCGA-FV-A496        TCGA-FV-A4ZP 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-FV-A4ZQ        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-G3-A3CJ        TCGA-G3-A3CK        TCGA-G3-A5SJ        TCGA-G3-A5SK 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-G3-A5SL        TCGA-G3-A5SM 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
[1] "hr=" "1.2"
D51V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  6P LOSS MUTATED         5        3         0          4          0          1
  6P LOSS WILD-TYPE      40       22         2         21          3          3
                   vv
clus                STAGE IV STAGE IVA STAGE IVB
  6P LOSS MUTATED          0         0         0
  6P LOSS WILD-TYPE        1         1         1
D51V3, multiclass
                   vv
clus                T1 T2 T3 T4
  6P LOSS MUTATED    6  3  4  0
  6P LOSS WILD-TYPE 42 25 30  6
D51V4, multiclass
    clus
vv   6P LOSS MUTATED 6P LOSS WILD-TYPE
  T1               6                42
  T2               3                25
  T3               4                30
  T4               0                 6
D51V5, binary
                   cls
clus                 0  1
  6P LOSS MUTATED   10  1
  6P LOSS WILD-TYPE 64  2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED     10    1
  6P LOSS WILD-TYPE   64    2
   clus
vv  6P LOSS MUTATED 6P LOSS WILD-TYPE
  0              10                64
  1               1                 2
                   vv
clus                M0 M1 MX
  6P LOSS MUTATED   13  0  0
  6P LOSS WILD-TYPE 77  2 25
D51V6, multiclass
    clus
vv   6P LOSS MUTATED 6P LOSS WILD-TYPE
  M0              13                77
  M1               0                 2
  MX               0                25
D51V7, binary
                   cls
clus                 0  1
  6P LOSS MUTATED    5  8
  6P LOSS WILD-TYPE 39 65
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED      5    8
  6P LOSS WILD-TYPE   39   65
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  FEMALE               5                39
  MALE                 8                65
                   vv
clus                R0 R1 R2 RX
  6P LOSS MUTATED   11  1  0  1
  6P LOSS WILD-TYPE 82  9  1  7
D51V8, multiclass
    clus
vv   6P LOSS MUTATED 6P LOSS WILD-TYPE
  R0              11                82
  R1               1                 9
  R2               0                 1
  RX               1                 7

Clustering(52) Variable = 6Q LOSS MUTATION ANALYSIS
D52V1, survival
                   sevent
clus2                0  1
  6Q LOSS MUTATED   21 14
  6Q LOSS WILD-TYPE 40 39
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               35                79 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               14                39 
$`6Q LOSS MUTATED`
TCGA-BC-A10Q TCGA-BC-A3KF TCGA-BC-A5W4 TCGA-CC-5260 TCGA-CC-A3M9 TCGA-CC-A3MA 
       37.32         0.26         9.50         2.86         0.10         0.07 
TCGA-DD-A118 TCGA-DD-A11A TCGA-DD-A11C TCGA-DD-A1E9 TCGA-DD-A1EC TCGA-DD-A1EE 
      112.96         2.60        21.76        90.67        19.76         6.67 
TCGA-DD-A1EF TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A39X TCGA-DD-A39Z TCGA-DD-A3A1 
       12.95         6.02        29.16        55.66        19.73         7.66 
TCGA-DD-A3A8 TCGA-DD-A4NA TCGA-DD-A4NG TCGA-DD-A4NH TCGA-DD-A4NJ TCGA-DD-A4NK 
        0.36        33.14        14.93        14.24        15.06        39.75 
TCGA-EP-A12J TCGA-EP-A3RK TCGA-ES-A2HS TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-A3I0 
       10.85         0.43        23.01        32.45        19.07         0.20 
TCGA-FV-A3R2 TCGA-FV-A4ZP TCGA-G3-A25T TCGA-G3-A25X TCGA-G3-A5SL 
        6.35        60.36        51.02        58.49         7.99 

$`6Q LOSS WILD-TYPE`
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U 
       48.99        27.91        10.13        46.78        27.52        27.52 
TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 
        2.99        25.32        23.34         1.12        69.57         5.03 
TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KG TCGA-CC-5258 TCGA-CC-5261 TCGA-CC-5262 
       44.42        13.81        16.37         0.07         3.02         3.39 
TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A113 TCGA-DD-A114 
        4.24         3.32         0.10         0.13        79.73        37.74 
TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A119 TCGA-DD-A11B TCGA-DD-A11D TCGA-DD-A1EA 
       83.57        53.29         7.33         0.46        51.25        79.36 
TCGA-DD-A1EB TCGA-DD-A1ED TCGA-DD-A1EH TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39Y 
       66.31        75.65        49.15        13.64        21.14         5.59 
TCGA-DD-A3A0 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 
       25.81        70.06        17.59        20.12       102.74       107.11 
TCGA-DD-A3A7 TCGA-DD-A3A9 TCGA-DD-A4ND TCGA-DD-A4NE TCGA-DD-A4NF TCGA-DD-A4NI 
       13.78        30.58        73.38        21.67        14.07        10.78 
TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-ED-A459 
       56.25        29.56        61.45        93.67        12.26         0.23 
TCGA-ED-A5KG TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL 
        0.20         7.76        11.74         1.97         0.62         3.19 
TCGA-ES-A2HT TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZQ TCGA-G3-A25S 
       14.40         0.13         0.03         0.33         0.39         1.22 
TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG 
       53.79        28.27        30.71        14.86        21.53        22.13 
TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SJ TCGA-G3-A5SK 
       25.64         5.88        19.53        19.23        11.97         9.93 
TCGA-G3-A5SM 
        4.37 

  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
             0.07              0.03 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
           112.96            107.11 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
            14.93             17.59 
[1] "0.1 - 113.0 (14.9)" "0.0 - 107.1 (17.6)"
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" 
       TCGA-BC-A3KG        TCGA-BC-A5W4        TCGA-CC-5258        TCGA-CC-5260 
"6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" 
       TCGA-CC-5261        TCGA-CC-5262        TCGA-CC-5263        TCGA-CC-A1HT 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-CC-A3M9        TCGA-CC-A3MA        TCGA-CC-A3MB        TCGA-CC-A3MC 
  "6Q LOSS MUTATED"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-DD-A113        TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-DD-A118        TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B 
  "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" 
       TCGA-DD-A11C        TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EA 
  "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" 
       TCGA-DD-A1EB        TCGA-DD-A1EC        TCGA-DD-A1ED        TCGA-DD-A1EE 
"6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" 
       TCGA-DD-A1EF        TCGA-DD-A1EH        TCGA-DD-A1EI        TCGA-DD-A1EJ 
  "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED"   "6Q LOSS MUTATED" 
       TCGA-DD-A1EL        TCGA-DD-A39V        TCGA-DD-A39X        TCGA-DD-A39Y 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" 
       TCGA-DD-A39Z        TCGA-DD-A3A0        TCGA-DD-A3A1        TCGA-DD-A3A2 
  "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" 
       TCGA-DD-A3A3        TCGA-DD-A3A4        TCGA-DD-A3A5        TCGA-DD-A3A6 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-DD-A3A7        TCGA-DD-A3A8        TCGA-DD-A3A9        TCGA-DD-A4NA 
"6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" 
       TCGA-DD-A4ND        TCGA-DD-A4NE        TCGA-DD-A4NF        TCGA-DD-A4NG 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" 
       TCGA-DD-A4NH        TCGA-DD-A4NI        TCGA-DD-A4NJ        TCGA-DD-A4NK 
  "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED"   "6Q LOSS MUTATED" 
       TCGA-DD-A4NL        TCGA-DD-A4NN        TCGA-DD-A4NO        TCGA-DD-A4NP 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-DD-A4NQ        TCGA-ED-A459        TCGA-ED-A5KG        TCGA-EP-A12J 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" 
       TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-EP-A3JL        TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT 
"6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" 
       TCGA-FV-A23B        TCGA-FV-A2QR        TCGA-FV-A3I0        TCGA-FV-A3R2 
  "6Q LOSS MUTATED"   "6Q LOSS MUTATED"   "6Q LOSS MUTATED"   "6Q LOSS MUTATED" 
       TCGA-FV-A3R3        TCGA-FV-A495        TCGA-FV-A496        TCGA-FV-A4ZP 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" 
       TCGA-FV-A4ZQ        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-G3-A3CJ        TCGA-G3-A3CK        TCGA-G3-A5SJ        TCGA-G3-A5SK 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-G3-A5SL        TCGA-G3-A5SM 
  "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" 
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" 
       TCGA-BC-A3KG        TCGA-BC-A5W4        TCGA-CC-5258        TCGA-CC-5260 
"6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" 
       TCGA-CC-5261        TCGA-CC-5262        TCGA-CC-5263        TCGA-CC-A1HT 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-CC-A3M9        TCGA-CC-A3MA        TCGA-CC-A3MB        TCGA-CC-A3MC 
  "6Q LOSS MUTATED"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-DD-A113        TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-DD-A118        TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B 
  "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" 
       TCGA-DD-A11C        TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EA 
  "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" 
       TCGA-DD-A1EB        TCGA-DD-A1EC        TCGA-DD-A1ED        TCGA-DD-A1EE 
"6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" 
       TCGA-DD-A1EF        TCGA-DD-A1EH        TCGA-DD-A1EI        TCGA-DD-A1EJ 
  "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED"   "6Q LOSS MUTATED" 
       TCGA-DD-A1EL        TCGA-DD-A39V        TCGA-DD-A39X        TCGA-DD-A39Y 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" 
       TCGA-DD-A39Z        TCGA-DD-A3A0        TCGA-DD-A3A1        TCGA-DD-A3A2 
  "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" 
       TCGA-DD-A3A3        TCGA-DD-A3A4        TCGA-DD-A3A5        TCGA-DD-A3A6 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-DD-A3A7        TCGA-DD-A3A8        TCGA-DD-A3A9        TCGA-DD-A4NA 
"6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" 
       TCGA-DD-A4ND        TCGA-DD-A4NE        TCGA-DD-A4NF        TCGA-DD-A4NG 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" 
       TCGA-DD-A4NH        TCGA-DD-A4NI        TCGA-DD-A4NJ        TCGA-DD-A4NK 
  "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED"   "6Q LOSS MUTATED" 
       TCGA-DD-A4NL        TCGA-DD-A4NN        TCGA-DD-A4NO        TCGA-DD-A4NP 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-DD-A4NQ        TCGA-ED-A459        TCGA-ED-A5KG        TCGA-EP-A12J 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" 
       TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-EP-A3JL        TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT 
"6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" 
       TCGA-FV-A23B        TCGA-FV-A2QR        TCGA-FV-A3I0        TCGA-FV-A3R2 
  "6Q LOSS MUTATED"   "6Q LOSS MUTATED"   "6Q LOSS MUTATED"   "6Q LOSS MUTATED" 
       TCGA-FV-A3R3        TCGA-FV-A495        TCGA-FV-A496        TCGA-FV-A4ZP 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" 
       TCGA-FV-A4ZQ        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-G3-A3CJ        TCGA-G3-A3CK        TCGA-G3-A5SJ        TCGA-G3-A5SK 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-G3-A5SL        TCGA-G3-A5SM 
  "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" 
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" 
       TCGA-BC-A3KG        TCGA-BC-A5W4        TCGA-CC-5258        TCGA-CC-5260 
"6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" 
       TCGA-CC-5261        TCGA-CC-5262        TCGA-CC-5263        TCGA-CC-A1HT 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-CC-A3M9        TCGA-CC-A3MA        TCGA-CC-A3MB        TCGA-CC-A3MC 
  "6Q LOSS MUTATED"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-DD-A113        TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-DD-A118        TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B 
  "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" 
       TCGA-DD-A11C        TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EA 
  "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" 
       TCGA-DD-A1EB        TCGA-DD-A1EC        TCGA-DD-A1ED        TCGA-DD-A1EE 
"6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" 
       TCGA-DD-A1EF        TCGA-DD-A1EH        TCGA-DD-A1EI        TCGA-DD-A1EJ 
  "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED"   "6Q LOSS MUTATED" 
       TCGA-DD-A1EL        TCGA-DD-A39V        TCGA-DD-A39X        TCGA-DD-A39Y 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" 
       TCGA-DD-A39Z        TCGA-DD-A3A0        TCGA-DD-A3A1        TCGA-DD-A3A2 
  "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" 
       TCGA-DD-A3A3        TCGA-DD-A3A4        TCGA-DD-A3A5        TCGA-DD-A3A6 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-DD-A3A7        TCGA-DD-A3A8        TCGA-DD-A3A9        TCGA-DD-A4NA 
"6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" 
       TCGA-DD-A4ND        TCGA-DD-A4NE        TCGA-DD-A4NF        TCGA-DD-A4NG 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" 
       TCGA-DD-A4NH        TCGA-DD-A4NI        TCGA-DD-A4NJ        TCGA-DD-A4NK 
  "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED"   "6Q LOSS MUTATED" 
       TCGA-DD-A4NL        TCGA-DD-A4NN        TCGA-DD-A4NO        TCGA-DD-A4NP 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-DD-A4NQ        TCGA-ED-A459        TCGA-ED-A5KG        TCGA-EP-A12J 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" 
       TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-EP-A3JL        TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT 
"6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" 
       TCGA-FV-A23B        TCGA-FV-A2QR        TCGA-FV-A3I0        TCGA-FV-A3R2 
  "6Q LOSS MUTATED"   "6Q LOSS MUTATED"   "6Q LOSS MUTATED"   "6Q LOSS MUTATED" 
       TCGA-FV-A3R3        TCGA-FV-A495        TCGA-FV-A496        TCGA-FV-A4ZP 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" 
       TCGA-FV-A4ZQ        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-G3-A3CJ        TCGA-G3-A3CK        TCGA-G3-A5SJ        TCGA-G3-A5SK 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-G3-A5SL        TCGA-G3-A5SM 
  "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" 
[1] "hr=" "1.1"
D52V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  6Q LOSS MUTATED        12        7         0         10          1          3
  6Q LOSS WILD-TYPE      33       18         2         15          2          1
                   vv
clus                STAGE IV STAGE IVA STAGE IVB
  6Q LOSS MUTATED          0         0         0
  6Q LOSS WILD-TYPE        1         1         1
D52V3, multiclass
                   vv
clus                T1 T2 T3 T4
  6Q LOSS MUTATED   13  9 11  1
  6Q LOSS WILD-TYPE 35 19 23  5
D52V4, multiclass
    clus
vv   6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  T1              13                35
  T2               9                19
  T3              11                23
  T4               1                 5
D52V5, binary
                   cls
clus                 0  1
  6Q LOSS MUTATED   20  2
  6Q LOSS WILD-TYPE 54  1
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED     20    2
  6Q LOSS WILD-TYPE   54    1
   clus
vv  6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  0              20                54
  1               2                 1
                   vv
clus                M0 M1 MX
  6Q LOSS MUTATED   30  0  5
  6Q LOSS WILD-TYPE 60  2 20
D52V6, multiclass
    clus
vv   6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  M0              30                60
  M1               0                 2
  MX               5                20
D52V7, binary
                   cls
clus                 0  1
  6Q LOSS MUTATED   16 19
  6Q LOSS WILD-TYPE 28 54
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED     16   19
  6Q LOSS WILD-TYPE   28   54
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  FEMALE              16                28
  MALE                19                54
                   vv
clus                R0 R1 R2 RX
  6Q LOSS MUTATED   28  3  0  3
  6Q LOSS WILD-TYPE 65  7  1  5
D52V8, multiclass
    clus
vv   6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  R0              28                65
  R1               3                 7
  R2               0                 1
  RX               3                 5

Clustering(53) Variable = 7P LOSS MUTATION ANALYSIS
D53V1, survival
                   sevent
clus2                0  1
  7P LOSS MUTATED    4  3
  7P LOSS WILD-TYPE 57 50
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
                7               107 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
                3                50 
$`7P LOSS MUTATED`
TCGA-BC-A217 TCGA-BC-A3KG TCGA-CC-5261 TCGA-CC-A3M9 TCGA-DD-A1EF TCGA-DD-A39X 
       13.81        16.37         3.02         0.10        12.95        55.66 
TCGA-EP-A2KB 
        1.97 

$`7P LOSS WILD-TYPE`
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T 
       48.99        27.91        37.32        10.13        46.78        27.52 
TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 
       27.52         2.99        25.32        23.34         1.12        69.57 
TCGA-BC-A112 TCGA-BC-A216 TCGA-BC-A3KF TCGA-BC-A5W4 TCGA-CC-5258 TCGA-CC-5260 
        5.03        44.42         0.26         9.50         0.07         2.86 
TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC 
        3.39         4.24         3.32         0.07         0.10         0.13 
TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 
       79.73        37.74        83.57        53.29       112.96         7.33 
TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA 
        2.60         0.46        21.76        51.25        90.67        79.36 
TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EH TCGA-DD-A1EI 
       66.31        19.76        75.65         6.67        49.15         6.02 
TCGA-DD-A1EJ TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A0 
       29.16        13.64        21.14         5.59        19.73        25.81 
TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 
        7.66        70.06        17.59        20.12       102.74       107.11 
TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4ND TCGA-DD-A4NE 
       13.78         0.36        30.58        33.14        73.38        21.67 
TCGA-DD-A4NF TCGA-DD-A4NG TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK 
       14.07        14.93        14.24        10.78        15.06        39.75 
TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-ED-A459 
       56.25        29.56        61.45        93.67        12.26         0.23 
TCGA-ED-A5KG TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KC TCGA-EP-A3JL 
        0.20        10.85         7.76        11.74         0.62         3.19 
TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-A3I0 
        0.43        23.01        14.40        32.45        19.07         0.20 
TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZP TCGA-FV-A4ZQ 
        6.35         0.13         0.03         0.33        60.36         0.39 
TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25X 
        1.22        51.02        53.79        28.27        30.71        58.49 
TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ 
       14.86        21.53        22.13        25.64         5.88        19.53 
TCGA-G3-A3CK TCGA-G3-A5SJ TCGA-G3-A5SK TCGA-G3-A5SL TCGA-G3-A5SM 
       19.23        11.97         9.93         7.99         4.37 

  7P LOSS MUTATED 7P LOSS WILD-TYPE 
             0.10              0.03 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
            55.66            112.96 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
            12.95             19.07 
[1] "0.1 - 55.7 (12.9)"  "0.0 - 113.0 (19.1)"
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE"   "7P LOSS MUTATED" "7P LOSS WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-BC-A5W4        TCGA-CC-5258        TCGA-CC-5260 
  "7P LOSS MUTATED" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-CC-5261        TCGA-CC-5262        TCGA-CC-5263        TCGA-CC-A1HT 
  "7P LOSS MUTATED" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-CC-A3M9        TCGA-CC-A3MA        TCGA-CC-A3MB        TCGA-CC-A3MC 
  "7P LOSS MUTATED" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DD-A113        TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DD-A118        TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DD-A11C        TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EA 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DD-A1EB        TCGA-DD-A1EC        TCGA-DD-A1ED        TCGA-DD-A1EE 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DD-A1EF        TCGA-DD-A1EH        TCGA-DD-A1EI        TCGA-DD-A1EJ 
  "7P LOSS MUTATED" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DD-A1EL        TCGA-DD-A39V        TCGA-DD-A39X        TCGA-DD-A39Y 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE"   "7P LOSS MUTATED" "7P LOSS WILD-TYPE" 
       TCGA-DD-A39Z        TCGA-DD-A3A0        TCGA-DD-A3A1        TCGA-DD-A3A2 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DD-A3A3        TCGA-DD-A3A4        TCGA-DD-A3A5        TCGA-DD-A3A6 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DD-A3A7        TCGA-DD-A3A8        TCGA-DD-A3A9        TCGA-DD-A4NA 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DD-A4ND        TCGA-DD-A4NE        TCGA-DD-A4NF        TCGA-DD-A4NG 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DD-A4NH        TCGA-DD-A4NI        TCGA-DD-A4NJ        TCGA-DD-A4NK 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DD-A4NL        TCGA-DD-A4NN        TCGA-DD-A4NO        TCGA-DD-A4NP 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DD-A4NQ        TCGA-ED-A459        TCGA-ED-A5KG        TCGA-EP-A12J 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE"   "7P LOSS MUTATED" "7P LOSS WILD-TYPE" 
       TCGA-EP-A3JL        TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-FV-A23B        TCGA-FV-A2QR        TCGA-FV-A3I0        TCGA-FV-A3R2 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-FV-A3R3        TCGA-FV-A495        TCGA-FV-A496        TCGA-FV-A4ZP 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-FV-A4ZQ        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-G3-A3CJ        TCGA-G3-A3CK        TCGA-G3-A5SJ        TCGA-G3-A5SK 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-G3-A5SL        TCGA-G3-A5SM 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE"   "7P LOSS MUTATED" "7P LOSS WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-BC-A5W4        TCGA-CC-5258        TCGA-CC-5260 
  "7P LOSS MUTATED" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-CC-5261        TCGA-CC-5262        TCGA-CC-5263        TCGA-CC-A1HT 
  "7P LOSS MUTATED" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-CC-A3M9        TCGA-CC-A3MA        TCGA-CC-A3MB        TCGA-CC-A3MC 
  "7P LOSS MUTATED" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DD-A113        TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DD-A118        TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DD-A11C        TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EA 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DD-A1EB        TCGA-DD-A1EC        TCGA-DD-A1ED        TCGA-DD-A1EE 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DD-A1EF        TCGA-DD-A1EH        TCGA-DD-A1EI        TCGA-DD-A1EJ 
  "7P LOSS MUTATED" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DD-A1EL        TCGA-DD-A39V        TCGA-DD-A39X        TCGA-DD-A39Y 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE"   "7P LOSS MUTATED" "7P LOSS WILD-TYPE" 
       TCGA-DD-A39Z        TCGA-DD-A3A0        TCGA-DD-A3A1        TCGA-DD-A3A2 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DD-A3A3        TCGA-DD-A3A4        TCGA-DD-A3A5        TCGA-DD-A3A6 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DD-A3A7        TCGA-DD-A3A8        TCGA-DD-A3A9        TCGA-DD-A4NA 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DD-A4ND        TCGA-DD-A4NE        TCGA-DD-A4NF        TCGA-DD-A4NG 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DD-A4NH        TCGA-DD-A4NI        TCGA-DD-A4NJ        TCGA-DD-A4NK 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DD-A4NL        TCGA-DD-A4NN        TCGA-DD-A4NO        TCGA-DD-A4NP 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DD-A4NQ        TCGA-ED-A459        TCGA-ED-A5KG        TCGA-EP-A12J 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE"   "7P LOSS MUTATED" "7P LOSS WILD-TYPE" 
       TCGA-EP-A3JL        TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-FV-A23B        TCGA-FV-A2QR        TCGA-FV-A3I0        TCGA-FV-A3R2 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-FV-A3R3        TCGA-FV-A495        TCGA-FV-A496        TCGA-FV-A4ZP 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-FV-A4ZQ        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-G3-A3CJ        TCGA-G3-A3CK        TCGA-G3-A5SJ        TCGA-G3-A5SK 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-G3-A5SL        TCGA-G3-A5SM 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE"   "7P LOSS MUTATED" "7P LOSS WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-BC-A5W4        TCGA-CC-5258        TCGA-CC-5260 
  "7P LOSS MUTATED" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-CC-5261        TCGA-CC-5262        TCGA-CC-5263        TCGA-CC-A1HT 
  "7P LOSS MUTATED" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-CC-A3M9        TCGA-CC-A3MA        TCGA-CC-A3MB        TCGA-CC-A3MC 
  "7P LOSS MUTATED" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DD-A113        TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DD-A118        TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DD-A11C        TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EA 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DD-A1EB        TCGA-DD-A1EC        TCGA-DD-A1ED        TCGA-DD-A1EE 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DD-A1EF        TCGA-DD-A1EH        TCGA-DD-A1EI        TCGA-DD-A1EJ 
  "7P LOSS MUTATED" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DD-A1EL        TCGA-DD-A39V        TCGA-DD-A39X        TCGA-DD-A39Y 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE"   "7P LOSS MUTATED" "7P LOSS WILD-TYPE" 
       TCGA-DD-A39Z        TCGA-DD-A3A0        TCGA-DD-A3A1        TCGA-DD-A3A2 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DD-A3A3        TCGA-DD-A3A4        TCGA-DD-A3A5        TCGA-DD-A3A6 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DD-A3A7        TCGA-DD-A3A8        TCGA-DD-A3A9        TCGA-DD-A4NA 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DD-A4ND        TCGA-DD-A4NE        TCGA-DD-A4NF        TCGA-DD-A4NG 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DD-A4NH        TCGA-DD-A4NI        TCGA-DD-A4NJ        TCGA-DD-A4NK 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DD-A4NL        TCGA-DD-A4NN        TCGA-DD-A4NO        TCGA-DD-A4NP 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DD-A4NQ        TCGA-ED-A459        TCGA-ED-A5KG        TCGA-EP-A12J 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE"   "7P LOSS MUTATED" "7P LOSS WILD-TYPE" 
       TCGA-EP-A3JL        TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-FV-A23B        TCGA-FV-A2QR        TCGA-FV-A3I0        TCGA-FV-A3R2 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-FV-A3R3        TCGA-FV-A495        TCGA-FV-A496        TCGA-FV-A4ZP 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-FV-A4ZQ        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-G3-A3CJ        TCGA-G3-A3CK        TCGA-G3-A5SJ        TCGA-G3-A5SK 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-G3-A5SL        TCGA-G3-A5SM 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
[1] "hr=" "1.6"
D53V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  7P LOSS MUTATED         3        4         0          1          0          0
  7P LOSS WILD-TYPE      42       21         2         24          3          4
                   vv
clus                STAGE IV STAGE IVA STAGE IVB
  7P LOSS MUTATED          0         0         0
  7P LOSS WILD-TYPE        1         1         1
D53V3, multiclass
                   vv
clus                T1 T2 T3 T4
  7P LOSS MUTATED    3  4  1  0
  7P LOSS WILD-TYPE 45 24 33  6
D53V4, multiclass
    clus
vv   7P LOSS MUTATED 7P LOSS WILD-TYPE
  T1               3                45
  T2               4                24
  T3               1                33
  T4               0                 6
D53V5, binary
                   cls
clus                 0  1
  7P LOSS MUTATED    5  0
  7P LOSS WILD-TYPE 69  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED      5    0
  7P LOSS WILD-TYPE   69    3
   clus
vv  7P LOSS MUTATED 7P LOSS WILD-TYPE
  0               5                69
  1               0                 3
                   vv
clus                M0 M1 MX
  7P LOSS MUTATED    6  0  2
  7P LOSS WILD-TYPE 84  2 23
D53V6, multiclass
    clus
vv   7P LOSS MUTATED 7P LOSS WILD-TYPE
  M0               6                84
  M1               0                 2
  MX               2                23
D53V7, binary
                   cls
clus                 0  1
  7P LOSS MUTATED    6  2
  7P LOSS WILD-TYPE 38 71
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED      6    2
  7P LOSS WILD-TYPE   38   71
        clus
vv       7P LOSS MUTATED 7P LOSS WILD-TYPE
  FEMALE               6                38
  MALE                 2                71
                   vv
clus                R0 R1 R2 RX
  7P LOSS MUTATED    7  0  0  1
  7P LOSS WILD-TYPE 86 10  1  7
D53V8, multiclass
    clus
vv   7P LOSS MUTATED 7P LOSS WILD-TYPE
  R0               7                86
  R1               0                10
  R2               0                 1
  RX               1                 7

Clustering(54) Variable = 7Q LOSS MUTATION ANALYSIS
D54V1, survival
                   sevent
clus2                0  1
  7Q LOSS MUTATED    5  6
  7Q LOSS WILD-TYPE 56 47
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
               11               103 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
                6                47 
$`7Q LOSS MUTATED`
TCGA-BC-4072 TCGA-BC-A217 TCGA-BC-A3KG TCGA-CC-5261 TCGA-DD-A1EF TCGA-DD-A1EL 
       48.99        13.81        16.37         3.02        12.95        13.64 
TCGA-DD-A39X TCGA-DD-A4ND TCGA-EP-A2KB TCGA-FV-A496 TCGA-G3-A25S 
       55.66        73.38         1.97         0.33         1.22 

$`7Q LOSS WILD-TYPE`
TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U 
       27.91        37.32        10.13        46.78        27.52        27.52 
TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 
        2.99        25.32        23.34         1.12        69.57         5.03 
TCGA-BC-A216 TCGA-BC-A3KF TCGA-BC-A5W4 TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5262 
       44.42         0.26         9.50         0.07         2.86         3.39 
TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC 
        4.24         3.32         0.10         0.07         0.10         0.13 
TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 
       79.73        37.74        83.57        53.29       112.96         7.33 
TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA 
        2.60         0.46        21.76        51.25        90.67        79.36 
TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EH TCGA-DD-A1EI 
       66.31        19.76        75.65         6.67        49.15         6.02 
TCGA-DD-A1EJ TCGA-DD-A39V TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 
       29.16        21.14         5.59        19.73        25.81         7.66 
TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 
       70.06        17.59        20.12       102.74       107.11        13.78 
TCGA-DD-A3A8 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NE TCGA-DD-A4NF TCGA-DD-A4NG 
        0.36        30.58        33.14        21.67        14.07        14.93 
TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN 
       14.24        10.78        15.06        39.75        56.25        29.56 
TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-ED-A459 TCGA-ED-A5KG TCGA-EP-A12J 
       61.45        93.67        12.26         0.23         0.20        10.85 
TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS 
        7.76        11.74         0.62         3.19         0.43        23.01 
TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3R2 TCGA-FV-A3R3 
       14.40        32.45        19.07         0.20         6.35         0.13 
TCGA-FV-A495 TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V 
        0.03        60.36         0.39        51.02        53.79        28.27 
TCGA-G3-A25W TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CH 
       30.71        58.49        14.86        21.53        22.13        25.64 
TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SJ TCGA-G3-A5SK TCGA-G3-A5SL 
        5.88        19.53        19.23        11.97         9.93         7.99 
TCGA-G3-A5SM 
        4.37 

  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
             0.33              0.03 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
            73.38            112.96 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
            13.64             19.07 
[1] "0.3 - 73.4 (13.6)"  "0.0 - 113.0 (19.1)"
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
  "7Q LOSS MUTATED" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE"   "7Q LOSS MUTATED" "7Q LOSS WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-BC-A5W4        TCGA-CC-5258        TCGA-CC-5260 
  "7Q LOSS MUTATED" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-CC-5261        TCGA-CC-5262        TCGA-CC-5263        TCGA-CC-A1HT 
  "7Q LOSS MUTATED" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-CC-A3M9        TCGA-CC-A3MA        TCGA-CC-A3MB        TCGA-CC-A3MC 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-DD-A113        TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-DD-A118        TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-DD-A11C        TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EA 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-DD-A1EB        TCGA-DD-A1EC        TCGA-DD-A1ED        TCGA-DD-A1EE 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-DD-A1EF        TCGA-DD-A1EH        TCGA-DD-A1EI        TCGA-DD-A1EJ 
  "7Q LOSS MUTATED" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-DD-A1EL        TCGA-DD-A39V        TCGA-DD-A39X        TCGA-DD-A39Y 
  "7Q LOSS MUTATED" "7Q LOSS WILD-TYPE"   "7Q LOSS MUTATED" "7Q LOSS WILD-TYPE" 
       TCGA-DD-A39Z        TCGA-DD-A3A0        TCGA-DD-A3A1        TCGA-DD-A3A2 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-DD-A3A3        TCGA-DD-A3A4        TCGA-DD-A3A5        TCGA-DD-A3A6 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-DD-A3A7        TCGA-DD-A3A8        TCGA-DD-A3A9        TCGA-DD-A4NA 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-DD-A4ND        TCGA-DD-A4NE        TCGA-DD-A4NF        TCGA-DD-A4NG 
  "7Q LOSS MUTATED" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-DD-A4NH        TCGA-DD-A4NI        TCGA-DD-A4NJ        TCGA-DD-A4NK 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-DD-A4NL        TCGA-DD-A4NN        TCGA-DD-A4NO        TCGA-DD-A4NP 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-DD-A4NQ        TCGA-ED-A459        TCGA-ED-A5KG        TCGA-EP-A12J 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE"   "7Q LOSS MUTATED" "7Q LOSS WILD-TYPE" 
       TCGA-EP-A3JL        TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-FV-A23B        TCGA-FV-A2QR        TCGA-FV-A3I0        TCGA-FV-A3R2 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-FV-A3R3        TCGA-FV-A495        TCGA-FV-A496        TCGA-FV-A4ZP 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE"   "7Q LOSS MUTATED" "7Q LOSS WILD-TYPE" 
       TCGA-FV-A4ZQ        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"7Q LOSS WILD-TYPE"   "7Q LOSS MUTATED" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-G3-A3CJ        TCGA-G3-A3CK        TCGA-G3-A5SJ        TCGA-G3-A5SK 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-G3-A5SL        TCGA-G3-A5SM 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
  "7Q LOSS MUTATED" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE"   "7Q LOSS MUTATED" "7Q LOSS WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-BC-A5W4        TCGA-CC-5258        TCGA-CC-5260 
  "7Q LOSS MUTATED" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-CC-5261        TCGA-CC-5262        TCGA-CC-5263        TCGA-CC-A1HT 
  "7Q LOSS MUTATED" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-CC-A3M9        TCGA-CC-A3MA        TCGA-CC-A3MB        TCGA-CC-A3MC 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-DD-A113        TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-DD-A118        TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-DD-A11C        TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EA 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-DD-A1EB        TCGA-DD-A1EC        TCGA-DD-A1ED        TCGA-DD-A1EE 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-DD-A1EF        TCGA-DD-A1EH        TCGA-DD-A1EI        TCGA-DD-A1EJ 
  "7Q LOSS MUTATED" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-DD-A1EL        TCGA-DD-A39V        TCGA-DD-A39X        TCGA-DD-A39Y 
  "7Q LOSS MUTATED" "7Q LOSS WILD-TYPE"   "7Q LOSS MUTATED" "7Q LOSS WILD-TYPE" 
       TCGA-DD-A39Z        TCGA-DD-A3A0        TCGA-DD-A3A1        TCGA-DD-A3A2 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-DD-A3A3        TCGA-DD-A3A4        TCGA-DD-A3A5        TCGA-DD-A3A6 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-DD-A3A7        TCGA-DD-A3A8        TCGA-DD-A3A9        TCGA-DD-A4NA 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-DD-A4ND        TCGA-DD-A4NE        TCGA-DD-A4NF        TCGA-DD-A4NG 
  "7Q LOSS MUTATED" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-DD-A4NH        TCGA-DD-A4NI        TCGA-DD-A4NJ        TCGA-DD-A4NK 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-DD-A4NL        TCGA-DD-A4NN        TCGA-DD-A4NO        TCGA-DD-A4NP 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-DD-A4NQ        TCGA-ED-A459        TCGA-ED-A5KG        TCGA-EP-A12J 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE"   "7Q LOSS MUTATED" "7Q LOSS WILD-TYPE" 
       TCGA-EP-A3JL        TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-FV-A23B        TCGA-FV-A2QR        TCGA-FV-A3I0        TCGA-FV-A3R2 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-FV-A3R3        TCGA-FV-A495        TCGA-FV-A496        TCGA-FV-A4ZP 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE"   "7Q LOSS MUTATED" "7Q LOSS WILD-TYPE" 
       TCGA-FV-A4ZQ        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"7Q LOSS WILD-TYPE"   "7Q LOSS MUTATED" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-G3-A3CJ        TCGA-G3-A3CK        TCGA-G3-A5SJ        TCGA-G3-A5SK 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-G3-A5SL        TCGA-G3-A5SM 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
  "7Q LOSS MUTATED" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE"   "7Q LOSS MUTATED" "7Q LOSS WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-BC-A5W4        TCGA-CC-5258        TCGA-CC-5260 
  "7Q LOSS MUTATED" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-CC-5261        TCGA-CC-5262        TCGA-CC-5263        TCGA-CC-A1HT 
  "7Q LOSS MUTATED" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-CC-A3M9        TCGA-CC-A3MA        TCGA-CC-A3MB        TCGA-CC-A3MC 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-DD-A113        TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-DD-A118        TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-DD-A11C        TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EA 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-DD-A1EB        TCGA-DD-A1EC        TCGA-DD-A1ED        TCGA-DD-A1EE 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-DD-A1EF        TCGA-DD-A1EH        TCGA-DD-A1EI        TCGA-DD-A1EJ 
  "7Q LOSS MUTATED" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-DD-A1EL        TCGA-DD-A39V        TCGA-DD-A39X        TCGA-DD-A39Y 
  "7Q LOSS MUTATED" "7Q LOSS WILD-TYPE"   "7Q LOSS MUTATED" "7Q LOSS WILD-TYPE" 
       TCGA-DD-A39Z        TCGA-DD-A3A0        TCGA-DD-A3A1        TCGA-DD-A3A2 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-DD-A3A3        TCGA-DD-A3A4        TCGA-DD-A3A5        TCGA-DD-A3A6 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-DD-A3A7        TCGA-DD-A3A8        TCGA-DD-A3A9        TCGA-DD-A4NA 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-DD-A4ND        TCGA-DD-A4NE        TCGA-DD-A4NF        TCGA-DD-A4NG 
  "7Q LOSS MUTATED" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-DD-A4NH        TCGA-DD-A4NI        TCGA-DD-A4NJ        TCGA-DD-A4NK 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-DD-A4NL        TCGA-DD-A4NN        TCGA-DD-A4NO        TCGA-DD-A4NP 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-DD-A4NQ        TCGA-ED-A459        TCGA-ED-A5KG        TCGA-EP-A12J 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE"   "7Q LOSS MUTATED" "7Q LOSS WILD-TYPE" 
       TCGA-EP-A3JL        TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-FV-A23B        TCGA-FV-A2QR        TCGA-FV-A3I0        TCGA-FV-A3R2 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-FV-A3R3        TCGA-FV-A495        TCGA-FV-A496        TCGA-FV-A4ZP 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE"   "7Q LOSS MUTATED" "7Q LOSS WILD-TYPE" 
       TCGA-FV-A4ZQ        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"7Q LOSS WILD-TYPE"   "7Q LOSS MUTATED" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-G3-A3CJ        TCGA-G3-A3CK        TCGA-G3-A5SJ        TCGA-G3-A5SK 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-G3-A5SL        TCGA-G3-A5SM 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
[1] "hr=" "1.5"
D54V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  7Q LOSS MUTATED         6        4         0          1          0          0
  7Q LOSS WILD-TYPE      39       21         2         24          3          4
                   vv
clus                STAGE IV STAGE IVA STAGE IVB
  7Q LOSS MUTATED          0         0         0
  7Q LOSS WILD-TYPE        1         1         1
D54V3, multiclass
                   vv
clus                T1 T2 T3 T4
  7Q LOSS MUTATED    6  4  1  0
  7Q LOSS WILD-TYPE 42 24 33  6
D54V4, multiclass
    clus
vv   7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  T1               6                42
  T2               4                24
  T3               1                33
  T4               0                 6
D54V5, binary
                   cls
clus                 0  1
  7Q LOSS MUTATED    7  0
  7Q LOSS WILD-TYPE 67  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED      7    0
  7Q LOSS WILD-TYPE   67    3
   clus
vv  7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  0               7                67
  1               0                 3
                   vv
clus                M0 M1 MX
  7Q LOSS MUTATED   10  0  1
  7Q LOSS WILD-TYPE 80  2 24
D54V6, multiclass
    clus
vv   7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  M0              10                80
  M1               0                 2
  MX               1                24
D54V7, binary
                   cls
clus                 0  1
  7Q LOSS MUTATED    8  3
  7Q LOSS WILD-TYPE 36 70
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED      8    3
  7Q LOSS WILD-TYPE   36   70
        clus
vv       7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  FEMALE               8                36
  MALE                 3                70
                   vv
clus                R0 R1 R2 RX
  7Q LOSS MUTATED    8  2  0  1
  7Q LOSS WILD-TYPE 85  8  1  7
D54V8, multiclass
    clus
vv   7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  R0               8                85
  R1               2                 8
  R2               0                 1
  RX               1                 7

Clustering(55) Variable = 8P LOSS MUTATION ANALYSIS
D55V1, survival
                   sevent
clus2                0  1
  8P LOSS MUTATED   24 30
  8P LOSS WILD-TYPE 37 23
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               54                60 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               30                23 
$`8P LOSS MUTATED`
TCGA-BC-4072 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A112 
       48.99        37.32        10.13        27.52        27.52         5.03 
TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-CC-5261 TCGA-CC-5262 
       44.42        13.81         0.26        16.37         3.02         3.39 
TCGA-DD-A113 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A11C TCGA-DD-A1EE 
       79.73        83.57        53.29       112.96        21.76         6.67 
TCGA-DD-A1EJ TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A39Z 
       29.16        13.64        21.14        55.66         5.59        19.73 
TCGA-DD-A3A0 TCGA-DD-A3A3 TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A3A9 TCGA-DD-A4NA 
       25.81        17.59        13.78         0.36        30.58        33.14 
TCGA-DD-A4ND TCGA-DD-A4NE TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-EP-A12J 
       73.38        21.67        10.78        15.06        39.75        10.85 
TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KC TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT 
        7.76        11.74         0.62         0.43        23.01        14.40 
TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3R2 TCGA-FV-A495 TCGA-FV-A4ZP TCGA-FV-A4ZQ 
       19.07         0.20         6.35         0.03        60.36         0.39 
TCGA-G3-A25S TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A3CG TCGA-G3-A3CJ TCGA-G3-A5SL 
        1.22        28.27        30.71        22.13        19.53         7.99 

$`8P LOSS WILD-TYPE`
TCGA-BC-4073 TCGA-BC-A10S TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z 
       27.91        46.78         2.99        25.32        23.34         1.12 
TCGA-BC-A110 TCGA-BC-A5W4 TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5263 TCGA-CC-A1HT 
       69.57         9.50         0.07         2.86         4.24         3.32 
TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A114 TCGA-DD-A119 
        0.10         0.07         0.10         0.13        37.74         7.33 
TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB 
        2.60         0.46        51.25        90.67        79.36        66.31 
TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EF TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A3A1 
       19.76        75.65        12.95        49.15         6.02         7.66 
TCGA-DD-A3A2 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A4NF TCGA-DD-A4NG 
       70.06        20.12       102.74       107.11        14.07        14.93 
TCGA-DD-A4NH TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ 
       14.24        56.25        29.56        61.45        93.67        12.26 
TCGA-ED-A459 TCGA-ED-A5KG TCGA-EP-A2KB TCGA-EP-A3JL TCGA-FV-A23B TCGA-FV-A3R3 
        0.23         0.20         1.97         3.19        32.45         0.13 
TCGA-FV-A496 TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A25Z 
        0.33        51.02        53.79        58.49        14.86        21.53 
TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CK TCGA-G3-A5SJ TCGA-G3-A5SK TCGA-G3-A5SM 
       25.64         5.88        19.23        11.97         9.93         4.37 

  8P LOSS MUTATED 8P LOSS WILD-TYPE 
             0.03              0.07 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
           112.96            107.11 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
            18.33             14.55 
[1] "0.0 - 113.0 (18.3)" "0.1 - 107.1 (14.6)"
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
  "8P LOSS MUTATED" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED"   "8P LOSS MUTATED" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"8P LOSS WILD-TYPE"   "8P LOSS MUTATED"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
  "8P LOSS MUTATED"   "8P LOSS MUTATED"   "8P LOSS MUTATED"   "8P LOSS MUTATED" 
       TCGA-BC-A3KG        TCGA-BC-A5W4        TCGA-CC-5258        TCGA-CC-5260 
  "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-CC-5261        TCGA-CC-5262        TCGA-CC-5263        TCGA-CC-A1HT 
  "8P LOSS MUTATED"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-CC-A3M9        TCGA-CC-A3MA        TCGA-CC-A3MB        TCGA-CC-A3MC 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-DD-A113        TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116 
  "8P LOSS MUTATED" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED"   "8P LOSS MUTATED" 
       TCGA-DD-A118        TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B 
  "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-DD-A11C        TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EA 
  "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-DD-A1EB        TCGA-DD-A1EC        TCGA-DD-A1ED        TCGA-DD-A1EE 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" 
       TCGA-DD-A1EF        TCGA-DD-A1EH        TCGA-DD-A1EI        TCGA-DD-A1EJ 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" 
       TCGA-DD-A1EL        TCGA-DD-A39V        TCGA-DD-A39X        TCGA-DD-A39Y 
  "8P LOSS MUTATED"   "8P LOSS MUTATED"   "8P LOSS MUTATED"   "8P LOSS MUTATED" 
       TCGA-DD-A39Z        TCGA-DD-A3A0        TCGA-DD-A3A1        TCGA-DD-A3A2 
  "8P LOSS MUTATED"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-DD-A3A3        TCGA-DD-A3A4        TCGA-DD-A3A5        TCGA-DD-A3A6 
  "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-DD-A3A7        TCGA-DD-A3A8        TCGA-DD-A3A9        TCGA-DD-A4NA 
  "8P LOSS MUTATED"   "8P LOSS MUTATED"   "8P LOSS MUTATED"   "8P LOSS MUTATED" 
       TCGA-DD-A4ND        TCGA-DD-A4NE        TCGA-DD-A4NF        TCGA-DD-A4NG 
  "8P LOSS MUTATED"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-DD-A4NH        TCGA-DD-A4NI        TCGA-DD-A4NJ        TCGA-DD-A4NK 
"8P LOSS WILD-TYPE"   "8P LOSS MUTATED"   "8P LOSS MUTATED"   "8P LOSS MUTATED" 
       TCGA-DD-A4NL        TCGA-DD-A4NN        TCGA-DD-A4NO        TCGA-DD-A4NP 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-DD-A4NQ        TCGA-ED-A459        TCGA-ED-A5KG        TCGA-EP-A12J 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" 
       TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC 
  "8P LOSS MUTATED"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" 
       TCGA-EP-A3JL        TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT 
"8P LOSS WILD-TYPE"   "8P LOSS MUTATED"   "8P LOSS MUTATED"   "8P LOSS MUTATED" 
       TCGA-FV-A23B        TCGA-FV-A2QR        TCGA-FV-A3I0        TCGA-FV-A3R2 
"8P LOSS WILD-TYPE"   "8P LOSS MUTATED"   "8P LOSS MUTATED"   "8P LOSS MUTATED" 
       TCGA-FV-A3R3        TCGA-FV-A495        TCGA-FV-A496        TCGA-FV-A4ZP 
"8P LOSS WILD-TYPE"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" 
       TCGA-FV-A4ZQ        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
  "8P LOSS MUTATED"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
  "8P LOSS MUTATED"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI 
"8P LOSS WILD-TYPE"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-G3-A3CJ        TCGA-G3-A3CK        TCGA-G3-A5SJ        TCGA-G3-A5SK 
  "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-G3-A5SL        TCGA-G3-A5SM 
  "8P LOSS MUTATED" "8P LOSS WILD-TYPE" 
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
  "8P LOSS MUTATED" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED"   "8P LOSS MUTATED" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"8P LOSS WILD-TYPE"   "8P LOSS MUTATED"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
  "8P LOSS MUTATED"   "8P LOSS MUTATED"   "8P LOSS MUTATED"   "8P LOSS MUTATED" 
       TCGA-BC-A3KG        TCGA-BC-A5W4        TCGA-CC-5258        TCGA-CC-5260 
  "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-CC-5261        TCGA-CC-5262        TCGA-CC-5263        TCGA-CC-A1HT 
  "8P LOSS MUTATED"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-CC-A3M9        TCGA-CC-A3MA        TCGA-CC-A3MB        TCGA-CC-A3MC 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-DD-A113        TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116 
  "8P LOSS MUTATED" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED"   "8P LOSS MUTATED" 
       TCGA-DD-A118        TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B 
  "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-DD-A11C        TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EA 
  "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-DD-A1EB        TCGA-DD-A1EC        TCGA-DD-A1ED        TCGA-DD-A1EE 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" 
       TCGA-DD-A1EF        TCGA-DD-A1EH        TCGA-DD-A1EI        TCGA-DD-A1EJ 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" 
       TCGA-DD-A1EL        TCGA-DD-A39V        TCGA-DD-A39X        TCGA-DD-A39Y 
  "8P LOSS MUTATED"   "8P LOSS MUTATED"   "8P LOSS MUTATED"   "8P LOSS MUTATED" 
       TCGA-DD-A39Z        TCGA-DD-A3A0        TCGA-DD-A3A1        TCGA-DD-A3A2 
  "8P LOSS MUTATED"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-DD-A3A3        TCGA-DD-A3A4        TCGA-DD-A3A5        TCGA-DD-A3A6 
  "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-DD-A3A7        TCGA-DD-A3A8        TCGA-DD-A3A9        TCGA-DD-A4NA 
  "8P LOSS MUTATED"   "8P LOSS MUTATED"   "8P LOSS MUTATED"   "8P LOSS MUTATED" 
       TCGA-DD-A4ND        TCGA-DD-A4NE        TCGA-DD-A4NF        TCGA-DD-A4NG 
  "8P LOSS MUTATED"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-DD-A4NH        TCGA-DD-A4NI        TCGA-DD-A4NJ        TCGA-DD-A4NK 
"8P LOSS WILD-TYPE"   "8P LOSS MUTATED"   "8P LOSS MUTATED"   "8P LOSS MUTATED" 
       TCGA-DD-A4NL        TCGA-DD-A4NN        TCGA-DD-A4NO        TCGA-DD-A4NP 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-DD-A4NQ        TCGA-ED-A459        TCGA-ED-A5KG        TCGA-EP-A12J 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" 
       TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC 
  "8P LOSS MUTATED"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" 
       TCGA-EP-A3JL        TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT 
"8P LOSS WILD-TYPE"   "8P LOSS MUTATED"   "8P LOSS MUTATED"   "8P LOSS MUTATED" 
       TCGA-FV-A23B        TCGA-FV-A2QR        TCGA-FV-A3I0        TCGA-FV-A3R2 
"8P LOSS WILD-TYPE"   "8P LOSS MUTATED"   "8P LOSS MUTATED"   "8P LOSS MUTATED" 
       TCGA-FV-A3R3        TCGA-FV-A495        TCGA-FV-A496        TCGA-FV-A4ZP 
"8P LOSS WILD-TYPE"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" 
       TCGA-FV-A4ZQ        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
  "8P LOSS MUTATED"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
  "8P LOSS MUTATED"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI 
"8P LOSS WILD-TYPE"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-G3-A3CJ        TCGA-G3-A3CK        TCGA-G3-A5SJ        TCGA-G3-A5SK 
  "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-G3-A5SL        TCGA-G3-A5SM 
  "8P LOSS MUTATED" "8P LOSS WILD-TYPE" 
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
  "8P LOSS MUTATED" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED"   "8P LOSS MUTATED" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"8P LOSS WILD-TYPE"   "8P LOSS MUTATED"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
  "8P LOSS MUTATED"   "8P LOSS MUTATED"   "8P LOSS MUTATED"   "8P LOSS MUTATED" 
       TCGA-BC-A3KG        TCGA-BC-A5W4        TCGA-CC-5258        TCGA-CC-5260 
  "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-CC-5261        TCGA-CC-5262        TCGA-CC-5263        TCGA-CC-A1HT 
  "8P LOSS MUTATED"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-CC-A3M9        TCGA-CC-A3MA        TCGA-CC-A3MB        TCGA-CC-A3MC 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-DD-A113        TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116 
  "8P LOSS MUTATED" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED"   "8P LOSS MUTATED" 
       TCGA-DD-A118        TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B 
  "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-DD-A11C        TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EA 
  "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-DD-A1EB        TCGA-DD-A1EC        TCGA-DD-A1ED        TCGA-DD-A1EE 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" 
       TCGA-DD-A1EF        TCGA-DD-A1EH        TCGA-DD-A1EI        TCGA-DD-A1EJ 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" 
       TCGA-DD-A1EL        TCGA-DD-A39V        TCGA-DD-A39X        TCGA-DD-A39Y 
  "8P LOSS MUTATED"   "8P LOSS MUTATED"   "8P LOSS MUTATED"   "8P LOSS MUTATED" 
       TCGA-DD-A39Z        TCGA-DD-A3A0        TCGA-DD-A3A1        TCGA-DD-A3A2 
  "8P LOSS MUTATED"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-DD-A3A3        TCGA-DD-A3A4        TCGA-DD-A3A5        TCGA-DD-A3A6 
  "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-DD-A3A7        TCGA-DD-A3A8        TCGA-DD-A3A9        TCGA-DD-A4NA 
  "8P LOSS MUTATED"   "8P LOSS MUTATED"   "8P LOSS MUTATED"   "8P LOSS MUTATED" 
       TCGA-DD-A4ND        TCGA-DD-A4NE        TCGA-DD-A4NF        TCGA-DD-A4NG 
  "8P LOSS MUTATED"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-DD-A4NH        TCGA-DD-A4NI        TCGA-DD-A4NJ        TCGA-DD-A4NK 
"8P LOSS WILD-TYPE"   "8P LOSS MUTATED"   "8P LOSS MUTATED"   "8P LOSS MUTATED" 
       TCGA-DD-A4NL        TCGA-DD-A4NN        TCGA-DD-A4NO        TCGA-DD-A4NP 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-DD-A4NQ        TCGA-ED-A459        TCGA-ED-A5KG        TCGA-EP-A12J 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" 
       TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC 
  "8P LOSS MUTATED"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" 
       TCGA-EP-A3JL        TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT 
"8P LOSS WILD-TYPE"   "8P LOSS MUTATED"   "8P LOSS MUTATED"   "8P LOSS MUTATED" 
       TCGA-FV-A23B        TCGA-FV-A2QR        TCGA-FV-A3I0        TCGA-FV-A3R2 
"8P LOSS WILD-TYPE"   "8P LOSS MUTATED"   "8P LOSS MUTATED"   "8P LOSS MUTATED" 
       TCGA-FV-A3R3        TCGA-FV-A495        TCGA-FV-A496        TCGA-FV-A4ZP 
"8P LOSS WILD-TYPE"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" 
       TCGA-FV-A4ZQ        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
  "8P LOSS MUTATED"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
  "8P LOSS MUTATED"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI 
"8P LOSS WILD-TYPE"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-G3-A3CJ        TCGA-G3-A3CK        TCGA-G3-A5SJ        TCGA-G3-A5SK 
  "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-G3-A5SL        TCGA-G3-A5SM 
  "8P LOSS MUTATED" "8P LOSS WILD-TYPE" 
[1] "hr=" "1.6"
D55V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  8P LOSS MUTATED        18       15         0         11          2          3
  8P LOSS WILD-TYPE      27       10         2         14          1          1
                   vv
clus                STAGE IV STAGE IVA STAGE IVB
  8P LOSS MUTATED          0         1         1
  8P LOSS WILD-TYPE        1         0         0
D55V3, multiclass
                   vv
clus                T1 T2 T3 T4
  8P LOSS MUTATED   20 18 15  3
  8P LOSS WILD-TYPE 28 10 19  3
D55V4, multiclass
    clus
vv   8P LOSS MUTATED 8P LOSS WILD-TYPE
  T1              20                28
  T2              18                10
  T3              15                19
  T4               3                 3
D55V5, binary
                   cls
clus                 0  1
  8P LOSS MUTATED   27  3
  8P LOSS WILD-TYPE 47  0
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED     27    3
  8P LOSS WILD-TYPE   47    0
   clus
vv  8P LOSS MUTATED 8P LOSS WILD-TYPE
  0              27                47
  1               3                 0
                   vv
clus                M0 M1 MX
  8P LOSS MUTATED   40  1 15
  8P LOSS WILD-TYPE 50  1 10
D55V6, multiclass
    clus
vv   8P LOSS MUTATED 8P LOSS WILD-TYPE
  M0              40                50
  M1               1                 1
  MX              15                10
D55V7, binary
                   cls
clus                 0  1
  8P LOSS MUTATED   23 33
  8P LOSS WILD-TYPE 21 40
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED     23   33
  8P LOSS WILD-TYPE   21   40
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  FEMALE              23                21
  MALE                33                40
                   vv
clus                R0 R1 R2 RX
  8P LOSS MUTATED   43  7  0  3
  8P LOSS WILD-TYPE 50  3  1  5
D55V8, multiclass
    clus
vv   8P LOSS MUTATED 8P LOSS WILD-TYPE
  R0              43                50
  R1               7                 3
  R2               0                 1
  RX               3                 5

Clustering(56) Variable = 8Q LOSS MUTATION ANALYSIS
D56V1, survival
                   sevent
clus2                0  1
  8Q LOSS MUTATED    7  7
  8Q LOSS WILD-TYPE 54 46
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               14               100 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                7                46 
$`8Q LOSS MUTATED`
TCGA-BC-A10T TCGA-BC-A217 TCGA-BC-A3KG TCGA-CC-5261 TCGA-DD-A115 TCGA-DD-A39Z 
       27.52        13.81        16.37         3.02        83.57        19.73 
TCGA-DD-A3A0 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NI TCGA-DD-A4NK TCGA-FV-A3I0 
       25.81        30.58        33.14        10.78        39.75         0.20 
TCGA-FV-A495 TCGA-G3-A25V 
        0.03        28.27 

$`8Q LOSS WILD-TYPE`
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10U 
       48.99        27.91        37.32        10.13        46.78        27.52 
TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 
        2.99        25.32        23.34         1.12        69.57         5.03 
TCGA-BC-A216 TCGA-BC-A3KF TCGA-BC-A5W4 TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5262 
       44.42         0.26         9.50         0.07         2.86         3.39 
TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC 
        4.24         3.32         0.10         0.07         0.10         0.13 
TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A 
       79.73        37.74        53.29       112.96         7.33         2.60 
TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB 
        0.46        21.76        51.25        90.67        79.36        66.31 
TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EH TCGA-DD-A1EI 
       19.76        75.65         6.67        12.95        49.15         6.02 
TCGA-DD-A1EJ TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A3A1 
       29.16        13.64        21.14        55.66         5.59         7.66 
TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 
       70.06        17.59        20.12       102.74       107.11        13.78 
TCGA-DD-A3A8 TCGA-DD-A4ND TCGA-DD-A4NE TCGA-DD-A4NF TCGA-DD-A4NG TCGA-DD-A4NH 
        0.36        73.38        21.67        14.07        14.93        14.24 
TCGA-DD-A4NJ TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ 
       15.06        56.25        29.56        61.45        93.67        12.26 
TCGA-ED-A459 TCGA-ED-A5KG TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB 
        0.23         0.20        10.85         7.76        11.74         1.97 
TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A23B 
        0.62         3.19         0.43        23.01        14.40        32.45 
TCGA-FV-A2QR TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A496 TCGA-FV-A4ZP TCGA-FV-A4ZQ 
       19.07         6.35         0.13         0.33        60.36         0.39 
TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25W TCGA-G3-A25X TCGA-G3-A25Y 
        1.22        51.02        53.79        30.71        58.49        14.86 
TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK 
       21.53        22.13        25.64         5.88        19.53        19.23 
TCGA-G3-A5SJ TCGA-G3-A5SK TCGA-G3-A5SL TCGA-G3-A5SM 
       11.97         9.93         7.99         4.37 

  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
             0.03              0.07 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
            83.57            112.96 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
           22.770            14.895 
[1] "0.0 - 83.6 (22.8)"  "0.1 - 113.0 (14.9)"
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"8Q LOSS WILD-TYPE"   "8Q LOSS MUTATED" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE"   "8Q LOSS MUTATED" "8Q LOSS WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-BC-A5W4        TCGA-CC-5258        TCGA-CC-5260 
  "8Q LOSS MUTATED" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-CC-5261        TCGA-CC-5262        TCGA-CC-5263        TCGA-CC-A1HT 
  "8Q LOSS MUTATED" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-CC-A3M9        TCGA-CC-A3MA        TCGA-CC-A3MB        TCGA-CC-A3MC 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DD-A113        TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE"   "8Q LOSS MUTATED" "8Q LOSS WILD-TYPE" 
       TCGA-DD-A118        TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DD-A11C        TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EA 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DD-A1EB        TCGA-DD-A1EC        TCGA-DD-A1ED        TCGA-DD-A1EE 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DD-A1EF        TCGA-DD-A1EH        TCGA-DD-A1EI        TCGA-DD-A1EJ 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DD-A1EL        TCGA-DD-A39V        TCGA-DD-A39X        TCGA-DD-A39Y 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DD-A39Z        TCGA-DD-A3A0        TCGA-DD-A3A1        TCGA-DD-A3A2 
  "8Q LOSS MUTATED"   "8Q LOSS MUTATED" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DD-A3A3        TCGA-DD-A3A4        TCGA-DD-A3A5        TCGA-DD-A3A6 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DD-A3A7        TCGA-DD-A3A8        TCGA-DD-A3A9        TCGA-DD-A4NA 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE"   "8Q LOSS MUTATED"   "8Q LOSS MUTATED" 
       TCGA-DD-A4ND        TCGA-DD-A4NE        TCGA-DD-A4NF        TCGA-DD-A4NG 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DD-A4NH        TCGA-DD-A4NI        TCGA-DD-A4NJ        TCGA-DD-A4NK 
"8Q LOSS WILD-TYPE"   "8Q LOSS MUTATED" "8Q LOSS WILD-TYPE"   "8Q LOSS MUTATED" 
       TCGA-DD-A4NL        TCGA-DD-A4NN        TCGA-DD-A4NO        TCGA-DD-A4NP 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DD-A4NQ        TCGA-ED-A459        TCGA-ED-A5KG        TCGA-EP-A12J 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EP-A3JL        TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-FV-A23B        TCGA-FV-A2QR        TCGA-FV-A3I0        TCGA-FV-A3R2 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE"   "8Q LOSS MUTATED" "8Q LOSS WILD-TYPE" 
       TCGA-FV-A3R3        TCGA-FV-A495        TCGA-FV-A496        TCGA-FV-A4ZP 
"8Q LOSS WILD-TYPE"   "8Q LOSS MUTATED" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-FV-A4ZQ        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
  "8Q LOSS MUTATED" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-G3-A3CJ        TCGA-G3-A3CK        TCGA-G3-A5SJ        TCGA-G3-A5SK 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-G3-A5SL        TCGA-G3-A5SM 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"8Q LOSS WILD-TYPE"   "8Q LOSS MUTATED" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE"   "8Q LOSS MUTATED" "8Q LOSS WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-BC-A5W4        TCGA-CC-5258        TCGA-CC-5260 
  "8Q LOSS MUTATED" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-CC-5261        TCGA-CC-5262        TCGA-CC-5263        TCGA-CC-A1HT 
  "8Q LOSS MUTATED" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-CC-A3M9        TCGA-CC-A3MA        TCGA-CC-A3MB        TCGA-CC-A3MC 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DD-A113        TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE"   "8Q LOSS MUTATED" "8Q LOSS WILD-TYPE" 
       TCGA-DD-A118        TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DD-A11C        TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EA 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DD-A1EB        TCGA-DD-A1EC        TCGA-DD-A1ED        TCGA-DD-A1EE 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DD-A1EF        TCGA-DD-A1EH        TCGA-DD-A1EI        TCGA-DD-A1EJ 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DD-A1EL        TCGA-DD-A39V        TCGA-DD-A39X        TCGA-DD-A39Y 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DD-A39Z        TCGA-DD-A3A0        TCGA-DD-A3A1        TCGA-DD-A3A2 
  "8Q LOSS MUTATED"   "8Q LOSS MUTATED" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DD-A3A3        TCGA-DD-A3A4        TCGA-DD-A3A5        TCGA-DD-A3A6 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DD-A3A7        TCGA-DD-A3A8        TCGA-DD-A3A9        TCGA-DD-A4NA 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE"   "8Q LOSS MUTATED"   "8Q LOSS MUTATED" 
       TCGA-DD-A4ND        TCGA-DD-A4NE        TCGA-DD-A4NF        TCGA-DD-A4NG 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DD-A4NH        TCGA-DD-A4NI        TCGA-DD-A4NJ        TCGA-DD-A4NK 
"8Q LOSS WILD-TYPE"   "8Q LOSS MUTATED" "8Q LOSS WILD-TYPE"   "8Q LOSS MUTATED" 
       TCGA-DD-A4NL        TCGA-DD-A4NN        TCGA-DD-A4NO        TCGA-DD-A4NP 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DD-A4NQ        TCGA-ED-A459        TCGA-ED-A5KG        TCGA-EP-A12J 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EP-A3JL        TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-FV-A23B        TCGA-FV-A2QR        TCGA-FV-A3I0        TCGA-FV-A3R2 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE"   "8Q LOSS MUTATED" "8Q LOSS WILD-TYPE" 
       TCGA-FV-A3R3        TCGA-FV-A495        TCGA-FV-A496        TCGA-FV-A4ZP 
"8Q LOSS WILD-TYPE"   "8Q LOSS MUTATED" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-FV-A4ZQ        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
  "8Q LOSS MUTATED" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-G3-A3CJ        TCGA-G3-A3CK        TCGA-G3-A5SJ        TCGA-G3-A5SK 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-G3-A5SL        TCGA-G3-A5SM 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"8Q LOSS WILD-TYPE"   "8Q LOSS MUTATED" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE"   "8Q LOSS MUTATED" "8Q LOSS WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-BC-A5W4        TCGA-CC-5258        TCGA-CC-5260 
  "8Q LOSS MUTATED" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-CC-5261        TCGA-CC-5262        TCGA-CC-5263        TCGA-CC-A1HT 
  "8Q LOSS MUTATED" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-CC-A3M9        TCGA-CC-A3MA        TCGA-CC-A3MB        TCGA-CC-A3MC 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DD-A113        TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE"   "8Q LOSS MUTATED" "8Q LOSS WILD-TYPE" 
       TCGA-DD-A118        TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DD-A11C        TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EA 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DD-A1EB        TCGA-DD-A1EC        TCGA-DD-A1ED        TCGA-DD-A1EE 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DD-A1EF        TCGA-DD-A1EH        TCGA-DD-A1EI        TCGA-DD-A1EJ 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DD-A1EL        TCGA-DD-A39V        TCGA-DD-A39X        TCGA-DD-A39Y 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DD-A39Z        TCGA-DD-A3A0        TCGA-DD-A3A1        TCGA-DD-A3A2 
  "8Q LOSS MUTATED"   "8Q LOSS MUTATED" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DD-A3A3        TCGA-DD-A3A4        TCGA-DD-A3A5        TCGA-DD-A3A6 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DD-A3A7        TCGA-DD-A3A8        TCGA-DD-A3A9        TCGA-DD-A4NA 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE"   "8Q LOSS MUTATED"   "8Q LOSS MUTATED" 
       TCGA-DD-A4ND        TCGA-DD-A4NE        TCGA-DD-A4NF        TCGA-DD-A4NG 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DD-A4NH        TCGA-DD-A4NI        TCGA-DD-A4NJ        TCGA-DD-A4NK 
"8Q LOSS WILD-TYPE"   "8Q LOSS MUTATED" "8Q LOSS WILD-TYPE"   "8Q LOSS MUTATED" 
       TCGA-DD-A4NL        TCGA-DD-A4NN        TCGA-DD-A4NO        TCGA-DD-A4NP 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DD-A4NQ        TCGA-ED-A459        TCGA-ED-A5KG        TCGA-EP-A12J 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EP-A3JL        TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-FV-A23B        TCGA-FV-A2QR        TCGA-FV-A3I0        TCGA-FV-A3R2 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE"   "8Q LOSS MUTATED" "8Q LOSS WILD-TYPE" 
       TCGA-FV-A3R3        TCGA-FV-A495        TCGA-FV-A496        TCGA-FV-A4ZP 
"8Q LOSS WILD-TYPE"   "8Q LOSS MUTATED" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-FV-A4ZQ        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
  "8Q LOSS MUTATED" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-G3-A3CJ        TCGA-G3-A3CK        TCGA-G3-A5SJ        TCGA-G3-A5SK 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-G3-A5SL        TCGA-G3-A5SM 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
[1] "hr=" "1.1"
D56V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  8Q LOSS MUTATED         2        7         0          2          0          1
  8Q LOSS WILD-TYPE      43       18         2         23          3          3
                   vv
clus                STAGE IV STAGE IVA STAGE IVB
  8Q LOSS MUTATED          0         0         1
  8Q LOSS WILD-TYPE        1         1         0
D56V3, multiclass
                   vv
clus                T1 T2 T3 T4
  8Q LOSS MUTATED    2  8  2  2
  8Q LOSS WILD-TYPE 46 20 32  4
D56V4, multiclass
    clus
vv   8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  T1               2                46
  T2               8                20
  T3               2                32
  T4               2                 4
D56V5, binary
                   cls
clus                 0  1
  8Q LOSS MUTATED    6  1
  8Q LOSS WILD-TYPE 68  2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED      6    1
  8Q LOSS WILD-TYPE   68    2
   clus
vv  8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  0               6                68
  1               1                 2
                   vv
clus                M0 M1 MX
  8Q LOSS MUTATED   12  1  1
  8Q LOSS WILD-TYPE 78  1 24
D56V6, multiclass
    clus
vv   8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  M0              12                78
  M1               1                 1
  MX               1                24
D56V7, binary
                   cls
clus                 0  1
  8Q LOSS MUTATED    8  6
  8Q LOSS WILD-TYPE 36 67
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED      8    6
  8Q LOSS WILD-TYPE   36   67
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  FEMALE               8                36
  MALE                 6                67
                   vv
clus                R0 R1 R2 RX
  8Q LOSS MUTATED   12  1  0  1
  8Q LOSS WILD-TYPE 81  9  1  7
D56V8, multiclass
    clus
vv   8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  R0              12                81
  R1               1                 9
  R2               0                 1
  RX               1                 7

Clustering(57) Variable = 9P LOSS MUTATION ANALYSIS
D57V1, survival
                   sevent
clus2                0  1
  9P LOSS MUTATED   16 18
  9P LOSS WILD-TYPE 45 35
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               34                80 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               18                35 
$`9P LOSS MUTATED`
TCGA-BC-4072 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10U TCGA-BC-A112 
       48.99        37.32        10.13        46.78        27.52         5.03 
TCGA-BC-A217 TCGA-BC-A5W4 TCGA-CC-5258 TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3M9 
       13.81         9.50         0.07         4.24         3.32         0.10 
TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A113 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A119 
        0.10         0.13        79.73        83.57        53.29         7.33 
TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A39X 
        2.60         0.46        21.76         6.02        29.16        55.66 
TCGA-DD-A3A0 TCGA-DD-A3A9 TCGA-DD-A4ND TCGA-DD-A4NO TCGA-ED-A459 TCGA-EP-A2KC 
       25.81        30.58        73.38        61.45         0.23         0.62 
TCGA-EP-A3RK TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A3CH 
        0.43         1.22        51.02        25.64 

$`9P LOSS WILD-TYPE`
TCGA-BC-4073 TCGA-BC-A10T TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z 
       27.91        27.52         2.99        25.32        23.34         1.12 
TCGA-BC-A110 TCGA-BC-A216 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-CC-5260 TCGA-CC-5261 
       69.57        44.42         0.26        16.37         2.86         3.02 
TCGA-CC-5262 TCGA-CC-A3MA TCGA-DD-A114 TCGA-DD-A118 TCGA-DD-A11D TCGA-DD-A1E9 
        3.39         0.07        37.74       112.96        51.25        90.67 
TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EF 
       79.36        66.31        19.76        75.65         6.67        12.95 
TCGA-DD-A1EH TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A1 
       49.15        13.64        21.14         5.59        19.73         7.66 
TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 
       70.06        17.59        20.12       102.74       107.11        13.78 
TCGA-DD-A3A8 TCGA-DD-A4NA TCGA-DD-A4NE TCGA-DD-A4NF TCGA-DD-A4NG TCGA-DD-A4NH 
        0.36        33.14        21.67        14.07        14.93        14.24 
TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NP 
       10.78        15.06        39.75        56.25        29.56        93.67 
TCGA-DD-A4NQ TCGA-ED-A5KG TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB 
       12.26         0.20        10.85         7.76        11.74         1.97 
TCGA-EP-A3JL TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-A3I0 
        3.19        23.01        14.40        32.45        19.07         0.20 
TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZP TCGA-FV-A4ZQ 
        6.35         0.13         0.03         0.33        60.36         0.39 
TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A25Z 
       53.79        28.27        30.71        58.49        14.86        21.53 
TCGA-G3-A3CG TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SJ TCGA-G3-A5SK 
       22.13         5.88        19.53        19.23        11.97         9.93 
TCGA-G3-A5SL TCGA-G3-A5SM 
        7.99         4.37 

  9P LOSS MUTATED 9P LOSS WILD-TYPE 
             0.07              0.03 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
            83.57            112.96 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
            11.97             16.98 
[1] "0.1 - 83.6 (12.0)"  "0.0 - 113.0 (17.0)"
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
  "9P LOSS MUTATED" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED"   "9P LOSS MUTATED" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
  "9P LOSS MUTATED" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
  "9P LOSS MUTATED" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-BC-A5W4        TCGA-CC-5258        TCGA-CC-5260 
"9P LOSS WILD-TYPE"   "9P LOSS MUTATED"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" 
       TCGA-CC-5261        TCGA-CC-5262        TCGA-CC-5263        TCGA-CC-A1HT 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED"   "9P LOSS MUTATED" 
       TCGA-CC-A3M9        TCGA-CC-A3MA        TCGA-CC-A3MB        TCGA-CC-A3MC 
  "9P LOSS MUTATED" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED"   "9P LOSS MUTATED" 
       TCGA-DD-A113        TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116 
  "9P LOSS MUTATED" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED"   "9P LOSS MUTATED" 
       TCGA-DD-A118        TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B 
"9P LOSS WILD-TYPE"   "9P LOSS MUTATED"   "9P LOSS MUTATED"   "9P LOSS MUTATED" 
       TCGA-DD-A11C        TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EA 
  "9P LOSS MUTATED" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-DD-A1EB        TCGA-DD-A1EC        TCGA-DD-A1ED        TCGA-DD-A1EE 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-DD-A1EF        TCGA-DD-A1EH        TCGA-DD-A1EI        TCGA-DD-A1EJ 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED"   "9P LOSS MUTATED" 
       TCGA-DD-A1EL        TCGA-DD-A39V        TCGA-DD-A39X        TCGA-DD-A39Y 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" 
       TCGA-DD-A39Z        TCGA-DD-A3A0        TCGA-DD-A3A1        TCGA-DD-A3A2 
"9P LOSS WILD-TYPE"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-DD-A3A3        TCGA-DD-A3A4        TCGA-DD-A3A5        TCGA-DD-A3A6 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-DD-A3A7        TCGA-DD-A3A8        TCGA-DD-A3A9        TCGA-DD-A4NA 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" 
       TCGA-DD-A4ND        TCGA-DD-A4NE        TCGA-DD-A4NF        TCGA-DD-A4NG 
  "9P LOSS MUTATED" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-DD-A4NH        TCGA-DD-A4NI        TCGA-DD-A4NJ        TCGA-DD-A4NK 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-DD-A4NL        TCGA-DD-A4NN        TCGA-DD-A4NO        TCGA-DD-A4NP 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" 
       TCGA-DD-A4NQ        TCGA-ED-A459        TCGA-ED-A5KG        TCGA-EP-A12J 
"9P LOSS WILD-TYPE"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" 
       TCGA-EP-A3JL        TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT 
"9P LOSS WILD-TYPE"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-FV-A23B        TCGA-FV-A2QR        TCGA-FV-A3I0        TCGA-FV-A3R2 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-FV-A3R3        TCGA-FV-A495        TCGA-FV-A496        TCGA-FV-A4ZP 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-FV-A4ZQ        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"9P LOSS WILD-TYPE"   "9P LOSS MUTATED"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" 
       TCGA-G3-A3CJ        TCGA-G3-A3CK        TCGA-G3-A5SJ        TCGA-G3-A5SK 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-G3-A5SL        TCGA-G3-A5SM 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
  "9P LOSS MUTATED" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED"   "9P LOSS MUTATED" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
  "9P LOSS MUTATED" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
  "9P LOSS MUTATED" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-BC-A5W4        TCGA-CC-5258        TCGA-CC-5260 
"9P LOSS WILD-TYPE"   "9P LOSS MUTATED"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" 
       TCGA-CC-5261        TCGA-CC-5262        TCGA-CC-5263        TCGA-CC-A1HT 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED"   "9P LOSS MUTATED" 
       TCGA-CC-A3M9        TCGA-CC-A3MA        TCGA-CC-A3MB        TCGA-CC-A3MC 
  "9P LOSS MUTATED" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED"   "9P LOSS MUTATED" 
       TCGA-DD-A113        TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116 
  "9P LOSS MUTATED" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED"   "9P LOSS MUTATED" 
       TCGA-DD-A118        TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B 
"9P LOSS WILD-TYPE"   "9P LOSS MUTATED"   "9P LOSS MUTATED"   "9P LOSS MUTATED" 
       TCGA-DD-A11C        TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EA 
  "9P LOSS MUTATED" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-DD-A1EB        TCGA-DD-A1EC        TCGA-DD-A1ED        TCGA-DD-A1EE 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-DD-A1EF        TCGA-DD-A1EH        TCGA-DD-A1EI        TCGA-DD-A1EJ 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED"   "9P LOSS MUTATED" 
       TCGA-DD-A1EL        TCGA-DD-A39V        TCGA-DD-A39X        TCGA-DD-A39Y 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" 
       TCGA-DD-A39Z        TCGA-DD-A3A0        TCGA-DD-A3A1        TCGA-DD-A3A2 
"9P LOSS WILD-TYPE"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-DD-A3A3        TCGA-DD-A3A4        TCGA-DD-A3A5        TCGA-DD-A3A6 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-DD-A3A7        TCGA-DD-A3A8        TCGA-DD-A3A9        TCGA-DD-A4NA 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" 
       TCGA-DD-A4ND        TCGA-DD-A4NE        TCGA-DD-A4NF        TCGA-DD-A4NG 
  "9P LOSS MUTATED" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-DD-A4NH        TCGA-DD-A4NI        TCGA-DD-A4NJ        TCGA-DD-A4NK 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-DD-A4NL        TCGA-DD-A4NN        TCGA-DD-A4NO        TCGA-DD-A4NP 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" 
       TCGA-DD-A4NQ        TCGA-ED-A459        TCGA-ED-A5KG        TCGA-EP-A12J 
"9P LOSS WILD-TYPE"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" 
       TCGA-EP-A3JL        TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT 
"9P LOSS WILD-TYPE"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-FV-A23B        TCGA-FV-A2QR        TCGA-FV-A3I0        TCGA-FV-A3R2 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-FV-A3R3        TCGA-FV-A495        TCGA-FV-A496        TCGA-FV-A4ZP 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-FV-A4ZQ        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"9P LOSS WILD-TYPE"   "9P LOSS MUTATED"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" 
       TCGA-G3-A3CJ        TCGA-G3-A3CK        TCGA-G3-A5SJ        TCGA-G3-A5SK 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-G3-A5SL        TCGA-G3-A5SM 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
  "9P LOSS MUTATED" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED"   "9P LOSS MUTATED" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
  "9P LOSS MUTATED" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
  "9P LOSS MUTATED" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-BC-A5W4        TCGA-CC-5258        TCGA-CC-5260 
"9P LOSS WILD-TYPE"   "9P LOSS MUTATED"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" 
       TCGA-CC-5261        TCGA-CC-5262        TCGA-CC-5263        TCGA-CC-A1HT 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED"   "9P LOSS MUTATED" 
       TCGA-CC-A3M9        TCGA-CC-A3MA        TCGA-CC-A3MB        TCGA-CC-A3MC 
  "9P LOSS MUTATED" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED"   "9P LOSS MUTATED" 
       TCGA-DD-A113        TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116 
  "9P LOSS MUTATED" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED"   "9P LOSS MUTATED" 
       TCGA-DD-A118        TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B 
"9P LOSS WILD-TYPE"   "9P LOSS MUTATED"   "9P LOSS MUTATED"   "9P LOSS MUTATED" 
       TCGA-DD-A11C        TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EA 
  "9P LOSS MUTATED" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-DD-A1EB        TCGA-DD-A1EC        TCGA-DD-A1ED        TCGA-DD-A1EE 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-DD-A1EF        TCGA-DD-A1EH        TCGA-DD-A1EI        TCGA-DD-A1EJ 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED"   "9P LOSS MUTATED" 
       TCGA-DD-A1EL        TCGA-DD-A39V        TCGA-DD-A39X        TCGA-DD-A39Y 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" 
       TCGA-DD-A39Z        TCGA-DD-A3A0        TCGA-DD-A3A1        TCGA-DD-A3A2 
"9P LOSS WILD-TYPE"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-DD-A3A3        TCGA-DD-A3A4        TCGA-DD-A3A5        TCGA-DD-A3A6 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-DD-A3A7        TCGA-DD-A3A8        TCGA-DD-A3A9        TCGA-DD-A4NA 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" 
       TCGA-DD-A4ND        TCGA-DD-A4NE        TCGA-DD-A4NF        TCGA-DD-A4NG 
  "9P LOSS MUTATED" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-DD-A4NH        TCGA-DD-A4NI        TCGA-DD-A4NJ        TCGA-DD-A4NK 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-DD-A4NL        TCGA-DD-A4NN        TCGA-DD-A4NO        TCGA-DD-A4NP 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" 
       TCGA-DD-A4NQ        TCGA-ED-A459        TCGA-ED-A5KG        TCGA-EP-A12J 
"9P LOSS WILD-TYPE"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" 
       TCGA-EP-A3JL        TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT 
"9P LOSS WILD-TYPE"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-FV-A23B        TCGA-FV-A2QR        TCGA-FV-A3I0        TCGA-FV-A3R2 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-FV-A3R3        TCGA-FV-A495        TCGA-FV-A496        TCGA-FV-A4ZP 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-FV-A4ZQ        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"9P LOSS WILD-TYPE"   "9P LOSS MUTATED"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" 
       TCGA-G3-A3CJ        TCGA-G3-A3CK        TCGA-G3-A5SJ        TCGA-G3-A5SK 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-G3-A5SL        TCGA-G3-A5SM 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
[1] "hr=" "1.4"
D57V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  9P LOSS MUTATED        10        5         0         11          0          1
  9P LOSS WILD-TYPE      35       20         2         14          3          3
                   vv
clus                STAGE IV STAGE IVA STAGE IVB
  9P LOSS MUTATED          1         1         1
  9P LOSS WILD-TYPE        0         0         0
D57V3, multiclass
                   vv
clus                T1 T2 T3 T4
  9P LOSS MUTATED   12  7 15  1
  9P LOSS WILD-TYPE 36 21 19  5
D57V4, multiclass
    clus
vv   9P LOSS MUTATED 9P LOSS WILD-TYPE
  T1              12                36
  T2               7                21
  T3              15                19
  T4               1                 5
D57V5, binary
                   cls
clus                 0  1
  9P LOSS MUTATED   23  2
  9P LOSS WILD-TYPE 51  1
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED     23    2
  9P LOSS WILD-TYPE   51    1
   clus
vv  9P LOSS MUTATED 9P LOSS WILD-TYPE
  0              23                51
  1               2                 1
                   vv
clus                M0 M1 MX
  9P LOSS MUTATED   25  2  9
  9P LOSS WILD-TYPE 65  0 16
D57V6, multiclass
    clus
vv   9P LOSS MUTATED 9P LOSS WILD-TYPE
  M0              25                65
  M1               2                 0
  MX               9                16
D57V7, binary
                   cls
clus                 0  1
  9P LOSS MUTATED   11 25
  9P LOSS WILD-TYPE 33 48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED     11   25
  9P LOSS WILD-TYPE   33   48
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  FEMALE              11                33
  MALE                25                48
                   vv
clus                R0 R1 R2 RX
  9P LOSS MUTATED   24  5  1  4
  9P LOSS WILD-TYPE 69  5  0  4
D57V8, multiclass
    clus
vv   9P LOSS MUTATED 9P LOSS WILD-TYPE
  R0              24                69
  R1               5                 5
  R2               1                 0
  RX               4                 4

Clustering(58) Variable = 9Q LOSS MUTATION ANALYSIS
D58V1, survival
                   sevent
clus2                0  1
  9Q LOSS MUTATED   18 17
  9Q LOSS WILD-TYPE 43 36
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               35                79 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               17                36 
$`9Q LOSS MUTATED`
TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10U TCGA-BC-A112 TCGA-BC-A217 
       37.32        10.13        46.78        27.52         5.03        13.81 
TCGA-BC-A5W4 TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3M9 
        9.50         0.07         2.86         4.24         3.32         0.10 
TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A113 TCGA-DD-A116 TCGA-DD-A119 TCGA-DD-A11A 
        0.10         0.13        79.73        53.29         7.33         2.60 
TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A39X TCGA-DD-A3A9 
        0.46        21.76         6.02        29.16        55.66        30.58 
TCGA-DD-A4NA TCGA-DD-A4NO TCGA-ED-A459 TCGA-EP-A2KC TCGA-EP-A3RK TCGA-FV-A3I0 
       33.14        61.45         0.23         0.62         0.43         0.20 
TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A3CH 
        6.35         0.13         1.22        51.02        25.64 

$`9Q LOSS WILD-TYPE`
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10T TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y 
       48.99        27.91        27.52         2.99        25.32        23.34 
TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A216 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-CC-5261 
        1.12        69.57        44.42         0.26        16.37         3.02 
TCGA-CC-5262 TCGA-CC-A3MA TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A118 TCGA-DD-A11D 
        3.39         0.07        37.74        83.57       112.96        51.25 
TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE 
       90.67        79.36        66.31        19.76        75.65         6.67 
TCGA-DD-A1EF TCGA-DD-A1EH TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39Y TCGA-DD-A39Z 
       12.95        49.15        13.64        21.14         5.59        19.73 
TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 
       25.81         7.66        70.06        17.59        20.12       102.74 
TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A4ND TCGA-DD-A4NE TCGA-DD-A4NF 
      107.11        13.78         0.36        73.38        21.67        14.07 
TCGA-DD-A4NG TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL 
       14.93        14.24        10.78        15.06        39.75        56.25 
TCGA-DD-A4NN TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-ED-A5KG TCGA-EP-A12J TCGA-EP-A26S 
       29.56        93.67        12.26         0.20        10.85         7.76 
TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A3JL TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A23B 
       11.74         1.97         3.19        23.01        14.40        32.45 
TCGA-FV-A2QR TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25U 
       19.07         0.03         0.33        60.36         0.39        53.79 
TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG 
       28.27        30.71        58.49        14.86        21.53        22.13 
TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SJ TCGA-G3-A5SK TCGA-G3-A5SL 
        5.88        19.53        19.23        11.97         9.93         7.99 
TCGA-G3-A5SM 
        4.37 

  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
             0.07              0.03 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
            79.73            112.96 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
             6.35             19.53 
[1] "0.1 - 79.7 (6.3)"   "0.0 - 113.0 (19.5)"
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED"   "9Q LOSS MUTATED" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
  "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
  "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-BC-A5W4        TCGA-CC-5258        TCGA-CC-5260 
"9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED"   "9Q LOSS MUTATED"   "9Q LOSS MUTATED" 
       TCGA-CC-5261        TCGA-CC-5262        TCGA-CC-5263        TCGA-CC-A1HT 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED"   "9Q LOSS MUTATED" 
       TCGA-CC-A3M9        TCGA-CC-A3MA        TCGA-CC-A3MB        TCGA-CC-A3MC 
  "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED"   "9Q LOSS MUTATED" 
       TCGA-DD-A113        TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116 
  "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" 
       TCGA-DD-A118        TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B 
"9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED"   "9Q LOSS MUTATED"   "9Q LOSS MUTATED" 
       TCGA-DD-A11C        TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EA 
  "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-DD-A1EB        TCGA-DD-A1EC        TCGA-DD-A1ED        TCGA-DD-A1EE 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-DD-A1EF        TCGA-DD-A1EH        TCGA-DD-A1EI        TCGA-DD-A1EJ 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED"   "9Q LOSS MUTATED" 
       TCGA-DD-A1EL        TCGA-DD-A39V        TCGA-DD-A39X        TCGA-DD-A39Y 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" 
       TCGA-DD-A39Z        TCGA-DD-A3A0        TCGA-DD-A3A1        TCGA-DD-A3A2 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-DD-A3A3        TCGA-DD-A3A4        TCGA-DD-A3A5        TCGA-DD-A3A6 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-DD-A3A7        TCGA-DD-A3A8        TCGA-DD-A3A9        TCGA-DD-A4NA 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED"   "9Q LOSS MUTATED" 
       TCGA-DD-A4ND        TCGA-DD-A4NE        TCGA-DD-A4NF        TCGA-DD-A4NG 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-DD-A4NH        TCGA-DD-A4NI        TCGA-DD-A4NJ        TCGA-DD-A4NK 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-DD-A4NL        TCGA-DD-A4NN        TCGA-DD-A4NO        TCGA-DD-A4NP 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" 
       TCGA-DD-A4NQ        TCGA-ED-A459        TCGA-ED-A5KG        TCGA-EP-A12J 
"9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" 
       TCGA-EP-A3JL        TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT 
"9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-FV-A23B        TCGA-FV-A2QR        TCGA-FV-A3I0        TCGA-FV-A3R2 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED"   "9Q LOSS MUTATED" 
       TCGA-FV-A3R3        TCGA-FV-A495        TCGA-FV-A496        TCGA-FV-A4ZP 
  "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-FV-A4ZQ        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" 
       TCGA-G3-A3CJ        TCGA-G3-A3CK        TCGA-G3-A5SJ        TCGA-G3-A5SK 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-G3-A5SL        TCGA-G3-A5SM 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED"   "9Q LOSS MUTATED" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
  "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
  "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-BC-A5W4        TCGA-CC-5258        TCGA-CC-5260 
"9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED"   "9Q LOSS MUTATED"   "9Q LOSS MUTATED" 
       TCGA-CC-5261        TCGA-CC-5262        TCGA-CC-5263        TCGA-CC-A1HT 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED"   "9Q LOSS MUTATED" 
       TCGA-CC-A3M9        TCGA-CC-A3MA        TCGA-CC-A3MB        TCGA-CC-A3MC 
  "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED"   "9Q LOSS MUTATED" 
       TCGA-DD-A113        TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116 
  "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" 
       TCGA-DD-A118        TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B 
"9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED"   "9Q LOSS MUTATED"   "9Q LOSS MUTATED" 
       TCGA-DD-A11C        TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EA 
  "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-DD-A1EB        TCGA-DD-A1EC        TCGA-DD-A1ED        TCGA-DD-A1EE 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-DD-A1EF        TCGA-DD-A1EH        TCGA-DD-A1EI        TCGA-DD-A1EJ 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED"   "9Q LOSS MUTATED" 
       TCGA-DD-A1EL        TCGA-DD-A39V        TCGA-DD-A39X        TCGA-DD-A39Y 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" 
       TCGA-DD-A39Z        TCGA-DD-A3A0        TCGA-DD-A3A1        TCGA-DD-A3A2 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-DD-A3A3        TCGA-DD-A3A4        TCGA-DD-A3A5        TCGA-DD-A3A6 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-DD-A3A7        TCGA-DD-A3A8        TCGA-DD-A3A9        TCGA-DD-A4NA 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED"   "9Q LOSS MUTATED" 
       TCGA-DD-A4ND        TCGA-DD-A4NE        TCGA-DD-A4NF        TCGA-DD-A4NG 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-DD-A4NH        TCGA-DD-A4NI        TCGA-DD-A4NJ        TCGA-DD-A4NK 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-DD-A4NL        TCGA-DD-A4NN        TCGA-DD-A4NO        TCGA-DD-A4NP 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" 
       TCGA-DD-A4NQ        TCGA-ED-A459        TCGA-ED-A5KG        TCGA-EP-A12J 
"9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" 
       TCGA-EP-A3JL        TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT 
"9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-FV-A23B        TCGA-FV-A2QR        TCGA-FV-A3I0        TCGA-FV-A3R2 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED"   "9Q LOSS MUTATED" 
       TCGA-FV-A3R3        TCGA-FV-A495        TCGA-FV-A496        TCGA-FV-A4ZP 
  "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-FV-A4ZQ        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" 
       TCGA-G3-A3CJ        TCGA-G3-A3CK        TCGA-G3-A5SJ        TCGA-G3-A5SK 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-G3-A5SL        TCGA-G3-A5SM 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED"   "9Q LOSS MUTATED" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
  "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
  "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-BC-A5W4        TCGA-CC-5258        TCGA-CC-5260 
"9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED"   "9Q LOSS MUTATED"   "9Q LOSS MUTATED" 
       TCGA-CC-5261        TCGA-CC-5262        TCGA-CC-5263        TCGA-CC-A1HT 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED"   "9Q LOSS MUTATED" 
       TCGA-CC-A3M9        TCGA-CC-A3MA        TCGA-CC-A3MB        TCGA-CC-A3MC 
  "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED"   "9Q LOSS MUTATED" 
       TCGA-DD-A113        TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116 
  "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" 
       TCGA-DD-A118        TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B 
"9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED"   "9Q LOSS MUTATED"   "9Q LOSS MUTATED" 
       TCGA-DD-A11C        TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EA 
  "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-DD-A1EB        TCGA-DD-A1EC        TCGA-DD-A1ED        TCGA-DD-A1EE 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-DD-A1EF        TCGA-DD-A1EH        TCGA-DD-A1EI        TCGA-DD-A1EJ 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED"   "9Q LOSS MUTATED" 
       TCGA-DD-A1EL        TCGA-DD-A39V        TCGA-DD-A39X        TCGA-DD-A39Y 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" 
       TCGA-DD-A39Z        TCGA-DD-A3A0        TCGA-DD-A3A1        TCGA-DD-A3A2 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-DD-A3A3        TCGA-DD-A3A4        TCGA-DD-A3A5        TCGA-DD-A3A6 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-DD-A3A7        TCGA-DD-A3A8        TCGA-DD-A3A9        TCGA-DD-A4NA 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED"   "9Q LOSS MUTATED" 
       TCGA-DD-A4ND        TCGA-DD-A4NE        TCGA-DD-A4NF        TCGA-DD-A4NG 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-DD-A4NH        TCGA-DD-A4NI        TCGA-DD-A4NJ        TCGA-DD-A4NK 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-DD-A4NL        TCGA-DD-A4NN        TCGA-DD-A4NO        TCGA-DD-A4NP 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" 
       TCGA-DD-A4NQ        TCGA-ED-A459        TCGA-ED-A5KG        TCGA-EP-A12J 
"9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" 
       TCGA-EP-A3JL        TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT 
"9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-FV-A23B        TCGA-FV-A2QR        TCGA-FV-A3I0        TCGA-FV-A3R2 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED"   "9Q LOSS MUTATED" 
       TCGA-FV-A3R3        TCGA-FV-A495        TCGA-FV-A496        TCGA-FV-A4ZP 
  "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-FV-A4ZQ        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" 
       TCGA-G3-A3CJ        TCGA-G3-A3CK        TCGA-G3-A5SJ        TCGA-G3-A5SK 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-G3-A5SL        TCGA-G3-A5SM 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
[1] "hr=" "1.8"
D58V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  9Q LOSS MUTATED        10        6         0          9          0          3
  9Q LOSS WILD-TYPE      35       19         2         16          3          1
                   vv
clus                STAGE IV STAGE IVA STAGE IVB
  9Q LOSS MUTATED          1         1         1
  9Q LOSS WILD-TYPE        0         0         0
D58V3, multiclass
                   vv
clus                T1 T2 T3 T4
  9Q LOSS MUTATED   12  9 13  2
  9Q LOSS WILD-TYPE 36 19 21  4
D58V4, multiclass
    clus
vv   9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  T1              12                36
  T2               9                19
  T3              13                21
  T4               2                 4
D58V5, binary
                   cls
clus                 0  1
  9Q LOSS MUTATED   21  3
  9Q LOSS WILD-TYPE 53  0
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED     21    3
  9Q LOSS WILD-TYPE   53    0
   clus
vv  9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  0              21                53
  1               3                 0
                   vv
clus                M0 M1 MX
  9Q LOSS MUTATED   24  2 11
  9Q LOSS WILD-TYPE 66  0 14
D58V6, multiclass
    clus
vv   9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  M0              24                66
  M1               2                 0
  MX              11                14
D58V7, binary
                   cls
clus                 0  1
  9Q LOSS MUTATED   13 24
  9Q LOSS WILD-TYPE 31 49
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED     13   24
  9Q LOSS WILD-TYPE   31   49
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  FEMALE              13                31
  MALE                24                49
                   vv
clus                R0 R1 R2 RX
  9Q LOSS MUTATED   25  4  1  5
  9Q LOSS WILD-TYPE 68  6  0  3
D58V8, multiclass
    clus
vv   9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  R0              25                68
  R1               4                 6
  R2               1                 0
  RX               5                 3

Clustering(59) Variable = 10P LOSS MUTATION ANALYSIS
D59V1, survival
                    sevent
clus2                 0  1
  10P LOSS MUTATED    9  3
  10P LOSS WILD-TYPE 52 50
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                12                102 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                 3                 50 
$`10P LOSS MUTATED`
TCGA-BC-A112 TCGA-BC-A217 TCGA-BC-A5W4 TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MC 
        5.03        13.81         9.50         0.10         0.07         0.13 
TCGA-DD-A11A TCGA-DD-A11C TCGA-DD-A4NE TCGA-DD-A4NQ TCGA-FV-A3I0 TCGA-G3-A25X 
        2.60        21.76        21.67        12.26         0.20        58.49 

$`10P LOSS WILD-TYPE`
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T 
       48.99        27.91        37.32        10.13        46.78        27.52 
TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 
       27.52         2.99        25.32        23.34         1.12        69.57 
TCGA-BC-A216 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5261 
       44.42         0.26        16.37         0.07         2.86         3.02 
TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3MB TCGA-DD-A113 TCGA-DD-A114 
        3.39         4.24         3.32         0.10        79.73        37.74 
TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11B TCGA-DD-A11D 
       83.57        53.29       112.96         7.33         0.46        51.25 
TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE 
       90.67        79.36        66.31        19.76        75.65         6.67 
TCGA-DD-A1EF TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EL TCGA-DD-A39V 
       12.95        49.15         6.02        29.16        13.64        21.14 
TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 
       55.66         5.59        19.73        25.81         7.66        70.06 
TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A8 
       17.59        20.12       102.74       107.11        13.78         0.36 
TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4ND TCGA-DD-A4NF TCGA-DD-A4NG TCGA-DD-A4NH 
       30.58        33.14        73.38        14.07        14.93        14.24 
TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO 
       10.78        15.06        39.75        56.25        29.56        61.45 
TCGA-DD-A4NP TCGA-ED-A459 TCGA-ED-A5KG TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA 
       93.67         0.23         0.20        10.85         7.76        11.74 
TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT 
        1.97         0.62         3.19         0.43        23.01        14.40 
TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 
       32.45        19.07         6.35         0.13         0.03         0.33 
TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V 
       60.36         0.39         1.22        51.02        53.79        28.27 
TCGA-G3-A25W TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CH TCGA-G3-A3CI 
       30.71        14.86        21.53        22.13        25.64         5.88 
TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SJ TCGA-G3-A5SK TCGA-G3-A5SL TCGA-G3-A5SM 
       19.53        19.23        11.97         9.93         7.99         4.37 

  10P LOSS MUTATED 10P LOSS WILD-TYPE 
              0.07               0.03 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
             58.49             112.96 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
             7.265             19.150 
[1] "0.1 - 58.5 (7.3)"   "0.0 - 113.0 (19.1)"
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
  "10P LOSS MUTATED" "10P LOSS WILD-TYPE"   "10P LOSS MUTATED" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-BC-A5W4 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE"   "10P LOSS MUTATED" 
        TCGA-CC-5258         TCGA-CC-5260         TCGA-CC-5261 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-CC-5262         TCGA-CC-5263         TCGA-CC-A1HT 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-CC-A3M9         TCGA-CC-A3MA         TCGA-CC-A3MB 
  "10P LOSS MUTATED"   "10P LOSS MUTATED" "10P LOSS WILD-TYPE" 
        TCGA-CC-A3MC         TCGA-DD-A113         TCGA-DD-A114 
  "10P LOSS MUTATED" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"10P LOSS WILD-TYPE"   "10P LOSS MUTATED" "10P LOSS WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
  "10P LOSS MUTATED" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-DD-A1EA         TCGA-DD-A1EB         TCGA-DD-A1EC 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-DD-A1ED         TCGA-DD-A1EE         TCGA-DD-A1EF 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-DD-A1EH         TCGA-DD-A1EI         TCGA-DD-A1EJ 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-DD-A1EL         TCGA-DD-A39V         TCGA-DD-A39X 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-DD-A39Y         TCGA-DD-A39Z         TCGA-DD-A3A0 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-DD-A3A1         TCGA-DD-A3A2         TCGA-DD-A3A3 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-DD-A3A4         TCGA-DD-A3A5         TCGA-DD-A3A6 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-DD-A3A7         TCGA-DD-A3A8         TCGA-DD-A3A9 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-DD-A4NA         TCGA-DD-A4ND         TCGA-DD-A4NE 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE"   "10P LOSS MUTATED" 
        TCGA-DD-A4NF         TCGA-DD-A4NG         TCGA-DD-A4NH 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-DD-A4NI         TCGA-DD-A4NJ         TCGA-DD-A4NK 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-DD-A4NL         TCGA-DD-A4NN         TCGA-DD-A4NO 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-DD-A4NP         TCGA-DD-A4NQ         TCGA-ED-A459 
"10P LOSS WILD-TYPE"   "10P LOSS MUTATED" "10P LOSS WILD-TYPE" 
        TCGA-ED-A5KG         TCGA-EP-A12J         TCGA-EP-A26S 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-EP-A2KA         TCGA-EP-A2KB         TCGA-EP-A2KC 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-EP-A3JL         TCGA-EP-A3RK         TCGA-ES-A2HS 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-ES-A2HT         TCGA-FV-A23B         TCGA-FV-A2QR 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-FV-A3I0         TCGA-FV-A3R2         TCGA-FV-A3R3 
  "10P LOSS MUTATED" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-FV-A495         TCGA-FV-A496         TCGA-FV-A4ZP 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-FV-A4ZQ         TCGA-G3-A25S         TCGA-G3-A25T 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-G3-A25U         TCGA-G3-A25V         TCGA-G3-A25W 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-G3-A25X         TCGA-G3-A25Y         TCGA-G3-A25Z 
  "10P LOSS MUTATED" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-G3-A3CG         TCGA-G3-A3CH         TCGA-G3-A3CI 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK         TCGA-G3-A5SJ 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-G3-A5SK         TCGA-G3-A5SL         TCGA-G3-A5SM 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
  "10P LOSS MUTATED" "10P LOSS WILD-TYPE"   "10P LOSS MUTATED" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-BC-A5W4 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE"   "10P LOSS MUTATED" 
        TCGA-CC-5258         TCGA-CC-5260         TCGA-CC-5261 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-CC-5262         TCGA-CC-5263         TCGA-CC-A1HT 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-CC-A3M9         TCGA-CC-A3MA         TCGA-CC-A3MB 
  "10P LOSS MUTATED"   "10P LOSS MUTATED" "10P LOSS WILD-TYPE" 
        TCGA-CC-A3MC         TCGA-DD-A113         TCGA-DD-A114 
  "10P LOSS MUTATED" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"10P LOSS WILD-TYPE"   "10P LOSS MUTATED" "10P LOSS WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
  "10P LOSS MUTATED" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-DD-A1EA         TCGA-DD-A1EB         TCGA-DD-A1EC 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-DD-A1ED         TCGA-DD-A1EE         TCGA-DD-A1EF 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-DD-A1EH         TCGA-DD-A1EI         TCGA-DD-A1EJ 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-DD-A1EL         TCGA-DD-A39V         TCGA-DD-A39X 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-DD-A39Y         TCGA-DD-A39Z         TCGA-DD-A3A0 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-DD-A3A1         TCGA-DD-A3A2         TCGA-DD-A3A3 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-DD-A3A4         TCGA-DD-A3A5         TCGA-DD-A3A6 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-DD-A3A7         TCGA-DD-A3A8         TCGA-DD-A3A9 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-DD-A4NA         TCGA-DD-A4ND         TCGA-DD-A4NE 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE"   "10P LOSS MUTATED" 
        TCGA-DD-A4NF         TCGA-DD-A4NG         TCGA-DD-A4NH 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-DD-A4NI         TCGA-DD-A4NJ         TCGA-DD-A4NK 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-DD-A4NL         TCGA-DD-A4NN         TCGA-DD-A4NO 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-DD-A4NP         TCGA-DD-A4NQ         TCGA-ED-A459 
"10P LOSS WILD-TYPE"   "10P LOSS MUTATED" "10P LOSS WILD-TYPE" 
        TCGA-ED-A5KG         TCGA-EP-A12J         TCGA-EP-A26S 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-EP-A2KA         TCGA-EP-A2KB         TCGA-EP-A2KC 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-EP-A3JL         TCGA-EP-A3RK         TCGA-ES-A2HS 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-ES-A2HT         TCGA-FV-A23B         TCGA-FV-A2QR 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-FV-A3I0         TCGA-FV-A3R2         TCGA-FV-A3R3 
  "10P LOSS MUTATED" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-FV-A495         TCGA-FV-A496         TCGA-FV-A4ZP 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-FV-A4ZQ         TCGA-G3-A25S         TCGA-G3-A25T 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-G3-A25U         TCGA-G3-A25V         TCGA-G3-A25W 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-G3-A25X         TCGA-G3-A25Y         TCGA-G3-A25Z 
  "10P LOSS MUTATED" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-G3-A3CG         TCGA-G3-A3CH         TCGA-G3-A3CI 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK         TCGA-G3-A5SJ 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-G3-A5SK         TCGA-G3-A5SL         TCGA-G3-A5SM 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
  "10P LOSS MUTATED" "10P LOSS WILD-TYPE"   "10P LOSS MUTATED" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-BC-A5W4 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE"   "10P LOSS MUTATED" 
        TCGA-CC-5258         TCGA-CC-5260         TCGA-CC-5261 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-CC-5262         TCGA-CC-5263         TCGA-CC-A1HT 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-CC-A3M9         TCGA-CC-A3MA         TCGA-CC-A3MB 
  "10P LOSS MUTATED"   "10P LOSS MUTATED" "10P LOSS WILD-TYPE" 
        TCGA-CC-A3MC         TCGA-DD-A113         TCGA-DD-A114 
  "10P LOSS MUTATED" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"10P LOSS WILD-TYPE"   "10P LOSS MUTATED" "10P LOSS WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
  "10P LOSS MUTATED" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-DD-A1EA         TCGA-DD-A1EB         TCGA-DD-A1EC 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-DD-A1ED         TCGA-DD-A1EE         TCGA-DD-A1EF 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-DD-A1EH         TCGA-DD-A1EI         TCGA-DD-A1EJ 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-DD-A1EL         TCGA-DD-A39V         TCGA-DD-A39X 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-DD-A39Y         TCGA-DD-A39Z         TCGA-DD-A3A0 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-DD-A3A1         TCGA-DD-A3A2         TCGA-DD-A3A3 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-DD-A3A4         TCGA-DD-A3A5         TCGA-DD-A3A6 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-DD-A3A7         TCGA-DD-A3A8         TCGA-DD-A3A9 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-DD-A4NA         TCGA-DD-A4ND         TCGA-DD-A4NE 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE"   "10P LOSS MUTATED" 
        TCGA-DD-A4NF         TCGA-DD-A4NG         TCGA-DD-A4NH 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-DD-A4NI         TCGA-DD-A4NJ         TCGA-DD-A4NK 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-DD-A4NL         TCGA-DD-A4NN         TCGA-DD-A4NO 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-DD-A4NP         TCGA-DD-A4NQ         TCGA-ED-A459 
"10P LOSS WILD-TYPE"   "10P LOSS MUTATED" "10P LOSS WILD-TYPE" 
        TCGA-ED-A5KG         TCGA-EP-A12J         TCGA-EP-A26S 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-EP-A2KA         TCGA-EP-A2KB         TCGA-EP-A2KC 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-EP-A3JL         TCGA-EP-A3RK         TCGA-ES-A2HS 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-ES-A2HT         TCGA-FV-A23B         TCGA-FV-A2QR 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-FV-A3I0         TCGA-FV-A3R2         TCGA-FV-A3R3 
  "10P LOSS MUTATED" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-FV-A495         TCGA-FV-A496         TCGA-FV-A4ZP 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-FV-A4ZQ         TCGA-G3-A25S         TCGA-G3-A25T 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-G3-A25U         TCGA-G3-A25V         TCGA-G3-A25W 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-G3-A25X         TCGA-G3-A25Y         TCGA-G3-A25Z 
  "10P LOSS MUTATED" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-G3-A3CG         TCGA-G3-A3CH         TCGA-G3-A3CI 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK         TCGA-G3-A5SJ 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-G3-A5SK         TCGA-G3-A5SL         TCGA-G3-A5SM 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
[1] "hr=" "1.1"
D59V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  10P LOSS MUTATED         2        4         0          5          0
  10P LOSS WILD-TYPE      43       21         2         20          3
                    vv
clus                 STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  10P LOSS MUTATED            0        0         1         0
  10P LOSS WILD-TYPE          4        1         0         1
D59V3, multiclass
                    vv
clus                 T1 T2 T3 T4
  10P LOSS MUTATED    3  4  6  0
  10P LOSS WILD-TYPE 45 24 28  6
D59V4, multiclass
    clus
vv   10P LOSS MUTATED 10P LOSS WILD-TYPE
  T1                3                 45
  T2                4                 24
  T3                6                 28
  T4                0                  6
D59V5, binary
                    cls
clus                  0  1
  10P LOSS MUTATED    8  1
  10P LOSS WILD-TYPE 66  2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED      8    1
  10P LOSS WILD-TYPE   66    2
   clus
vv  10P LOSS MUTATED 10P LOSS WILD-TYPE
  0                8                 66
  1                1                  2
                    vv
clus                 M0 M1 MX
  10P LOSS MUTATED   11  0  2
  10P LOSS WILD-TYPE 79  2 23
D59V6, multiclass
    clus
vv   10P LOSS MUTATED 10P LOSS WILD-TYPE
  M0               11                 79
  M1                0                  2
  MX                2                 23
D59V7, binary
                    cls
clus                  0  1
  10P LOSS MUTATED    3 10
  10P LOSS WILD-TYPE 41 63
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED      3   10
  10P LOSS WILD-TYPE   41   63
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  FEMALE                3                 41
  MALE                 10                 63
                    vv
clus                 R0 R1 R2 RX
  10P LOSS MUTATED   11  1  0  1
  10P LOSS WILD-TYPE 82  9  1  7
D59V8, multiclass
    clus
vv   10P LOSS MUTATED 10P LOSS WILD-TYPE
  R0               11                 82
  R1                1                  9
  R2                0                  1
  RX                1                  7

Clustering(60) Variable = 10Q LOSS MUTATION ANALYSIS
D60V1, survival
                    sevent
clus2                 0  1
  10Q LOSS MUTATED   14 10
  10Q LOSS WILD-TYPE 47 43
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                24                 90 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                10                 43 
$`10Q LOSS MUTATED`
TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10W TCGA-BC-A112 TCGA-BC-A217 TCGA-BC-A5W4 
       37.32        10.13         2.99         5.03        13.81         9.50 
TCGA-CC-5260 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MC TCGA-DD-A114 
        2.86         3.32         0.10         0.07         0.13        37.74 
TCGA-DD-A11A TCGA-DD-A11C TCGA-DD-A1EL TCGA-DD-A4NE TCGA-DD-A4NQ TCGA-ED-A459 
        2.60        21.76        13.64        21.67        12.26         0.23 
TCGA-FV-A3I0 TCGA-FV-A496 TCGA-G3-A25U TCGA-G3-A25X TCGA-G3-A5SJ TCGA-G3-A5SK 
        0.20         0.33        53.79        58.49        11.97         9.93 

$`10Q LOSS WILD-TYPE`
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10X 
       48.99        27.91        46.78        27.52        27.52        25.32 
TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A216 TCGA-BC-A3KF TCGA-BC-A3KG 
       23.34         1.12        69.57        44.42         0.26        16.37 
TCGA-CC-5258 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A3MB TCGA-DD-A113 
        0.07         3.02         3.39         4.24         0.10        79.73 
TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11B TCGA-DD-A11D 
       83.57        53.29       112.96         7.33         0.46        51.25 
TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE 
       90.67        79.36        66.31        19.76        75.65         6.67 
TCGA-DD-A1EF TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A39V TCGA-DD-A39X 
       12.95        49.15         6.02        29.16        21.14        55.66 
TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 
        5.59        19.73        25.81         7.66        70.06        17.59 
TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A3A9 
       20.12       102.74       107.11        13.78         0.36        30.58 
TCGA-DD-A4NA TCGA-DD-A4ND TCGA-DD-A4NF TCGA-DD-A4NG TCGA-DD-A4NH TCGA-DD-A4NI 
       33.14        73.38        14.07        14.93        14.24        10.78 
TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP 
       15.06        39.75        56.25        29.56        61.45        93.67 
TCGA-ED-A5KG TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC 
        0.20        10.85         7.76        11.74         1.97         0.62 
TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QR 
        3.19         0.43        23.01        14.40        32.45        19.07 
TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25S 
        6.35         0.13         0.03        60.36         0.39         1.22 
TCGA-G3-A25T TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG 
       51.02        28.27        30.71        14.86        21.53        22.13 
TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SL TCGA-G3-A5SM 
       25.64         5.88        19.53        19.23         7.99         4.37 

  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
              0.07               0.03 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
             58.49             112.96 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
             9.715             19.745 
[1] "0.1 - 58.5 (9.7)"   "0.0 - 113.0 (19.7)"
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-BC-A5W4 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" 
        TCGA-CC-5258         TCGA-CC-5260         TCGA-CC-5261 
"10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-CC-5262         TCGA-CC-5263         TCGA-CC-A1HT 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" 
        TCGA-CC-A3M9         TCGA-CC-A3MA         TCGA-CC-A3MB 
  "10Q LOSS MUTATED"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-CC-A3MC         TCGA-DD-A113         TCGA-DD-A114 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-DD-A1EA         TCGA-DD-A1EB         TCGA-DD-A1EC 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-DD-A1ED         TCGA-DD-A1EE         TCGA-DD-A1EF 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-DD-A1EH         TCGA-DD-A1EI         TCGA-DD-A1EJ 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-DD-A1EL         TCGA-DD-A39V         TCGA-DD-A39X 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-DD-A39Y         TCGA-DD-A39Z         TCGA-DD-A3A0 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-DD-A3A1         TCGA-DD-A3A2         TCGA-DD-A3A3 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-DD-A3A4         TCGA-DD-A3A5         TCGA-DD-A3A6 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-DD-A3A7         TCGA-DD-A3A8         TCGA-DD-A3A9 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-DD-A4NA         TCGA-DD-A4ND         TCGA-DD-A4NE 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" 
        TCGA-DD-A4NF         TCGA-DD-A4NG         TCGA-DD-A4NH 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-DD-A4NI         TCGA-DD-A4NJ         TCGA-DD-A4NK 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-DD-A4NL         TCGA-DD-A4NN         TCGA-DD-A4NO 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-DD-A4NP         TCGA-DD-A4NQ         TCGA-ED-A459 
"10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED"   "10Q LOSS MUTATED" 
        TCGA-ED-A5KG         TCGA-EP-A12J         TCGA-EP-A26S 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EP-A2KA         TCGA-EP-A2KB         TCGA-EP-A2KC 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EP-A3JL         TCGA-EP-A3RK         TCGA-ES-A2HS 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-ES-A2HT         TCGA-FV-A23B         TCGA-FV-A2QR 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-FV-A3I0         TCGA-FV-A3R2         TCGA-FV-A3R3 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-FV-A495         TCGA-FV-A496         TCGA-FV-A4ZP 
"10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-FV-A4ZQ         TCGA-G3-A25S         TCGA-G3-A25T 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-G3-A25U         TCGA-G3-A25V         TCGA-G3-A25W 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-G3-A25X         TCGA-G3-A25Y         TCGA-G3-A25Z 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-G3-A3CG         TCGA-G3-A3CH         TCGA-G3-A3CI 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK         TCGA-G3-A5SJ 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" 
        TCGA-G3-A5SK         TCGA-G3-A5SL         TCGA-G3-A5SM 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-BC-A5W4 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" 
        TCGA-CC-5258         TCGA-CC-5260         TCGA-CC-5261 
"10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-CC-5262         TCGA-CC-5263         TCGA-CC-A1HT 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" 
        TCGA-CC-A3M9         TCGA-CC-A3MA         TCGA-CC-A3MB 
  "10Q LOSS MUTATED"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-CC-A3MC         TCGA-DD-A113         TCGA-DD-A114 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-DD-A1EA         TCGA-DD-A1EB         TCGA-DD-A1EC 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-DD-A1ED         TCGA-DD-A1EE         TCGA-DD-A1EF 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-DD-A1EH         TCGA-DD-A1EI         TCGA-DD-A1EJ 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-DD-A1EL         TCGA-DD-A39V         TCGA-DD-A39X 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-DD-A39Y         TCGA-DD-A39Z         TCGA-DD-A3A0 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-DD-A3A1         TCGA-DD-A3A2         TCGA-DD-A3A3 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-DD-A3A4         TCGA-DD-A3A5         TCGA-DD-A3A6 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-DD-A3A7         TCGA-DD-A3A8         TCGA-DD-A3A9 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-DD-A4NA         TCGA-DD-A4ND         TCGA-DD-A4NE 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" 
        TCGA-DD-A4NF         TCGA-DD-A4NG         TCGA-DD-A4NH 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-DD-A4NI         TCGA-DD-A4NJ         TCGA-DD-A4NK 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-DD-A4NL         TCGA-DD-A4NN         TCGA-DD-A4NO 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-DD-A4NP         TCGA-DD-A4NQ         TCGA-ED-A459 
"10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED"   "10Q LOSS MUTATED" 
        TCGA-ED-A5KG         TCGA-EP-A12J         TCGA-EP-A26S 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EP-A2KA         TCGA-EP-A2KB         TCGA-EP-A2KC 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EP-A3JL         TCGA-EP-A3RK         TCGA-ES-A2HS 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-ES-A2HT         TCGA-FV-A23B         TCGA-FV-A2QR 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-FV-A3I0         TCGA-FV-A3R2         TCGA-FV-A3R3 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-FV-A495         TCGA-FV-A496         TCGA-FV-A4ZP 
"10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-FV-A4ZQ         TCGA-G3-A25S         TCGA-G3-A25T 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-G3-A25U         TCGA-G3-A25V         TCGA-G3-A25W 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-G3-A25X         TCGA-G3-A25Y         TCGA-G3-A25Z 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-G3-A3CG         TCGA-G3-A3CH         TCGA-G3-A3CI 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK         TCGA-G3-A5SJ 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" 
        TCGA-G3-A5SK         TCGA-G3-A5SL         TCGA-G3-A5SM 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-BC-A5W4 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" 
        TCGA-CC-5258         TCGA-CC-5260         TCGA-CC-5261 
"10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-CC-5262         TCGA-CC-5263         TCGA-CC-A1HT 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" 
        TCGA-CC-A3M9         TCGA-CC-A3MA         TCGA-CC-A3MB 
  "10Q LOSS MUTATED"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-CC-A3MC         TCGA-DD-A113         TCGA-DD-A114 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-DD-A1EA         TCGA-DD-A1EB         TCGA-DD-A1EC 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-DD-A1ED         TCGA-DD-A1EE         TCGA-DD-A1EF 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-DD-A1EH         TCGA-DD-A1EI         TCGA-DD-A1EJ 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-DD-A1EL         TCGA-DD-A39V         TCGA-DD-A39X 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-DD-A39Y         TCGA-DD-A39Z         TCGA-DD-A3A0 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-DD-A3A1         TCGA-DD-A3A2         TCGA-DD-A3A3 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-DD-A3A4         TCGA-DD-A3A5         TCGA-DD-A3A6 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-DD-A3A7         TCGA-DD-A3A8         TCGA-DD-A3A9 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-DD-A4NA         TCGA-DD-A4ND         TCGA-DD-A4NE 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" 
        TCGA-DD-A4NF         TCGA-DD-A4NG         TCGA-DD-A4NH 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-DD-A4NI         TCGA-DD-A4NJ         TCGA-DD-A4NK 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-DD-A4NL         TCGA-DD-A4NN         TCGA-DD-A4NO 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-DD-A4NP         TCGA-DD-A4NQ         TCGA-ED-A459 
"10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED"   "10Q LOSS MUTATED" 
        TCGA-ED-A5KG         TCGA-EP-A12J         TCGA-EP-A26S 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EP-A2KA         TCGA-EP-A2KB         TCGA-EP-A2KC 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EP-A3JL         TCGA-EP-A3RK         TCGA-ES-A2HS 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-ES-A2HT         TCGA-FV-A23B         TCGA-FV-A2QR 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-FV-A3I0         TCGA-FV-A3R2         TCGA-FV-A3R3 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-FV-A495         TCGA-FV-A496         TCGA-FV-A4ZP 
"10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-FV-A4ZQ         TCGA-G3-A25S         TCGA-G3-A25T 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-G3-A25U         TCGA-G3-A25V         TCGA-G3-A25W 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-G3-A25X         TCGA-G3-A25Y         TCGA-G3-A25Z 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-G3-A3CG         TCGA-G3-A3CH         TCGA-G3-A3CI 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK         TCGA-G3-A5SJ 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" 
        TCGA-G3-A5SK         TCGA-G3-A5SL         TCGA-G3-A5SM 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
[1] "hr=" "1.8"
D60V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  10Q LOSS MUTATED         6        7         0          7          0
  10Q LOSS WILD-TYPE      39       18         2         18          3
                    vv
clus                 STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  10Q LOSS MUTATED            1        0         1         0
  10Q LOSS WILD-TYPE          3        1         0         1
D60V3, multiclass
                    vv
clus                 T1 T2 T3 T4
  10Q LOSS MUTATED    7  8  9  2
  10Q LOSS WILD-TYPE 41 20 25  4
D60V4, multiclass
    clus
vv   10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  T1                7                 41
  T2                8                 20
  T3                9                 25
  T4                2                  4
D60V5, binary
                    cls
clus                  0  1
  10Q LOSS MUTATED   14  1
  10Q LOSS WILD-TYPE 60  2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED     14    1
  10Q LOSS WILD-TYPE   60    2
   clus
vv  10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  0               14                 60
  1                1                  2
                    vv
clus                 M0 M1 MX
  10Q LOSS MUTATED   21  0  5
  10Q LOSS WILD-TYPE 69  2 20
D60V6, multiclass
    clus
vv   10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  M0               21                 69
  M1                0                  2
  MX                5                 20
D60V7, binary
                    cls
clus                  0  1
  10Q LOSS MUTATED    8 18
  10Q LOSS WILD-TYPE 36 55
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED      8   18
  10Q LOSS WILD-TYPE   36   55
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  FEMALE                8                 36
  MALE                 18                 55
                    vv
clus                 R0 R1 R2 RX
  10Q LOSS MUTATED   19  3  0  3
  10Q LOSS WILD-TYPE 74  7  1  5
D60V8, multiclass
    clus
vv   10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  R0               19                 74
  R1                3                  7
  R2                0                  1
  RX                3                  5

Clustering(61) Variable = 11P LOSS MUTATION ANALYSIS
D61V1, survival
                    sevent
clus2                 0  1
  11P LOSS MUTATED    8 10
  11P LOSS WILD-TYPE 53 43
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                18                 96 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                10                 43 
$`11P LOSS MUTATED`
TCGA-BC-A10Q TCGA-BC-A10S TCGA-BC-A112 TCGA-BC-A217 TCGA-CC-A3MA TCGA-CC-A3MC 
       37.32        46.78         5.03        13.81         0.07         0.13 
TCGA-DD-A113 TCGA-DD-A115 TCGA-DD-A1E9 TCGA-DD-A1EJ TCGA-DD-A39X TCGA-DD-A4ND 
       79.73        83.57        90.67        29.16        55.66        73.38 
TCGA-DD-A4NE TCGA-EP-A2KC TCGA-FV-A496 TCGA-FV-A4ZP TCGA-G3-A25S TCGA-G3-A5SJ 
       21.67         0.62         0.33        60.36         1.22        11.97 

$`11P LOSS WILD-TYPE`
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W 
       48.99        27.91        10.13        27.52        27.52         2.99 
TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A216 TCGA-BC-A3KF 
       25.32        23.34         1.12        69.57        44.42         0.26 
TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 
       16.37         9.50         0.07         2.86         3.02         3.39 
TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MB TCGA-DD-A114 TCGA-DD-A116 
        4.24         3.32         0.10         0.10        37.74        53.29 
TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D 
      112.96         7.33         2.60         0.46        21.76        51.25 
TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EF 
       79.36        66.31        19.76        75.65         6.67        12.95 
TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39Y TCGA-DD-A39Z 
       49.15         6.02        13.64        21.14         5.59        19.73 
TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 
       25.81         7.66        70.06        17.59        20.12       102.74 
TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NF 
      107.11        13.78         0.36        30.58        33.14        14.07 
TCGA-DD-A4NG TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL 
       14.93        14.24        10.78        15.06        39.75        56.25 
TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-ED-A459 TCGA-ED-A5KG 
       29.56        61.45        93.67        12.26         0.23         0.20 
TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A3JL TCGA-EP-A3RK 
       10.85         7.76        11.74         1.97         3.19         0.43 
TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3R2 
       23.01        14.40        32.45        19.07         0.20         6.35 
TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A4ZQ TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V 
        0.13         0.03         0.39        51.02        53.79        28.27 
TCGA-G3-A25W TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CH 
       30.71        58.49        14.86        21.53        22.13        25.64 
TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SK TCGA-G3-A5SL TCGA-G3-A5SM 
        5.88        19.53        19.23         9.93         7.99         4.37 

  11P LOSS MUTATED 11P LOSS WILD-TYPE 
              0.07               0.03 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
             90.67             112.96 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
            25.415             14.995 
[1] "0.1 - 90.7 (25.4)"  "0.0 - 113.0 (15.0)"
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE"   "11P LOSS MUTATED" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
"11P LOSS WILD-TYPE"   "11P LOSS MUTATED" "11P LOSS WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE"   "11P LOSS MUTATED" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-BC-A5W4 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-CC-5258         TCGA-CC-5260         TCGA-CC-5261 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-CC-5262         TCGA-CC-5263         TCGA-CC-A1HT 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-CC-A3M9         TCGA-CC-A3MA         TCGA-CC-A3MB 
"11P LOSS WILD-TYPE"   "11P LOSS MUTATED" "11P LOSS WILD-TYPE" 
        TCGA-CC-A3MC         TCGA-DD-A113         TCGA-DD-A114 
  "11P LOSS MUTATED"   "11P LOSS MUTATED" "11P LOSS WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE"   "11P LOSS MUTATED" 
        TCGA-DD-A1EA         TCGA-DD-A1EB         TCGA-DD-A1EC 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-DD-A1ED         TCGA-DD-A1EE         TCGA-DD-A1EF 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-DD-A1EH         TCGA-DD-A1EI         TCGA-DD-A1EJ 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE"   "11P LOSS MUTATED" 
        TCGA-DD-A1EL         TCGA-DD-A39V         TCGA-DD-A39X 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE"   "11P LOSS MUTATED" 
        TCGA-DD-A39Y         TCGA-DD-A39Z         TCGA-DD-A3A0 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-DD-A3A1         TCGA-DD-A3A2         TCGA-DD-A3A3 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-DD-A3A4         TCGA-DD-A3A5         TCGA-DD-A3A6 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-DD-A3A7         TCGA-DD-A3A8         TCGA-DD-A3A9 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-DD-A4NA         TCGA-DD-A4ND         TCGA-DD-A4NE 
"11P LOSS WILD-TYPE"   "11P LOSS MUTATED"   "11P LOSS MUTATED" 
        TCGA-DD-A4NF         TCGA-DD-A4NG         TCGA-DD-A4NH 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-DD-A4NI         TCGA-DD-A4NJ         TCGA-DD-A4NK 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-DD-A4NL         TCGA-DD-A4NN         TCGA-DD-A4NO 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-DD-A4NP         TCGA-DD-A4NQ         TCGA-ED-A459 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-ED-A5KG         TCGA-EP-A12J         TCGA-EP-A26S 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-EP-A2KA         TCGA-EP-A2KB         TCGA-EP-A2KC 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE"   "11P LOSS MUTATED" 
        TCGA-EP-A3JL         TCGA-EP-A3RK         TCGA-ES-A2HS 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-ES-A2HT         TCGA-FV-A23B         TCGA-FV-A2QR 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-FV-A3I0         TCGA-FV-A3R2         TCGA-FV-A3R3 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-FV-A495         TCGA-FV-A496         TCGA-FV-A4ZP 
"11P LOSS WILD-TYPE"   "11P LOSS MUTATED"   "11P LOSS MUTATED" 
        TCGA-FV-A4ZQ         TCGA-G3-A25S         TCGA-G3-A25T 
"11P LOSS WILD-TYPE"   "11P LOSS MUTATED" "11P LOSS WILD-TYPE" 
        TCGA-G3-A25U         TCGA-G3-A25V         TCGA-G3-A25W 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-G3-A25X         TCGA-G3-A25Y         TCGA-G3-A25Z 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-G3-A3CG         TCGA-G3-A3CH         TCGA-G3-A3CI 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK         TCGA-G3-A5SJ 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE"   "11P LOSS MUTATED" 
        TCGA-G3-A5SK         TCGA-G3-A5SL         TCGA-G3-A5SM 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE"   "11P LOSS MUTATED" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
"11P LOSS WILD-TYPE"   "11P LOSS MUTATED" "11P LOSS WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE"   "11P LOSS MUTATED" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-BC-A5W4 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-CC-5258         TCGA-CC-5260         TCGA-CC-5261 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-CC-5262         TCGA-CC-5263         TCGA-CC-A1HT 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-CC-A3M9         TCGA-CC-A3MA         TCGA-CC-A3MB 
"11P LOSS WILD-TYPE"   "11P LOSS MUTATED" "11P LOSS WILD-TYPE" 
        TCGA-CC-A3MC         TCGA-DD-A113         TCGA-DD-A114 
  "11P LOSS MUTATED"   "11P LOSS MUTATED" "11P LOSS WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE"   "11P LOSS MUTATED" 
        TCGA-DD-A1EA         TCGA-DD-A1EB         TCGA-DD-A1EC 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-DD-A1ED         TCGA-DD-A1EE         TCGA-DD-A1EF 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-DD-A1EH         TCGA-DD-A1EI         TCGA-DD-A1EJ 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE"   "11P LOSS MUTATED" 
        TCGA-DD-A1EL         TCGA-DD-A39V         TCGA-DD-A39X 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE"   "11P LOSS MUTATED" 
        TCGA-DD-A39Y         TCGA-DD-A39Z         TCGA-DD-A3A0 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-DD-A3A1         TCGA-DD-A3A2         TCGA-DD-A3A3 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-DD-A3A4         TCGA-DD-A3A5         TCGA-DD-A3A6 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-DD-A3A7         TCGA-DD-A3A8         TCGA-DD-A3A9 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-DD-A4NA         TCGA-DD-A4ND         TCGA-DD-A4NE 
"11P LOSS WILD-TYPE"   "11P LOSS MUTATED"   "11P LOSS MUTATED" 
        TCGA-DD-A4NF         TCGA-DD-A4NG         TCGA-DD-A4NH 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-DD-A4NI         TCGA-DD-A4NJ         TCGA-DD-A4NK 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-DD-A4NL         TCGA-DD-A4NN         TCGA-DD-A4NO 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-DD-A4NP         TCGA-DD-A4NQ         TCGA-ED-A459 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-ED-A5KG         TCGA-EP-A12J         TCGA-EP-A26S 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-EP-A2KA         TCGA-EP-A2KB         TCGA-EP-A2KC 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE"   "11P LOSS MUTATED" 
        TCGA-EP-A3JL         TCGA-EP-A3RK         TCGA-ES-A2HS 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-ES-A2HT         TCGA-FV-A23B         TCGA-FV-A2QR 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-FV-A3I0         TCGA-FV-A3R2         TCGA-FV-A3R3 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-FV-A495         TCGA-FV-A496         TCGA-FV-A4ZP 
"11P LOSS WILD-TYPE"   "11P LOSS MUTATED"   "11P LOSS MUTATED" 
        TCGA-FV-A4ZQ         TCGA-G3-A25S         TCGA-G3-A25T 
"11P LOSS WILD-TYPE"   "11P LOSS MUTATED" "11P LOSS WILD-TYPE" 
        TCGA-G3-A25U         TCGA-G3-A25V         TCGA-G3-A25W 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-G3-A25X         TCGA-G3-A25Y         TCGA-G3-A25Z 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-G3-A3CG         TCGA-G3-A3CH         TCGA-G3-A3CI 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK         TCGA-G3-A5SJ 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE"   "11P LOSS MUTATED" 
        TCGA-G3-A5SK         TCGA-G3-A5SL         TCGA-G3-A5SM 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE"   "11P LOSS MUTATED" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
"11P LOSS WILD-TYPE"   "11P LOSS MUTATED" "11P LOSS WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE"   "11P LOSS MUTATED" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-BC-A5W4 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-CC-5258         TCGA-CC-5260         TCGA-CC-5261 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-CC-5262         TCGA-CC-5263         TCGA-CC-A1HT 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-CC-A3M9         TCGA-CC-A3MA         TCGA-CC-A3MB 
"11P LOSS WILD-TYPE"   "11P LOSS MUTATED" "11P LOSS WILD-TYPE" 
        TCGA-CC-A3MC         TCGA-DD-A113         TCGA-DD-A114 
  "11P LOSS MUTATED"   "11P LOSS MUTATED" "11P LOSS WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE"   "11P LOSS MUTATED" 
        TCGA-DD-A1EA         TCGA-DD-A1EB         TCGA-DD-A1EC 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-DD-A1ED         TCGA-DD-A1EE         TCGA-DD-A1EF 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-DD-A1EH         TCGA-DD-A1EI         TCGA-DD-A1EJ 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE"   "11P LOSS MUTATED" 
        TCGA-DD-A1EL         TCGA-DD-A39V         TCGA-DD-A39X 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE"   "11P LOSS MUTATED" 
        TCGA-DD-A39Y         TCGA-DD-A39Z         TCGA-DD-A3A0 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-DD-A3A1         TCGA-DD-A3A2         TCGA-DD-A3A3 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-DD-A3A4         TCGA-DD-A3A5         TCGA-DD-A3A6 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-DD-A3A7         TCGA-DD-A3A8         TCGA-DD-A3A9 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-DD-A4NA         TCGA-DD-A4ND         TCGA-DD-A4NE 
"11P LOSS WILD-TYPE"   "11P LOSS MUTATED"   "11P LOSS MUTATED" 
        TCGA-DD-A4NF         TCGA-DD-A4NG         TCGA-DD-A4NH 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-DD-A4NI         TCGA-DD-A4NJ         TCGA-DD-A4NK 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-DD-A4NL         TCGA-DD-A4NN         TCGA-DD-A4NO 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-DD-A4NP         TCGA-DD-A4NQ         TCGA-ED-A459 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-ED-A5KG         TCGA-EP-A12J         TCGA-EP-A26S 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-EP-A2KA         TCGA-EP-A2KB         TCGA-EP-A2KC 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE"   "11P LOSS MUTATED" 
        TCGA-EP-A3JL         TCGA-EP-A3RK         TCGA-ES-A2HS 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-ES-A2HT         TCGA-FV-A23B         TCGA-FV-A2QR 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-FV-A3I0         TCGA-FV-A3R2         TCGA-FV-A3R3 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-FV-A495         TCGA-FV-A496         TCGA-FV-A4ZP 
"11P LOSS WILD-TYPE"   "11P LOSS MUTATED"   "11P LOSS MUTATED" 
        TCGA-FV-A4ZQ         TCGA-G3-A25S         TCGA-G3-A25T 
"11P LOSS WILD-TYPE"   "11P LOSS MUTATED" "11P LOSS WILD-TYPE" 
        TCGA-G3-A25U         TCGA-G3-A25V         TCGA-G3-A25W 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-G3-A25X         TCGA-G3-A25Y         TCGA-G3-A25Z 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-G3-A3CG         TCGA-G3-A3CH         TCGA-G3-A3CI 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK         TCGA-G3-A5SJ 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE"   "11P LOSS MUTATED" 
        TCGA-G3-A5SK         TCGA-G3-A5SL         TCGA-G3-A5SM 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
[1] "hr=" "1"  
D61V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  11P LOSS MUTATED         7        2         0          6          0
  11P LOSS WILD-TYPE      38       23         2         19          3
                    vv
clus                 STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  11P LOSS MUTATED            1        0         1         0
  11P LOSS WILD-TYPE          3        1         0         1
D61V3, multiclass
                    vv
clus                 T1 T2 T3 T4
  11P LOSS MUTATED    9  3  8  0
  11P LOSS WILD-TYPE 39 25 26  6
D61V4, multiclass
    clus
vv   11P LOSS MUTATED 11P LOSS WILD-TYPE
  T1                9                 39
  T2                3                 25
  T3                8                 26
  T4                0                  6
D61V5, binary
                    cls
clus                  0  1
  11P LOSS MUTATED    9  2
  11P LOSS WILD-TYPE 65  1
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED      9    2
  11P LOSS WILD-TYPE   65    1
   clus
vv  11P LOSS MUTATED 11P LOSS WILD-TYPE
  0                9                 65
  1                2                  1
                    vv
clus                 M0 M1 MX
  11P LOSS MUTATED   15  0  5
  11P LOSS WILD-TYPE 75  2 20
D61V6, multiclass
    clus
vv   11P LOSS MUTATED 11P LOSS WILD-TYPE
  M0               15                 75
  M1                0                  2
  MX                5                 20
D61V7, binary
                    cls
clus                  0  1
  11P LOSS MUTATED    8 12
  11P LOSS WILD-TYPE 36 61
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED      8   12
  11P LOSS WILD-TYPE   36   61
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  FEMALE                8                 36
  MALE                 12                 61
                    vv
clus                 R0 R1 R2 RX
  11P LOSS MUTATED   16  3  0  1
  11P LOSS WILD-TYPE 77  7  1  7
D61V8, multiclass
    clus
vv   11P LOSS MUTATED 11P LOSS WILD-TYPE
  R0               16                 77
  R1                3                  7
  R2                0                  1
  RX                1                  7

Clustering(62) Variable = 11Q LOSS MUTATION ANALYSIS
D62V1, survival
                    sevent
clus2                 0  1
  11Q LOSS MUTATED    9 11
  11Q LOSS WILD-TYPE 52 42
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                20                 94 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                11                 42 
$`11Q LOSS MUTATED`
TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10S TCGA-BC-A112 TCGA-BC-A217 TCGA-CC-5263 
       27.91        37.32        46.78         5.03        13.81         4.24 
TCGA-CC-A3MC TCGA-DD-A113 TCGA-DD-A115 TCGA-DD-A11A TCGA-DD-A1E9 TCGA-DD-A1EJ 
        0.13        79.73        83.57         2.60        90.67        29.16 
TCGA-DD-A39X TCGA-DD-A4ND TCGA-DD-A4NE TCGA-EP-A2KC TCGA-FV-A496 TCGA-FV-A4ZP 
       55.66        73.38        21.67         0.62         0.33        60.36 
TCGA-G3-A25S TCGA-G3-A5SJ 
        1.22        11.97 

$`11Q LOSS WILD-TYPE`
TCGA-BC-4072 TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X 
       48.99        10.13        27.52        27.52         2.99        25.32 
TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A216 TCGA-BC-A3KF TCGA-BC-A3KG 
       23.34         1.12        69.57        44.42         0.26        16.37 
TCGA-BC-A5W4 TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-A1HT 
        9.50         0.07         2.86         3.02         3.39         3.32 
TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-DD-A114 TCGA-DD-A116 TCGA-DD-A118 
        0.10         0.07         0.10        37.74        53.29       112.96 
TCGA-DD-A119 TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1EA TCGA-DD-A1EB 
        7.33         0.46        21.76        51.25        79.36        66.31 
TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EH TCGA-DD-A1EI 
       19.76        75.65         6.67        12.95        49.15         6.02 
TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 
       13.64        21.14         5.59        19.73        25.81         7.66 
TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 
       70.06        17.59        20.12       102.74       107.11        13.78 
TCGA-DD-A3A8 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NF TCGA-DD-A4NG TCGA-DD-A4NH 
        0.36        30.58        33.14        14.07        14.93        14.24 
TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO 
       10.78        15.06        39.75        56.25        29.56        61.45 
TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-ED-A459 TCGA-ED-A5KG TCGA-EP-A12J TCGA-EP-A26S 
       93.67        12.26         0.23         0.20        10.85         7.76 
TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT 
       11.74         1.97         3.19         0.43        23.01        14.40 
TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 
       32.45        19.07         0.20         6.35         0.13         0.03 
TCGA-FV-A4ZQ TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25X 
        0.39        51.02        53.79        28.27        30.71        58.49 
TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ 
       14.86        21.53        22.13        25.64         5.88        19.53 
TCGA-G3-A3CK TCGA-G3-A5SK TCGA-G3-A5SL TCGA-G3-A5SM 
       19.23         9.93         7.99         4.37 

  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
              0.13               0.03 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
             90.67             112.96 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
            24.790             14.995 
[1] "0.1 - 90.7 (24.8)"  "0.0 - 113.0 (15.0)"
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED"   "11Q LOSS MUTATED" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
"11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-BC-A5W4 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-CC-5258         TCGA-CC-5260         TCGA-CC-5261 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-CC-5262         TCGA-CC-5263         TCGA-CC-A1HT 
"11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" 
        TCGA-CC-A3M9         TCGA-CC-A3MA         TCGA-CC-A3MB 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-CC-A3MC         TCGA-DD-A113         TCGA-DD-A114 
  "11Q LOSS MUTATED"   "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" 
        TCGA-DD-A1EA         TCGA-DD-A1EB         TCGA-DD-A1EC 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-DD-A1ED         TCGA-DD-A1EE         TCGA-DD-A1EF 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-DD-A1EH         TCGA-DD-A1EI         TCGA-DD-A1EJ 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" 
        TCGA-DD-A1EL         TCGA-DD-A39V         TCGA-DD-A39X 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" 
        TCGA-DD-A39Y         TCGA-DD-A39Z         TCGA-DD-A3A0 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-DD-A3A1         TCGA-DD-A3A2         TCGA-DD-A3A3 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-DD-A3A4         TCGA-DD-A3A5         TCGA-DD-A3A6 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-DD-A3A7         TCGA-DD-A3A8         TCGA-DD-A3A9 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-DD-A4NA         TCGA-DD-A4ND         TCGA-DD-A4NE 
"11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED"   "11Q LOSS MUTATED" 
        TCGA-DD-A4NF         TCGA-DD-A4NG         TCGA-DD-A4NH 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-DD-A4NI         TCGA-DD-A4NJ         TCGA-DD-A4NK 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-DD-A4NL         TCGA-DD-A4NN         TCGA-DD-A4NO 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-DD-A4NP         TCGA-DD-A4NQ         TCGA-ED-A459 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-ED-A5KG         TCGA-EP-A12J         TCGA-EP-A26S 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-EP-A2KA         TCGA-EP-A2KB         TCGA-EP-A2KC 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" 
        TCGA-EP-A3JL         TCGA-EP-A3RK         TCGA-ES-A2HS 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-ES-A2HT         TCGA-FV-A23B         TCGA-FV-A2QR 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-FV-A3I0         TCGA-FV-A3R2         TCGA-FV-A3R3 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-FV-A495         TCGA-FV-A496         TCGA-FV-A4ZP 
"11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED"   "11Q LOSS MUTATED" 
        TCGA-FV-A4ZQ         TCGA-G3-A25S         TCGA-G3-A25T 
"11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" 
        TCGA-G3-A25U         TCGA-G3-A25V         TCGA-G3-A25W 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-G3-A25X         TCGA-G3-A25Y         TCGA-G3-A25Z 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-G3-A3CG         TCGA-G3-A3CH         TCGA-G3-A3CI 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK         TCGA-G3-A5SJ 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" 
        TCGA-G3-A5SK         TCGA-G3-A5SL         TCGA-G3-A5SM 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED"   "11Q LOSS MUTATED" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
"11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-BC-A5W4 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-CC-5258         TCGA-CC-5260         TCGA-CC-5261 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-CC-5262         TCGA-CC-5263         TCGA-CC-A1HT 
"11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" 
        TCGA-CC-A3M9         TCGA-CC-A3MA         TCGA-CC-A3MB 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-CC-A3MC         TCGA-DD-A113         TCGA-DD-A114 
  "11Q LOSS MUTATED"   "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" 
        TCGA-DD-A1EA         TCGA-DD-A1EB         TCGA-DD-A1EC 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-DD-A1ED         TCGA-DD-A1EE         TCGA-DD-A1EF 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-DD-A1EH         TCGA-DD-A1EI         TCGA-DD-A1EJ 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" 
        TCGA-DD-A1EL         TCGA-DD-A39V         TCGA-DD-A39X 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" 
        TCGA-DD-A39Y         TCGA-DD-A39Z         TCGA-DD-A3A0 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-DD-A3A1         TCGA-DD-A3A2         TCGA-DD-A3A3 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-DD-A3A4         TCGA-DD-A3A5         TCGA-DD-A3A6 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-DD-A3A7         TCGA-DD-A3A8         TCGA-DD-A3A9 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-DD-A4NA         TCGA-DD-A4ND         TCGA-DD-A4NE 
"11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED"   "11Q LOSS MUTATED" 
        TCGA-DD-A4NF         TCGA-DD-A4NG         TCGA-DD-A4NH 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-DD-A4NI         TCGA-DD-A4NJ         TCGA-DD-A4NK 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-DD-A4NL         TCGA-DD-A4NN         TCGA-DD-A4NO 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-DD-A4NP         TCGA-DD-A4NQ         TCGA-ED-A459 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-ED-A5KG         TCGA-EP-A12J         TCGA-EP-A26S 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-EP-A2KA         TCGA-EP-A2KB         TCGA-EP-A2KC 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" 
        TCGA-EP-A3JL         TCGA-EP-A3RK         TCGA-ES-A2HS 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-ES-A2HT         TCGA-FV-A23B         TCGA-FV-A2QR 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-FV-A3I0         TCGA-FV-A3R2         TCGA-FV-A3R3 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-FV-A495         TCGA-FV-A496         TCGA-FV-A4ZP 
"11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED"   "11Q LOSS MUTATED" 
        TCGA-FV-A4ZQ         TCGA-G3-A25S         TCGA-G3-A25T 
"11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" 
        TCGA-G3-A25U         TCGA-G3-A25V         TCGA-G3-A25W 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-G3-A25X         TCGA-G3-A25Y         TCGA-G3-A25Z 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-G3-A3CG         TCGA-G3-A3CH         TCGA-G3-A3CI 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK         TCGA-G3-A5SJ 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" 
        TCGA-G3-A5SK         TCGA-G3-A5SL         TCGA-G3-A5SM 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED"   "11Q LOSS MUTATED" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
"11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-BC-A5W4 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-CC-5258         TCGA-CC-5260         TCGA-CC-5261 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-CC-5262         TCGA-CC-5263         TCGA-CC-A1HT 
"11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" 
        TCGA-CC-A3M9         TCGA-CC-A3MA         TCGA-CC-A3MB 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-CC-A3MC         TCGA-DD-A113         TCGA-DD-A114 
  "11Q LOSS MUTATED"   "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" 
        TCGA-DD-A1EA         TCGA-DD-A1EB         TCGA-DD-A1EC 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-DD-A1ED         TCGA-DD-A1EE         TCGA-DD-A1EF 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-DD-A1EH         TCGA-DD-A1EI         TCGA-DD-A1EJ 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" 
        TCGA-DD-A1EL         TCGA-DD-A39V         TCGA-DD-A39X 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" 
        TCGA-DD-A39Y         TCGA-DD-A39Z         TCGA-DD-A3A0 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-DD-A3A1         TCGA-DD-A3A2         TCGA-DD-A3A3 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-DD-A3A4         TCGA-DD-A3A5         TCGA-DD-A3A6 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-DD-A3A7         TCGA-DD-A3A8         TCGA-DD-A3A9 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-DD-A4NA         TCGA-DD-A4ND         TCGA-DD-A4NE 
"11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED"   "11Q LOSS MUTATED" 
        TCGA-DD-A4NF         TCGA-DD-A4NG         TCGA-DD-A4NH 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-DD-A4NI         TCGA-DD-A4NJ         TCGA-DD-A4NK 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-DD-A4NL         TCGA-DD-A4NN         TCGA-DD-A4NO 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-DD-A4NP         TCGA-DD-A4NQ         TCGA-ED-A459 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-ED-A5KG         TCGA-EP-A12J         TCGA-EP-A26S 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-EP-A2KA         TCGA-EP-A2KB         TCGA-EP-A2KC 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" 
        TCGA-EP-A3JL         TCGA-EP-A3RK         TCGA-ES-A2HS 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-ES-A2HT         TCGA-FV-A23B         TCGA-FV-A2QR 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-FV-A3I0         TCGA-FV-A3R2         TCGA-FV-A3R3 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-FV-A495         TCGA-FV-A496         TCGA-FV-A4ZP 
"11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED"   "11Q LOSS MUTATED" 
        TCGA-FV-A4ZQ         TCGA-G3-A25S         TCGA-G3-A25T 
"11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" 
        TCGA-G3-A25U         TCGA-G3-A25V         TCGA-G3-A25W 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-G3-A25X         TCGA-G3-A25Y         TCGA-G3-A25Z 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-G3-A3CG         TCGA-G3-A3CH         TCGA-G3-A3CI 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK         TCGA-G3-A5SJ 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" 
        TCGA-G3-A5SK         TCGA-G3-A5SL         TCGA-G3-A5SM 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
[1] "hr=" "1"  
D62V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  11Q LOSS MUTATED         8        2         0          7          0
  11Q LOSS WILD-TYPE      37       23         2         18          3
                    vv
clus                 STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  11Q LOSS MUTATED            1        0         1         0
  11Q LOSS WILD-TYPE          3        1         0         1
D62V3, multiclass
                    vv
clus                 T1 T2 T3 T4
  11Q LOSS MUTATED   10  3  9  0
  11Q LOSS WILD-TYPE 38 25 25  6
D62V4, multiclass
    clus
vv   11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  T1               10                 38
  T2                3                 25
  T3                9                 25
  T4                0                  6
D62V5, binary
                    cls
clus                  0  1
  11Q LOSS MUTATED   11  2
  11Q LOSS WILD-TYPE 63  1
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED     11    2
  11Q LOSS WILD-TYPE   63    1
   clus
vv  11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  0               11                 63
  1                2                  1
                    vv
clus                 M0 M1 MX
  11Q LOSS MUTATED   16  0  6
  11Q LOSS WILD-TYPE 74  2 19
D62V6, multiclass
    clus
vv   11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  M0               16                 74
  M1                0                  2
  MX                6                 19
D62V7, binary
                    cls
clus                  0  1
  11Q LOSS MUTATED    8 14
  11Q LOSS WILD-TYPE 36 59
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED      8   14
  11Q LOSS WILD-TYPE   36   59
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  FEMALE                8                 36
  MALE                 14                 59
                    vv
clus                 R0 R1 R2 RX
  11Q LOSS MUTATED   16  4  0  2
  11Q LOSS WILD-TYPE 77  6  1  6
D62V8, multiclass
    clus
vv   11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  R0               16                 77
  R1                4                  6
  R2                0                  1
  RX                2                  6

Clustering(63) Variable = 12P LOSS MUTATION ANALYSIS
D63V1, survival
                    sevent
clus2                 0  1
  12P LOSS MUTATED   10 10
  12P LOSS WILD-TYPE 51 43
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                20                 94 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                10                 43 
$`12P LOSS MUTATED`
TCGA-BC-A217 TCGA-BC-A5W4 TCGA-CC-A1HT TCGA-CC-A3MC TCGA-DD-A119 TCGA-DD-A1EH 
       13.81         9.50         3.32         0.13         7.33        49.15 
TCGA-DD-A1EJ TCGA-DD-A1EL TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A3A1 TCGA-DD-A4NA 
       29.16        13.64        55.66         5.59         7.66        33.14 
TCGA-DD-A4NH TCGA-DD-A4NJ TCGA-DD-A4NO TCGA-EP-A2KC TCGA-FV-A3R2 TCGA-FV-A496 
       14.24        15.06        61.45         0.62         6.35         0.33 
TCGA-G3-A25S TCGA-G3-A25Z 
        1.22        21.53 

$`12P LOSS WILD-TYPE`
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T 
       48.99        27.91        37.32        10.13        46.78        27.52 
TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 
       27.52         2.99        25.32        23.34         1.12        69.57 
TCGA-BC-A112 TCGA-BC-A216 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-CC-5258 TCGA-CC-5260 
        5.03        44.42         0.26        16.37         0.07         2.86 
TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB 
        3.02         3.39         4.24         0.10         0.07         0.10 
TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A11A 
       79.73        37.74        83.57        53.29       112.96         2.60 
TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB 
        0.46        21.76        51.25        90.67        79.36        66.31 
TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EI TCGA-DD-A39V 
       19.76        75.65         6.67        12.95         6.02        21.14 
TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 
       19.73        25.81        70.06        17.59        20.12       102.74 
TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A3A9 TCGA-DD-A4ND TCGA-DD-A4NE 
      107.11        13.78         0.36        30.58        73.38        21.67 
TCGA-DD-A4NF TCGA-DD-A4NG TCGA-DD-A4NI TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN 
       14.07        14.93        10.78        39.75        56.25        29.56 
TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-ED-A459 TCGA-ED-A5KG TCGA-EP-A12J TCGA-EP-A26S 
       93.67        12.26         0.23         0.20        10.85         7.76 
TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT 
       11.74         1.97         3.19         0.43        23.01        14.40 
TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A4ZP 
       32.45        19.07         0.20         0.13         0.03        60.36 
TCGA-FV-A4ZQ TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25X 
        0.39        51.02        53.79        28.27        30.71        58.49 
TCGA-G3-A25Y TCGA-G3-A3CG TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK 
       14.86        22.13        25.64         5.88        19.53        19.23 
TCGA-G3-A5SJ TCGA-G3-A5SK TCGA-G3-A5SL TCGA-G3-A5SM 
       11.97         9.93         7.99         4.37 

  12P LOSS MUTATED 12P LOSS WILD-TYPE 
              0.13               0.03 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
             61.45             112.96 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
             11.57              19.38 
[1] "0.1 - 61.5 (11.6)"  "0.0 - 113.0 (19.4)"
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE"   "12P LOSS MUTATED" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-BC-A5W4 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE"   "12P LOSS MUTATED" 
        TCGA-CC-5258         TCGA-CC-5260         TCGA-CC-5261 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-CC-5262         TCGA-CC-5263         TCGA-CC-A1HT 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE"   "12P LOSS MUTATED" 
        TCGA-CC-A3M9         TCGA-CC-A3MA         TCGA-CC-A3MB 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-CC-A3MC         TCGA-DD-A113         TCGA-DD-A114 
  "12P LOSS MUTATED" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
  "12P LOSS MUTATED" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DD-A1EA         TCGA-DD-A1EB         TCGA-DD-A1EC 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DD-A1ED         TCGA-DD-A1EE         TCGA-DD-A1EF 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DD-A1EH         TCGA-DD-A1EI         TCGA-DD-A1EJ 
  "12P LOSS MUTATED" "12P LOSS WILD-TYPE"   "12P LOSS MUTATED" 
        TCGA-DD-A1EL         TCGA-DD-A39V         TCGA-DD-A39X 
  "12P LOSS MUTATED" "12P LOSS WILD-TYPE"   "12P LOSS MUTATED" 
        TCGA-DD-A39Y         TCGA-DD-A39Z         TCGA-DD-A3A0 
  "12P LOSS MUTATED" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DD-A3A1         TCGA-DD-A3A2         TCGA-DD-A3A3 
  "12P LOSS MUTATED" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DD-A3A4         TCGA-DD-A3A5         TCGA-DD-A3A6 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DD-A3A7         TCGA-DD-A3A8         TCGA-DD-A3A9 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DD-A4NA         TCGA-DD-A4ND         TCGA-DD-A4NE 
  "12P LOSS MUTATED" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DD-A4NF         TCGA-DD-A4NG         TCGA-DD-A4NH 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE"   "12P LOSS MUTATED" 
        TCGA-DD-A4NI         TCGA-DD-A4NJ         TCGA-DD-A4NK 
"12P LOSS WILD-TYPE"   "12P LOSS MUTATED" "12P LOSS WILD-TYPE" 
        TCGA-DD-A4NL         TCGA-DD-A4NN         TCGA-DD-A4NO 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE"   "12P LOSS MUTATED" 
        TCGA-DD-A4NP         TCGA-DD-A4NQ         TCGA-ED-A459 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-ED-A5KG         TCGA-EP-A12J         TCGA-EP-A26S 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EP-A2KA         TCGA-EP-A2KB         TCGA-EP-A2KC 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE"   "12P LOSS MUTATED" 
        TCGA-EP-A3JL         TCGA-EP-A3RK         TCGA-ES-A2HS 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-ES-A2HT         TCGA-FV-A23B         TCGA-FV-A2QR 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-FV-A3I0         TCGA-FV-A3R2         TCGA-FV-A3R3 
"12P LOSS WILD-TYPE"   "12P LOSS MUTATED" "12P LOSS WILD-TYPE" 
        TCGA-FV-A495         TCGA-FV-A496         TCGA-FV-A4ZP 
"12P LOSS WILD-TYPE"   "12P LOSS MUTATED" "12P LOSS WILD-TYPE" 
        TCGA-FV-A4ZQ         TCGA-G3-A25S         TCGA-G3-A25T 
"12P LOSS WILD-TYPE"   "12P LOSS MUTATED" "12P LOSS WILD-TYPE" 
        TCGA-G3-A25U         TCGA-G3-A25V         TCGA-G3-A25W 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-G3-A25X         TCGA-G3-A25Y         TCGA-G3-A25Z 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE"   "12P LOSS MUTATED" 
        TCGA-G3-A3CG         TCGA-G3-A3CH         TCGA-G3-A3CI 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK         TCGA-G3-A5SJ 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-G3-A5SK         TCGA-G3-A5SL         TCGA-G3-A5SM 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE"   "12P LOSS MUTATED" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-BC-A5W4 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE"   "12P LOSS MUTATED" 
        TCGA-CC-5258         TCGA-CC-5260         TCGA-CC-5261 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-CC-5262         TCGA-CC-5263         TCGA-CC-A1HT 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE"   "12P LOSS MUTATED" 
        TCGA-CC-A3M9         TCGA-CC-A3MA         TCGA-CC-A3MB 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-CC-A3MC         TCGA-DD-A113         TCGA-DD-A114 
  "12P LOSS MUTATED" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
  "12P LOSS MUTATED" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DD-A1EA         TCGA-DD-A1EB         TCGA-DD-A1EC 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DD-A1ED         TCGA-DD-A1EE         TCGA-DD-A1EF 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DD-A1EH         TCGA-DD-A1EI         TCGA-DD-A1EJ 
  "12P LOSS MUTATED" "12P LOSS WILD-TYPE"   "12P LOSS MUTATED" 
        TCGA-DD-A1EL         TCGA-DD-A39V         TCGA-DD-A39X 
  "12P LOSS MUTATED" "12P LOSS WILD-TYPE"   "12P LOSS MUTATED" 
        TCGA-DD-A39Y         TCGA-DD-A39Z         TCGA-DD-A3A0 
  "12P LOSS MUTATED" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DD-A3A1         TCGA-DD-A3A2         TCGA-DD-A3A3 
  "12P LOSS MUTATED" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DD-A3A4         TCGA-DD-A3A5         TCGA-DD-A3A6 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DD-A3A7         TCGA-DD-A3A8         TCGA-DD-A3A9 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DD-A4NA         TCGA-DD-A4ND         TCGA-DD-A4NE 
  "12P LOSS MUTATED" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DD-A4NF         TCGA-DD-A4NG         TCGA-DD-A4NH 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE"   "12P LOSS MUTATED" 
        TCGA-DD-A4NI         TCGA-DD-A4NJ         TCGA-DD-A4NK 
"12P LOSS WILD-TYPE"   "12P LOSS MUTATED" "12P LOSS WILD-TYPE" 
        TCGA-DD-A4NL         TCGA-DD-A4NN         TCGA-DD-A4NO 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE"   "12P LOSS MUTATED" 
        TCGA-DD-A4NP         TCGA-DD-A4NQ         TCGA-ED-A459 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-ED-A5KG         TCGA-EP-A12J         TCGA-EP-A26S 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EP-A2KA         TCGA-EP-A2KB         TCGA-EP-A2KC 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE"   "12P LOSS MUTATED" 
        TCGA-EP-A3JL         TCGA-EP-A3RK         TCGA-ES-A2HS 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-ES-A2HT         TCGA-FV-A23B         TCGA-FV-A2QR 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-FV-A3I0         TCGA-FV-A3R2         TCGA-FV-A3R3 
"12P LOSS WILD-TYPE"   "12P LOSS MUTATED" "12P LOSS WILD-TYPE" 
        TCGA-FV-A495         TCGA-FV-A496         TCGA-FV-A4ZP 
"12P LOSS WILD-TYPE"   "12P LOSS MUTATED" "12P LOSS WILD-TYPE" 
        TCGA-FV-A4ZQ         TCGA-G3-A25S         TCGA-G3-A25T 
"12P LOSS WILD-TYPE"   "12P LOSS MUTATED" "12P LOSS WILD-TYPE" 
        TCGA-G3-A25U         TCGA-G3-A25V         TCGA-G3-A25W 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-G3-A25X         TCGA-G3-A25Y         TCGA-G3-A25Z 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE"   "12P LOSS MUTATED" 
        TCGA-G3-A3CG         TCGA-G3-A3CH         TCGA-G3-A3CI 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK         TCGA-G3-A5SJ 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-G3-A5SK         TCGA-G3-A5SL         TCGA-G3-A5SM 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE"   "12P LOSS MUTATED" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-BC-A5W4 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE"   "12P LOSS MUTATED" 
        TCGA-CC-5258         TCGA-CC-5260         TCGA-CC-5261 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-CC-5262         TCGA-CC-5263         TCGA-CC-A1HT 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE"   "12P LOSS MUTATED" 
        TCGA-CC-A3M9         TCGA-CC-A3MA         TCGA-CC-A3MB 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-CC-A3MC         TCGA-DD-A113         TCGA-DD-A114 
  "12P LOSS MUTATED" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
  "12P LOSS MUTATED" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DD-A1EA         TCGA-DD-A1EB         TCGA-DD-A1EC 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DD-A1ED         TCGA-DD-A1EE         TCGA-DD-A1EF 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DD-A1EH         TCGA-DD-A1EI         TCGA-DD-A1EJ 
  "12P LOSS MUTATED" "12P LOSS WILD-TYPE"   "12P LOSS MUTATED" 
        TCGA-DD-A1EL         TCGA-DD-A39V         TCGA-DD-A39X 
  "12P LOSS MUTATED" "12P LOSS WILD-TYPE"   "12P LOSS MUTATED" 
        TCGA-DD-A39Y         TCGA-DD-A39Z         TCGA-DD-A3A0 
  "12P LOSS MUTATED" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DD-A3A1         TCGA-DD-A3A2         TCGA-DD-A3A3 
  "12P LOSS MUTATED" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DD-A3A4         TCGA-DD-A3A5         TCGA-DD-A3A6 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DD-A3A7         TCGA-DD-A3A8         TCGA-DD-A3A9 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DD-A4NA         TCGA-DD-A4ND         TCGA-DD-A4NE 
  "12P LOSS MUTATED" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DD-A4NF         TCGA-DD-A4NG         TCGA-DD-A4NH 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE"   "12P LOSS MUTATED" 
        TCGA-DD-A4NI         TCGA-DD-A4NJ         TCGA-DD-A4NK 
"12P LOSS WILD-TYPE"   "12P LOSS MUTATED" "12P LOSS WILD-TYPE" 
        TCGA-DD-A4NL         TCGA-DD-A4NN         TCGA-DD-A4NO 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE"   "12P LOSS MUTATED" 
        TCGA-DD-A4NP         TCGA-DD-A4NQ         TCGA-ED-A459 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-ED-A5KG         TCGA-EP-A12J         TCGA-EP-A26S 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EP-A2KA         TCGA-EP-A2KB         TCGA-EP-A2KC 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE"   "12P LOSS MUTATED" 
        TCGA-EP-A3JL         TCGA-EP-A3RK         TCGA-ES-A2HS 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-ES-A2HT         TCGA-FV-A23B         TCGA-FV-A2QR 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-FV-A3I0         TCGA-FV-A3R2         TCGA-FV-A3R3 
"12P LOSS WILD-TYPE"   "12P LOSS MUTATED" "12P LOSS WILD-TYPE" 
        TCGA-FV-A495         TCGA-FV-A496         TCGA-FV-A4ZP 
"12P LOSS WILD-TYPE"   "12P LOSS MUTATED" "12P LOSS WILD-TYPE" 
        TCGA-FV-A4ZQ         TCGA-G3-A25S         TCGA-G3-A25T 
"12P LOSS WILD-TYPE"   "12P LOSS MUTATED" "12P LOSS WILD-TYPE" 
        TCGA-G3-A25U         TCGA-G3-A25V         TCGA-G3-A25W 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-G3-A25X         TCGA-G3-A25Y         TCGA-G3-A25Z 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE"   "12P LOSS MUTATED" 
        TCGA-G3-A3CG         TCGA-G3-A3CH         TCGA-G3-A3CI 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK         TCGA-G3-A5SJ 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-G3-A5SK         TCGA-G3-A5SL         TCGA-G3-A5SM 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
[1] "hr=" "1.7"
D63V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  12P LOSS MUTATED         8        4         1          4          1
  12P LOSS WILD-TYPE      37       21         1         21          2
                    vv
clus                 STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  12P LOSS MUTATED            2        1         0         0
  12P LOSS WILD-TYPE          2        0         1         1
D63V3, multiclass
                    vv
clus                 T1 T2 T3 T4
  12P LOSS MUTATED    9  5  7  0
  12P LOSS WILD-TYPE 39 23 27  6
D63V4, multiclass
    clus
vv   12P LOSS MUTATED 12P LOSS WILD-TYPE
  T1                9                 39
  T2                5                 23
  T3                7                 27
  T4                0                  6
D63V5, binary
                    cls
clus                  0  1
  12P LOSS MUTATED   12  2
  12P LOSS WILD-TYPE 62  1
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED     12    2
  12P LOSS WILD-TYPE   62    1
   clus
vv  12P LOSS MUTATED 12P LOSS WILD-TYPE
  0               12                 62
  1                2                  1
                    vv
clus                 M0 M1 MX
  12P LOSS MUTATED   17  1  3
  12P LOSS WILD-TYPE 73  1 22
D63V6, multiclass
    clus
vv   12P LOSS MUTATED 12P LOSS WILD-TYPE
  M0               17                 73
  M1                1                  1
  MX                3                 22
D63V7, binary
                    cls
clus                  0  1
  12P LOSS MUTATED    8 13
  12P LOSS WILD-TYPE 36 60
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED      8   13
  12P LOSS WILD-TYPE   36   60
        clus
vv       12P LOSS MUTATED 12P LOSS WILD-TYPE
  FEMALE                8                 36
  MALE                 13                 60
                    vv
clus                 R0 R1 R2 RX
  12P LOSS MUTATED   17  2  1  0
  12P LOSS WILD-TYPE 76  8  0  8
D63V8, multiclass
    clus
vv   12P LOSS MUTATED 12P LOSS WILD-TYPE
  R0               17                 76
  R1                2                  8
  R2                1                  0
  RX                0                  8

Clustering(64) Variable = 12Q LOSS MUTATION ANALYSIS
D64V1, survival
                    sevent
clus2                 0  1
  12Q LOSS MUTATED    6  5
  12Q LOSS WILD-TYPE 55 48
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                11                103 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                 5                 48 
$`12Q LOSS MUTATED`
TCGA-BC-A217 TCGA-CC-A1HT TCGA-CC-A3MC TCGA-DD-A119 TCGA-DD-A1EH TCGA-DD-A1EL 
       13.81         3.32         0.13         7.33        49.15        13.64 
TCGA-DD-A39X TCGA-DD-A4NO TCGA-EP-A2KC TCGA-FV-A496 TCGA-G3-A25Z 
       55.66        61.45         0.62         0.33        21.53 

$`12Q LOSS WILD-TYPE`
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T 
       48.99        27.91        37.32        10.13        46.78        27.52 
TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 
       27.52         2.99        25.32        23.34         1.12        69.57 
TCGA-BC-A112 TCGA-BC-A216 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-CC-5258 
        5.03        44.42         0.26        16.37         9.50         0.07 
TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A3M9 TCGA-CC-A3MA 
        2.86         3.02         3.39         4.24         0.10         0.07 
TCGA-CC-A3MB TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 
        0.10        79.73        37.74        83.57        53.29       112.96 
TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA 
        2.60         0.46        21.76        51.25        90.67        79.36 
TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EI 
       66.31        19.76        75.65         6.67        12.95         6.02 
TCGA-DD-A1EJ TCGA-DD-A39V TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 
       29.16        21.14         5.59        19.73        25.81         7.66 
TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 
       70.06        17.59        20.12       102.74       107.11        13.78 
TCGA-DD-A3A8 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4ND TCGA-DD-A4NE TCGA-DD-A4NF 
        0.36        30.58        33.14        73.38        21.67        14.07 
TCGA-DD-A4NG TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL 
       14.93        14.24        10.78        15.06        39.75        56.25 
TCGA-DD-A4NN TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-ED-A459 TCGA-ED-A5KG TCGA-EP-A12J 
       29.56        93.67        12.26         0.23         0.20        10.85 
TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS 
        7.76        11.74         1.97         3.19         0.43        23.01 
TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3R2 TCGA-FV-A3R3 
       14.40        32.45        19.07         0.20         6.35         0.13 
TCGA-FV-A495 TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25U 
        0.03        60.36         0.39         1.22        51.02        53.79 
TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A3CG TCGA-G3-A3CH 
       28.27        30.71        58.49        14.86        22.13        25.64 
TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SJ TCGA-G3-A5SK TCGA-G3-A5SL 
        5.88        19.53        19.23        11.97         9.93         7.99 
TCGA-G3-A5SM 
        4.37 

  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
              0.13               0.03 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
             61.45             112.96 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
             13.64              17.59 
[1] "0.1 - 61.5 (13.6)"  "0.0 - 113.0 (17.6)"
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE"   "12Q LOSS MUTATED" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-BC-A5W4 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-CC-5258         TCGA-CC-5260         TCGA-CC-5261 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-CC-5262         TCGA-CC-5263         TCGA-CC-A1HT 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE"   "12Q LOSS MUTATED" 
        TCGA-CC-A3M9         TCGA-CC-A3MA         TCGA-CC-A3MB 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-CC-A3MC         TCGA-DD-A113         TCGA-DD-A114 
  "12Q LOSS MUTATED" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
  "12Q LOSS MUTATED" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DD-A1EA         TCGA-DD-A1EB         TCGA-DD-A1EC 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DD-A1ED         TCGA-DD-A1EE         TCGA-DD-A1EF 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DD-A1EH         TCGA-DD-A1EI         TCGA-DD-A1EJ 
  "12Q LOSS MUTATED" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DD-A1EL         TCGA-DD-A39V         TCGA-DD-A39X 
  "12Q LOSS MUTATED" "12Q LOSS WILD-TYPE"   "12Q LOSS MUTATED" 
        TCGA-DD-A39Y         TCGA-DD-A39Z         TCGA-DD-A3A0 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DD-A3A1         TCGA-DD-A3A2         TCGA-DD-A3A3 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DD-A3A4         TCGA-DD-A3A5         TCGA-DD-A3A6 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DD-A3A7         TCGA-DD-A3A8         TCGA-DD-A3A9 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DD-A4NA         TCGA-DD-A4ND         TCGA-DD-A4NE 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DD-A4NF         TCGA-DD-A4NG         TCGA-DD-A4NH 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DD-A4NI         TCGA-DD-A4NJ         TCGA-DD-A4NK 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DD-A4NL         TCGA-DD-A4NN         TCGA-DD-A4NO 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE"   "12Q LOSS MUTATED" 
        TCGA-DD-A4NP         TCGA-DD-A4NQ         TCGA-ED-A459 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-ED-A5KG         TCGA-EP-A12J         TCGA-EP-A26S 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-EP-A2KA         TCGA-EP-A2KB         TCGA-EP-A2KC 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE"   "12Q LOSS MUTATED" 
        TCGA-EP-A3JL         TCGA-EP-A3RK         TCGA-ES-A2HS 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-ES-A2HT         TCGA-FV-A23B         TCGA-FV-A2QR 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-FV-A3I0         TCGA-FV-A3R2         TCGA-FV-A3R3 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-FV-A495         TCGA-FV-A496         TCGA-FV-A4ZP 
"12Q LOSS WILD-TYPE"   "12Q LOSS MUTATED" "12Q LOSS WILD-TYPE" 
        TCGA-FV-A4ZQ         TCGA-G3-A25S         TCGA-G3-A25T 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-G3-A25U         TCGA-G3-A25V         TCGA-G3-A25W 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-G3-A25X         TCGA-G3-A25Y         TCGA-G3-A25Z 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE"   "12Q LOSS MUTATED" 
        TCGA-G3-A3CG         TCGA-G3-A3CH         TCGA-G3-A3CI 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK         TCGA-G3-A5SJ 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-G3-A5SK         TCGA-G3-A5SL         TCGA-G3-A5SM 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE"   "12Q LOSS MUTATED" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-BC-A5W4 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-CC-5258         TCGA-CC-5260         TCGA-CC-5261 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-CC-5262         TCGA-CC-5263         TCGA-CC-A1HT 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE"   "12Q LOSS MUTATED" 
        TCGA-CC-A3M9         TCGA-CC-A3MA         TCGA-CC-A3MB 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-CC-A3MC         TCGA-DD-A113         TCGA-DD-A114 
  "12Q LOSS MUTATED" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
  "12Q LOSS MUTATED" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DD-A1EA         TCGA-DD-A1EB         TCGA-DD-A1EC 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DD-A1ED         TCGA-DD-A1EE         TCGA-DD-A1EF 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DD-A1EH         TCGA-DD-A1EI         TCGA-DD-A1EJ 
  "12Q LOSS MUTATED" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DD-A1EL         TCGA-DD-A39V         TCGA-DD-A39X 
  "12Q LOSS MUTATED" "12Q LOSS WILD-TYPE"   "12Q LOSS MUTATED" 
        TCGA-DD-A39Y         TCGA-DD-A39Z         TCGA-DD-A3A0 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DD-A3A1         TCGA-DD-A3A2         TCGA-DD-A3A3 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DD-A3A4         TCGA-DD-A3A5         TCGA-DD-A3A6 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DD-A3A7         TCGA-DD-A3A8         TCGA-DD-A3A9 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DD-A4NA         TCGA-DD-A4ND         TCGA-DD-A4NE 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DD-A4NF         TCGA-DD-A4NG         TCGA-DD-A4NH 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DD-A4NI         TCGA-DD-A4NJ         TCGA-DD-A4NK 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DD-A4NL         TCGA-DD-A4NN         TCGA-DD-A4NO 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE"   "12Q LOSS MUTATED" 
        TCGA-DD-A4NP         TCGA-DD-A4NQ         TCGA-ED-A459 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-ED-A5KG         TCGA-EP-A12J         TCGA-EP-A26S 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-EP-A2KA         TCGA-EP-A2KB         TCGA-EP-A2KC 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE"   "12Q LOSS MUTATED" 
        TCGA-EP-A3JL         TCGA-EP-A3RK         TCGA-ES-A2HS 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-ES-A2HT         TCGA-FV-A23B         TCGA-FV-A2QR 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-FV-A3I0         TCGA-FV-A3R2         TCGA-FV-A3R3 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-FV-A495         TCGA-FV-A496         TCGA-FV-A4ZP 
"12Q LOSS WILD-TYPE"   "12Q LOSS MUTATED" "12Q LOSS WILD-TYPE" 
        TCGA-FV-A4ZQ         TCGA-G3-A25S         TCGA-G3-A25T 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-G3-A25U         TCGA-G3-A25V         TCGA-G3-A25W 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-G3-A25X         TCGA-G3-A25Y         TCGA-G3-A25Z 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE"   "12Q LOSS MUTATED" 
        TCGA-G3-A3CG         TCGA-G3-A3CH         TCGA-G3-A3CI 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK         TCGA-G3-A5SJ 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-G3-A5SK         TCGA-G3-A5SL         TCGA-G3-A5SM 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE"   "12Q LOSS MUTATED" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-BC-A5W4 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-CC-5258         TCGA-CC-5260         TCGA-CC-5261 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-CC-5262         TCGA-CC-5263         TCGA-CC-A1HT 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE"   "12Q LOSS MUTATED" 
        TCGA-CC-A3M9         TCGA-CC-A3MA         TCGA-CC-A3MB 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-CC-A3MC         TCGA-DD-A113         TCGA-DD-A114 
  "12Q LOSS MUTATED" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
  "12Q LOSS MUTATED" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DD-A1EA         TCGA-DD-A1EB         TCGA-DD-A1EC 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DD-A1ED         TCGA-DD-A1EE         TCGA-DD-A1EF 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DD-A1EH         TCGA-DD-A1EI         TCGA-DD-A1EJ 
  "12Q LOSS MUTATED" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DD-A1EL         TCGA-DD-A39V         TCGA-DD-A39X 
  "12Q LOSS MUTATED" "12Q LOSS WILD-TYPE"   "12Q LOSS MUTATED" 
        TCGA-DD-A39Y         TCGA-DD-A39Z         TCGA-DD-A3A0 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DD-A3A1         TCGA-DD-A3A2         TCGA-DD-A3A3 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DD-A3A4         TCGA-DD-A3A5         TCGA-DD-A3A6 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DD-A3A7         TCGA-DD-A3A8         TCGA-DD-A3A9 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DD-A4NA         TCGA-DD-A4ND         TCGA-DD-A4NE 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DD-A4NF         TCGA-DD-A4NG         TCGA-DD-A4NH 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DD-A4NI         TCGA-DD-A4NJ         TCGA-DD-A4NK 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DD-A4NL         TCGA-DD-A4NN         TCGA-DD-A4NO 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE"   "12Q LOSS MUTATED" 
        TCGA-DD-A4NP         TCGA-DD-A4NQ         TCGA-ED-A459 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-ED-A5KG         TCGA-EP-A12J         TCGA-EP-A26S 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-EP-A2KA         TCGA-EP-A2KB         TCGA-EP-A2KC 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE"   "12Q LOSS MUTATED" 
        TCGA-EP-A3JL         TCGA-EP-A3RK         TCGA-ES-A2HS 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-ES-A2HT         TCGA-FV-A23B         TCGA-FV-A2QR 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-FV-A3I0         TCGA-FV-A3R2         TCGA-FV-A3R3 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-FV-A495         TCGA-FV-A496         TCGA-FV-A4ZP 
"12Q LOSS WILD-TYPE"   "12Q LOSS MUTATED" "12Q LOSS WILD-TYPE" 
        TCGA-FV-A4ZQ         TCGA-G3-A25S         TCGA-G3-A25T 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-G3-A25U         TCGA-G3-A25V         TCGA-G3-A25W 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-G3-A25X         TCGA-G3-A25Y         TCGA-G3-A25Z 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE"   "12Q LOSS MUTATED" 
        TCGA-G3-A3CG         TCGA-G3-A3CH         TCGA-G3-A3CI 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK         TCGA-G3-A5SJ 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-G3-A5SK         TCGA-G3-A5SL         TCGA-G3-A5SM 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
[1] "hr=" "1.3"
D64V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  12Q LOSS MUTATED         5        3         1          2          0
  12Q LOSS WILD-TYPE      40       22         1         23          3
                    vv
clus                 STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  12Q LOSS MUTATED            0        1         0         0
  12Q LOSS WILD-TYPE          4        0         1         1
D64V3, multiclass
                    vv
clus                 T1 T2 T3 T4
  12Q LOSS MUTATED    5  3  4  0
  12Q LOSS WILD-TYPE 43 25 30  6
D64V4, multiclass
    clus
vv   12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  T1                5                 43
  T2                3                 25
  T3                4                 30
  T4                0                  6
D64V5, binary
                    cls
clus                  0  1
  12Q LOSS MUTATED    8  0
  12Q LOSS WILD-TYPE 66  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED      8    0
  12Q LOSS WILD-TYPE   66    3
   clus
vv  12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  0                8                 66
  1                0                  3
                    vv
clus                 M0 M1 MX
  12Q LOSS MUTATED    9  1  2
  12Q LOSS WILD-TYPE 81  1 23
D64V6, multiclass
    clus
vv   12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  M0                9                 81
  M1                1                  1
  MX                2                 23
D64V7, binary
                    cls
clus                  0  1
  12Q LOSS MUTATED    4  8
  12Q LOSS WILD-TYPE 40 65
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED      4    8
  12Q LOSS WILD-TYPE   40   65
        clus
vv       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  FEMALE                4                 40
  MALE                  8                 65
                    vv
clus                 R0 R1 R2 RX
  12Q LOSS MUTATED   10  0  1  0
  12Q LOSS WILD-TYPE 83 10  0  8
D64V8, multiclass
    clus
vv   12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  R0               10                 83
  R1                0                 10
  R2                1                  0
  RX                0                  8

Clustering(65) Variable = 13Q LOSS MUTATION ANALYSIS
D65V1, survival
                    sevent
clus2                 0  1
  13Q LOSS MUTATED   21 18
  13Q LOSS WILD-TYPE 40 35
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                39                 75 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                18                 35 
$`13Q LOSS MUTATED`
TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A112 TCGA-BC-A217 TCGA-BC-A3KG 
       37.32        10.13        27.52         5.03        13.81        16.37 
TCGA-BC-A5W4 TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-A3M9 
        9.50         0.07         2.86         3.02         3.39         0.10 
TCGA-CC-A3MA TCGA-DD-A113 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A11A 
        0.07        79.73        83.57        53.29       112.96         2.60 
TCGA-DD-A11C TCGA-DD-A1EF TCGA-DD-A1EI TCGA-DD-A39X TCGA-DD-A3A0 TCGA-DD-A3A5 
       21.76        12.95         6.02        55.66        25.81       102.74 
TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NG TCGA-DD-A4NH TCGA-DD-A4NN TCGA-DD-A4NO 
       30.58        33.14        14.93        14.24        29.56        61.45 
TCGA-DD-A4NQ TCGA-EP-A3RK TCGA-FV-A3I0 TCGA-FV-A3R2 TCGA-G3-A25S TCGA-G3-A25T 
       12.26         0.43         0.20         6.35         1.22        51.02 
TCGA-G3-A25X TCGA-G3-A3CH TCGA-G3-A5SM 
       58.49        25.64         4.37 

$`13Q LOSS WILD-TYPE`
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10S TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X 
       48.99        27.91        46.78        27.52         2.99        25.32 
TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A216 TCGA-BC-A3KF TCGA-CC-5263 
       23.34         1.12        69.57        44.42         0.26         4.24 
TCGA-CC-A1HT TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A114 TCGA-DD-A119 TCGA-DD-A11B 
        3.32         0.10         0.13        37.74         7.33         0.46 
TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED 
       51.25        90.67        79.36        66.31        19.76        75.65 
TCGA-DD-A1EE TCGA-DD-A1EH TCGA-DD-A1EJ TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39Y 
        6.67        49.15        29.16        13.64        21.14         5.59 
TCGA-DD-A39Z TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A6 
       19.73         7.66        70.06        17.59        20.12       107.11 
TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A4ND TCGA-DD-A4NE TCGA-DD-A4NF TCGA-DD-A4NI 
       13.78         0.36        73.38        21.67        14.07        10.78 
TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NP TCGA-ED-A459 TCGA-ED-A5KG 
       15.06        39.75        56.25        93.67         0.23         0.20 
TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL 
       10.85         7.76        11.74         1.97         0.62         3.19 
TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-A3R3 TCGA-FV-A495 
       23.01        14.40        32.45        19.07         0.13         0.03 
TCGA-FV-A496 TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W 
        0.33        60.36         0.39        53.79        28.27        30.71 
TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK 
       14.86        21.53        22.13         5.88        19.53        19.23 
TCGA-G3-A5SJ TCGA-G3-A5SK TCGA-G3-A5SL 
       11.97         9.93         7.99 

  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
              0.07               0.03 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
            112.96             107.11 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
             14.24              19.07 
[1] "0.1 - 113.0 (14.2)" "0.0 - 107.1 (19.1)"
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
  "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
  "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-BC-A5W4 
"13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED"   "13Q LOSS MUTATED" 
        TCGA-CC-5258         TCGA-CC-5260         TCGA-CC-5261 
  "13Q LOSS MUTATED"   "13Q LOSS MUTATED"   "13Q LOSS MUTATED" 
        TCGA-CC-5262         TCGA-CC-5263         TCGA-CC-A1HT 
  "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CC-A3M9         TCGA-CC-A3MA         TCGA-CC-A3MB 
  "13Q LOSS MUTATED"   "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" 
        TCGA-CC-A3MC         TCGA-DD-A113         TCGA-DD-A114 
"13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
  "13Q LOSS MUTATED"   "13Q LOSS MUTATED"   "13Q LOSS MUTATED" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
  "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-DD-A1EA         TCGA-DD-A1EB         TCGA-DD-A1EC 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-DD-A1ED         TCGA-DD-A1EE         TCGA-DD-A1EF 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" 
        TCGA-DD-A1EH         TCGA-DD-A1EI         TCGA-DD-A1EJ 
"13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" 
        TCGA-DD-A1EL         TCGA-DD-A39V         TCGA-DD-A39X 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" 
        TCGA-DD-A39Y         TCGA-DD-A39Z         TCGA-DD-A3A0 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" 
        TCGA-DD-A3A1         TCGA-DD-A3A2         TCGA-DD-A3A3 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-DD-A3A4         TCGA-DD-A3A5         TCGA-DD-A3A6 
"13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" 
        TCGA-DD-A3A7         TCGA-DD-A3A8         TCGA-DD-A3A9 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" 
        TCGA-DD-A4NA         TCGA-DD-A4ND         TCGA-DD-A4NE 
  "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-DD-A4NF         TCGA-DD-A4NG         TCGA-DD-A4NH 
"13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED"   "13Q LOSS MUTATED" 
        TCGA-DD-A4NI         TCGA-DD-A4NJ         TCGA-DD-A4NK 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-DD-A4NL         TCGA-DD-A4NN         TCGA-DD-A4NO 
"13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED"   "13Q LOSS MUTATED" 
        TCGA-DD-A4NP         TCGA-DD-A4NQ         TCGA-ED-A459 
"13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" 
        TCGA-ED-A5KG         TCGA-EP-A12J         TCGA-EP-A26S 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EP-A2KA         TCGA-EP-A2KB         TCGA-EP-A2KC 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EP-A3JL         TCGA-EP-A3RK         TCGA-ES-A2HS 
"13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" 
        TCGA-ES-A2HT         TCGA-FV-A23B         TCGA-FV-A2QR 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-FV-A3I0         TCGA-FV-A3R2         TCGA-FV-A3R3 
  "13Q LOSS MUTATED"   "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" 
        TCGA-FV-A495         TCGA-FV-A496         TCGA-FV-A4ZP 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-FV-A4ZQ         TCGA-G3-A25S         TCGA-G3-A25T 
"13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED"   "13Q LOSS MUTATED" 
        TCGA-G3-A25U         TCGA-G3-A25V         TCGA-G3-A25W 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-G3-A25X         TCGA-G3-A25Y         TCGA-G3-A25Z 
  "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-G3-A3CG         TCGA-G3-A3CH         TCGA-G3-A3CI 
"13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK         TCGA-G3-A5SJ 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-G3-A5SK         TCGA-G3-A5SL         TCGA-G3-A5SM 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" 
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
  "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
  "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-BC-A5W4 
"13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED"   "13Q LOSS MUTATED" 
        TCGA-CC-5258         TCGA-CC-5260         TCGA-CC-5261 
  "13Q LOSS MUTATED"   "13Q LOSS MUTATED"   "13Q LOSS MUTATED" 
        TCGA-CC-5262         TCGA-CC-5263         TCGA-CC-A1HT 
  "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CC-A3M9         TCGA-CC-A3MA         TCGA-CC-A3MB 
  "13Q LOSS MUTATED"   "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" 
        TCGA-CC-A3MC         TCGA-DD-A113         TCGA-DD-A114 
"13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
  "13Q LOSS MUTATED"   "13Q LOSS MUTATED"   "13Q LOSS MUTATED" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
  "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-DD-A1EA         TCGA-DD-A1EB         TCGA-DD-A1EC 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-DD-A1ED         TCGA-DD-A1EE         TCGA-DD-A1EF 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" 
        TCGA-DD-A1EH         TCGA-DD-A1EI         TCGA-DD-A1EJ 
"13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" 
        TCGA-DD-A1EL         TCGA-DD-A39V         TCGA-DD-A39X 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" 
        TCGA-DD-A39Y         TCGA-DD-A39Z         TCGA-DD-A3A0 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" 
        TCGA-DD-A3A1         TCGA-DD-A3A2         TCGA-DD-A3A3 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-DD-A3A4         TCGA-DD-A3A5         TCGA-DD-A3A6 
"13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" 
        TCGA-DD-A3A7         TCGA-DD-A3A8         TCGA-DD-A3A9 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" 
        TCGA-DD-A4NA         TCGA-DD-A4ND         TCGA-DD-A4NE 
  "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-DD-A4NF         TCGA-DD-A4NG         TCGA-DD-A4NH 
"13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED"   "13Q LOSS MUTATED" 
        TCGA-DD-A4NI         TCGA-DD-A4NJ         TCGA-DD-A4NK 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-DD-A4NL         TCGA-DD-A4NN         TCGA-DD-A4NO 
"13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED"   "13Q LOSS MUTATED" 
        TCGA-DD-A4NP         TCGA-DD-A4NQ         TCGA-ED-A459 
"13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" 
        TCGA-ED-A5KG         TCGA-EP-A12J         TCGA-EP-A26S 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EP-A2KA         TCGA-EP-A2KB         TCGA-EP-A2KC 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EP-A3JL         TCGA-EP-A3RK         TCGA-ES-A2HS 
"13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" 
        TCGA-ES-A2HT         TCGA-FV-A23B         TCGA-FV-A2QR 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-FV-A3I0         TCGA-FV-A3R2         TCGA-FV-A3R3 
  "13Q LOSS MUTATED"   "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" 
        TCGA-FV-A495         TCGA-FV-A496         TCGA-FV-A4ZP 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-FV-A4ZQ         TCGA-G3-A25S         TCGA-G3-A25T 
"13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED"   "13Q LOSS MUTATED" 
        TCGA-G3-A25U         TCGA-G3-A25V         TCGA-G3-A25W 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-G3-A25X         TCGA-G3-A25Y         TCGA-G3-A25Z 
  "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-G3-A3CG         TCGA-G3-A3CH         TCGA-G3-A3CI 
"13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK         TCGA-G3-A5SJ 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-G3-A5SK         TCGA-G3-A5SL         TCGA-G3-A5SM 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" 
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
  "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
  "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-BC-A5W4 
"13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED"   "13Q LOSS MUTATED" 
        TCGA-CC-5258         TCGA-CC-5260         TCGA-CC-5261 
  "13Q LOSS MUTATED"   "13Q LOSS MUTATED"   "13Q LOSS MUTATED" 
        TCGA-CC-5262         TCGA-CC-5263         TCGA-CC-A1HT 
  "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CC-A3M9         TCGA-CC-A3MA         TCGA-CC-A3MB 
  "13Q LOSS MUTATED"   "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" 
        TCGA-CC-A3MC         TCGA-DD-A113         TCGA-DD-A114 
"13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
  "13Q LOSS MUTATED"   "13Q LOSS MUTATED"   "13Q LOSS MUTATED" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
  "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-DD-A1EA         TCGA-DD-A1EB         TCGA-DD-A1EC 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-DD-A1ED         TCGA-DD-A1EE         TCGA-DD-A1EF 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" 
        TCGA-DD-A1EH         TCGA-DD-A1EI         TCGA-DD-A1EJ 
"13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" 
        TCGA-DD-A1EL         TCGA-DD-A39V         TCGA-DD-A39X 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" 
        TCGA-DD-A39Y         TCGA-DD-A39Z         TCGA-DD-A3A0 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" 
        TCGA-DD-A3A1         TCGA-DD-A3A2         TCGA-DD-A3A3 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-DD-A3A4         TCGA-DD-A3A5         TCGA-DD-A3A6 
"13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" 
        TCGA-DD-A3A7         TCGA-DD-A3A8         TCGA-DD-A3A9 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" 
        TCGA-DD-A4NA         TCGA-DD-A4ND         TCGA-DD-A4NE 
  "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-DD-A4NF         TCGA-DD-A4NG         TCGA-DD-A4NH 
"13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED"   "13Q LOSS MUTATED" 
        TCGA-DD-A4NI         TCGA-DD-A4NJ         TCGA-DD-A4NK 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-DD-A4NL         TCGA-DD-A4NN         TCGA-DD-A4NO 
"13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED"   "13Q LOSS MUTATED" 
        TCGA-DD-A4NP         TCGA-DD-A4NQ         TCGA-ED-A459 
"13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" 
        TCGA-ED-A5KG         TCGA-EP-A12J         TCGA-EP-A26S 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EP-A2KA         TCGA-EP-A2KB         TCGA-EP-A2KC 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EP-A3JL         TCGA-EP-A3RK         TCGA-ES-A2HS 
"13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" 
        TCGA-ES-A2HT         TCGA-FV-A23B         TCGA-FV-A2QR 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-FV-A3I0         TCGA-FV-A3R2         TCGA-FV-A3R3 
  "13Q LOSS MUTATED"   "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" 
        TCGA-FV-A495         TCGA-FV-A496         TCGA-FV-A4ZP 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-FV-A4ZQ         TCGA-G3-A25S         TCGA-G3-A25T 
"13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED"   "13Q LOSS MUTATED" 
        TCGA-G3-A25U         TCGA-G3-A25V         TCGA-G3-A25W 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-G3-A25X         TCGA-G3-A25Y         TCGA-G3-A25Z 
  "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-G3-A3CG         TCGA-G3-A3CH         TCGA-G3-A3CI 
"13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK         TCGA-G3-A5SJ 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-G3-A5SK         TCGA-G3-A5SL         TCGA-G3-A5SM 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" 
[1] "hr=" "1.1"
D65V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  13Q LOSS MUTATED        10       10         1          9          1
  13Q LOSS WILD-TYPE      35       15         1         16          2
                    vv
clus                 STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  13Q LOSS MUTATED            3        0         0         1
  13Q LOSS WILD-TYPE          1        1         1         0
D65V3, multiclass
                    vv
clus                 T1 T2 T3 T4
  13Q LOSS MUTATED   10 12 13  4
  13Q LOSS WILD-TYPE 38 16 21  2
D65V4, multiclass
    clus
vv   13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  T1               10                 38
  T2               12                 16
  T3               13                 21
  T4                4                  2
D65V5, binary
                    cls
clus                  0  1
  13Q LOSS MUTATED   26  1
  13Q LOSS WILD-TYPE 48  2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED     26    1
  13Q LOSS WILD-TYPE   48    2
   clus
vv  13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  0               26                 48
  1                1                  2
                    vv
clus                 M0 M1 MX
  13Q LOSS MUTATED   33  1  6
  13Q LOSS WILD-TYPE 57  1 19
D65V6, multiclass
    clus
vv   13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  M0               33                 57
  M1                1                  1
  MX                6                 19
D65V7, binary
                    cls
clus                  0  1
  13Q LOSS MUTATED   16 24
  13Q LOSS WILD-TYPE 28 49
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED     16   24
  13Q LOSS WILD-TYPE   28   49
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  FEMALE               16                 28
  MALE                 24                 49
                    vv
clus                 R0 R1 R2 RX
  13Q LOSS MUTATED   29  4  0  5
  13Q LOSS WILD-TYPE 64  6  1  3
D65V8, multiclass
    clus
vv   13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  R0               29                 64
  R1                4                  6
  R2                0                  1
  RX                5                  3

Clustering(66) Variable = 14Q LOSS MUTATION ANALYSIS
D66V1, survival
                    sevent
clus2                 0  1
  14Q LOSS MUTATED   20 17
  14Q LOSS WILD-TYPE 41 36
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                37                 77 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                17                 36 
$`14Q LOSS MUTATED`
TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A112 TCGA-BC-A217 TCGA-BC-A3KF 
       37.32        10.13        27.52         5.03        13.81         0.26 
TCGA-BC-A3KG TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-A1HT TCGA-CC-A3MA 
       16.37         0.07         2.86         3.02         3.32         0.07 
TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A113 TCGA-DD-A115 TCGA-DD-A118 TCGA-DD-A11A 
        0.10         0.13        79.73        83.57       112.96         2.60 
TCGA-DD-A11C TCGA-DD-A1E9 TCGA-DD-A1EJ TCGA-DD-A1EL TCGA-DD-A39X TCGA-DD-A3A1 
       21.76        90.67        29.16        13.64        55.66         7.66 
TCGA-DD-A3A7 TCGA-DD-A3A9 TCGA-DD-A4NH TCGA-DD-A4NO TCGA-DD-A4NQ TCGA-ED-A459 
       13.78        30.58        14.24        61.45        12.26         0.23 
TCGA-EP-A2KB TCGA-EP-A3RK TCGA-FV-A4ZP TCGA-G3-A25S TCGA-G3-A25X TCGA-G3-A3CH 
        1.97         0.43        60.36         1.22        58.49        25.64 
TCGA-G3-A5SM 
        4.37 

$`14Q LOSS WILD-TYPE`
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10S TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X 
       48.99        27.91        46.78        27.52         2.99        25.32 
TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A216 TCGA-BC-A5W4 TCGA-CC-5262 
       23.34         1.12        69.57        44.42         9.50         3.39 
TCGA-CC-5263 TCGA-CC-A3M9 TCGA-DD-A114 TCGA-DD-A116 TCGA-DD-A119 TCGA-DD-A11B 
        4.24         0.10        37.74        53.29         7.33         0.46 
TCGA-DD-A11D TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE 
       51.25        79.36        66.31        19.76        75.65         6.67 
TCGA-DD-A1EF TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A39V TCGA-DD-A39Y TCGA-DD-A39Z 
       12.95        49.15         6.02        21.14         5.59        19.73 
TCGA-DD-A3A0 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 
       25.81        70.06        17.59        20.12       102.74       107.11 
TCGA-DD-A3A8 TCGA-DD-A4NA TCGA-DD-A4ND TCGA-DD-A4NE TCGA-DD-A4NF TCGA-DD-A4NG 
        0.36        33.14        73.38        21.67        14.07        14.93 
TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NP 
       10.78        15.06        39.75        56.25        29.56        93.67 
TCGA-ED-A5KG TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KC TCGA-EP-A3JL 
        0.20        10.85         7.76        11.74         0.62         3.19 
TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3R2 
       23.01        14.40        32.45        19.07         0.20         6.35 
TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZQ TCGA-G3-A25T TCGA-G3-A25U 
        0.13         0.03         0.33         0.39        51.02        53.79 
TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CI 
       28.27        30.71        14.86        21.53        22.13         5.88 
TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SJ TCGA-G3-A5SK TCGA-G3-A5SL 
       19.53        19.23        11.97         9.93         7.99 

  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
              0.07               0.03 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
            112.96             107.11 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
             13.64              19.53 
[1] "0.1 - 113.0 (13.6)" "0.0 - 107.1 (19.5)"
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-BC-A5W4 
  "14Q LOSS MUTATED"   "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" 
        TCGA-CC-5258         TCGA-CC-5260         TCGA-CC-5261 
  "14Q LOSS MUTATED"   "14Q LOSS MUTATED"   "14Q LOSS MUTATED" 
        TCGA-CC-5262         TCGA-CC-5263         TCGA-CC-A1HT 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-CC-A3M9         TCGA-CC-A3MA         TCGA-CC-A3MB 
"14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED"   "14Q LOSS MUTATED" 
        TCGA-CC-A3MC         TCGA-DD-A113         TCGA-DD-A114 
  "14Q LOSS MUTATED"   "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-DD-A1EA         TCGA-DD-A1EB         TCGA-DD-A1EC 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-DD-A1ED         TCGA-DD-A1EE         TCGA-DD-A1EF 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-DD-A1EH         TCGA-DD-A1EI         TCGA-DD-A1EJ 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-DD-A1EL         TCGA-DD-A39V         TCGA-DD-A39X 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-DD-A39Y         TCGA-DD-A39Z         TCGA-DD-A3A0 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-DD-A3A1         TCGA-DD-A3A2         TCGA-DD-A3A3 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-DD-A3A4         TCGA-DD-A3A5         TCGA-DD-A3A6 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-DD-A3A7         TCGA-DD-A3A8         TCGA-DD-A3A9 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-DD-A4NA         TCGA-DD-A4ND         TCGA-DD-A4NE 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-DD-A4NF         TCGA-DD-A4NG         TCGA-DD-A4NH 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-DD-A4NI         TCGA-DD-A4NJ         TCGA-DD-A4NK 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-DD-A4NL         TCGA-DD-A4NN         TCGA-DD-A4NO 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-DD-A4NP         TCGA-DD-A4NQ         TCGA-ED-A459 
"14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED"   "14Q LOSS MUTATED" 
        TCGA-ED-A5KG         TCGA-EP-A12J         TCGA-EP-A26S 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-EP-A2KA         TCGA-EP-A2KB         TCGA-EP-A2KC 
"14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" 
        TCGA-EP-A3JL         TCGA-EP-A3RK         TCGA-ES-A2HS 
"14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" 
        TCGA-ES-A2HT         TCGA-FV-A23B         TCGA-FV-A2QR 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-FV-A3I0         TCGA-FV-A3R2         TCGA-FV-A3R3 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-FV-A495         TCGA-FV-A496         TCGA-FV-A4ZP 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-FV-A4ZQ         TCGA-G3-A25S         TCGA-G3-A25T 
"14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" 
        TCGA-G3-A25U         TCGA-G3-A25V         TCGA-G3-A25W 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-G3-A25X         TCGA-G3-A25Y         TCGA-G3-A25Z 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-G3-A3CG         TCGA-G3-A3CH         TCGA-G3-A3CI 
"14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK         TCGA-G3-A5SJ 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-G3-A5SK         TCGA-G3-A5SL         TCGA-G3-A5SM 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-BC-A5W4 
  "14Q LOSS MUTATED"   "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" 
        TCGA-CC-5258         TCGA-CC-5260         TCGA-CC-5261 
  "14Q LOSS MUTATED"   "14Q LOSS MUTATED"   "14Q LOSS MUTATED" 
        TCGA-CC-5262         TCGA-CC-5263         TCGA-CC-A1HT 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-CC-A3M9         TCGA-CC-A3MA         TCGA-CC-A3MB 
"14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED"   "14Q LOSS MUTATED" 
        TCGA-CC-A3MC         TCGA-DD-A113         TCGA-DD-A114 
  "14Q LOSS MUTATED"   "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-DD-A1EA         TCGA-DD-A1EB         TCGA-DD-A1EC 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-DD-A1ED         TCGA-DD-A1EE         TCGA-DD-A1EF 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-DD-A1EH         TCGA-DD-A1EI         TCGA-DD-A1EJ 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-DD-A1EL         TCGA-DD-A39V         TCGA-DD-A39X 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-DD-A39Y         TCGA-DD-A39Z         TCGA-DD-A3A0 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-DD-A3A1         TCGA-DD-A3A2         TCGA-DD-A3A3 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-DD-A3A4         TCGA-DD-A3A5         TCGA-DD-A3A6 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-DD-A3A7         TCGA-DD-A3A8         TCGA-DD-A3A9 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-DD-A4NA         TCGA-DD-A4ND         TCGA-DD-A4NE 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-DD-A4NF         TCGA-DD-A4NG         TCGA-DD-A4NH 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-DD-A4NI         TCGA-DD-A4NJ         TCGA-DD-A4NK 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-DD-A4NL         TCGA-DD-A4NN         TCGA-DD-A4NO 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-DD-A4NP         TCGA-DD-A4NQ         TCGA-ED-A459 
"14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED"   "14Q LOSS MUTATED" 
        TCGA-ED-A5KG         TCGA-EP-A12J         TCGA-EP-A26S 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-EP-A2KA         TCGA-EP-A2KB         TCGA-EP-A2KC 
"14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" 
        TCGA-EP-A3JL         TCGA-EP-A3RK         TCGA-ES-A2HS 
"14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" 
        TCGA-ES-A2HT         TCGA-FV-A23B         TCGA-FV-A2QR 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-FV-A3I0         TCGA-FV-A3R2         TCGA-FV-A3R3 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-FV-A495         TCGA-FV-A496         TCGA-FV-A4ZP 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-FV-A4ZQ         TCGA-G3-A25S         TCGA-G3-A25T 
"14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" 
        TCGA-G3-A25U         TCGA-G3-A25V         TCGA-G3-A25W 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-G3-A25X         TCGA-G3-A25Y         TCGA-G3-A25Z 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-G3-A3CG         TCGA-G3-A3CH         TCGA-G3-A3CI 
"14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK         TCGA-G3-A5SJ 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-G3-A5SK         TCGA-G3-A5SL         TCGA-G3-A5SM 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-BC-A5W4 
  "14Q LOSS MUTATED"   "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" 
        TCGA-CC-5258         TCGA-CC-5260         TCGA-CC-5261 
  "14Q LOSS MUTATED"   "14Q LOSS MUTATED"   "14Q LOSS MUTATED" 
        TCGA-CC-5262         TCGA-CC-5263         TCGA-CC-A1HT 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-CC-A3M9         TCGA-CC-A3MA         TCGA-CC-A3MB 
"14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED"   "14Q LOSS MUTATED" 
        TCGA-CC-A3MC         TCGA-DD-A113         TCGA-DD-A114 
  "14Q LOSS MUTATED"   "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-DD-A1EA         TCGA-DD-A1EB         TCGA-DD-A1EC 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-DD-A1ED         TCGA-DD-A1EE         TCGA-DD-A1EF 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-DD-A1EH         TCGA-DD-A1EI         TCGA-DD-A1EJ 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-DD-A1EL         TCGA-DD-A39V         TCGA-DD-A39X 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-DD-A39Y         TCGA-DD-A39Z         TCGA-DD-A3A0 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-DD-A3A1         TCGA-DD-A3A2         TCGA-DD-A3A3 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-DD-A3A4         TCGA-DD-A3A5         TCGA-DD-A3A6 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-DD-A3A7         TCGA-DD-A3A8         TCGA-DD-A3A9 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-DD-A4NA         TCGA-DD-A4ND         TCGA-DD-A4NE 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-DD-A4NF         TCGA-DD-A4NG         TCGA-DD-A4NH 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-DD-A4NI         TCGA-DD-A4NJ         TCGA-DD-A4NK 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-DD-A4NL         TCGA-DD-A4NN         TCGA-DD-A4NO 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-DD-A4NP         TCGA-DD-A4NQ         TCGA-ED-A459 
"14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED"   "14Q LOSS MUTATED" 
        TCGA-ED-A5KG         TCGA-EP-A12J         TCGA-EP-A26S 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-EP-A2KA         TCGA-EP-A2KB         TCGA-EP-A2KC 
"14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" 
        TCGA-EP-A3JL         TCGA-EP-A3RK         TCGA-ES-A2HS 
"14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" 
        TCGA-ES-A2HT         TCGA-FV-A23B         TCGA-FV-A2QR 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-FV-A3I0         TCGA-FV-A3R2         TCGA-FV-A3R3 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-FV-A495         TCGA-FV-A496         TCGA-FV-A4ZP 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-FV-A4ZQ         TCGA-G3-A25S         TCGA-G3-A25T 
"14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" 
        TCGA-G3-A25U         TCGA-G3-A25V         TCGA-G3-A25W 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-G3-A25X         TCGA-G3-A25Y         TCGA-G3-A25Z 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-G3-A3CG         TCGA-G3-A3CH         TCGA-G3-A3CI 
"14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK         TCGA-G3-A5SJ 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-G3-A5SK         TCGA-G3-A5SL         TCGA-G3-A5SM 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
[1] "hr=" "1.1"
D66V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  14Q LOSS MUTATED         8       11         0         10          2
  14Q LOSS WILD-TYPE      37       14         2         15          1
                    vv
clus                 STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  14Q LOSS MUTATED            2        0         0         1
  14Q LOSS WILD-TYPE          2        1         1         0
D66V3, multiclass
                    vv
clus                 T1 T2 T3 T4
  14Q LOSS MUTATED    9 12 14  3
  14Q LOSS WILD-TYPE 39 16 20  3
D66V4, multiclass
    clus
vv   14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  T1                9                 39
  T2               12                 16
  T3               14                 20
  T4                3                  3
D66V5, binary
                    cls
clus                  0  1
  14Q LOSS MUTATED   26  1
  14Q LOSS WILD-TYPE 48  2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED     26    1
  14Q LOSS WILD-TYPE   48    2
   clus
vv  14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  0               26                 48
  1                1                  2
                    vv
clus                 M0 M1 MX
  14Q LOSS MUTATED   31  1  6
  14Q LOSS WILD-TYPE 59  1 19
D66V6, multiclass
    clus
vv   14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  M0               31                 59
  M1                1                  1
  MX                6                 19
D66V7, binary
                    cls
clus                  0  1
  14Q LOSS MUTATED   13 25
  14Q LOSS WILD-TYPE 31 48
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED     13   25
  14Q LOSS WILD-TYPE   31   48
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  FEMALE               13                 31
  MALE                 25                 48
                    vv
clus                 R0 R1 R2 RX
  14Q LOSS MUTATED   27  4  0  5
  14Q LOSS WILD-TYPE 66  6  1  3
D66V8, multiclass
    clus
vv   14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  R0               27                 66
  R1                4                  6
  R2                0                  1
  RX                5                  3

Clustering(67) Variable = 15Q LOSS MUTATION ANALYSIS
D67V1, survival
                    sevent
clus2                 0  1
  15Q LOSS MUTATED   13  8
  15Q LOSS WILD-TYPE 48 45
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                21                 93 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                 8                 45 
$`15Q LOSS MUTATED`
TCGA-BC-A112 TCGA-BC-A5W4 TCGA-CC-5258 TCGA-CC-A3MA TCGA-DD-A113 TCGA-DD-A114 
        5.03         9.50         0.07         0.07        79.73        37.74 
TCGA-DD-A115 TCGA-DD-A11A TCGA-DD-A1E9 TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EL 
       83.57         2.60        90.67         6.02        29.16        13.64 
TCGA-DD-A3A5 TCGA-DD-A4NA TCGA-DD-A4NQ TCGA-ED-A459 TCGA-EP-A2KB TCGA-FV-A496 
      102.74        33.14        12.26         0.23         1.97         0.33 
TCGA-FV-A4ZP TCGA-G3-A25Z TCGA-G3-A5SM 
       60.36        21.53         4.37 

$`15Q LOSS WILD-TYPE`
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T 
       48.99        27.91        37.32        10.13        46.78        27.52 
TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 
       27.52         2.99        25.32        23.34         1.12        69.57 
TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-CC-5260 TCGA-CC-5261 
       44.42        13.81         0.26        16.37         2.86         3.02 
TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MB TCGA-CC-A3MC 
        3.39         4.24         3.32         0.10         0.10         0.13 
TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D 
       53.29       112.96         7.33         0.46        21.76        51.25 
TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EF 
       79.36        66.31        19.76        75.65         6.67        12.95 
TCGA-DD-A1EH TCGA-DD-A39V TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A0 
       49.15        21.14        55.66         5.59        19.73        25.81 
TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A6 TCGA-DD-A3A7 
        7.66        70.06        17.59        20.12       107.11        13.78 
TCGA-DD-A3A8 TCGA-DD-A3A9 TCGA-DD-A4ND TCGA-DD-A4NE TCGA-DD-A4NF TCGA-DD-A4NG 
        0.36        30.58        73.38        21.67        14.07        14.93 
TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN 
       14.24        10.78        15.06        39.75        56.25        29.56 
TCGA-DD-A4NO TCGA-DD-A4NP TCGA-ED-A5KG TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA 
       61.45        93.67         0.20        10.85         7.76        11.74 
TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A23B 
        0.62         3.19         0.43        23.01        14.40        32.45 
TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A4ZQ 
       19.07         0.20         6.35         0.13         0.03         0.39 
TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25X 
        1.22        51.02        53.79        28.27        30.71        58.49 
TCGA-G3-A25Y TCGA-G3-A3CG TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK 
       14.86        22.13        25.64         5.88        19.53        19.23 
TCGA-G3-A5SJ TCGA-G3-A5SK TCGA-G3-A5SL 
       11.97         9.93         7.99 

  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
              0.07               0.03 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
            102.74             112.96 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
             12.26              17.59 
[1] "0.1 - 102.7 (12.3)" "0.0 - 113.0 (17.6)"
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
  "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-BC-A5W4 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" 
        TCGA-CC-5258         TCGA-CC-5260         TCGA-CC-5261 
  "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-CC-5262         TCGA-CC-5263         TCGA-CC-A1HT 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-CC-A3M9         TCGA-CC-A3MA         TCGA-CC-A3MB 
"15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" 
        TCGA-CC-A3MC         TCGA-DD-A113         TCGA-DD-A114 
"15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED"   "15Q LOSS MUTATED" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
  "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" 
        TCGA-DD-A1EA         TCGA-DD-A1EB         TCGA-DD-A1EC 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-DD-A1ED         TCGA-DD-A1EE         TCGA-DD-A1EF 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-DD-A1EH         TCGA-DD-A1EI         TCGA-DD-A1EJ 
"15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED"   "15Q LOSS MUTATED" 
        TCGA-DD-A1EL         TCGA-DD-A39V         TCGA-DD-A39X 
  "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-DD-A39Y         TCGA-DD-A39Z         TCGA-DD-A3A0 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-DD-A3A1         TCGA-DD-A3A2         TCGA-DD-A3A3 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-DD-A3A4         TCGA-DD-A3A5         TCGA-DD-A3A6 
"15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" 
        TCGA-DD-A3A7         TCGA-DD-A3A8         TCGA-DD-A3A9 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-DD-A4NA         TCGA-DD-A4ND         TCGA-DD-A4NE 
  "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-DD-A4NF         TCGA-DD-A4NG         TCGA-DD-A4NH 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-DD-A4NI         TCGA-DD-A4NJ         TCGA-DD-A4NK 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-DD-A4NL         TCGA-DD-A4NN         TCGA-DD-A4NO 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-DD-A4NP         TCGA-DD-A4NQ         TCGA-ED-A459 
"15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED"   "15Q LOSS MUTATED" 
        TCGA-ED-A5KG         TCGA-EP-A12J         TCGA-EP-A26S 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-EP-A2KA         TCGA-EP-A2KB         TCGA-EP-A2KC 
"15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" 
        TCGA-EP-A3JL         TCGA-EP-A3RK         TCGA-ES-A2HS 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-ES-A2HT         TCGA-FV-A23B         TCGA-FV-A2QR 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-FV-A3I0         TCGA-FV-A3R2         TCGA-FV-A3R3 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-FV-A495         TCGA-FV-A496         TCGA-FV-A4ZP 
"15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED"   "15Q LOSS MUTATED" 
        TCGA-FV-A4ZQ         TCGA-G3-A25S         TCGA-G3-A25T 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-G3-A25U         TCGA-G3-A25V         TCGA-G3-A25W 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-G3-A25X         TCGA-G3-A25Y         TCGA-G3-A25Z 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" 
        TCGA-G3-A3CG         TCGA-G3-A3CH         TCGA-G3-A3CI 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK         TCGA-G3-A5SJ 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-G3-A5SK         TCGA-G3-A5SL         TCGA-G3-A5SM 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" 
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
  "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-BC-A5W4 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" 
        TCGA-CC-5258         TCGA-CC-5260         TCGA-CC-5261 
  "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-CC-5262         TCGA-CC-5263         TCGA-CC-A1HT 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-CC-A3M9         TCGA-CC-A3MA         TCGA-CC-A3MB 
"15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" 
        TCGA-CC-A3MC         TCGA-DD-A113         TCGA-DD-A114 
"15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED"   "15Q LOSS MUTATED" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
  "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" 
        TCGA-DD-A1EA         TCGA-DD-A1EB         TCGA-DD-A1EC 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-DD-A1ED         TCGA-DD-A1EE         TCGA-DD-A1EF 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-DD-A1EH         TCGA-DD-A1EI         TCGA-DD-A1EJ 
"15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED"   "15Q LOSS MUTATED" 
        TCGA-DD-A1EL         TCGA-DD-A39V         TCGA-DD-A39X 
  "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-DD-A39Y         TCGA-DD-A39Z         TCGA-DD-A3A0 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-DD-A3A1         TCGA-DD-A3A2         TCGA-DD-A3A3 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-DD-A3A4         TCGA-DD-A3A5         TCGA-DD-A3A6 
"15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" 
        TCGA-DD-A3A7         TCGA-DD-A3A8         TCGA-DD-A3A9 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-DD-A4NA         TCGA-DD-A4ND         TCGA-DD-A4NE 
  "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-DD-A4NF         TCGA-DD-A4NG         TCGA-DD-A4NH 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-DD-A4NI         TCGA-DD-A4NJ         TCGA-DD-A4NK 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-DD-A4NL         TCGA-DD-A4NN         TCGA-DD-A4NO 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-DD-A4NP         TCGA-DD-A4NQ         TCGA-ED-A459 
"15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED"   "15Q LOSS MUTATED" 
        TCGA-ED-A5KG         TCGA-EP-A12J         TCGA-EP-A26S 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-EP-A2KA         TCGA-EP-A2KB         TCGA-EP-A2KC 
"15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" 
        TCGA-EP-A3JL         TCGA-EP-A3RK         TCGA-ES-A2HS 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-ES-A2HT         TCGA-FV-A23B         TCGA-FV-A2QR 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-FV-A3I0         TCGA-FV-A3R2         TCGA-FV-A3R3 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-FV-A495         TCGA-FV-A496         TCGA-FV-A4ZP 
"15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED"   "15Q LOSS MUTATED" 
        TCGA-FV-A4ZQ         TCGA-G3-A25S         TCGA-G3-A25T 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-G3-A25U         TCGA-G3-A25V         TCGA-G3-A25W 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-G3-A25X         TCGA-G3-A25Y         TCGA-G3-A25Z 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" 
        TCGA-G3-A3CG         TCGA-G3-A3CH         TCGA-G3-A3CI 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK         TCGA-G3-A5SJ 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-G3-A5SK         TCGA-G3-A5SL         TCGA-G3-A5SM 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" 
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
  "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-BC-A5W4 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" 
        TCGA-CC-5258         TCGA-CC-5260         TCGA-CC-5261 
  "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-CC-5262         TCGA-CC-5263         TCGA-CC-A1HT 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-CC-A3M9         TCGA-CC-A3MA         TCGA-CC-A3MB 
"15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" 
        TCGA-CC-A3MC         TCGA-DD-A113         TCGA-DD-A114 
"15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED"   "15Q LOSS MUTATED" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
  "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" 
        TCGA-DD-A1EA         TCGA-DD-A1EB         TCGA-DD-A1EC 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-DD-A1ED         TCGA-DD-A1EE         TCGA-DD-A1EF 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-DD-A1EH         TCGA-DD-A1EI         TCGA-DD-A1EJ 
"15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED"   "15Q LOSS MUTATED" 
        TCGA-DD-A1EL         TCGA-DD-A39V         TCGA-DD-A39X 
  "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-DD-A39Y         TCGA-DD-A39Z         TCGA-DD-A3A0 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-DD-A3A1         TCGA-DD-A3A2         TCGA-DD-A3A3 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-DD-A3A4         TCGA-DD-A3A5         TCGA-DD-A3A6 
"15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" 
        TCGA-DD-A3A7         TCGA-DD-A3A8         TCGA-DD-A3A9 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-DD-A4NA         TCGA-DD-A4ND         TCGA-DD-A4NE 
  "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-DD-A4NF         TCGA-DD-A4NG         TCGA-DD-A4NH 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-DD-A4NI         TCGA-DD-A4NJ         TCGA-DD-A4NK 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-DD-A4NL         TCGA-DD-A4NN         TCGA-DD-A4NO 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-DD-A4NP         TCGA-DD-A4NQ         TCGA-ED-A459 
"15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED"   "15Q LOSS MUTATED" 
        TCGA-ED-A5KG         TCGA-EP-A12J         TCGA-EP-A26S 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-EP-A2KA         TCGA-EP-A2KB         TCGA-EP-A2KC 
"15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" 
        TCGA-EP-A3JL         TCGA-EP-A3RK         TCGA-ES-A2HS 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-ES-A2HT         TCGA-FV-A23B         TCGA-FV-A2QR 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-FV-A3I0         TCGA-FV-A3R2         TCGA-FV-A3R3 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-FV-A495         TCGA-FV-A496         TCGA-FV-A4ZP 
"15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED"   "15Q LOSS MUTATED" 
        TCGA-FV-A4ZQ         TCGA-G3-A25S         TCGA-G3-A25T 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-G3-A25U         TCGA-G3-A25V         TCGA-G3-A25W 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-G3-A25X         TCGA-G3-A25Y         TCGA-G3-A25Z 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" 
        TCGA-G3-A3CG         TCGA-G3-A3CH         TCGA-G3-A3CI 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK         TCGA-G3-A5SJ 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-G3-A5SK         TCGA-G3-A5SL         TCGA-G3-A5SM 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" 
[1] "hr=" "1.4"
D67V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  15Q LOSS MUTATED         6        7         1          5          0
  15Q LOSS WILD-TYPE      39       18         1         20          3
                    vv
clus                 STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  15Q LOSS MUTATED            2        0         0         0
  15Q LOSS WILD-TYPE          2        1         1         1
D67V3, multiclass
                    vv
clus                 T1 T2 T3 T4
  15Q LOSS MUTATED    7  8  7  0
  15Q LOSS WILD-TYPE 41 20 27  6
D67V4, multiclass
    clus
vv   15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  T1                7                 41
  T2                8                 20
  T3                7                 27
  T4                0                  6
D67V5, binary
                    cls
clus                  0  1
  15Q LOSS MUTATED   13  2
  15Q LOSS WILD-TYPE 61  1
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED     13    2
  15Q LOSS WILD-TYPE   61    1
   clus
vv  15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  0               13                 61
  1                2                  1
                    vv
clus                 M0 M1 MX
  15Q LOSS MUTATED   20  0  2
  15Q LOSS WILD-TYPE 70  2 23
D67V6, multiclass
    clus
vv   15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  M0               20                 70
  M1                0                  2
  MX                2                 23
D67V7, binary
                    cls
clus                  0  1
  15Q LOSS MUTATED    6 16
  15Q LOSS WILD-TYPE 38 57
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED      6   16
  15Q LOSS WILD-TYPE   38   57
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  FEMALE                6                 38
  MALE                 16                 57
                    vv
clus                 R0 R1 R2 RX
  15Q LOSS MUTATED   18  2  0  2
  15Q LOSS WILD-TYPE 75  8  1  6
D67V8, multiclass
    clus
vv   15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  R0               18                 75
  R1                2                  8
  R2                0                  1
  RX                2                  6

Clustering(68) Variable = 16P LOSS MUTATION ANALYSIS
D68V1, survival
                    sevent
clus2                 0  1
  16P LOSS MUTATED   16 15
  16P LOSS WILD-TYPE 45 38
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                31                 83 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                15                 38 
$`16P LOSS MUTATED`
TCGA-BC-A217 TCGA-BC-A5W4 TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 
       13.81         9.50         0.07         2.86         3.02         3.39 
TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A114 TCGA-DD-A11B 
        0.10         0.07         0.10         0.13        37.74         0.46 
TCGA-DD-A1EF TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A39Z TCGA-DD-A3A8 
       12.95        49.15         6.02        29.16        19.73         0.36 
TCGA-DD-A3A9 TCGA-DD-A4ND TCGA-DD-A4NH TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NQ 
       30.58        73.38        14.24        29.56        61.45        12.26 
TCGA-EP-A2KB TCGA-ES-A2HS TCGA-FV-A23B TCGA-FV-A3I0 TCGA-FV-A3R2 TCGA-G3-A25X 
        1.97        23.01        32.45         0.20         6.35        58.49 
TCGA-G3-A25Y 
       14.86 

$`16P LOSS WILD-TYPE`
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T 
       48.99        27.91        37.32        10.13        46.78        27.52 
TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 
       27.52         2.99        25.32        23.34         1.12        69.57 
TCGA-BC-A112 TCGA-BC-A216 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-CC-5263 TCGA-CC-A1HT 
        5.03        44.42         0.26        16.37         4.24         3.32 
TCGA-DD-A113 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A 
       79.73        83.57        53.29       112.96         7.33         2.60 
TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC 
       21.76        51.25        90.67        79.36        66.31        19.76 
TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39X TCGA-DD-A39Y 
       75.65         6.67        13.64        21.14        55.66         5.59 
TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 
       25.81         7.66        70.06        17.59        20.12       102.74 
TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A4NA TCGA-DD-A4NE TCGA-DD-A4NF TCGA-DD-A4NG 
      107.11        13.78        33.14        21.67        14.07        14.93 
TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NP TCGA-ED-A459 
       10.78        15.06        39.75        56.25        93.67         0.23 
TCGA-ED-A5KG TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KC TCGA-EP-A3JL 
        0.20        10.85         7.76        11.74         0.62         3.19 
TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A2QR TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 
        0.43        14.40        19.07         0.13         0.03         0.33 
TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V 
       60.36         0.39         1.22        51.02        53.79        28.27 
TCGA-G3-A25W TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ 
       30.71        21.53        22.13        25.64         5.88        19.53 
TCGA-G3-A3CK TCGA-G3-A5SJ TCGA-G3-A5SK TCGA-G3-A5SL TCGA-G3-A5SM 
       19.23        11.97         9.93         7.99         4.37 

  16P LOSS MUTATED 16P LOSS WILD-TYPE 
              0.07               0.03 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
             73.38             112.96 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
             12.26              19.53 
[1] "0.1 - 73.4 (12.3)"  "0.0 - 113.0 (19.5)"
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE"   "16P LOSS MUTATED" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-BC-A5W4 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE"   "16P LOSS MUTATED" 
        TCGA-CC-5258         TCGA-CC-5260         TCGA-CC-5261 
  "16P LOSS MUTATED"   "16P LOSS MUTATED"   "16P LOSS MUTATED" 
        TCGA-CC-5262         TCGA-CC-5263         TCGA-CC-A1HT 
  "16P LOSS MUTATED" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-CC-A3M9         TCGA-CC-A3MA         TCGA-CC-A3MB 
  "16P LOSS MUTATED"   "16P LOSS MUTATED"   "16P LOSS MUTATED" 
        TCGA-CC-A3MC         TCGA-DD-A113         TCGA-DD-A114 
  "16P LOSS MUTATED" "16P LOSS WILD-TYPE"   "16P LOSS MUTATED" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE"   "16P LOSS MUTATED" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DD-A1EA         TCGA-DD-A1EB         TCGA-DD-A1EC 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DD-A1ED         TCGA-DD-A1EE         TCGA-DD-A1EF 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE"   "16P LOSS MUTATED" 
        TCGA-DD-A1EH         TCGA-DD-A1EI         TCGA-DD-A1EJ 
  "16P LOSS MUTATED"   "16P LOSS MUTATED"   "16P LOSS MUTATED" 
        TCGA-DD-A1EL         TCGA-DD-A39V         TCGA-DD-A39X 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DD-A39Y         TCGA-DD-A39Z         TCGA-DD-A3A0 
"16P LOSS WILD-TYPE"   "16P LOSS MUTATED" "16P LOSS WILD-TYPE" 
        TCGA-DD-A3A1         TCGA-DD-A3A2         TCGA-DD-A3A3 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DD-A3A4         TCGA-DD-A3A5         TCGA-DD-A3A6 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DD-A3A7         TCGA-DD-A3A8         TCGA-DD-A3A9 
"16P LOSS WILD-TYPE"   "16P LOSS MUTATED"   "16P LOSS MUTATED" 
        TCGA-DD-A4NA         TCGA-DD-A4ND         TCGA-DD-A4NE 
"16P LOSS WILD-TYPE"   "16P LOSS MUTATED" "16P LOSS WILD-TYPE" 
        TCGA-DD-A4NF         TCGA-DD-A4NG         TCGA-DD-A4NH 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE"   "16P LOSS MUTATED" 
        TCGA-DD-A4NI         TCGA-DD-A4NJ         TCGA-DD-A4NK 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DD-A4NL         TCGA-DD-A4NN         TCGA-DD-A4NO 
"16P LOSS WILD-TYPE"   "16P LOSS MUTATED"   "16P LOSS MUTATED" 
        TCGA-DD-A4NP         TCGA-DD-A4NQ         TCGA-ED-A459 
"16P LOSS WILD-TYPE"   "16P LOSS MUTATED" "16P LOSS WILD-TYPE" 
        TCGA-ED-A5KG         TCGA-EP-A12J         TCGA-EP-A26S 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EP-A2KA         TCGA-EP-A2KB         TCGA-EP-A2KC 
"16P LOSS WILD-TYPE"   "16P LOSS MUTATED" "16P LOSS WILD-TYPE" 
        TCGA-EP-A3JL         TCGA-EP-A3RK         TCGA-ES-A2HS 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE"   "16P LOSS MUTATED" 
        TCGA-ES-A2HT         TCGA-FV-A23B         TCGA-FV-A2QR 
"16P LOSS WILD-TYPE"   "16P LOSS MUTATED" "16P LOSS WILD-TYPE" 
        TCGA-FV-A3I0         TCGA-FV-A3R2         TCGA-FV-A3R3 
  "16P LOSS MUTATED"   "16P LOSS MUTATED" "16P LOSS WILD-TYPE" 
        TCGA-FV-A495         TCGA-FV-A496         TCGA-FV-A4ZP 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-FV-A4ZQ         TCGA-G3-A25S         TCGA-G3-A25T 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-G3-A25U         TCGA-G3-A25V         TCGA-G3-A25W 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-G3-A25X         TCGA-G3-A25Y         TCGA-G3-A25Z 
  "16P LOSS MUTATED"   "16P LOSS MUTATED" "16P LOSS WILD-TYPE" 
        TCGA-G3-A3CG         TCGA-G3-A3CH         TCGA-G3-A3CI 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK         TCGA-G3-A5SJ 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-G3-A5SK         TCGA-G3-A5SL         TCGA-G3-A5SM 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE"   "16P LOSS MUTATED" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-BC-A5W4 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE"   "16P LOSS MUTATED" 
        TCGA-CC-5258         TCGA-CC-5260         TCGA-CC-5261 
  "16P LOSS MUTATED"   "16P LOSS MUTATED"   "16P LOSS MUTATED" 
        TCGA-CC-5262         TCGA-CC-5263         TCGA-CC-A1HT 
  "16P LOSS MUTATED" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-CC-A3M9         TCGA-CC-A3MA         TCGA-CC-A3MB 
  "16P LOSS MUTATED"   "16P LOSS MUTATED"   "16P LOSS MUTATED" 
        TCGA-CC-A3MC         TCGA-DD-A113         TCGA-DD-A114 
  "16P LOSS MUTATED" "16P LOSS WILD-TYPE"   "16P LOSS MUTATED" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE"   "16P LOSS MUTATED" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DD-A1EA         TCGA-DD-A1EB         TCGA-DD-A1EC 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DD-A1ED         TCGA-DD-A1EE         TCGA-DD-A1EF 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE"   "16P LOSS MUTATED" 
        TCGA-DD-A1EH         TCGA-DD-A1EI         TCGA-DD-A1EJ 
  "16P LOSS MUTATED"   "16P LOSS MUTATED"   "16P LOSS MUTATED" 
        TCGA-DD-A1EL         TCGA-DD-A39V         TCGA-DD-A39X 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DD-A39Y         TCGA-DD-A39Z         TCGA-DD-A3A0 
"16P LOSS WILD-TYPE"   "16P LOSS MUTATED" "16P LOSS WILD-TYPE" 
        TCGA-DD-A3A1         TCGA-DD-A3A2         TCGA-DD-A3A3 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DD-A3A4         TCGA-DD-A3A5         TCGA-DD-A3A6 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DD-A3A7         TCGA-DD-A3A8         TCGA-DD-A3A9 
"16P LOSS WILD-TYPE"   "16P LOSS MUTATED"   "16P LOSS MUTATED" 
        TCGA-DD-A4NA         TCGA-DD-A4ND         TCGA-DD-A4NE 
"16P LOSS WILD-TYPE"   "16P LOSS MUTATED" "16P LOSS WILD-TYPE" 
        TCGA-DD-A4NF         TCGA-DD-A4NG         TCGA-DD-A4NH 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE"   "16P LOSS MUTATED" 
        TCGA-DD-A4NI         TCGA-DD-A4NJ         TCGA-DD-A4NK 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DD-A4NL         TCGA-DD-A4NN         TCGA-DD-A4NO 
"16P LOSS WILD-TYPE"   "16P LOSS MUTATED"   "16P LOSS MUTATED" 
        TCGA-DD-A4NP         TCGA-DD-A4NQ         TCGA-ED-A459 
"16P LOSS WILD-TYPE"   "16P LOSS MUTATED" "16P LOSS WILD-TYPE" 
        TCGA-ED-A5KG         TCGA-EP-A12J         TCGA-EP-A26S 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EP-A2KA         TCGA-EP-A2KB         TCGA-EP-A2KC 
"16P LOSS WILD-TYPE"   "16P LOSS MUTATED" "16P LOSS WILD-TYPE" 
        TCGA-EP-A3JL         TCGA-EP-A3RK         TCGA-ES-A2HS 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE"   "16P LOSS MUTATED" 
        TCGA-ES-A2HT         TCGA-FV-A23B         TCGA-FV-A2QR 
"16P LOSS WILD-TYPE"   "16P LOSS MUTATED" "16P LOSS WILD-TYPE" 
        TCGA-FV-A3I0         TCGA-FV-A3R2         TCGA-FV-A3R3 
  "16P LOSS MUTATED"   "16P LOSS MUTATED" "16P LOSS WILD-TYPE" 
        TCGA-FV-A495         TCGA-FV-A496         TCGA-FV-A4ZP 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-FV-A4ZQ         TCGA-G3-A25S         TCGA-G3-A25T 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-G3-A25U         TCGA-G3-A25V         TCGA-G3-A25W 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-G3-A25X         TCGA-G3-A25Y         TCGA-G3-A25Z 
  "16P LOSS MUTATED"   "16P LOSS MUTATED" "16P LOSS WILD-TYPE" 
        TCGA-G3-A3CG         TCGA-G3-A3CH         TCGA-G3-A3CI 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK         TCGA-G3-A5SJ 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-G3-A5SK         TCGA-G3-A5SL         TCGA-G3-A5SM 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE"   "16P LOSS MUTATED" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-BC-A5W4 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE"   "16P LOSS MUTATED" 
        TCGA-CC-5258         TCGA-CC-5260         TCGA-CC-5261 
  "16P LOSS MUTATED"   "16P LOSS MUTATED"   "16P LOSS MUTATED" 
        TCGA-CC-5262         TCGA-CC-5263         TCGA-CC-A1HT 
  "16P LOSS MUTATED" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-CC-A3M9         TCGA-CC-A3MA         TCGA-CC-A3MB 
  "16P LOSS MUTATED"   "16P LOSS MUTATED"   "16P LOSS MUTATED" 
        TCGA-CC-A3MC         TCGA-DD-A113         TCGA-DD-A114 
  "16P LOSS MUTATED" "16P LOSS WILD-TYPE"   "16P LOSS MUTATED" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE"   "16P LOSS MUTATED" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DD-A1EA         TCGA-DD-A1EB         TCGA-DD-A1EC 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DD-A1ED         TCGA-DD-A1EE         TCGA-DD-A1EF 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE"   "16P LOSS MUTATED" 
        TCGA-DD-A1EH         TCGA-DD-A1EI         TCGA-DD-A1EJ 
  "16P LOSS MUTATED"   "16P LOSS MUTATED"   "16P LOSS MUTATED" 
        TCGA-DD-A1EL         TCGA-DD-A39V         TCGA-DD-A39X 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DD-A39Y         TCGA-DD-A39Z         TCGA-DD-A3A0 
"16P LOSS WILD-TYPE"   "16P LOSS MUTATED" "16P LOSS WILD-TYPE" 
        TCGA-DD-A3A1         TCGA-DD-A3A2         TCGA-DD-A3A3 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DD-A3A4         TCGA-DD-A3A5         TCGA-DD-A3A6 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DD-A3A7         TCGA-DD-A3A8         TCGA-DD-A3A9 
"16P LOSS WILD-TYPE"   "16P LOSS MUTATED"   "16P LOSS MUTATED" 
        TCGA-DD-A4NA         TCGA-DD-A4ND         TCGA-DD-A4NE 
"16P LOSS WILD-TYPE"   "16P LOSS MUTATED" "16P LOSS WILD-TYPE" 
        TCGA-DD-A4NF         TCGA-DD-A4NG         TCGA-DD-A4NH 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE"   "16P LOSS MUTATED" 
        TCGA-DD-A4NI         TCGA-DD-A4NJ         TCGA-DD-A4NK 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DD-A4NL         TCGA-DD-A4NN         TCGA-DD-A4NO 
"16P LOSS WILD-TYPE"   "16P LOSS MUTATED"   "16P LOSS MUTATED" 
        TCGA-DD-A4NP         TCGA-DD-A4NQ         TCGA-ED-A459 
"16P LOSS WILD-TYPE"   "16P LOSS MUTATED" "16P LOSS WILD-TYPE" 
        TCGA-ED-A5KG         TCGA-EP-A12J         TCGA-EP-A26S 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EP-A2KA         TCGA-EP-A2KB         TCGA-EP-A2KC 
"16P LOSS WILD-TYPE"   "16P LOSS MUTATED" "16P LOSS WILD-TYPE" 
        TCGA-EP-A3JL         TCGA-EP-A3RK         TCGA-ES-A2HS 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE"   "16P LOSS MUTATED" 
        TCGA-ES-A2HT         TCGA-FV-A23B         TCGA-FV-A2QR 
"16P LOSS WILD-TYPE"   "16P LOSS MUTATED" "16P LOSS WILD-TYPE" 
        TCGA-FV-A3I0         TCGA-FV-A3R2         TCGA-FV-A3R3 
  "16P LOSS MUTATED"   "16P LOSS MUTATED" "16P LOSS WILD-TYPE" 
        TCGA-FV-A495         TCGA-FV-A496         TCGA-FV-A4ZP 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-FV-A4ZQ         TCGA-G3-A25S         TCGA-G3-A25T 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-G3-A25U         TCGA-G3-A25V         TCGA-G3-A25W 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-G3-A25X         TCGA-G3-A25Y         TCGA-G3-A25Z 
  "16P LOSS MUTATED"   "16P LOSS MUTATED" "16P LOSS WILD-TYPE" 
        TCGA-G3-A3CG         TCGA-G3-A3CH         TCGA-G3-A3CI 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK         TCGA-G3-A5SJ 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-G3-A5SK         TCGA-G3-A5SL         TCGA-G3-A5SM 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
[1] "hr=" "1.7"
D68V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  16P LOSS MUTATED        10       10         1          6          1
  16P LOSS WILD-TYPE      35       15         1         19          2
                    vv
clus                 STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  16P LOSS MUTATED            3        0         1         1
  16P LOSS WILD-TYPE          1        1         0         0
D68V3, multiclass
                    vv
clus                 T1 T2 T3 T4
  16P LOSS MUTATED   12 10  8  3
  16P LOSS WILD-TYPE 36 18 26  3
D68V4, multiclass
    clus
vv   16P LOSS MUTATED 16P LOSS WILD-TYPE
  T1               12                 36
  T2               10                 18
  T3                8                 26
  T4                3                  3
D68V5, binary
                    cls
clus                  0  1
  16P LOSS MUTATED   23  2
  16P LOSS WILD-TYPE 51  1
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED     23    2
  16P LOSS WILD-TYPE   51    1
   clus
vv  16P LOSS MUTATED 16P LOSS WILD-TYPE
  0               23                 51
  1                2                  1
                    vv
clus                 M0 M1 MX
  16P LOSS MUTATED   28  1  4
  16P LOSS WILD-TYPE 62  1 21
D68V6, multiclass
    clus
vv   16P LOSS MUTATED 16P LOSS WILD-TYPE
  M0               28                 62
  M1                1                  1
  MX                4                 21
D68V7, binary
                    cls
clus                  0  1
  16P LOSS MUTATED   13 20
  16P LOSS WILD-TYPE 31 53
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED     13   20
  16P LOSS WILD-TYPE   31   53
        clus
vv       16P LOSS MUTATED 16P LOSS WILD-TYPE
  FEMALE               13                 31
  MALE                 20                 53
                    vv
clus                 R0 R1 R2 RX
  16P LOSS MUTATED   26  1  0  5
  16P LOSS WILD-TYPE 67  9  1  3
D68V8, multiclass
    clus
vv   16P LOSS MUTATED 16P LOSS WILD-TYPE
  R0               26                 67
  R1                1                  9
  R2                0                  1
  RX                5                  3

Clustering(69) Variable = 16Q LOSS MUTATION ANALYSIS
D69V1, survival
                    sevent
clus2                 0  1
  16Q LOSS MUTATED   21 20
  16Q LOSS WILD-TYPE 40 33
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                41                 73 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                20                 33 
$`16Q LOSS MUTATED`
TCGA-BC-A10S TCGA-BC-A10W TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KG TCGA-CC-5258 
       46.78         2.99        44.42        13.81        16.37         0.07 
TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5263 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC 
        2.86         3.02         4.24         0.07         0.10         0.13 
TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A116 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A1EF 
       79.73        37.74        53.29         2.60         0.46        12.95 
TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A39Z TCGA-DD-A3A8 TCGA-DD-A3A9 
       49.15         6.02        29.16        19.73         0.36        30.58 
TCGA-DD-A4ND TCGA-DD-A4NE TCGA-DD-A4NH TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NQ 
       73.38        21.67        14.24        29.56        61.45        12.26 
TCGA-ED-A459 TCGA-EP-A2KB TCGA-ES-A2HS TCGA-FV-A23B TCGA-FV-A3I0 TCGA-FV-A3R2 
        0.23         1.97        23.01        32.45         0.20         6.35 
TCGA-G3-A25S TCGA-G3-A25U TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A3CH 
        1.22        53.79        58.49        14.86        25.64 

$`16Q LOSS WILD-TYPE`
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A10U 
       48.99        27.91        37.32        10.13        27.52        27.52 
TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A3KF 
       25.32        23.34         1.12        69.57         5.03         0.26 
TCGA-BC-A5W4 TCGA-CC-5262 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-DD-A115 TCGA-DD-A118 
        9.50         3.39         3.32         0.10        83.57       112.96 
TCGA-DD-A119 TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB 
        7.33        21.76        51.25        90.67        79.36        66.31 
TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39X 
       19.76        75.65         6.67        13.64        21.14        55.66 
TCGA-DD-A39Y TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 
        5.59        25.81         7.66        70.06        17.59        20.12 
TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A4NA TCGA-DD-A4NF TCGA-DD-A4NG 
      102.74       107.11        13.78        33.14        14.07        14.93 
TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NP TCGA-ED-A5KG 
       10.78        15.06        39.75        56.25        93.67         0.20 
TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK 
       10.85         7.76        11.74         0.62         3.19         0.43 
TCGA-ES-A2HT TCGA-FV-A2QR TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZP 
       14.40        19.07         0.13         0.03         0.33        60.36 
TCGA-FV-A4ZQ TCGA-G3-A25T TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25Z TCGA-G3-A3CG 
        0.39        51.02        28.27        30.71        21.53        22.13 
TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SJ TCGA-G3-A5SK TCGA-G3-A5SL 
        5.88        19.53        19.23        11.97         9.93         7.99 
TCGA-G3-A5SM 
        4.37 

  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
              0.07               0.03 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
             79.73             112.96 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
             14.24              19.07 
[1] "0.1 - 79.7 (14.2)"  "0.0 - 113.0 (19.1)"
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
"16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
"16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED"   "16Q LOSS MUTATED" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-BC-A5W4 
"16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" 
        TCGA-CC-5258         TCGA-CC-5260         TCGA-CC-5261 
  "16Q LOSS MUTATED"   "16Q LOSS MUTATED"   "16Q LOSS MUTATED" 
        TCGA-CC-5262         TCGA-CC-5263         TCGA-CC-A1HT 
"16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" 
        TCGA-CC-A3M9         TCGA-CC-A3MA         TCGA-CC-A3MB 
"16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED"   "16Q LOSS MUTATED" 
        TCGA-CC-A3MC         TCGA-DD-A113         TCGA-DD-A114 
  "16Q LOSS MUTATED"   "16Q LOSS MUTATED"   "16Q LOSS MUTATED" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED"   "16Q LOSS MUTATED" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DD-A1EA         TCGA-DD-A1EB         TCGA-DD-A1EC 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DD-A1ED         TCGA-DD-A1EE         TCGA-DD-A1EF 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" 
        TCGA-DD-A1EH         TCGA-DD-A1EI         TCGA-DD-A1EJ 
  "16Q LOSS MUTATED"   "16Q LOSS MUTATED"   "16Q LOSS MUTATED" 
        TCGA-DD-A1EL         TCGA-DD-A39V         TCGA-DD-A39X 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DD-A39Y         TCGA-DD-A39Z         TCGA-DD-A3A0 
"16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" 
        TCGA-DD-A3A1         TCGA-DD-A3A2         TCGA-DD-A3A3 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DD-A3A4         TCGA-DD-A3A5         TCGA-DD-A3A6 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DD-A3A7         TCGA-DD-A3A8         TCGA-DD-A3A9 
"16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED"   "16Q LOSS MUTATED" 
        TCGA-DD-A4NA         TCGA-DD-A4ND         TCGA-DD-A4NE 
"16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED"   "16Q LOSS MUTATED" 
        TCGA-DD-A4NF         TCGA-DD-A4NG         TCGA-DD-A4NH 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" 
        TCGA-DD-A4NI         TCGA-DD-A4NJ         TCGA-DD-A4NK 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DD-A4NL         TCGA-DD-A4NN         TCGA-DD-A4NO 
"16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED"   "16Q LOSS MUTATED" 
        TCGA-DD-A4NP         TCGA-DD-A4NQ         TCGA-ED-A459 
"16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED"   "16Q LOSS MUTATED" 
        TCGA-ED-A5KG         TCGA-EP-A12J         TCGA-EP-A26S 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EP-A2KA         TCGA-EP-A2KB         TCGA-EP-A2KC 
"16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" 
        TCGA-EP-A3JL         TCGA-EP-A3RK         TCGA-ES-A2HS 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" 
        TCGA-ES-A2HT         TCGA-FV-A23B         TCGA-FV-A2QR 
"16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" 
        TCGA-FV-A3I0         TCGA-FV-A3R2         TCGA-FV-A3R3 
  "16Q LOSS MUTATED"   "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" 
        TCGA-FV-A495         TCGA-FV-A496         TCGA-FV-A4ZP 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-FV-A4ZQ         TCGA-G3-A25S         TCGA-G3-A25T 
"16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" 
        TCGA-G3-A25U         TCGA-G3-A25V         TCGA-G3-A25W 
  "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-G3-A25X         TCGA-G3-A25Y         TCGA-G3-A25Z 
  "16Q LOSS MUTATED"   "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" 
        TCGA-G3-A3CG         TCGA-G3-A3CH         TCGA-G3-A3CI 
"16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK         TCGA-G3-A5SJ 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-G3-A5SK         TCGA-G3-A5SL         TCGA-G3-A5SM 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
"16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
"16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED"   "16Q LOSS MUTATED" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-BC-A5W4 
"16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" 
        TCGA-CC-5258         TCGA-CC-5260         TCGA-CC-5261 
  "16Q LOSS MUTATED"   "16Q LOSS MUTATED"   "16Q LOSS MUTATED" 
        TCGA-CC-5262         TCGA-CC-5263         TCGA-CC-A1HT 
"16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" 
        TCGA-CC-A3M9         TCGA-CC-A3MA         TCGA-CC-A3MB 
"16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED"   "16Q LOSS MUTATED" 
        TCGA-CC-A3MC         TCGA-DD-A113         TCGA-DD-A114 
  "16Q LOSS MUTATED"   "16Q LOSS MUTATED"   "16Q LOSS MUTATED" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED"   "16Q LOSS MUTATED" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DD-A1EA         TCGA-DD-A1EB         TCGA-DD-A1EC 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DD-A1ED         TCGA-DD-A1EE         TCGA-DD-A1EF 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" 
        TCGA-DD-A1EH         TCGA-DD-A1EI         TCGA-DD-A1EJ 
  "16Q LOSS MUTATED"   "16Q LOSS MUTATED"   "16Q LOSS MUTATED" 
        TCGA-DD-A1EL         TCGA-DD-A39V         TCGA-DD-A39X 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DD-A39Y         TCGA-DD-A39Z         TCGA-DD-A3A0 
"16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" 
        TCGA-DD-A3A1         TCGA-DD-A3A2         TCGA-DD-A3A3 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DD-A3A4         TCGA-DD-A3A5         TCGA-DD-A3A6 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DD-A3A7         TCGA-DD-A3A8         TCGA-DD-A3A9 
"16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED"   "16Q LOSS MUTATED" 
        TCGA-DD-A4NA         TCGA-DD-A4ND         TCGA-DD-A4NE 
"16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED"   "16Q LOSS MUTATED" 
        TCGA-DD-A4NF         TCGA-DD-A4NG         TCGA-DD-A4NH 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" 
        TCGA-DD-A4NI         TCGA-DD-A4NJ         TCGA-DD-A4NK 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DD-A4NL         TCGA-DD-A4NN         TCGA-DD-A4NO 
"16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED"   "16Q LOSS MUTATED" 
        TCGA-DD-A4NP         TCGA-DD-A4NQ         TCGA-ED-A459 
"16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED"   "16Q LOSS MUTATED" 
        TCGA-ED-A5KG         TCGA-EP-A12J         TCGA-EP-A26S 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EP-A2KA         TCGA-EP-A2KB         TCGA-EP-A2KC 
"16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" 
        TCGA-EP-A3JL         TCGA-EP-A3RK         TCGA-ES-A2HS 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" 
        TCGA-ES-A2HT         TCGA-FV-A23B         TCGA-FV-A2QR 
"16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" 
        TCGA-FV-A3I0         TCGA-FV-A3R2         TCGA-FV-A3R3 
  "16Q LOSS MUTATED"   "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" 
        TCGA-FV-A495         TCGA-FV-A496         TCGA-FV-A4ZP 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-FV-A4ZQ         TCGA-G3-A25S         TCGA-G3-A25T 
"16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" 
        TCGA-G3-A25U         TCGA-G3-A25V         TCGA-G3-A25W 
  "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-G3-A25X         TCGA-G3-A25Y         TCGA-G3-A25Z 
  "16Q LOSS MUTATED"   "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" 
        TCGA-G3-A3CG         TCGA-G3-A3CH         TCGA-G3-A3CI 
"16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK         TCGA-G3-A5SJ 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-G3-A5SK         TCGA-G3-A5SL         TCGA-G3-A5SM 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
"16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
"16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED"   "16Q LOSS MUTATED" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-BC-A5W4 
"16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" 
        TCGA-CC-5258         TCGA-CC-5260         TCGA-CC-5261 
  "16Q LOSS MUTATED"   "16Q LOSS MUTATED"   "16Q LOSS MUTATED" 
        TCGA-CC-5262         TCGA-CC-5263         TCGA-CC-A1HT 
"16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" 
        TCGA-CC-A3M9         TCGA-CC-A3MA         TCGA-CC-A3MB 
"16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED"   "16Q LOSS MUTATED" 
        TCGA-CC-A3MC         TCGA-DD-A113         TCGA-DD-A114 
  "16Q LOSS MUTATED"   "16Q LOSS MUTATED"   "16Q LOSS MUTATED" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED"   "16Q LOSS MUTATED" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DD-A1EA         TCGA-DD-A1EB         TCGA-DD-A1EC 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DD-A1ED         TCGA-DD-A1EE         TCGA-DD-A1EF 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" 
        TCGA-DD-A1EH         TCGA-DD-A1EI         TCGA-DD-A1EJ 
  "16Q LOSS MUTATED"   "16Q LOSS MUTATED"   "16Q LOSS MUTATED" 
        TCGA-DD-A1EL         TCGA-DD-A39V         TCGA-DD-A39X 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DD-A39Y         TCGA-DD-A39Z         TCGA-DD-A3A0 
"16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" 
        TCGA-DD-A3A1         TCGA-DD-A3A2         TCGA-DD-A3A3 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DD-A3A4         TCGA-DD-A3A5         TCGA-DD-A3A6 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DD-A3A7         TCGA-DD-A3A8         TCGA-DD-A3A9 
"16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED"   "16Q LOSS MUTATED" 
        TCGA-DD-A4NA         TCGA-DD-A4ND         TCGA-DD-A4NE 
"16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED"   "16Q LOSS MUTATED" 
        TCGA-DD-A4NF         TCGA-DD-A4NG         TCGA-DD-A4NH 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" 
        TCGA-DD-A4NI         TCGA-DD-A4NJ         TCGA-DD-A4NK 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DD-A4NL         TCGA-DD-A4NN         TCGA-DD-A4NO 
"16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED"   "16Q LOSS MUTATED" 
        TCGA-DD-A4NP         TCGA-DD-A4NQ         TCGA-ED-A459 
"16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED"   "16Q LOSS MUTATED" 
        TCGA-ED-A5KG         TCGA-EP-A12J         TCGA-EP-A26S 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EP-A2KA         TCGA-EP-A2KB         TCGA-EP-A2KC 
"16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" 
        TCGA-EP-A3JL         TCGA-EP-A3RK         TCGA-ES-A2HS 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" 
        TCGA-ES-A2HT         TCGA-FV-A23B         TCGA-FV-A2QR 
"16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" 
        TCGA-FV-A3I0         TCGA-FV-A3R2         TCGA-FV-A3R3 
  "16Q LOSS MUTATED"   "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" 
        TCGA-FV-A495         TCGA-FV-A496         TCGA-FV-A4ZP 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-FV-A4ZQ         TCGA-G3-A25S         TCGA-G3-A25T 
"16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" 
        TCGA-G3-A25U         TCGA-G3-A25V         TCGA-G3-A25W 
  "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-G3-A25X         TCGA-G3-A25Y         TCGA-G3-A25Z 
  "16Q LOSS MUTATED"   "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" 
        TCGA-G3-A3CG         TCGA-G3-A3CH         TCGA-G3-A3CI 
"16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK         TCGA-G3-A5SJ 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-G3-A5SK         TCGA-G3-A5SL         TCGA-G3-A5SM 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
[1] "hr=" "1.4"
D69V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  16Q LOSS MUTATED        13       13         1          9          1
  16Q LOSS WILD-TYPE      32       12         1         16          2
                    vv
clus                 STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  16Q LOSS MUTATED            2        0         1         1
  16Q LOSS WILD-TYPE          2        1         0         0
D69V3, multiclass
                    vv
clus                 T1 T2 T3 T4
  16Q LOSS MUTATED   15 13 12  3
  16Q LOSS WILD-TYPE 33 15 22  3
D69V4, multiclass
    clus
vv   16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  T1               15                 33
  T2               13                 15
  T3               12                 22
  T4                3                  3
D69V5, binary
                    cls
clus                  0  1
  16Q LOSS MUTATED   31  2
  16Q LOSS WILD-TYPE 43  1
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED     31    2
  16Q LOSS WILD-TYPE   43    1
   clus
vv  16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  0               31                 43
  1                2                  1
                    vv
clus                 M0 M1 MX
  16Q LOSS MUTATED   36  1  6
  16Q LOSS WILD-TYPE 54  1 19
D69V6, multiclass
    clus
vv   16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  M0               36                 54
  M1                1                  1
  MX                6                 19
D69V7, binary
                    cls
clus                  0  1
  16Q LOSS MUTATED   18 25
  16Q LOSS WILD-TYPE 26 48
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED     18   25
  16Q LOSS WILD-TYPE   26   48
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  FEMALE               18                 26
  MALE                 25                 48
                    vv
clus                 R0 R1 R2 RX
  16Q LOSS MUTATED   35  2  0  6
  16Q LOSS WILD-TYPE 58  8  1  2
D69V8, multiclass
    clus
vv   16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  R0               35                 58
  R1                2                  8
  R2                0                  1
  RX                6                  2

Clustering(70) Variable = 17P LOSS MUTATION ANALYSIS
D70V1, survival
                    sevent
clus2                 0  1
  17P LOSS MUTATED   29 27
  17P LOSS WILD-TYPE 32 26
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                56                 58 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                27                 26 
$`17P LOSS MUTATED`
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10R TCGA-BC-A10U TCGA-BC-A10Y TCGA-BC-A10Z 
       48.99        27.91        10.13        27.52        23.34         1.12 
TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 
       69.57         5.03        13.81         0.26        16.37         9.50 
TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A1HT 
        0.07         2.86         3.02         3.39         4.24         3.32 
TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 
        0.10         0.13        83.57        53.29       112.96         7.33 
TCGA-DD-A11A TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EH 
        2.60        21.76        51.25        79.36        66.31        49.15 
TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EL TCGA-DD-A39Y TCGA-DD-A3A3 TCGA-DD-A3A4 
        6.02        29.16        13.64         5.59        17.59        20.12 
TCGA-DD-A3A5 TCGA-DD-A4NA TCGA-DD-A4NH TCGA-DD-A4NJ TCGA-DD-A4NQ TCGA-ED-A459 
      102.74        33.14        14.24        15.06        12.26         0.23 
TCGA-EP-A2KC TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A495 TCGA-G3-A25S 
        0.62        32.45        19.07         0.20         0.03         1.22 
TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CH TCGA-G3-A5SK 
       53.79        28.27        14.86        21.53        25.64         9.93 
TCGA-G3-A5SL TCGA-G3-A5SM 
        7.99         4.37 

$`17P LOSS WILD-TYPE`
TCGA-BC-A10Q TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A216 
       37.32        46.78        27.52         2.99        25.32        44.42 
TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A11B TCGA-DD-A1E9 
        0.10         0.07        79.73        37.74         0.46        90.67 
TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A39V TCGA-DD-A39X 
       19.76        75.65         6.67        12.95        21.14        55.66 
TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A6 TCGA-DD-A3A7 
       19.73        25.81         7.66        70.06       107.11        13.78 
TCGA-DD-A3A8 TCGA-DD-A3A9 TCGA-DD-A4ND TCGA-DD-A4NE TCGA-DD-A4NF TCGA-DD-A4NG 
        0.36        30.58        73.38        21.67        14.07        14.93 
TCGA-DD-A4NI TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP 
       10.78        39.75        56.25        29.56        61.45        93.67 
TCGA-ED-A5KG TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A3JL 
        0.20        10.85         7.76        11.74         1.97         3.19 
TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A496 
        0.43        23.01        14.40         6.35         0.13         0.33 
TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25T TCGA-G3-A25W TCGA-G3-A25X TCGA-G3-A3CG 
       60.36         0.39        51.02        30.71        58.49        22.13 
TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SJ 
        5.88        19.53        19.23        11.97 

  17P LOSS MUTATED 17P LOSS WILD-TYPE 
              0.03               0.07 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
            112.96             107.11 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
            14.025             19.745 
[1] "0.0 - 113.0 (14.0)" "0.1 - 107.1 (19.7)"
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
  "17P LOSS MUTATED"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
  "17P LOSS MUTATED"   "17P LOSS MUTATED"   "17P LOSS MUTATED" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-BC-A5W4 
  "17P LOSS MUTATED"   "17P LOSS MUTATED"   "17P LOSS MUTATED" 
        TCGA-CC-5258         TCGA-CC-5260         TCGA-CC-5261 
  "17P LOSS MUTATED"   "17P LOSS MUTATED"   "17P LOSS MUTATED" 
        TCGA-CC-5262         TCGA-CC-5263         TCGA-CC-A1HT 
  "17P LOSS MUTATED"   "17P LOSS MUTATED"   "17P LOSS MUTATED" 
        TCGA-CC-A3M9         TCGA-CC-A3MA         TCGA-CC-A3MB 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-CC-A3MC         TCGA-DD-A113         TCGA-DD-A114 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
  "17P LOSS MUTATED"   "17P LOSS MUTATED"   "17P LOSS MUTATED" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
  "17P LOSS MUTATED"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
  "17P LOSS MUTATED"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-DD-A1EA         TCGA-DD-A1EB         TCGA-DD-A1EC 
  "17P LOSS MUTATED"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-DD-A1ED         TCGA-DD-A1EE         TCGA-DD-A1EF 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-DD-A1EH         TCGA-DD-A1EI         TCGA-DD-A1EJ 
  "17P LOSS MUTATED"   "17P LOSS MUTATED"   "17P LOSS MUTATED" 
        TCGA-DD-A1EL         TCGA-DD-A39V         TCGA-DD-A39X 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-DD-A39Y         TCGA-DD-A39Z         TCGA-DD-A3A0 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-DD-A3A1         TCGA-DD-A3A2         TCGA-DD-A3A3 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-DD-A3A4         TCGA-DD-A3A5         TCGA-DD-A3A6 
  "17P LOSS MUTATED"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-DD-A3A7         TCGA-DD-A3A8         TCGA-DD-A3A9 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-DD-A4NA         TCGA-DD-A4ND         TCGA-DD-A4NE 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-DD-A4NF         TCGA-DD-A4NG         TCGA-DD-A4NH 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-DD-A4NI         TCGA-DD-A4NJ         TCGA-DD-A4NK 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-DD-A4NL         TCGA-DD-A4NN         TCGA-DD-A4NO 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-DD-A4NP         TCGA-DD-A4NQ         TCGA-ED-A459 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED"   "17P LOSS MUTATED" 
        TCGA-ED-A5KG         TCGA-EP-A12J         TCGA-EP-A26S 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-EP-A2KA         TCGA-EP-A2KB         TCGA-EP-A2KC 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-EP-A3JL         TCGA-EP-A3RK         TCGA-ES-A2HS 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-ES-A2HT         TCGA-FV-A23B         TCGA-FV-A2QR 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED"   "17P LOSS MUTATED" 
        TCGA-FV-A3I0         TCGA-FV-A3R2         TCGA-FV-A3R3 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-FV-A495         TCGA-FV-A496         TCGA-FV-A4ZP 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-FV-A4ZQ         TCGA-G3-A25S         TCGA-G3-A25T 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-G3-A25U         TCGA-G3-A25V         TCGA-G3-A25W 
  "17P LOSS MUTATED"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-G3-A25X         TCGA-G3-A25Y         TCGA-G3-A25Z 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED"   "17P LOSS MUTATED" 
        TCGA-G3-A3CG         TCGA-G3-A3CH         TCGA-G3-A3CI 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK         TCGA-G3-A5SJ 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-G3-A5SK         TCGA-G3-A5SL         TCGA-G3-A5SM 
  "17P LOSS MUTATED"   "17P LOSS MUTATED"   "17P LOSS MUTATED" 
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
  "17P LOSS MUTATED"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
  "17P LOSS MUTATED"   "17P LOSS MUTATED"   "17P LOSS MUTATED" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-BC-A5W4 
  "17P LOSS MUTATED"   "17P LOSS MUTATED"   "17P LOSS MUTATED" 
        TCGA-CC-5258         TCGA-CC-5260         TCGA-CC-5261 
  "17P LOSS MUTATED"   "17P LOSS MUTATED"   "17P LOSS MUTATED" 
        TCGA-CC-5262         TCGA-CC-5263         TCGA-CC-A1HT 
  "17P LOSS MUTATED"   "17P LOSS MUTATED"   "17P LOSS MUTATED" 
        TCGA-CC-A3M9         TCGA-CC-A3MA         TCGA-CC-A3MB 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-CC-A3MC         TCGA-DD-A113         TCGA-DD-A114 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
  "17P LOSS MUTATED"   "17P LOSS MUTATED"   "17P LOSS MUTATED" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
  "17P LOSS MUTATED"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
  "17P LOSS MUTATED"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-DD-A1EA         TCGA-DD-A1EB         TCGA-DD-A1EC 
  "17P LOSS MUTATED"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-DD-A1ED         TCGA-DD-A1EE         TCGA-DD-A1EF 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-DD-A1EH         TCGA-DD-A1EI         TCGA-DD-A1EJ 
  "17P LOSS MUTATED"   "17P LOSS MUTATED"   "17P LOSS MUTATED" 
        TCGA-DD-A1EL         TCGA-DD-A39V         TCGA-DD-A39X 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-DD-A39Y         TCGA-DD-A39Z         TCGA-DD-A3A0 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-DD-A3A1         TCGA-DD-A3A2         TCGA-DD-A3A3 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-DD-A3A4         TCGA-DD-A3A5         TCGA-DD-A3A6 
  "17P LOSS MUTATED"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-DD-A3A7         TCGA-DD-A3A8         TCGA-DD-A3A9 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-DD-A4NA         TCGA-DD-A4ND         TCGA-DD-A4NE 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-DD-A4NF         TCGA-DD-A4NG         TCGA-DD-A4NH 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-DD-A4NI         TCGA-DD-A4NJ         TCGA-DD-A4NK 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-DD-A4NL         TCGA-DD-A4NN         TCGA-DD-A4NO 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-DD-A4NP         TCGA-DD-A4NQ         TCGA-ED-A459 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED"   "17P LOSS MUTATED" 
        TCGA-ED-A5KG         TCGA-EP-A12J         TCGA-EP-A26S 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-EP-A2KA         TCGA-EP-A2KB         TCGA-EP-A2KC 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-EP-A3JL         TCGA-EP-A3RK         TCGA-ES-A2HS 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-ES-A2HT         TCGA-FV-A23B         TCGA-FV-A2QR 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED"   "17P LOSS MUTATED" 
        TCGA-FV-A3I0         TCGA-FV-A3R2         TCGA-FV-A3R3 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-FV-A495         TCGA-FV-A496         TCGA-FV-A4ZP 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-FV-A4ZQ         TCGA-G3-A25S         TCGA-G3-A25T 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-G3-A25U         TCGA-G3-A25V         TCGA-G3-A25W 
  "17P LOSS MUTATED"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-G3-A25X         TCGA-G3-A25Y         TCGA-G3-A25Z 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED"   "17P LOSS MUTATED" 
        TCGA-G3-A3CG         TCGA-G3-A3CH         TCGA-G3-A3CI 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK         TCGA-G3-A5SJ 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-G3-A5SK         TCGA-G3-A5SL         TCGA-G3-A5SM 
  "17P LOSS MUTATED"   "17P LOSS MUTATED"   "17P LOSS MUTATED" 
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
  "17P LOSS MUTATED"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
  "17P LOSS MUTATED"   "17P LOSS MUTATED"   "17P LOSS MUTATED" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-BC-A5W4 
  "17P LOSS MUTATED"   "17P LOSS MUTATED"   "17P LOSS MUTATED" 
        TCGA-CC-5258         TCGA-CC-5260         TCGA-CC-5261 
  "17P LOSS MUTATED"   "17P LOSS MUTATED"   "17P LOSS MUTATED" 
        TCGA-CC-5262         TCGA-CC-5263         TCGA-CC-A1HT 
  "17P LOSS MUTATED"   "17P LOSS MUTATED"   "17P LOSS MUTATED" 
        TCGA-CC-A3M9         TCGA-CC-A3MA         TCGA-CC-A3MB 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-CC-A3MC         TCGA-DD-A113         TCGA-DD-A114 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
  "17P LOSS MUTATED"   "17P LOSS MUTATED"   "17P LOSS MUTATED" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
  "17P LOSS MUTATED"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
  "17P LOSS MUTATED"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-DD-A1EA         TCGA-DD-A1EB         TCGA-DD-A1EC 
  "17P LOSS MUTATED"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-DD-A1ED         TCGA-DD-A1EE         TCGA-DD-A1EF 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-DD-A1EH         TCGA-DD-A1EI         TCGA-DD-A1EJ 
  "17P LOSS MUTATED"   "17P LOSS MUTATED"   "17P LOSS MUTATED" 
        TCGA-DD-A1EL         TCGA-DD-A39V         TCGA-DD-A39X 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-DD-A39Y         TCGA-DD-A39Z         TCGA-DD-A3A0 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-DD-A3A1         TCGA-DD-A3A2         TCGA-DD-A3A3 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-DD-A3A4         TCGA-DD-A3A5         TCGA-DD-A3A6 
  "17P LOSS MUTATED"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-DD-A3A7         TCGA-DD-A3A8         TCGA-DD-A3A9 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-DD-A4NA         TCGA-DD-A4ND         TCGA-DD-A4NE 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-DD-A4NF         TCGA-DD-A4NG         TCGA-DD-A4NH 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-DD-A4NI         TCGA-DD-A4NJ         TCGA-DD-A4NK 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-DD-A4NL         TCGA-DD-A4NN         TCGA-DD-A4NO 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-DD-A4NP         TCGA-DD-A4NQ         TCGA-ED-A459 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED"   "17P LOSS MUTATED" 
        TCGA-ED-A5KG         TCGA-EP-A12J         TCGA-EP-A26S 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-EP-A2KA         TCGA-EP-A2KB         TCGA-EP-A2KC 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-EP-A3JL         TCGA-EP-A3RK         TCGA-ES-A2HS 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-ES-A2HT         TCGA-FV-A23B         TCGA-FV-A2QR 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED"   "17P LOSS MUTATED" 
        TCGA-FV-A3I0         TCGA-FV-A3R2         TCGA-FV-A3R3 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-FV-A495         TCGA-FV-A496         TCGA-FV-A4ZP 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-FV-A4ZQ         TCGA-G3-A25S         TCGA-G3-A25T 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-G3-A25U         TCGA-G3-A25V         TCGA-G3-A25W 
  "17P LOSS MUTATED"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-G3-A25X         TCGA-G3-A25Y         TCGA-G3-A25Z 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED"   "17P LOSS MUTATED" 
        TCGA-G3-A3CG         TCGA-G3-A3CH         TCGA-G3-A3CI 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK         TCGA-G3-A5SJ 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-G3-A5SK         TCGA-G3-A5SL         TCGA-G3-A5SM 
  "17P LOSS MUTATED"   "17P LOSS MUTATED"   "17P LOSS MUTATED" 
[1] "hr=" "1.3"
D70V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  17P LOSS MUTATED        17       14         2         13          1
  17P LOSS WILD-TYPE      28       11         0         12          2
                    vv
clus                 STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  17P LOSS MUTATED            4        1         1         0
  17P LOSS WILD-TYPE          0        0         0         1
D70V3, multiclass
                    vv
clus                 T1 T2 T3 T4
  17P LOSS MUTATED   20 16 19  3
  17P LOSS WILD-TYPE 28 12 15  3
D70V4, multiclass
    clus
vv   17P LOSS MUTATED 17P LOSS WILD-TYPE
  T1               20                 28
  T2               16                 12
  T3               19                 15
  T4                3                  3
D70V5, binary
                    cls
clus                  0  1
  17P LOSS MUTATED   40  3
  17P LOSS WILD-TYPE 34  0
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED     40    3
  17P LOSS WILD-TYPE   34    0
   clus
vv  17P LOSS MUTATED 17P LOSS WILD-TYPE
  0               40                 34
  1                3                  0
                    vv
clus                 M0 M1 MX
  17P LOSS MUTATED   48  1  9
  17P LOSS WILD-TYPE 42  1 16
D70V6, multiclass
    clus
vv   17P LOSS MUTATED 17P LOSS WILD-TYPE
  M0               48                 42
  M1                1                  1
  MX                9                 16
D70V7, binary
                    cls
clus                  0  1
  17P LOSS MUTATED   21 37
  17P LOSS WILD-TYPE 23 36
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED     21   37
  17P LOSS WILD-TYPE   23   36
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  FEMALE               21                 23
  MALE                 37                 36
                    vv
clus                 R0 R1 R2 RX
  17P LOSS MUTATED   43  5  1  7
  17P LOSS WILD-TYPE 50  5  0  1
D70V8, multiclass
    clus
vv   17P LOSS MUTATED 17P LOSS WILD-TYPE
  R0               43                 50
  R1                5                  5
  R2                1                  0
  RX                7                  1

Clustering(71) Variable = 17Q LOSS MUTATION ANALYSIS
D71V1, survival
                    sevent
clus2                 0  1
  17Q LOSS MUTATED    6  2
  17Q LOSS WILD-TYPE 55 51
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                 8                106 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                 2                 51 
$`17Q LOSS MUTATED`
TCGA-BC-A10R TCGA-BC-A5W4 TCGA-DD-A116 TCGA-DD-A1EB TCGA-DD-A4NJ TCGA-FV-A3I0 
       10.13         9.50        53.29        66.31        15.06         0.20 
TCGA-G3-A5SL TCGA-G3-A5SM 
        7.99         4.37 

$`17Q LOSS WILD-TYPE`
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U 
       48.99        27.91        37.32        46.78        27.52        27.52 
TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 
        2.99        25.32        23.34         1.12        69.57         5.03 
TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-CC-5258 TCGA-CC-5260 
       44.42        13.81         0.26        16.37         0.07         2.86 
TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA 
        3.02         3.39         4.24         3.32         0.10         0.07 
TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A118 
        0.10         0.13        79.73        37.74        83.57       112.96 
TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 
        7.33         2.60         0.46        21.76        51.25        90.67 
TCGA-DD-A1EA TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EH 
       79.36        19.76        75.65         6.67        12.95        49.15 
TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39X TCGA-DD-A39Y 
        6.02        29.16        13.64        21.14        55.66         5.59 
TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 
       19.73        25.81         7.66        70.06        17.59        20.12 
TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A3A9 TCGA-DD-A4NA 
      102.74       107.11        13.78         0.36        30.58        33.14 
TCGA-DD-A4ND TCGA-DD-A4NE TCGA-DD-A4NF TCGA-DD-A4NG TCGA-DD-A4NH TCGA-DD-A4NI 
       73.38        21.67        14.07        14.93        14.24        10.78 
TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ 
       39.75        56.25        29.56        61.45        93.67        12.26 
TCGA-ED-A459 TCGA-ED-A5KG TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB 
        0.23         0.20        10.85         7.76        11.74         1.97 
TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A23B 
        0.62         3.19         0.43        23.01        14.40        32.45 
TCGA-FV-A2QR TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZP 
       19.07         6.35         0.13         0.03         0.33        60.36 
TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W 
        0.39         1.22        51.02        53.79        28.27        30.71 
TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CH TCGA-G3-A3CI 
       58.49        14.86        21.53        22.13        25.64         5.88 
TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SJ TCGA-G3-A5SK 
       19.53        19.23        11.97         9.93 

  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
              0.20               0.03 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
             66.31             112.96 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
             9.815             18.330 
[1] "0.2 - 66.3 (9.8)"   "0.0 - 113.0 (18.3)"
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
  "17Q LOSS MUTATED" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-BC-A5W4 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE"   "17Q LOSS MUTATED" 
        TCGA-CC-5258         TCGA-CC-5260         TCGA-CC-5261 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-CC-5262         TCGA-CC-5263         TCGA-CC-A1HT 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-CC-A3M9         TCGA-CC-A3MA         TCGA-CC-A3MB 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-CC-A3MC         TCGA-DD-A113         TCGA-DD-A114 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"17Q LOSS WILD-TYPE"   "17Q LOSS MUTATED" "17Q LOSS WILD-TYPE" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DD-A1EA         TCGA-DD-A1EB         TCGA-DD-A1EC 
"17Q LOSS WILD-TYPE"   "17Q LOSS MUTATED" "17Q LOSS WILD-TYPE" 
        TCGA-DD-A1ED         TCGA-DD-A1EE         TCGA-DD-A1EF 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DD-A1EH         TCGA-DD-A1EI         TCGA-DD-A1EJ 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DD-A1EL         TCGA-DD-A39V         TCGA-DD-A39X 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DD-A39Y         TCGA-DD-A39Z         TCGA-DD-A3A0 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DD-A3A1         TCGA-DD-A3A2         TCGA-DD-A3A3 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DD-A3A4         TCGA-DD-A3A5         TCGA-DD-A3A6 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DD-A3A7         TCGA-DD-A3A8         TCGA-DD-A3A9 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DD-A4NA         TCGA-DD-A4ND         TCGA-DD-A4NE 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DD-A4NF         TCGA-DD-A4NG         TCGA-DD-A4NH 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DD-A4NI         TCGA-DD-A4NJ         TCGA-DD-A4NK 
"17Q LOSS WILD-TYPE"   "17Q LOSS MUTATED" "17Q LOSS WILD-TYPE" 
        TCGA-DD-A4NL         TCGA-DD-A4NN         TCGA-DD-A4NO 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DD-A4NP         TCGA-DD-A4NQ         TCGA-ED-A459 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-ED-A5KG         TCGA-EP-A12J         TCGA-EP-A26S 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EP-A2KA         TCGA-EP-A2KB         TCGA-EP-A2KC 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EP-A3JL         TCGA-EP-A3RK         TCGA-ES-A2HS 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-ES-A2HT         TCGA-FV-A23B         TCGA-FV-A2QR 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-FV-A3I0         TCGA-FV-A3R2         TCGA-FV-A3R3 
  "17Q LOSS MUTATED" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-FV-A495         TCGA-FV-A496         TCGA-FV-A4ZP 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-FV-A4ZQ         TCGA-G3-A25S         TCGA-G3-A25T 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-G3-A25U         TCGA-G3-A25V         TCGA-G3-A25W 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-G3-A25X         TCGA-G3-A25Y         TCGA-G3-A25Z 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-G3-A3CG         TCGA-G3-A3CH         TCGA-G3-A3CI 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK         TCGA-G3-A5SJ 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-G3-A5SK         TCGA-G3-A5SL         TCGA-G3-A5SM 
"17Q LOSS WILD-TYPE"   "17Q LOSS MUTATED"   "17Q LOSS MUTATED" 
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
  "17Q LOSS MUTATED" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-BC-A5W4 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE"   "17Q LOSS MUTATED" 
        TCGA-CC-5258         TCGA-CC-5260         TCGA-CC-5261 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-CC-5262         TCGA-CC-5263         TCGA-CC-A1HT 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-CC-A3M9         TCGA-CC-A3MA         TCGA-CC-A3MB 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-CC-A3MC         TCGA-DD-A113         TCGA-DD-A114 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"17Q LOSS WILD-TYPE"   "17Q LOSS MUTATED" "17Q LOSS WILD-TYPE" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DD-A1EA         TCGA-DD-A1EB         TCGA-DD-A1EC 
"17Q LOSS WILD-TYPE"   "17Q LOSS MUTATED" "17Q LOSS WILD-TYPE" 
        TCGA-DD-A1ED         TCGA-DD-A1EE         TCGA-DD-A1EF 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DD-A1EH         TCGA-DD-A1EI         TCGA-DD-A1EJ 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DD-A1EL         TCGA-DD-A39V         TCGA-DD-A39X 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DD-A39Y         TCGA-DD-A39Z         TCGA-DD-A3A0 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DD-A3A1         TCGA-DD-A3A2         TCGA-DD-A3A3 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DD-A3A4         TCGA-DD-A3A5         TCGA-DD-A3A6 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DD-A3A7         TCGA-DD-A3A8         TCGA-DD-A3A9 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DD-A4NA         TCGA-DD-A4ND         TCGA-DD-A4NE 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DD-A4NF         TCGA-DD-A4NG         TCGA-DD-A4NH 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DD-A4NI         TCGA-DD-A4NJ         TCGA-DD-A4NK 
"17Q LOSS WILD-TYPE"   "17Q LOSS MUTATED" "17Q LOSS WILD-TYPE" 
        TCGA-DD-A4NL         TCGA-DD-A4NN         TCGA-DD-A4NO 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DD-A4NP         TCGA-DD-A4NQ         TCGA-ED-A459 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-ED-A5KG         TCGA-EP-A12J         TCGA-EP-A26S 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EP-A2KA         TCGA-EP-A2KB         TCGA-EP-A2KC 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EP-A3JL         TCGA-EP-A3RK         TCGA-ES-A2HS 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-ES-A2HT         TCGA-FV-A23B         TCGA-FV-A2QR 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-FV-A3I0         TCGA-FV-A3R2         TCGA-FV-A3R3 
  "17Q LOSS MUTATED" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-FV-A495         TCGA-FV-A496         TCGA-FV-A4ZP 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-FV-A4ZQ         TCGA-G3-A25S         TCGA-G3-A25T 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-G3-A25U         TCGA-G3-A25V         TCGA-G3-A25W 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-G3-A25X         TCGA-G3-A25Y         TCGA-G3-A25Z 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-G3-A3CG         TCGA-G3-A3CH         TCGA-G3-A3CI 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK         TCGA-G3-A5SJ 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-G3-A5SK         TCGA-G3-A5SL         TCGA-G3-A5SM 
"17Q LOSS WILD-TYPE"   "17Q LOSS MUTATED"   "17Q LOSS MUTATED" 
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
  "17Q LOSS MUTATED" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-BC-A5W4 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE"   "17Q LOSS MUTATED" 
        TCGA-CC-5258         TCGA-CC-5260         TCGA-CC-5261 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-CC-5262         TCGA-CC-5263         TCGA-CC-A1HT 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-CC-A3M9         TCGA-CC-A3MA         TCGA-CC-A3MB 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-CC-A3MC         TCGA-DD-A113         TCGA-DD-A114 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"17Q LOSS WILD-TYPE"   "17Q LOSS MUTATED" "17Q LOSS WILD-TYPE" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DD-A1EA         TCGA-DD-A1EB         TCGA-DD-A1EC 
"17Q LOSS WILD-TYPE"   "17Q LOSS MUTATED" "17Q LOSS WILD-TYPE" 
        TCGA-DD-A1ED         TCGA-DD-A1EE         TCGA-DD-A1EF 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DD-A1EH         TCGA-DD-A1EI         TCGA-DD-A1EJ 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DD-A1EL         TCGA-DD-A39V         TCGA-DD-A39X 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DD-A39Y         TCGA-DD-A39Z         TCGA-DD-A3A0 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DD-A3A1         TCGA-DD-A3A2         TCGA-DD-A3A3 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DD-A3A4         TCGA-DD-A3A5         TCGA-DD-A3A6 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DD-A3A7         TCGA-DD-A3A8         TCGA-DD-A3A9 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DD-A4NA         TCGA-DD-A4ND         TCGA-DD-A4NE 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DD-A4NF         TCGA-DD-A4NG         TCGA-DD-A4NH 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DD-A4NI         TCGA-DD-A4NJ         TCGA-DD-A4NK 
"17Q LOSS WILD-TYPE"   "17Q LOSS MUTATED" "17Q LOSS WILD-TYPE" 
        TCGA-DD-A4NL         TCGA-DD-A4NN         TCGA-DD-A4NO 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DD-A4NP         TCGA-DD-A4NQ         TCGA-ED-A459 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-ED-A5KG         TCGA-EP-A12J         TCGA-EP-A26S 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EP-A2KA         TCGA-EP-A2KB         TCGA-EP-A2KC 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EP-A3JL         TCGA-EP-A3RK         TCGA-ES-A2HS 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-ES-A2HT         TCGA-FV-A23B         TCGA-FV-A2QR 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-FV-A3I0         TCGA-FV-A3R2         TCGA-FV-A3R3 
  "17Q LOSS MUTATED" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-FV-A495         TCGA-FV-A496         TCGA-FV-A4ZP 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-FV-A4ZQ         TCGA-G3-A25S         TCGA-G3-A25T 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-G3-A25U         TCGA-G3-A25V         TCGA-G3-A25W 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-G3-A25X         TCGA-G3-A25Y         TCGA-G3-A25Z 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-G3-A3CG         TCGA-G3-A3CH         TCGA-G3-A3CI 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK         TCGA-G3-A5SJ 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-G3-A5SK         TCGA-G3-A5SL         TCGA-G3-A5SM 
"17Q LOSS WILD-TYPE"   "17Q LOSS MUTATED"   "17Q LOSS MUTATED" 
[1] "hr=" "1.5"
D71V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  17Q LOSS MUTATED         1        3         0          3          0
  17Q LOSS WILD-TYPE      44       22         2         22          3
                    vv
clus                 STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  17Q LOSS MUTATED            0        0         1         0
  17Q LOSS WILD-TYPE          4        1         0         1
D71V3, multiclass
                    vv
clus                 T1 T2 T3 T4
  17Q LOSS MUTATED    2  3  4  0
  17Q LOSS WILD-TYPE 46 25 30  6
D71V4, multiclass
    clus
vv   17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  T1                2                 46
  T2                3                 25
  T3                4                 30
  T4                0                  6
D71V5, binary
                    cls
clus                  0  1
  17Q LOSS MUTATED    3  1
  17Q LOSS WILD-TYPE 71  2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED      3    1
  17Q LOSS WILD-TYPE   71    2
   clus
vv  17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  0                3                 71
  1                1                  2
                    vv
clus                 M0 M1 MX
  17Q LOSS MUTATED    7  0  2
  17Q LOSS WILD-TYPE 83  2 23
D71V6, multiclass
    clus
vv   17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  M0                7                 83
  M1                0                  2
  MX                2                 23
D71V7, binary
                    cls
clus                  0  1
  17Q LOSS MUTATED    4  5
  17Q LOSS WILD-TYPE 40 68
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED      4    5
  17Q LOSS WILD-TYPE   40   68
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  FEMALE                4                 40
  MALE                  5                 68
                    vv
clus                 R0 R1 R2 RX
  17Q LOSS MUTATED    8  1  0  0
  17Q LOSS WILD-TYPE 85  9  1  8
D71V8, multiclass
    clus
vv   17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  R0                8                 85
  R1                1                  9
  R2                0                  1
  RX                0                  8

Clustering(72) Variable = 18P LOSS MUTATION ANALYSIS
D72V1, survival
                    sevent
clus2                 0  1
  18P LOSS MUTATED    8 10
  18P LOSS WILD-TYPE 53 43
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                18                 96 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                10                 43 
$`18P LOSS MUTATED`
TCGA-BC-A10R TCGA-BC-A112 TCGA-BC-A217 TCGA-CC-A3MB TCGA-DD-A118 TCGA-DD-A11A 
       10.13         5.03        13.81         0.10       112.96         2.60 
TCGA-DD-A11B TCGA-DD-A1EJ TCGA-DD-A1EL TCGA-DD-A39X TCGA-DD-A3A4 TCGA-DD-A4NE 
        0.46        29.16        13.64        55.66        20.12        21.67 
TCGA-DD-A4NO TCGA-ED-A459 TCGA-ES-A2HS TCGA-FV-A3I0 TCGA-FV-A496 TCGA-G3-A25S 
       61.45         0.23        23.01         0.20         0.33         1.22 

$`18P LOSS WILD-TYPE`
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U 
       48.99        27.91        37.32        46.78        27.52        27.52 
TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A216 
        2.99        25.32        23.34         1.12        69.57        44.42 
TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5261 
        0.26        16.37         9.50         0.07         2.86         3.02 
TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MC 
        3.39         4.24         3.32         0.10         0.07         0.13 
TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A119 TCGA-DD-A11C 
       79.73        37.74        83.57        53.29         7.33        21.76 
TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED 
       51.25        90.67        79.36        66.31        19.76        75.65 
TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A39V TCGA-DD-A39Y 
        6.67        12.95        49.15         6.02        21.14         5.59 
TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A5 
       19.73        25.81         7.66        70.06        17.59       102.74 
TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4ND 
      107.11        13.78         0.36        30.58        33.14        73.38 
TCGA-DD-A4NF TCGA-DD-A4NG TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK 
       14.07        14.93        14.24        10.78        15.06        39.75 
TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-ED-A5KG TCGA-EP-A12J 
       56.25        29.56        93.67        12.26         0.20        10.85 
TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK 
        7.76        11.74         1.97         0.62         3.19         0.43 
TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 
       14.40        32.45        19.07         6.35         0.13         0.03 
TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W 
       60.36         0.39        51.02        53.79        28.27        30.71 
TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CH TCGA-G3-A3CI 
       58.49        14.86        21.53        22.13        25.64         5.88 
TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SJ TCGA-G3-A5SK TCGA-G3-A5SL TCGA-G3-A5SM 
       19.53        19.23        11.97         9.93         7.99         4.37 

  18P LOSS MUTATED 18P LOSS WILD-TYPE 
              0.10               0.03 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
            112.96             107.11 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
            11.885             18.330 
[1] "0.1 - 113.0 (11.9)" "0.0 - 107.1 (18.3)"
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
  "18P LOSS MUTATED" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
  "18P LOSS MUTATED" "18P LOSS WILD-TYPE"   "18P LOSS MUTATED" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-BC-A5W4 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-CC-5258         TCGA-CC-5260         TCGA-CC-5261 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-CC-5262         TCGA-CC-5263         TCGA-CC-A1HT 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-CC-A3M9         TCGA-CC-A3MA         TCGA-CC-A3MB 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE"   "18P LOSS MUTATED" 
        TCGA-CC-A3MC         TCGA-DD-A113         TCGA-DD-A114 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE"   "18P LOSS MUTATED" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"18P LOSS WILD-TYPE"   "18P LOSS MUTATED"   "18P LOSS MUTATED" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-DD-A1EA         TCGA-DD-A1EB         TCGA-DD-A1EC 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-DD-A1ED         TCGA-DD-A1EE         TCGA-DD-A1EF 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-DD-A1EH         TCGA-DD-A1EI         TCGA-DD-A1EJ 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE"   "18P LOSS MUTATED" 
        TCGA-DD-A1EL         TCGA-DD-A39V         TCGA-DD-A39X 
  "18P LOSS MUTATED" "18P LOSS WILD-TYPE"   "18P LOSS MUTATED" 
        TCGA-DD-A39Y         TCGA-DD-A39Z         TCGA-DD-A3A0 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-DD-A3A1         TCGA-DD-A3A2         TCGA-DD-A3A3 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-DD-A3A4         TCGA-DD-A3A5         TCGA-DD-A3A6 
  "18P LOSS MUTATED" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-DD-A3A7         TCGA-DD-A3A8         TCGA-DD-A3A9 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-DD-A4NA         TCGA-DD-A4ND         TCGA-DD-A4NE 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE"   "18P LOSS MUTATED" 
        TCGA-DD-A4NF         TCGA-DD-A4NG         TCGA-DD-A4NH 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-DD-A4NI         TCGA-DD-A4NJ         TCGA-DD-A4NK 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-DD-A4NL         TCGA-DD-A4NN         TCGA-DD-A4NO 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE"   "18P LOSS MUTATED" 
        TCGA-DD-A4NP         TCGA-DD-A4NQ         TCGA-ED-A459 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE"   "18P LOSS MUTATED" 
        TCGA-ED-A5KG         TCGA-EP-A12J         TCGA-EP-A26S 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EP-A2KA         TCGA-EP-A2KB         TCGA-EP-A2KC 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EP-A3JL         TCGA-EP-A3RK         TCGA-ES-A2HS 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE"   "18P LOSS MUTATED" 
        TCGA-ES-A2HT         TCGA-FV-A23B         TCGA-FV-A2QR 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-FV-A3I0         TCGA-FV-A3R2         TCGA-FV-A3R3 
  "18P LOSS MUTATED" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-FV-A495         TCGA-FV-A496         TCGA-FV-A4ZP 
"18P LOSS WILD-TYPE"   "18P LOSS MUTATED" "18P LOSS WILD-TYPE" 
        TCGA-FV-A4ZQ         TCGA-G3-A25S         TCGA-G3-A25T 
"18P LOSS WILD-TYPE"   "18P LOSS MUTATED" "18P LOSS WILD-TYPE" 
        TCGA-G3-A25U         TCGA-G3-A25V         TCGA-G3-A25W 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-G3-A25X         TCGA-G3-A25Y         TCGA-G3-A25Z 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-G3-A3CG         TCGA-G3-A3CH         TCGA-G3-A3CI 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK         TCGA-G3-A5SJ 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-G3-A5SK         TCGA-G3-A5SL         TCGA-G3-A5SM 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
  "18P LOSS MUTATED" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
  "18P LOSS MUTATED" "18P LOSS WILD-TYPE"   "18P LOSS MUTATED" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-BC-A5W4 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-CC-5258         TCGA-CC-5260         TCGA-CC-5261 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-CC-5262         TCGA-CC-5263         TCGA-CC-A1HT 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-CC-A3M9         TCGA-CC-A3MA         TCGA-CC-A3MB 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE"   "18P LOSS MUTATED" 
        TCGA-CC-A3MC         TCGA-DD-A113         TCGA-DD-A114 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE"   "18P LOSS MUTATED" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"18P LOSS WILD-TYPE"   "18P LOSS MUTATED"   "18P LOSS MUTATED" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-DD-A1EA         TCGA-DD-A1EB         TCGA-DD-A1EC 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-DD-A1ED         TCGA-DD-A1EE         TCGA-DD-A1EF 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-DD-A1EH         TCGA-DD-A1EI         TCGA-DD-A1EJ 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE"   "18P LOSS MUTATED" 
        TCGA-DD-A1EL         TCGA-DD-A39V         TCGA-DD-A39X 
  "18P LOSS MUTATED" "18P LOSS WILD-TYPE"   "18P LOSS MUTATED" 
        TCGA-DD-A39Y         TCGA-DD-A39Z         TCGA-DD-A3A0 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-DD-A3A1         TCGA-DD-A3A2         TCGA-DD-A3A3 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-DD-A3A4         TCGA-DD-A3A5         TCGA-DD-A3A6 
  "18P LOSS MUTATED" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-DD-A3A7         TCGA-DD-A3A8         TCGA-DD-A3A9 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-DD-A4NA         TCGA-DD-A4ND         TCGA-DD-A4NE 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE"   "18P LOSS MUTATED" 
        TCGA-DD-A4NF         TCGA-DD-A4NG         TCGA-DD-A4NH 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-DD-A4NI         TCGA-DD-A4NJ         TCGA-DD-A4NK 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-DD-A4NL         TCGA-DD-A4NN         TCGA-DD-A4NO 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE"   "18P LOSS MUTATED" 
        TCGA-DD-A4NP         TCGA-DD-A4NQ         TCGA-ED-A459 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE"   "18P LOSS MUTATED" 
        TCGA-ED-A5KG         TCGA-EP-A12J         TCGA-EP-A26S 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EP-A2KA         TCGA-EP-A2KB         TCGA-EP-A2KC 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EP-A3JL         TCGA-EP-A3RK         TCGA-ES-A2HS 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE"   "18P LOSS MUTATED" 
        TCGA-ES-A2HT         TCGA-FV-A23B         TCGA-FV-A2QR 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-FV-A3I0         TCGA-FV-A3R2         TCGA-FV-A3R3 
  "18P LOSS MUTATED" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-FV-A495         TCGA-FV-A496         TCGA-FV-A4ZP 
"18P LOSS WILD-TYPE"   "18P LOSS MUTATED" "18P LOSS WILD-TYPE" 
        TCGA-FV-A4ZQ         TCGA-G3-A25S         TCGA-G3-A25T 
"18P LOSS WILD-TYPE"   "18P LOSS MUTATED" "18P LOSS WILD-TYPE" 
        TCGA-G3-A25U         TCGA-G3-A25V         TCGA-G3-A25W 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-G3-A25X         TCGA-G3-A25Y         TCGA-G3-A25Z 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-G3-A3CG         TCGA-G3-A3CH         TCGA-G3-A3CI 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK         TCGA-G3-A5SJ 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-G3-A5SK         TCGA-G3-A5SL         TCGA-G3-A5SM 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
  "18P LOSS MUTATED" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
  "18P LOSS MUTATED" "18P LOSS WILD-TYPE"   "18P LOSS MUTATED" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-BC-A5W4 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-CC-5258         TCGA-CC-5260         TCGA-CC-5261 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-CC-5262         TCGA-CC-5263         TCGA-CC-A1HT 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-CC-A3M9         TCGA-CC-A3MA         TCGA-CC-A3MB 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE"   "18P LOSS MUTATED" 
        TCGA-CC-A3MC         TCGA-DD-A113         TCGA-DD-A114 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE"   "18P LOSS MUTATED" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"18P LOSS WILD-TYPE"   "18P LOSS MUTATED"   "18P LOSS MUTATED" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-DD-A1EA         TCGA-DD-A1EB         TCGA-DD-A1EC 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-DD-A1ED         TCGA-DD-A1EE         TCGA-DD-A1EF 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-DD-A1EH         TCGA-DD-A1EI         TCGA-DD-A1EJ 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE"   "18P LOSS MUTATED" 
        TCGA-DD-A1EL         TCGA-DD-A39V         TCGA-DD-A39X 
  "18P LOSS MUTATED" "18P LOSS WILD-TYPE"   "18P LOSS MUTATED" 
        TCGA-DD-A39Y         TCGA-DD-A39Z         TCGA-DD-A3A0 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-DD-A3A1         TCGA-DD-A3A2         TCGA-DD-A3A3 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-DD-A3A4         TCGA-DD-A3A5         TCGA-DD-A3A6 
  "18P LOSS MUTATED" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-DD-A3A7         TCGA-DD-A3A8         TCGA-DD-A3A9 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-DD-A4NA         TCGA-DD-A4ND         TCGA-DD-A4NE 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE"   "18P LOSS MUTATED" 
        TCGA-DD-A4NF         TCGA-DD-A4NG         TCGA-DD-A4NH 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-DD-A4NI         TCGA-DD-A4NJ         TCGA-DD-A4NK 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-DD-A4NL         TCGA-DD-A4NN         TCGA-DD-A4NO 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE"   "18P LOSS MUTATED" 
        TCGA-DD-A4NP         TCGA-DD-A4NQ         TCGA-ED-A459 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE"   "18P LOSS MUTATED" 
        TCGA-ED-A5KG         TCGA-EP-A12J         TCGA-EP-A26S 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EP-A2KA         TCGA-EP-A2KB         TCGA-EP-A2KC 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EP-A3JL         TCGA-EP-A3RK         TCGA-ES-A2HS 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE"   "18P LOSS MUTATED" 
        TCGA-ES-A2HT         TCGA-FV-A23B         TCGA-FV-A2QR 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-FV-A3I0         TCGA-FV-A3R2         TCGA-FV-A3R3 
  "18P LOSS MUTATED" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-FV-A495         TCGA-FV-A496         TCGA-FV-A4ZP 
"18P LOSS WILD-TYPE"   "18P LOSS MUTATED" "18P LOSS WILD-TYPE" 
        TCGA-FV-A4ZQ         TCGA-G3-A25S         TCGA-G3-A25T 
"18P LOSS WILD-TYPE"   "18P LOSS MUTATED" "18P LOSS WILD-TYPE" 
        TCGA-G3-A25U         TCGA-G3-A25V         TCGA-G3-A25W 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-G3-A25X         TCGA-G3-A25Y         TCGA-G3-A25Z 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-G3-A3CG         TCGA-G3-A3CH         TCGA-G3-A3CI 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK         TCGA-G3-A5SJ 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-G3-A5SK         TCGA-G3-A5SL         TCGA-G3-A5SM 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
[1] "hr=" "1.5"
D72V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  18P LOSS MUTATED         7        5         0          3          0
  18P LOSS WILD-TYPE      38       20         2         22          3
                    vv
clus                 STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  18P LOSS MUTATED            1        0         0         0
  18P LOSS WILD-TYPE          3        1         1         1
D72V3, multiclass
                    vv
clus                 T1 T2 T3 T4
  18P LOSS MUTATED    8  5  5  0
  18P LOSS WILD-TYPE 40 23 29  6
D72V4, multiclass
    clus
vv   18P LOSS MUTATED 18P LOSS WILD-TYPE
  T1                8                 40
  T2                5                 23
  T3                5                 29
  T4                0                  6
D72V5, binary
                    cls
clus                  0  1
  18P LOSS MUTATED   10  1
  18P LOSS WILD-TYPE 64  2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED     10    1
  18P LOSS WILD-TYPE   64    2
   clus
vv  18P LOSS MUTATED 18P LOSS WILD-TYPE
  0               10                 64
  1                1                  2
                    vv
clus                 M0 M1 MX
  18P LOSS MUTATED   15  0  3
  18P LOSS WILD-TYPE 75  2 22
D72V6, multiclass
    clus
vv   18P LOSS MUTATED 18P LOSS WILD-TYPE
  M0               15                 75
  M1                0                  2
  MX                3                 22
D72V7, binary
                    cls
clus                  0  1
  18P LOSS MUTATED    8 10
  18P LOSS WILD-TYPE 36 63
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED      8   10
  18P LOSS WILD-TYPE   36   63
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  FEMALE                8                 36
  MALE                 10                 63
                    vv
clus                 R0 R1 R2 RX
  18P LOSS MUTATED   16  1  0  1
  18P LOSS WILD-TYPE 77  9  1  7
D72V8, multiclass
    clus
vv   18P LOSS MUTATED 18P LOSS WILD-TYPE
  R0               16                 77
  R1                1                  9
  R2                0                  1
  RX                1                  7

Clustering(73) Variable = 18Q LOSS MUTATION ANALYSIS
D73V1, survival
                    sevent
clus2                 0  1
  18Q LOSS MUTATED    9 10
  18Q LOSS WILD-TYPE 52 43
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                19                 95 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                10                 43 
$`18Q LOSS MUTATED`
TCGA-BC-A10R TCGA-BC-A112 TCGA-BC-A216 TCGA-BC-A217 TCGA-CC-A3MB TCGA-DD-A118 
       10.13         5.03        44.42        13.81         0.10       112.96 
TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A1EJ TCGA-DD-A1EL TCGA-DD-A39X TCGA-DD-A3A9 
        2.60         0.46        29.16        13.64        55.66        30.58 
TCGA-DD-A4NE TCGA-DD-A4NO TCGA-ED-A459 TCGA-ES-A2HS TCGA-FV-A3I0 TCGA-FV-A496 
       21.67        61.45         0.23        23.01         0.20         0.33 
TCGA-G3-A25S 
        1.22 

$`18Q LOSS WILD-TYPE`
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U 
       48.99        27.91        37.32        46.78        27.52        27.52 
TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A3KF 
        2.99        25.32        23.34         1.12        69.57         0.26 
TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 
       16.37         9.50         0.07         2.86         3.02         3.39 
TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MC TCGA-DD-A113 
        4.24         3.32         0.10         0.07         0.13        79.73 
TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A119 TCGA-DD-A11C TCGA-DD-A11D 
       37.74        83.57        53.29         7.33        21.76        51.25 
TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE 
       90.67        79.36        66.31        19.76        75.65         6.67 
TCGA-DD-A1EF TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A39V TCGA-DD-A39Y TCGA-DD-A39Z 
       12.95        49.15         6.02        21.14         5.59        19.73 
TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 
       25.81         7.66        70.06        17.59        20.12       102.74 
TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A4NA TCGA-DD-A4ND TCGA-DD-A4NF 
      107.11        13.78         0.36        33.14        73.38        14.07 
TCGA-DD-A4NG TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL 
       14.93        14.24        10.78        15.06        39.75        56.25 
TCGA-DD-A4NN TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-ED-A5KG TCGA-EP-A12J TCGA-EP-A26S 
       29.56        93.67        12.26         0.20        10.85         7.76 
TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HT 
       11.74         1.97         0.62         3.19         0.43        14.40 
TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A4ZP 
       32.45        19.07         6.35         0.13         0.03        60.36 
TCGA-FV-A4ZQ TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25X 
        0.39        51.02        53.79        28.27        30.71        58.49 
TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ 
       14.86        21.53        22.13        25.64         5.88        19.53 
TCGA-G3-A3CK TCGA-G3-A5SJ TCGA-G3-A5SK TCGA-G3-A5SL TCGA-G3-A5SM 
       19.23        11.97         9.93         7.99         4.37 

  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
              0.10               0.03 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
            112.96             107.11 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
             13.64              17.59 
[1] "0.1 - 113.0 (13.6)" "0.0 - 107.1 (17.6)"
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
  "18Q LOSS MUTATED"   "18Q LOSS MUTATED"   "18Q LOSS MUTATED" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-BC-A5W4 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-CC-5258         TCGA-CC-5260         TCGA-CC-5261 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-CC-5262         TCGA-CC-5263         TCGA-CC-A1HT 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-CC-A3M9         TCGA-CC-A3MA         TCGA-CC-A3MB 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" 
        TCGA-CC-A3MC         TCGA-DD-A113         TCGA-DD-A114 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED"   "18Q LOSS MUTATED" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-DD-A1EA         TCGA-DD-A1EB         TCGA-DD-A1EC 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-DD-A1ED         TCGA-DD-A1EE         TCGA-DD-A1EF 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-DD-A1EH         TCGA-DD-A1EI         TCGA-DD-A1EJ 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" 
        TCGA-DD-A1EL         TCGA-DD-A39V         TCGA-DD-A39X 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" 
        TCGA-DD-A39Y         TCGA-DD-A39Z         TCGA-DD-A3A0 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-DD-A3A1         TCGA-DD-A3A2         TCGA-DD-A3A3 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-DD-A3A4         TCGA-DD-A3A5         TCGA-DD-A3A6 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-DD-A3A7         TCGA-DD-A3A8         TCGA-DD-A3A9 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" 
        TCGA-DD-A4NA         TCGA-DD-A4ND         TCGA-DD-A4NE 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" 
        TCGA-DD-A4NF         TCGA-DD-A4NG         TCGA-DD-A4NH 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-DD-A4NI         TCGA-DD-A4NJ         TCGA-DD-A4NK 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-DD-A4NL         TCGA-DD-A4NN         TCGA-DD-A4NO 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" 
        TCGA-DD-A4NP         TCGA-DD-A4NQ         TCGA-ED-A459 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" 
        TCGA-ED-A5KG         TCGA-EP-A12J         TCGA-EP-A26S 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EP-A2KA         TCGA-EP-A2KB         TCGA-EP-A2KC 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EP-A3JL         TCGA-EP-A3RK         TCGA-ES-A2HS 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" 
        TCGA-ES-A2HT         TCGA-FV-A23B         TCGA-FV-A2QR 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-FV-A3I0         TCGA-FV-A3R2         TCGA-FV-A3R3 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-FV-A495         TCGA-FV-A496         TCGA-FV-A4ZP 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" 
        TCGA-FV-A4ZQ         TCGA-G3-A25S         TCGA-G3-A25T 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" 
        TCGA-G3-A25U         TCGA-G3-A25V         TCGA-G3-A25W 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-G3-A25X         TCGA-G3-A25Y         TCGA-G3-A25Z 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-G3-A3CG         TCGA-G3-A3CH         TCGA-G3-A3CI 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK         TCGA-G3-A5SJ 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-G3-A5SK         TCGA-G3-A5SL         TCGA-G3-A5SM 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
  "18Q LOSS MUTATED"   "18Q LOSS MUTATED"   "18Q LOSS MUTATED" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-BC-A5W4 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-CC-5258         TCGA-CC-5260         TCGA-CC-5261 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-CC-5262         TCGA-CC-5263         TCGA-CC-A1HT 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-CC-A3M9         TCGA-CC-A3MA         TCGA-CC-A3MB 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" 
        TCGA-CC-A3MC         TCGA-DD-A113         TCGA-DD-A114 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED"   "18Q LOSS MUTATED" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-DD-A1EA         TCGA-DD-A1EB         TCGA-DD-A1EC 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-DD-A1ED         TCGA-DD-A1EE         TCGA-DD-A1EF 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-DD-A1EH         TCGA-DD-A1EI         TCGA-DD-A1EJ 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" 
        TCGA-DD-A1EL         TCGA-DD-A39V         TCGA-DD-A39X 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" 
        TCGA-DD-A39Y         TCGA-DD-A39Z         TCGA-DD-A3A0 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-DD-A3A1         TCGA-DD-A3A2         TCGA-DD-A3A3 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-DD-A3A4         TCGA-DD-A3A5         TCGA-DD-A3A6 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-DD-A3A7         TCGA-DD-A3A8         TCGA-DD-A3A9 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" 
        TCGA-DD-A4NA         TCGA-DD-A4ND         TCGA-DD-A4NE 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" 
        TCGA-DD-A4NF         TCGA-DD-A4NG         TCGA-DD-A4NH 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-DD-A4NI         TCGA-DD-A4NJ         TCGA-DD-A4NK 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-DD-A4NL         TCGA-DD-A4NN         TCGA-DD-A4NO 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" 
        TCGA-DD-A4NP         TCGA-DD-A4NQ         TCGA-ED-A459 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" 
        TCGA-ED-A5KG         TCGA-EP-A12J         TCGA-EP-A26S 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EP-A2KA         TCGA-EP-A2KB         TCGA-EP-A2KC 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EP-A3JL         TCGA-EP-A3RK         TCGA-ES-A2HS 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" 
        TCGA-ES-A2HT         TCGA-FV-A23B         TCGA-FV-A2QR 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-FV-A3I0         TCGA-FV-A3R2         TCGA-FV-A3R3 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-FV-A495         TCGA-FV-A496         TCGA-FV-A4ZP 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" 
        TCGA-FV-A4ZQ         TCGA-G3-A25S         TCGA-G3-A25T 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" 
        TCGA-G3-A25U         TCGA-G3-A25V         TCGA-G3-A25W 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-G3-A25X         TCGA-G3-A25Y         TCGA-G3-A25Z 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-G3-A3CG         TCGA-G3-A3CH         TCGA-G3-A3CI 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK         TCGA-G3-A5SJ 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-G3-A5SK         TCGA-G3-A5SL         TCGA-G3-A5SM 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
  "18Q LOSS MUTATED"   "18Q LOSS MUTATED"   "18Q LOSS MUTATED" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-BC-A5W4 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-CC-5258         TCGA-CC-5260         TCGA-CC-5261 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-CC-5262         TCGA-CC-5263         TCGA-CC-A1HT 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-CC-A3M9         TCGA-CC-A3MA         TCGA-CC-A3MB 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" 
        TCGA-CC-A3MC         TCGA-DD-A113         TCGA-DD-A114 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED"   "18Q LOSS MUTATED" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-DD-A1EA         TCGA-DD-A1EB         TCGA-DD-A1EC 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-DD-A1ED         TCGA-DD-A1EE         TCGA-DD-A1EF 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-DD-A1EH         TCGA-DD-A1EI         TCGA-DD-A1EJ 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" 
        TCGA-DD-A1EL         TCGA-DD-A39V         TCGA-DD-A39X 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" 
        TCGA-DD-A39Y         TCGA-DD-A39Z         TCGA-DD-A3A0 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-DD-A3A1         TCGA-DD-A3A2         TCGA-DD-A3A3 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-DD-A3A4         TCGA-DD-A3A5         TCGA-DD-A3A6 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-DD-A3A7         TCGA-DD-A3A8         TCGA-DD-A3A9 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" 
        TCGA-DD-A4NA         TCGA-DD-A4ND         TCGA-DD-A4NE 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" 
        TCGA-DD-A4NF         TCGA-DD-A4NG         TCGA-DD-A4NH 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-DD-A4NI         TCGA-DD-A4NJ         TCGA-DD-A4NK 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-DD-A4NL         TCGA-DD-A4NN         TCGA-DD-A4NO 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" 
        TCGA-DD-A4NP         TCGA-DD-A4NQ         TCGA-ED-A459 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" 
        TCGA-ED-A5KG         TCGA-EP-A12J         TCGA-EP-A26S 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EP-A2KA         TCGA-EP-A2KB         TCGA-EP-A2KC 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EP-A3JL         TCGA-EP-A3RK         TCGA-ES-A2HS 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" 
        TCGA-ES-A2HT         TCGA-FV-A23B         TCGA-FV-A2QR 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-FV-A3I0         TCGA-FV-A3R2         TCGA-FV-A3R3 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-FV-A495         TCGA-FV-A496         TCGA-FV-A4ZP 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" 
        TCGA-FV-A4ZQ         TCGA-G3-A25S         TCGA-G3-A25T 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" 
        TCGA-G3-A25U         TCGA-G3-A25V         TCGA-G3-A25W 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-G3-A25X         TCGA-G3-A25Y         TCGA-G3-A25Z 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-G3-A3CG         TCGA-G3-A3CH         TCGA-G3-A3CI 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK         TCGA-G3-A5SJ 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-G3-A5SK         TCGA-G3-A5SL         TCGA-G3-A5SM 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
[1] "hr=" "1.3"
D73V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  18Q LOSS MUTATED         7        5         0          3          0
  18Q LOSS WILD-TYPE      38       20         2         22          3
                    vv
clus                 STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  18Q LOSS MUTATED            1        0         0         1
  18Q LOSS WILD-TYPE          3        1         1         0
D73V3, multiclass
                    vv
clus                 T1 T2 T3 T4
  18Q LOSS MUTATED    8  5  5  1
  18Q LOSS WILD-TYPE 40 23 29  5
D73V4, multiclass
    clus
vv   18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  T1                8                 40
  T2                5                 23
  T3                5                 29
  T4                1                  5
D73V5, binary
                    cls
clus                  0  1
  18Q LOSS MUTATED   10  1
  18Q LOSS WILD-TYPE 64  2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED     10    1
  18Q LOSS WILD-TYPE   64    2
   clus
vv  18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  0               10                 64
  1                1                  2
                    vv
clus                 M0 M1 MX
  18Q LOSS MUTATED   15  1  3
  18Q LOSS WILD-TYPE 75  1 22
D73V6, multiclass
    clus
vv   18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  M0               15                 75
  M1                1                  1
  MX                3                 22
D73V7, binary
                    cls
clus                  0  1
  18Q LOSS MUTATED   10  9
  18Q LOSS WILD-TYPE 34 64
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED     10    9
  18Q LOSS WILD-TYPE   34   64
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  FEMALE               10                 34
  MALE                  9                 64
                    vv
clus                 R0 R1 R2 RX
  18Q LOSS MUTATED   17  1  0  1
  18Q LOSS WILD-TYPE 76  9  1  7
D73V8, multiclass
    clus
vv   18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  R0               17                 76
  R1                1                  9
  R2                0                  1
  RX                1                  7

Clustering(74) Variable = 19P LOSS MUTATION ANALYSIS
D74V1, survival
                    sevent
clus2                 0  1
  19P LOSS MUTATED    8  6
  19P LOSS WILD-TYPE 53 47
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                14                100 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                 6                 47 
$`19P LOSS MUTATED`
TCGA-BC-A10W TCGA-BC-A112 TCGA-BC-A3KF TCGA-CC-5258 TCGA-CC-5263 TCGA-CC-A1HT 
        2.99         5.03         0.26         0.07         4.24         3.32 
TCGA-DD-A11A TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A4NJ TCGA-FV-A496 TCGA-FV-A4ZP 
        2.60         6.02        29.16        15.06         0.33        60.36 
TCGA-G3-A25S TCGA-G3-A3CH 
        1.22        25.64 

$`19P LOSS WILD-TYPE`
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T 
       48.99        27.91        37.32        10.13        46.78        27.52 
TCGA-BC-A10U TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A216 
       27.52        25.32        23.34         1.12        69.57        44.42 
TCGA-BC-A217 TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 
       13.81        16.37         9.50         2.86         3.02         3.39 
TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A113 TCGA-DD-A114 
        0.10         0.07         0.10         0.13        79.73        37.74 
TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11B TCGA-DD-A11C 
       83.57        53.29       112.96         7.33         0.46        21.76 
TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED 
       51.25        90.67        79.36        66.31        19.76        75.65 
TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EH TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39X 
        6.67        12.95        49.15        13.64        21.14        55.66 
TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 
        5.59        19.73        25.81         7.66        70.06        17.59 
TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A3A9 
       20.12       102.74       107.11        13.78         0.36        30.58 
TCGA-DD-A4NA TCGA-DD-A4ND TCGA-DD-A4NE TCGA-DD-A4NF TCGA-DD-A4NG TCGA-DD-A4NH 
       33.14        73.38        21.67        14.07        14.93        14.24 
TCGA-DD-A4NI TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP 
       10.78        39.75        56.25        29.56        61.45        93.67 
TCGA-DD-A4NQ TCGA-ED-A459 TCGA-ED-A5KG TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA 
       12.26         0.23         0.20        10.85         7.76        11.74 
TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT 
        1.97         0.62         3.19         0.43        23.01        14.40 
TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 
       32.45        19.07         0.20         6.35         0.13         0.03 
TCGA-FV-A4ZQ TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25X 
        0.39        51.02        53.79        28.27        30.71        58.49 
TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK 
       14.86        21.53        22.13         5.88        19.53        19.23 
TCGA-G3-A5SJ TCGA-G3-A5SK TCGA-G3-A5SL TCGA-G3-A5SM 
       11.97         9.93         7.99         4.37 

  19P LOSS MUTATED 19P LOSS WILD-TYPE 
              0.07               0.03 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
             60.36             112.96 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
              3.78              19.38 
[1] "0.1 - 60.4 (3.8)"   "0.0 - 113.0 (19.4)"
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"19P LOSS WILD-TYPE"   "19P LOSS MUTATED" "19P LOSS WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
  "19P LOSS MUTATED" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-BC-A5W4 
  "19P LOSS MUTATED" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-CC-5258         TCGA-CC-5260         TCGA-CC-5261 
  "19P LOSS MUTATED" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-CC-5262         TCGA-CC-5263         TCGA-CC-A1HT 
"19P LOSS WILD-TYPE"   "19P LOSS MUTATED"   "19P LOSS MUTATED" 
        TCGA-CC-A3M9         TCGA-CC-A3MA         TCGA-CC-A3MB 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-CC-A3MC         TCGA-DD-A113         TCGA-DD-A114 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"19P LOSS WILD-TYPE"   "19P LOSS MUTATED" "19P LOSS WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DD-A1EA         TCGA-DD-A1EB         TCGA-DD-A1EC 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DD-A1ED         TCGA-DD-A1EE         TCGA-DD-A1EF 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DD-A1EH         TCGA-DD-A1EI         TCGA-DD-A1EJ 
"19P LOSS WILD-TYPE"   "19P LOSS MUTATED"   "19P LOSS MUTATED" 
        TCGA-DD-A1EL         TCGA-DD-A39V         TCGA-DD-A39X 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DD-A39Y         TCGA-DD-A39Z         TCGA-DD-A3A0 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DD-A3A1         TCGA-DD-A3A2         TCGA-DD-A3A3 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DD-A3A4         TCGA-DD-A3A5         TCGA-DD-A3A6 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DD-A3A7         TCGA-DD-A3A8         TCGA-DD-A3A9 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DD-A4NA         TCGA-DD-A4ND         TCGA-DD-A4NE 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DD-A4NF         TCGA-DD-A4NG         TCGA-DD-A4NH 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DD-A4NI         TCGA-DD-A4NJ         TCGA-DD-A4NK 
"19P LOSS WILD-TYPE"   "19P LOSS MUTATED" "19P LOSS WILD-TYPE" 
        TCGA-DD-A4NL         TCGA-DD-A4NN         TCGA-DD-A4NO 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DD-A4NP         TCGA-DD-A4NQ         TCGA-ED-A459 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-ED-A5KG         TCGA-EP-A12J         TCGA-EP-A26S 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EP-A2KA         TCGA-EP-A2KB         TCGA-EP-A2KC 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EP-A3JL         TCGA-EP-A3RK         TCGA-ES-A2HS 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-ES-A2HT         TCGA-FV-A23B         TCGA-FV-A2QR 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-FV-A3I0         TCGA-FV-A3R2         TCGA-FV-A3R3 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-FV-A495         TCGA-FV-A496         TCGA-FV-A4ZP 
"19P LOSS WILD-TYPE"   "19P LOSS MUTATED"   "19P LOSS MUTATED" 
        TCGA-FV-A4ZQ         TCGA-G3-A25S         TCGA-G3-A25T 
"19P LOSS WILD-TYPE"   "19P LOSS MUTATED" "19P LOSS WILD-TYPE" 
        TCGA-G3-A25U         TCGA-G3-A25V         TCGA-G3-A25W 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-G3-A25X         TCGA-G3-A25Y         TCGA-G3-A25Z 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-G3-A3CG         TCGA-G3-A3CH         TCGA-G3-A3CI 
"19P LOSS WILD-TYPE"   "19P LOSS MUTATED" "19P LOSS WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK         TCGA-G3-A5SJ 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-G3-A5SK         TCGA-G3-A5SL         TCGA-G3-A5SM 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"19P LOSS WILD-TYPE"   "19P LOSS MUTATED" "19P LOSS WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
  "19P LOSS MUTATED" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-BC-A5W4 
  "19P LOSS MUTATED" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-CC-5258         TCGA-CC-5260         TCGA-CC-5261 
  "19P LOSS MUTATED" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-CC-5262         TCGA-CC-5263         TCGA-CC-A1HT 
"19P LOSS WILD-TYPE"   "19P LOSS MUTATED"   "19P LOSS MUTATED" 
        TCGA-CC-A3M9         TCGA-CC-A3MA         TCGA-CC-A3MB 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-CC-A3MC         TCGA-DD-A113         TCGA-DD-A114 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"19P LOSS WILD-TYPE"   "19P LOSS MUTATED" "19P LOSS WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DD-A1EA         TCGA-DD-A1EB         TCGA-DD-A1EC 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DD-A1ED         TCGA-DD-A1EE         TCGA-DD-A1EF 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DD-A1EH         TCGA-DD-A1EI         TCGA-DD-A1EJ 
"19P LOSS WILD-TYPE"   "19P LOSS MUTATED"   "19P LOSS MUTATED" 
        TCGA-DD-A1EL         TCGA-DD-A39V         TCGA-DD-A39X 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DD-A39Y         TCGA-DD-A39Z         TCGA-DD-A3A0 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DD-A3A1         TCGA-DD-A3A2         TCGA-DD-A3A3 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DD-A3A4         TCGA-DD-A3A5         TCGA-DD-A3A6 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DD-A3A7         TCGA-DD-A3A8         TCGA-DD-A3A9 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DD-A4NA         TCGA-DD-A4ND         TCGA-DD-A4NE 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DD-A4NF         TCGA-DD-A4NG         TCGA-DD-A4NH 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DD-A4NI         TCGA-DD-A4NJ         TCGA-DD-A4NK 
"19P LOSS WILD-TYPE"   "19P LOSS MUTATED" "19P LOSS WILD-TYPE" 
        TCGA-DD-A4NL         TCGA-DD-A4NN         TCGA-DD-A4NO 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DD-A4NP         TCGA-DD-A4NQ         TCGA-ED-A459 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-ED-A5KG         TCGA-EP-A12J         TCGA-EP-A26S 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EP-A2KA         TCGA-EP-A2KB         TCGA-EP-A2KC 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EP-A3JL         TCGA-EP-A3RK         TCGA-ES-A2HS 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-ES-A2HT         TCGA-FV-A23B         TCGA-FV-A2QR 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-FV-A3I0         TCGA-FV-A3R2         TCGA-FV-A3R3 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-FV-A495         TCGA-FV-A496         TCGA-FV-A4ZP 
"19P LOSS WILD-TYPE"   "19P LOSS MUTATED"   "19P LOSS MUTATED" 
        TCGA-FV-A4ZQ         TCGA-G3-A25S         TCGA-G3-A25T 
"19P LOSS WILD-TYPE"   "19P LOSS MUTATED" "19P LOSS WILD-TYPE" 
        TCGA-G3-A25U         TCGA-G3-A25V         TCGA-G3-A25W 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-G3-A25X         TCGA-G3-A25Y         TCGA-G3-A25Z 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-G3-A3CG         TCGA-G3-A3CH         TCGA-G3-A3CI 
"19P LOSS WILD-TYPE"   "19P LOSS MUTATED" "19P LOSS WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK         TCGA-G3-A5SJ 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-G3-A5SK         TCGA-G3-A5SL         TCGA-G3-A5SM 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"19P LOSS WILD-TYPE"   "19P LOSS MUTATED" "19P LOSS WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
  "19P LOSS MUTATED" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-BC-A5W4 
  "19P LOSS MUTATED" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-CC-5258         TCGA-CC-5260         TCGA-CC-5261 
  "19P LOSS MUTATED" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-CC-5262         TCGA-CC-5263         TCGA-CC-A1HT 
"19P LOSS WILD-TYPE"   "19P LOSS MUTATED"   "19P LOSS MUTATED" 
        TCGA-CC-A3M9         TCGA-CC-A3MA         TCGA-CC-A3MB 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-CC-A3MC         TCGA-DD-A113         TCGA-DD-A114 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"19P LOSS WILD-TYPE"   "19P LOSS MUTATED" "19P LOSS WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DD-A1EA         TCGA-DD-A1EB         TCGA-DD-A1EC 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DD-A1ED         TCGA-DD-A1EE         TCGA-DD-A1EF 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DD-A1EH         TCGA-DD-A1EI         TCGA-DD-A1EJ 
"19P LOSS WILD-TYPE"   "19P LOSS MUTATED"   "19P LOSS MUTATED" 
        TCGA-DD-A1EL         TCGA-DD-A39V         TCGA-DD-A39X 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DD-A39Y         TCGA-DD-A39Z         TCGA-DD-A3A0 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DD-A3A1         TCGA-DD-A3A2         TCGA-DD-A3A3 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DD-A3A4         TCGA-DD-A3A5         TCGA-DD-A3A6 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DD-A3A7         TCGA-DD-A3A8         TCGA-DD-A3A9 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DD-A4NA         TCGA-DD-A4ND         TCGA-DD-A4NE 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DD-A4NF         TCGA-DD-A4NG         TCGA-DD-A4NH 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DD-A4NI         TCGA-DD-A4NJ         TCGA-DD-A4NK 
"19P LOSS WILD-TYPE"   "19P LOSS MUTATED" "19P LOSS WILD-TYPE" 
        TCGA-DD-A4NL         TCGA-DD-A4NN         TCGA-DD-A4NO 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DD-A4NP         TCGA-DD-A4NQ         TCGA-ED-A459 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-ED-A5KG         TCGA-EP-A12J         TCGA-EP-A26S 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EP-A2KA         TCGA-EP-A2KB         TCGA-EP-A2KC 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EP-A3JL         TCGA-EP-A3RK         TCGA-ES-A2HS 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-ES-A2HT         TCGA-FV-A23B         TCGA-FV-A2QR 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-FV-A3I0         TCGA-FV-A3R2         TCGA-FV-A3R3 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-FV-A495         TCGA-FV-A496         TCGA-FV-A4ZP 
"19P LOSS WILD-TYPE"   "19P LOSS MUTATED"   "19P LOSS MUTATED" 
        TCGA-FV-A4ZQ         TCGA-G3-A25S         TCGA-G3-A25T 
"19P LOSS WILD-TYPE"   "19P LOSS MUTATED" "19P LOSS WILD-TYPE" 
        TCGA-G3-A25U         TCGA-G3-A25V         TCGA-G3-A25W 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-G3-A25X         TCGA-G3-A25Y         TCGA-G3-A25Z 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-G3-A3CG         TCGA-G3-A3CH         TCGA-G3-A3CI 
"19P LOSS WILD-TYPE"   "19P LOSS MUTATED" "19P LOSS WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK         TCGA-G3-A5SJ 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-G3-A5SK         TCGA-G3-A5SL         TCGA-G3-A5SM 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
[1] "hr=" "2.1"
D74V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  19P LOSS MUTATED         5        2         0          4          0
  19P LOSS WILD-TYPE      40       23         2         21          3
                    vv
clus                 STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  19P LOSS MUTATED            1        0         0         0
  19P LOSS WILD-TYPE          3        1         1         1
D74V3, multiclass
                    vv
clus                 T1 T2 T3 T4
  19P LOSS MUTATED    6  2  5  1
  19P LOSS WILD-TYPE 42 26 29  5
D74V4, multiclass
    clus
vv   19P LOSS MUTATED 19P LOSS WILD-TYPE
  T1                6                 42
  T2                2                 26
  T3                5                 29
  T4                1                  5
D74V5, binary
                    cls
clus                  0  1
  19P LOSS MUTATED    8  1
  19P LOSS WILD-TYPE 66  2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED      8    1
  19P LOSS WILD-TYPE   66    2
   clus
vv  19P LOSS MUTATED 19P LOSS WILD-TYPE
  0                8                 66
  1                1                  2
                    vv
clus                 M0 M1 MX
  19P LOSS MUTATED   12  0  2
  19P LOSS WILD-TYPE 78  2 23
D74V6, multiclass
    clus
vv   19P LOSS MUTATED 19P LOSS WILD-TYPE
  M0               12                 78
  M1                0                  2
  MX                2                 23
D74V7, binary
                    cls
clus                  0  1
  19P LOSS MUTATED    4 10
  19P LOSS WILD-TYPE 40 63
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED      4   10
  19P LOSS WILD-TYPE   40   63
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  FEMALE                4                 40
  MALE                 10                 63
                    vv
clus                 R0 R1 R2 RX
  19P LOSS MUTATED    8  3  0  2
  19P LOSS WILD-TYPE 85  7  1  6
D74V8, multiclass
    clus
vv   19P LOSS MUTATED 19P LOSS WILD-TYPE
  R0                8                 85
  R1                3                  7
  R2                0                  1
  RX                2                  6

Clustering(75) Variable = 19Q LOSS MUTATION ANALYSIS
D75V1, survival
                    sevent
clus2                 0  1
  19Q LOSS MUTATED    6  4
  19Q LOSS WILD-TYPE 55 49
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                10                104 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                 4                 49 
$`19Q LOSS MUTATED`
TCGA-BC-A112 TCGA-BC-A3KF TCGA-CC-5258 TCGA-CC-5263 TCGA-CC-A1HT TCGA-DD-A11A 
        5.03         0.26         0.07         4.24         3.32         2.60 
TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A4NJ TCGA-FV-A4ZP 
        6.02        29.16        15.06        60.36 

$`19Q LOSS WILD-TYPE`
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T 
       48.99        27.91        37.32        10.13        46.78        27.52 
TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 
       27.52         2.99        25.32        23.34         1.12        69.57 
TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-CC-5260 TCGA-CC-5261 
       44.42        13.81        16.37         9.50         2.86         3.02 
TCGA-CC-5262 TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A113 
        3.39         0.10         0.07         0.10         0.13        79.73 
TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11B 
       37.74        83.57        53.29       112.96         7.33         0.46 
TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC 
       21.76        51.25        90.67        79.36        66.31        19.76 
TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EH TCGA-DD-A1EL TCGA-DD-A39V 
       75.65         6.67        12.95        49.15        13.64        21.14 
TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 
       55.66         5.59        19.73        25.81         7.66        70.06 
TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A8 
       17.59        20.12       102.74       107.11        13.78         0.36 
TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4ND TCGA-DD-A4NE TCGA-DD-A4NF TCGA-DD-A4NG 
       30.58        33.14        73.38        21.67        14.07        14.93 
TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO 
       14.24        10.78        39.75        56.25        29.56        61.45 
TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-ED-A459 TCGA-ED-A5KG TCGA-EP-A12J TCGA-EP-A26S 
       93.67        12.26         0.23         0.20        10.85         7.76 
TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS 
       11.74         1.97         0.62         3.19         0.43        23.01 
TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3R2 TCGA-FV-A3R3 
       14.40        32.45        19.07         0.20         6.35         0.13 
TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25U 
        0.03         0.33         0.39         1.22        51.02        53.79 
TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG 
       28.27        30.71        58.49        14.86        21.53        22.13 
TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SJ TCGA-G3-A5SK 
       25.64         5.88        19.53        19.23        11.97         9.93 
TCGA-G3-A5SL TCGA-G3-A5SM 
        7.99         4.37 

  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
              0.07               0.03 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
             60.36             112.96 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
             4.635             19.150 
[1] "0.1 - 60.4 (4.6)"   "0.0 - 113.0 (19.1)"
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
  "19Q LOSS MUTATED" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-BC-A5W4 
  "19Q LOSS MUTATED" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-CC-5258         TCGA-CC-5260         TCGA-CC-5261 
  "19Q LOSS MUTATED" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-CC-5262         TCGA-CC-5263         TCGA-CC-A1HT 
"19Q LOSS WILD-TYPE"   "19Q LOSS MUTATED"   "19Q LOSS MUTATED" 
        TCGA-CC-A3M9         TCGA-CC-A3MA         TCGA-CC-A3MB 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-CC-A3MC         TCGA-DD-A113         TCGA-DD-A114 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"19Q LOSS WILD-TYPE"   "19Q LOSS MUTATED" "19Q LOSS WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DD-A1EA         TCGA-DD-A1EB         TCGA-DD-A1EC 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DD-A1ED         TCGA-DD-A1EE         TCGA-DD-A1EF 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DD-A1EH         TCGA-DD-A1EI         TCGA-DD-A1EJ 
"19Q LOSS WILD-TYPE"   "19Q LOSS MUTATED"   "19Q LOSS MUTATED" 
        TCGA-DD-A1EL         TCGA-DD-A39V         TCGA-DD-A39X 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DD-A39Y         TCGA-DD-A39Z         TCGA-DD-A3A0 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DD-A3A1         TCGA-DD-A3A2         TCGA-DD-A3A3 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DD-A3A4         TCGA-DD-A3A5         TCGA-DD-A3A6 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DD-A3A7         TCGA-DD-A3A8         TCGA-DD-A3A9 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DD-A4NA         TCGA-DD-A4ND         TCGA-DD-A4NE 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DD-A4NF         TCGA-DD-A4NG         TCGA-DD-A4NH 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DD-A4NI         TCGA-DD-A4NJ         TCGA-DD-A4NK 
"19Q LOSS WILD-TYPE"   "19Q LOSS MUTATED" "19Q LOSS WILD-TYPE" 
        TCGA-DD-A4NL         TCGA-DD-A4NN         TCGA-DD-A4NO 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DD-A4NP         TCGA-DD-A4NQ         TCGA-ED-A459 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-ED-A5KG         TCGA-EP-A12J         TCGA-EP-A26S 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-EP-A2KA         TCGA-EP-A2KB         TCGA-EP-A2KC 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-EP-A3JL         TCGA-EP-A3RK         TCGA-ES-A2HS 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-ES-A2HT         TCGA-FV-A23B         TCGA-FV-A2QR 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-FV-A3I0         TCGA-FV-A3R2         TCGA-FV-A3R3 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-FV-A495         TCGA-FV-A496         TCGA-FV-A4ZP 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE"   "19Q LOSS MUTATED" 
        TCGA-FV-A4ZQ         TCGA-G3-A25S         TCGA-G3-A25T 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-G3-A25U         TCGA-G3-A25V         TCGA-G3-A25W 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-G3-A25X         TCGA-G3-A25Y         TCGA-G3-A25Z 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-G3-A3CG         TCGA-G3-A3CH         TCGA-G3-A3CI 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK         TCGA-G3-A5SJ 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-G3-A5SK         TCGA-G3-A5SL         TCGA-G3-A5SM 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
  "19Q LOSS MUTATED" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-BC-A5W4 
  "19Q LOSS MUTATED" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-CC-5258         TCGA-CC-5260         TCGA-CC-5261 
  "19Q LOSS MUTATED" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-CC-5262         TCGA-CC-5263         TCGA-CC-A1HT 
"19Q LOSS WILD-TYPE"   "19Q LOSS MUTATED"   "19Q LOSS MUTATED" 
        TCGA-CC-A3M9         TCGA-CC-A3MA         TCGA-CC-A3MB 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-CC-A3MC         TCGA-DD-A113         TCGA-DD-A114 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"19Q LOSS WILD-TYPE"   "19Q LOSS MUTATED" "19Q LOSS WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DD-A1EA         TCGA-DD-A1EB         TCGA-DD-A1EC 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DD-A1ED         TCGA-DD-A1EE         TCGA-DD-A1EF 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DD-A1EH         TCGA-DD-A1EI         TCGA-DD-A1EJ 
"19Q LOSS WILD-TYPE"   "19Q LOSS MUTATED"   "19Q LOSS MUTATED" 
        TCGA-DD-A1EL         TCGA-DD-A39V         TCGA-DD-A39X 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DD-A39Y         TCGA-DD-A39Z         TCGA-DD-A3A0 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DD-A3A1         TCGA-DD-A3A2         TCGA-DD-A3A3 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DD-A3A4         TCGA-DD-A3A5         TCGA-DD-A3A6 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DD-A3A7         TCGA-DD-A3A8         TCGA-DD-A3A9 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DD-A4NA         TCGA-DD-A4ND         TCGA-DD-A4NE 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DD-A4NF         TCGA-DD-A4NG         TCGA-DD-A4NH 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DD-A4NI         TCGA-DD-A4NJ         TCGA-DD-A4NK 
"19Q LOSS WILD-TYPE"   "19Q LOSS MUTATED" "19Q LOSS WILD-TYPE" 
        TCGA-DD-A4NL         TCGA-DD-A4NN         TCGA-DD-A4NO 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DD-A4NP         TCGA-DD-A4NQ         TCGA-ED-A459 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-ED-A5KG         TCGA-EP-A12J         TCGA-EP-A26S 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-EP-A2KA         TCGA-EP-A2KB         TCGA-EP-A2KC 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-EP-A3JL         TCGA-EP-A3RK         TCGA-ES-A2HS 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-ES-A2HT         TCGA-FV-A23B         TCGA-FV-A2QR 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-FV-A3I0         TCGA-FV-A3R2         TCGA-FV-A3R3 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-FV-A495         TCGA-FV-A496         TCGA-FV-A4ZP 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE"   "19Q LOSS MUTATED" 
        TCGA-FV-A4ZQ         TCGA-G3-A25S         TCGA-G3-A25T 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-G3-A25U         TCGA-G3-A25V         TCGA-G3-A25W 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-G3-A25X         TCGA-G3-A25Y         TCGA-G3-A25Z 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-G3-A3CG         TCGA-G3-A3CH         TCGA-G3-A3CI 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK         TCGA-G3-A5SJ 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-G3-A5SK         TCGA-G3-A5SL         TCGA-G3-A5SM 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
  "19Q LOSS MUTATED" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-BC-A5W4 
  "19Q LOSS MUTATED" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-CC-5258         TCGA-CC-5260         TCGA-CC-5261 
  "19Q LOSS MUTATED" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-CC-5262         TCGA-CC-5263         TCGA-CC-A1HT 
"19Q LOSS WILD-TYPE"   "19Q LOSS MUTATED"   "19Q LOSS MUTATED" 
        TCGA-CC-A3M9         TCGA-CC-A3MA         TCGA-CC-A3MB 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-CC-A3MC         TCGA-DD-A113         TCGA-DD-A114 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"19Q LOSS WILD-TYPE"   "19Q LOSS MUTATED" "19Q LOSS WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DD-A1EA         TCGA-DD-A1EB         TCGA-DD-A1EC 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DD-A1ED         TCGA-DD-A1EE         TCGA-DD-A1EF 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DD-A1EH         TCGA-DD-A1EI         TCGA-DD-A1EJ 
"19Q LOSS WILD-TYPE"   "19Q LOSS MUTATED"   "19Q LOSS MUTATED" 
        TCGA-DD-A1EL         TCGA-DD-A39V         TCGA-DD-A39X 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DD-A39Y         TCGA-DD-A39Z         TCGA-DD-A3A0 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DD-A3A1         TCGA-DD-A3A2         TCGA-DD-A3A3 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DD-A3A4         TCGA-DD-A3A5         TCGA-DD-A3A6 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DD-A3A7         TCGA-DD-A3A8         TCGA-DD-A3A9 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DD-A4NA         TCGA-DD-A4ND         TCGA-DD-A4NE 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DD-A4NF         TCGA-DD-A4NG         TCGA-DD-A4NH 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DD-A4NI         TCGA-DD-A4NJ         TCGA-DD-A4NK 
"19Q LOSS WILD-TYPE"   "19Q LOSS MUTATED" "19Q LOSS WILD-TYPE" 
        TCGA-DD-A4NL         TCGA-DD-A4NN         TCGA-DD-A4NO 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DD-A4NP         TCGA-DD-A4NQ         TCGA-ED-A459 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-ED-A5KG         TCGA-EP-A12J         TCGA-EP-A26S 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-EP-A2KA         TCGA-EP-A2KB         TCGA-EP-A2KC 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-EP-A3JL         TCGA-EP-A3RK         TCGA-ES-A2HS 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-ES-A2HT         TCGA-FV-A23B         TCGA-FV-A2QR 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-FV-A3I0         TCGA-FV-A3R2         TCGA-FV-A3R3 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-FV-A495         TCGA-FV-A496         TCGA-FV-A4ZP 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE"   "19Q LOSS MUTATED" 
        TCGA-FV-A4ZQ         TCGA-G3-A25S         TCGA-G3-A25T 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-G3-A25U         TCGA-G3-A25V         TCGA-G3-A25W 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-G3-A25X         TCGA-G3-A25Y         TCGA-G3-A25Z 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-G3-A3CG         TCGA-G3-A3CH         TCGA-G3-A3CI 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK         TCGA-G3-A5SJ 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-G3-A5SK         TCGA-G3-A5SL         TCGA-G3-A5SM 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
[1] "hr=" "1.7"
D75V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  19Q LOSS MUTATED         3        2         0          3          0
  19Q LOSS WILD-TYPE      42       23         2         22          3
                    vv
clus                 STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  19Q LOSS MUTATED            1        0         0         0
  19Q LOSS WILD-TYPE          3        1         1         1
D75V3, multiclass
                    vv
clus                 T1 T2 T3 T4
  19Q LOSS MUTATED    4  2  4  0
  19Q LOSS WILD-TYPE 44 26 30  6
D75V4, multiclass
    clus
vv   19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  T1                4                 44
  T2                2                 26
  T3                4                 30
  T4                0                  6
D75V5, binary
                    cls
clus                  0  1
  19Q LOSS MUTATED    6  1
  19Q LOSS WILD-TYPE 68  2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED      6    1
  19Q LOSS WILD-TYPE   68    2
   clus
vv  19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  0                6                 68
  1                1                  2
                    vv
clus                 M0 M1 MX
  19Q LOSS MUTATED    9  0  1
  19Q LOSS WILD-TYPE 81  2 24
D75V6, multiclass
    clus
vv   19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  M0                9                 81
  M1                0                  2
  MX                1                 24
D75V7, binary
                    cls
clus                  0  1
  19Q LOSS MUTATED    3  7
  19Q LOSS WILD-TYPE 41 66
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED      3    7
  19Q LOSS WILD-TYPE   41   66
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  FEMALE                3                 41
  MALE                  7                 66
                    vv
clus                 R0 R1 R2 RX
  19Q LOSS MUTATED    6  1  0  2
  19Q LOSS WILD-TYPE 87  9  1  6
D75V8, multiclass
    clus
vv   19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  R0                6                 87
  R1                1                  9
  R2                0                  1
  RX                2                  6

Clustering(76) Variable = 20P LOSS MUTATION ANALYSIS
D76V1, survival
                    sevent
clus2                 0  1
  20P LOSS MUTATED    3  4
  20P LOSS WILD-TYPE 58 49
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                 7                107 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                 4                 49 
$`20P LOSS MUTATED`
TCGA-BC-A10Z TCGA-CC-A3MC TCGA-DD-A113 TCGA-DD-A3A3 TCGA-DD-A3A5 TCGA-DD-A4NO 
        1.12         0.13        79.73        17.59       102.74        61.45 
TCGA-DD-A4NQ 
       12.26 

$`20P LOSS WILD-TYPE`
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T 
       48.99        27.91        37.32        10.13        46.78        27.52 
TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A110 TCGA-BC-A112 
       27.52         2.99        25.32        23.34        69.57         5.03 
TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-CC-5258 
       44.42        13.81         0.26        16.37         9.50         0.07 
TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3M9 
        2.86         3.02         3.39         4.24         3.32         0.10 
TCGA-CC-A3MA TCGA-CC-A3MB TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 
        0.07         0.10        37.74        83.57        53.29       112.96 
TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 
        7.33         2.60         0.46        21.76        51.25        90.67 
TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EF 
       79.36        66.31        19.76        75.65         6.67        12.95 
TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39X 
       49.15         6.02        29.16        13.64        21.14        55.66 
TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A4 
        5.59        19.73        25.81         7.66        70.06        20.12 
TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4ND 
      107.11        13.78         0.36        30.58        33.14        73.38 
TCGA-DD-A4NE TCGA-DD-A4NF TCGA-DD-A4NG TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ 
       21.67        14.07        14.93        14.24        10.78        15.06 
TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NP TCGA-ED-A459 TCGA-ED-A5KG 
       39.75        56.25        29.56        93.67         0.23         0.20 
TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL 
       10.85         7.76        11.74         1.97         0.62         3.19 
TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-A3I0 
        0.43        23.01        14.40        32.45        19.07         0.20 
TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZP TCGA-FV-A4ZQ 
        6.35         0.13         0.03         0.33        60.36         0.39 
TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25X 
        1.22        51.02        53.79        28.27        30.71        58.49 
TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ 
       14.86        21.53        22.13        25.64         5.88        19.53 
TCGA-G3-A3CK TCGA-G3-A5SJ TCGA-G3-A5SK TCGA-G3-A5SL TCGA-G3-A5SM 
       19.23        11.97         9.93         7.99         4.37 

  20P LOSS MUTATED 20P LOSS WILD-TYPE 
              0.13               0.03 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
            102.74             112.96 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
             17.59              15.06 
[1] "0.1 - 102.7 (17.6)" "0.0 - 113.0 (15.1)"
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"20P LOSS WILD-TYPE"   "20P LOSS MUTATED" "20P LOSS WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-BC-A5W4 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CC-5258         TCGA-CC-5260         TCGA-CC-5261 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CC-5262         TCGA-CC-5263         TCGA-CC-A1HT 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CC-A3M9         TCGA-CC-A3MA         TCGA-CC-A3MB 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CC-A3MC         TCGA-DD-A113         TCGA-DD-A114 
  "20P LOSS MUTATED"   "20P LOSS MUTATED" "20P LOSS WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DD-A1EA         TCGA-DD-A1EB         TCGA-DD-A1EC 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DD-A1ED         TCGA-DD-A1EE         TCGA-DD-A1EF 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DD-A1EH         TCGA-DD-A1EI         TCGA-DD-A1EJ 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DD-A1EL         TCGA-DD-A39V         TCGA-DD-A39X 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DD-A39Y         TCGA-DD-A39Z         TCGA-DD-A3A0 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DD-A3A1         TCGA-DD-A3A2         TCGA-DD-A3A3 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE"   "20P LOSS MUTATED" 
        TCGA-DD-A3A4         TCGA-DD-A3A5         TCGA-DD-A3A6 
"20P LOSS WILD-TYPE"   "20P LOSS MUTATED" "20P LOSS WILD-TYPE" 
        TCGA-DD-A3A7         TCGA-DD-A3A8         TCGA-DD-A3A9 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DD-A4NA         TCGA-DD-A4ND         TCGA-DD-A4NE 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DD-A4NF         TCGA-DD-A4NG         TCGA-DD-A4NH 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DD-A4NI         TCGA-DD-A4NJ         TCGA-DD-A4NK 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DD-A4NL         TCGA-DD-A4NN         TCGA-DD-A4NO 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE"   "20P LOSS MUTATED" 
        TCGA-DD-A4NP         TCGA-DD-A4NQ         TCGA-ED-A459 
"20P LOSS WILD-TYPE"   "20P LOSS MUTATED" "20P LOSS WILD-TYPE" 
        TCGA-ED-A5KG         TCGA-EP-A12J         TCGA-EP-A26S 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EP-A2KA         TCGA-EP-A2KB         TCGA-EP-A2KC 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EP-A3JL         TCGA-EP-A3RK         TCGA-ES-A2HS 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-ES-A2HT         TCGA-FV-A23B         TCGA-FV-A2QR 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-FV-A3I0         TCGA-FV-A3R2         TCGA-FV-A3R3 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-FV-A495         TCGA-FV-A496         TCGA-FV-A4ZP 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-FV-A4ZQ         TCGA-G3-A25S         TCGA-G3-A25T 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-G3-A25U         TCGA-G3-A25V         TCGA-G3-A25W 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-G3-A25X         TCGA-G3-A25Y         TCGA-G3-A25Z 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-G3-A3CG         TCGA-G3-A3CH         TCGA-G3-A3CI 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK         TCGA-G3-A5SJ 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-G3-A5SK         TCGA-G3-A5SL         TCGA-G3-A5SM 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"20P LOSS WILD-TYPE"   "20P LOSS MUTATED" "20P LOSS WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-BC-A5W4 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CC-5258         TCGA-CC-5260         TCGA-CC-5261 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CC-5262         TCGA-CC-5263         TCGA-CC-A1HT 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CC-A3M9         TCGA-CC-A3MA         TCGA-CC-A3MB 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CC-A3MC         TCGA-DD-A113         TCGA-DD-A114 
  "20P LOSS MUTATED"   "20P LOSS MUTATED" "20P LOSS WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DD-A1EA         TCGA-DD-A1EB         TCGA-DD-A1EC 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DD-A1ED         TCGA-DD-A1EE         TCGA-DD-A1EF 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DD-A1EH         TCGA-DD-A1EI         TCGA-DD-A1EJ 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DD-A1EL         TCGA-DD-A39V         TCGA-DD-A39X 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DD-A39Y         TCGA-DD-A39Z         TCGA-DD-A3A0 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DD-A3A1         TCGA-DD-A3A2         TCGA-DD-A3A3 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE"   "20P LOSS MUTATED" 
        TCGA-DD-A3A4         TCGA-DD-A3A5         TCGA-DD-A3A6 
"20P LOSS WILD-TYPE"   "20P LOSS MUTATED" "20P LOSS WILD-TYPE" 
        TCGA-DD-A3A7         TCGA-DD-A3A8         TCGA-DD-A3A9 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DD-A4NA         TCGA-DD-A4ND         TCGA-DD-A4NE 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DD-A4NF         TCGA-DD-A4NG         TCGA-DD-A4NH 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DD-A4NI         TCGA-DD-A4NJ         TCGA-DD-A4NK 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DD-A4NL         TCGA-DD-A4NN         TCGA-DD-A4NO 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE"   "20P LOSS MUTATED" 
        TCGA-DD-A4NP         TCGA-DD-A4NQ         TCGA-ED-A459 
"20P LOSS WILD-TYPE"   "20P LOSS MUTATED" "20P LOSS WILD-TYPE" 
        TCGA-ED-A5KG         TCGA-EP-A12J         TCGA-EP-A26S 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EP-A2KA         TCGA-EP-A2KB         TCGA-EP-A2KC 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EP-A3JL         TCGA-EP-A3RK         TCGA-ES-A2HS 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-ES-A2HT         TCGA-FV-A23B         TCGA-FV-A2QR 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-FV-A3I0         TCGA-FV-A3R2         TCGA-FV-A3R3 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-FV-A495         TCGA-FV-A496         TCGA-FV-A4ZP 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-FV-A4ZQ         TCGA-G3-A25S         TCGA-G3-A25T 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-G3-A25U         TCGA-G3-A25V         TCGA-G3-A25W 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-G3-A25X         TCGA-G3-A25Y         TCGA-G3-A25Z 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-G3-A3CG         TCGA-G3-A3CH         TCGA-G3-A3CI 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK         TCGA-G3-A5SJ 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-G3-A5SK         TCGA-G3-A5SL         TCGA-G3-A5SM 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"20P LOSS WILD-TYPE"   "20P LOSS MUTATED" "20P LOSS WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-BC-A5W4 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CC-5258         TCGA-CC-5260         TCGA-CC-5261 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CC-5262         TCGA-CC-5263         TCGA-CC-A1HT 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CC-A3M9         TCGA-CC-A3MA         TCGA-CC-A3MB 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CC-A3MC         TCGA-DD-A113         TCGA-DD-A114 
  "20P LOSS MUTATED"   "20P LOSS MUTATED" "20P LOSS WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DD-A1EA         TCGA-DD-A1EB         TCGA-DD-A1EC 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DD-A1ED         TCGA-DD-A1EE         TCGA-DD-A1EF 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DD-A1EH         TCGA-DD-A1EI         TCGA-DD-A1EJ 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DD-A1EL         TCGA-DD-A39V         TCGA-DD-A39X 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DD-A39Y         TCGA-DD-A39Z         TCGA-DD-A3A0 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DD-A3A1         TCGA-DD-A3A2         TCGA-DD-A3A3 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE"   "20P LOSS MUTATED" 
        TCGA-DD-A3A4         TCGA-DD-A3A5         TCGA-DD-A3A6 
"20P LOSS WILD-TYPE"   "20P LOSS MUTATED" "20P LOSS WILD-TYPE" 
        TCGA-DD-A3A7         TCGA-DD-A3A8         TCGA-DD-A3A9 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DD-A4NA         TCGA-DD-A4ND         TCGA-DD-A4NE 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DD-A4NF         TCGA-DD-A4NG         TCGA-DD-A4NH 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DD-A4NI         TCGA-DD-A4NJ         TCGA-DD-A4NK 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DD-A4NL         TCGA-DD-A4NN         TCGA-DD-A4NO 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE"   "20P LOSS MUTATED" 
        TCGA-DD-A4NP         TCGA-DD-A4NQ         TCGA-ED-A459 
"20P LOSS WILD-TYPE"   "20P LOSS MUTATED" "20P LOSS WILD-TYPE" 
        TCGA-ED-A5KG         TCGA-EP-A12J         TCGA-EP-A26S 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EP-A2KA         TCGA-EP-A2KB         TCGA-EP-A2KC 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EP-A3JL         TCGA-EP-A3RK         TCGA-ES-A2HS 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-ES-A2HT         TCGA-FV-A23B         TCGA-FV-A2QR 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-FV-A3I0         TCGA-FV-A3R2         TCGA-FV-A3R3 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-FV-A495         TCGA-FV-A496         TCGA-FV-A4ZP 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-FV-A4ZQ         TCGA-G3-A25S         TCGA-G3-A25T 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-G3-A25U         TCGA-G3-A25V         TCGA-G3-A25W 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-G3-A25X         TCGA-G3-A25Y         TCGA-G3-A25Z 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-G3-A3CG         TCGA-G3-A3CH         TCGA-G3-A3CI 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK         TCGA-G3-A5SJ 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-G3-A5SK         TCGA-G3-A5SL         TCGA-G3-A5SM 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
[1] "hr=" "1.2"
D76V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  20P LOSS MUTATED         3        2         1          1          0
  20P LOSS WILD-TYPE      42       23         1         24          3
                    vv
clus                 STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  20P LOSS MUTATED            0        0         0         0
  20P LOSS WILD-TYPE          4        1         1         1
D76V3, multiclass
                    vv
clus                 T1 T2 T3 T4
  20P LOSS MUTATED    3  2  2  0
  20P LOSS WILD-TYPE 45 26 32  6
D76V4, multiclass
    clus
vv   20P LOSS MUTATED 20P LOSS WILD-TYPE
  T1                3                 45
  T2                2                 26
  T3                2                 32
  T4                0                  6
D76V5, binary
                    cls
clus                  0  1
  20P LOSS MUTATED    7  0
  20P LOSS WILD-TYPE 67  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED      7    0
  20P LOSS WILD-TYPE   67    3
   clus
vv  20P LOSS MUTATED 20P LOSS WILD-TYPE
  0                7                 67
  1                0                  3
                    vv
clus                 M0 M1 MX
  20P LOSS MUTATED    6  0  1
  20P LOSS WILD-TYPE 84  2 24
D76V6, multiclass
    clus
vv   20P LOSS MUTATED 20P LOSS WILD-TYPE
  M0                6                 84
  M1                0                  2
  MX                1                 24
D76V7, binary
                    cls
clus                  0  1
  20P LOSS MUTATED    3  4
  20P LOSS WILD-TYPE 41 69
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED      3    4
  20P LOSS WILD-TYPE   41   69
        clus
vv       20P LOSS MUTATED 20P LOSS WILD-TYPE
  FEMALE                3                 41
  MALE                  4                 69
                    vv
clus                 R0 R1 R2 RX
  20P LOSS MUTATED    7  0  0  0
  20P LOSS WILD-TYPE 86 10  1  8
D76V8, multiclass
    clus
vv   20P LOSS MUTATED 20P LOSS WILD-TYPE
  R0                7                 86
  R1                0                 10
  R2                0                  1
  RX                0                  8

Clustering(77) Variable = 20Q LOSS MUTATION ANALYSIS
D77V1, survival
                    sevent
clus2                 0  1
  20Q LOSS MUTATED    2  2
  20Q LOSS WILD-TYPE 59 51
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 4                110 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 2                 51 
$`20Q LOSS MUTATED`
TCGA-DD-A113 TCGA-DD-A3A5 TCGA-DD-A4NO TCGA-DD-A4NQ 
       79.73       102.74        61.45        12.26 

$`20Q LOSS WILD-TYPE`
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T 
       48.99        27.91        37.32        10.13        46.78        27.52 
TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 
       27.52         2.99        25.32        23.34         1.12        69.57 
TCGA-BC-A112 TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 
        5.03        44.42        13.81         0.26        16.37         9.50 
TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A1HT 
        0.07         2.86         3.02         3.39         4.24         3.32 
TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A114 TCGA-DD-A115 
        0.10         0.07         0.10         0.13        37.74        83.57 
TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C 
       53.29       112.96         7.33         2.60         0.46        21.76 
TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED 
       51.25        90.67        79.36        66.31        19.76        75.65 
TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EL 
        6.67        12.95        49.15         6.02        29.16        13.64 
TCGA-DD-A39V TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 
       21.14        55.66         5.59        19.73        25.81         7.66 
TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A8 
       70.06        17.59        20.12       107.11        13.78         0.36 
TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4ND TCGA-DD-A4NE TCGA-DD-A4NF TCGA-DD-A4NG 
       30.58        33.14        73.38        21.67        14.07        14.93 
TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN 
       14.24        10.78        15.06        39.75        56.25        29.56 
TCGA-DD-A4NP TCGA-ED-A459 TCGA-ED-A5KG TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA 
       93.67         0.23         0.20        10.85         7.76        11.74 
TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT 
        1.97         0.62         3.19         0.43        23.01        14.40 
TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 
       32.45        19.07         0.20         6.35         0.13         0.03 
TCGA-FV-A496 TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25U 
        0.33        60.36         0.39         1.22        51.02        53.79 
TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG 
       28.27        30.71        58.49        14.86        21.53        22.13 
TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SJ TCGA-G3-A5SK 
       25.64         5.88        19.53        19.23        11.97         9.93 
TCGA-G3-A5SL TCGA-G3-A5SM 
        7.99         4.37 

  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
             12.26               0.03 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
            102.74             112.96 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
            70.590             14.995 
[1] "12.3 - 102.7 (70.6)" "0.0 - 113.0 (15.0)" 
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-BC-A5W4 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-CC-5258         TCGA-CC-5260         TCGA-CC-5261 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-CC-5262         TCGA-CC-5263         TCGA-CC-A1HT 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-CC-A3M9         TCGA-CC-A3MA         TCGA-CC-A3MB 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-CC-A3MC         TCGA-DD-A113         TCGA-DD-A114 
"20Q LOSS WILD-TYPE"   "20Q LOSS MUTATED" "20Q LOSS WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-DD-A1EA         TCGA-DD-A1EB         TCGA-DD-A1EC 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-DD-A1ED         TCGA-DD-A1EE         TCGA-DD-A1EF 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-DD-A1EH         TCGA-DD-A1EI         TCGA-DD-A1EJ 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-DD-A1EL         TCGA-DD-A39V         TCGA-DD-A39X 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-DD-A39Y         TCGA-DD-A39Z         TCGA-DD-A3A0 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-DD-A3A1         TCGA-DD-A3A2         TCGA-DD-A3A3 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-DD-A3A4         TCGA-DD-A3A5         TCGA-DD-A3A6 
"20Q LOSS WILD-TYPE"   "20Q LOSS MUTATED" "20Q LOSS WILD-TYPE" 
        TCGA-DD-A3A7         TCGA-DD-A3A8         TCGA-DD-A3A9 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-DD-A4NA         TCGA-DD-A4ND         TCGA-DD-A4NE 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-DD-A4NF         TCGA-DD-A4NG         TCGA-DD-A4NH 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-DD-A4NI         TCGA-DD-A4NJ         TCGA-DD-A4NK 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-DD-A4NL         TCGA-DD-A4NN         TCGA-DD-A4NO 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE"   "20Q LOSS MUTATED" 
        TCGA-DD-A4NP         TCGA-DD-A4NQ         TCGA-ED-A459 
"20Q LOSS WILD-TYPE"   "20Q LOSS MUTATED" "20Q LOSS WILD-TYPE" 
        TCGA-ED-A5KG         TCGA-EP-A12J         TCGA-EP-A26S 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-EP-A2KA         TCGA-EP-A2KB         TCGA-EP-A2KC 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-EP-A3JL         TCGA-EP-A3RK         TCGA-ES-A2HS 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-ES-A2HT         TCGA-FV-A23B         TCGA-FV-A2QR 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-FV-A3I0         TCGA-FV-A3R2         TCGA-FV-A3R3 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-FV-A495         TCGA-FV-A496         TCGA-FV-A4ZP 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-FV-A4ZQ         TCGA-G3-A25S         TCGA-G3-A25T 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-G3-A25U         TCGA-G3-A25V         TCGA-G3-A25W 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-G3-A25X         TCGA-G3-A25Y         TCGA-G3-A25Z 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-G3-A3CG         TCGA-G3-A3CH         TCGA-G3-A3CI 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK         TCGA-G3-A5SJ 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-G3-A5SK         TCGA-G3-A5SL         TCGA-G3-A5SM 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-BC-A5W4 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-CC-5258         TCGA-CC-5260         TCGA-CC-5261 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-CC-5262         TCGA-CC-5263         TCGA-CC-A1HT 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-CC-A3M9         TCGA-CC-A3MA         TCGA-CC-A3MB 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-CC-A3MC         TCGA-DD-A113         TCGA-DD-A114 
"20Q LOSS WILD-TYPE"   "20Q LOSS MUTATED" "20Q LOSS WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-DD-A1EA         TCGA-DD-A1EB         TCGA-DD-A1EC 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-DD-A1ED         TCGA-DD-A1EE         TCGA-DD-A1EF 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-DD-A1EH         TCGA-DD-A1EI         TCGA-DD-A1EJ 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-DD-A1EL         TCGA-DD-A39V         TCGA-DD-A39X 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-DD-A39Y         TCGA-DD-A39Z         TCGA-DD-A3A0 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-DD-A3A1         TCGA-DD-A3A2         TCGA-DD-A3A3 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-DD-A3A4         TCGA-DD-A3A5         TCGA-DD-A3A6 
"20Q LOSS WILD-TYPE"   "20Q LOSS MUTATED" "20Q LOSS WILD-TYPE" 
        TCGA-DD-A3A7         TCGA-DD-A3A8         TCGA-DD-A3A9 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-DD-A4NA         TCGA-DD-A4ND         TCGA-DD-A4NE 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-DD-A4NF         TCGA-DD-A4NG         TCGA-DD-A4NH 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-DD-A4NI         TCGA-DD-A4NJ         TCGA-DD-A4NK 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-DD-A4NL         TCGA-DD-A4NN         TCGA-DD-A4NO 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE"   "20Q LOSS MUTATED" 
        TCGA-DD-A4NP         TCGA-DD-A4NQ         TCGA-ED-A459 
"20Q LOSS WILD-TYPE"   "20Q LOSS MUTATED" "20Q LOSS WILD-TYPE" 
        TCGA-ED-A5KG         TCGA-EP-A12J         TCGA-EP-A26S 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-EP-A2KA         TCGA-EP-A2KB         TCGA-EP-A2KC 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-EP-A3JL         TCGA-EP-A3RK         TCGA-ES-A2HS 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-ES-A2HT         TCGA-FV-A23B         TCGA-FV-A2QR 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-FV-A3I0         TCGA-FV-A3R2         TCGA-FV-A3R3 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-FV-A495         TCGA-FV-A496         TCGA-FV-A4ZP 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-FV-A4ZQ         TCGA-G3-A25S         TCGA-G3-A25T 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-G3-A25U         TCGA-G3-A25V         TCGA-G3-A25W 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-G3-A25X         TCGA-G3-A25Y         TCGA-G3-A25Z 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-G3-A3CG         TCGA-G3-A3CH         TCGA-G3-A3CI 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK         TCGA-G3-A5SJ 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-G3-A5SK         TCGA-G3-A5SL         TCGA-G3-A5SM 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-BC-A5W4 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-CC-5258         TCGA-CC-5260         TCGA-CC-5261 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-CC-5262         TCGA-CC-5263         TCGA-CC-A1HT 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-CC-A3M9         TCGA-CC-A3MA         TCGA-CC-A3MB 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-CC-A3MC         TCGA-DD-A113         TCGA-DD-A114 
"20Q LOSS WILD-TYPE"   "20Q LOSS MUTATED" "20Q LOSS WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-DD-A1EA         TCGA-DD-A1EB         TCGA-DD-A1EC 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-DD-A1ED         TCGA-DD-A1EE         TCGA-DD-A1EF 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-DD-A1EH         TCGA-DD-A1EI         TCGA-DD-A1EJ 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-DD-A1EL         TCGA-DD-A39V         TCGA-DD-A39X 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-DD-A39Y         TCGA-DD-A39Z         TCGA-DD-A3A0 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-DD-A3A1         TCGA-DD-A3A2         TCGA-DD-A3A3 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-DD-A3A4         TCGA-DD-A3A5         TCGA-DD-A3A6 
"20Q LOSS WILD-TYPE"   "20Q LOSS MUTATED" "20Q LOSS WILD-TYPE" 
        TCGA-DD-A3A7         TCGA-DD-A3A8         TCGA-DD-A3A9 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-DD-A4NA         TCGA-DD-A4ND         TCGA-DD-A4NE 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-DD-A4NF         TCGA-DD-A4NG         TCGA-DD-A4NH 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-DD-A4NI         TCGA-DD-A4NJ         TCGA-DD-A4NK 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-DD-A4NL         TCGA-DD-A4NN         TCGA-DD-A4NO 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE"   "20Q LOSS MUTATED" 
        TCGA-DD-A4NP         TCGA-DD-A4NQ         TCGA-ED-A459 
"20Q LOSS WILD-TYPE"   "20Q LOSS MUTATED" "20Q LOSS WILD-TYPE" 
        TCGA-ED-A5KG         TCGA-EP-A12J         TCGA-EP-A26S 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-EP-A2KA         TCGA-EP-A2KB         TCGA-EP-A2KC 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-EP-A3JL         TCGA-EP-A3RK         TCGA-ES-A2HS 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-ES-A2HT         TCGA-FV-A23B         TCGA-FV-A2QR 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-FV-A3I0         TCGA-FV-A3R2         TCGA-FV-A3R3 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-FV-A495         TCGA-FV-A496         TCGA-FV-A4ZP 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-FV-A4ZQ         TCGA-G3-A25S         TCGA-G3-A25T 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-G3-A25U         TCGA-G3-A25V         TCGA-G3-A25W 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-G3-A25X         TCGA-G3-A25Y         TCGA-G3-A25Z 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-G3-A3CG         TCGA-G3-A3CH         TCGA-G3-A3CI 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK         TCGA-G3-A5SJ 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-G3-A5SK         TCGA-G3-A5SL         TCGA-G3-A5SM 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
[1] "hr=" "2.3"
D77V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  20Q LOSS MUTATED         1        2         1          0          0
  20Q LOSS WILD-TYPE      44       23         1         25          3
                    vv
clus                 STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  20Q LOSS MUTATED            0        0         0         0
  20Q LOSS WILD-TYPE          4        1         1         1
D77V3, multiclass
                    vv
clus                 T1 T2 T3 T4
  20Q LOSS MUTATED    1  2  1  0
  20Q LOSS WILD-TYPE 47 26 33  6
D77V4, multiclass
    clus
vv   20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  T1                1                 47
  T2                2                 26
  T3                1                 33
  T4                0                  6
D77V5, binary
                    cls
clus                  0  1
  20Q LOSS MUTATED    4  0
  20Q LOSS WILD-TYPE 70  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED      4    0
  20Q LOSS WILD-TYPE   70    3
   clus
vv  20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  0                4                 70
  1                0                  3
                    vv
clus                 M0 M1 MX
  20Q LOSS MUTATED    4  0  0
  20Q LOSS WILD-TYPE 86  2 25
D77V6, multiclass
    clus
vv   20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  M0                4                 86
  M1                0                  2
  MX                0                 25
D77V7, binary
                    cls
clus                  0  1
  20Q LOSS MUTATED    2  2
  20Q LOSS WILD-TYPE 42 71
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED      2    2
  20Q LOSS WILD-TYPE   42   71
        clus
vv       20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  FEMALE                2                 42
  MALE                  2                 71
                    vv
clus                 R0 R1 R2 RX
  20Q LOSS MUTATED    4  0  0  0
  20Q LOSS WILD-TYPE 89 10  1  8
D77V8, multiclass
    clus
vv   20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  R0                4                 89
  R1                0                 10
  R2                0                  1
  RX                0                  8

Clustering(78) Variable = 21Q LOSS MUTATION ANALYSIS
D78V1, survival
                    sevent
clus2                 0  1
  21Q LOSS MUTATED   12 15
  21Q LOSS WILD-TYPE 49 38
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                27                 87 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                15                 38 
$`21Q LOSS MUTATED`
TCGA-BC-A10U TCGA-BC-A112 TCGA-BC-A216 TCGA-CC-5262 TCGA-CC-A1HT TCGA-CC-A3MB 
       27.52         5.03        44.42         3.39         3.32         0.10 
TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A1E9 TCGA-DD-A1EH TCGA-DD-A1EJ TCGA-DD-A1EL 
        7.33         2.60        90.67        49.15        29.16        13.64 
TCGA-DD-A39V TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A7 TCGA-DD-A3A9 TCGA-DD-A4NG 
       21.14        25.81         7.66        13.78        30.58        14.93 
TCGA-ED-A459 TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK TCGA-FV-A23B TCGA-FV-A496 
        0.23         0.62         3.19         0.43        32.45         0.33 
TCGA-FV-A4ZP TCGA-G3-A25S TCGA-G3-A25Z 
       60.36         1.22        21.53 

$`21Q LOSS WILD-TYPE`
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T 
       48.99        27.91        37.32        10.13        46.78        27.52 
TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A217 
        2.99        25.32        23.34         1.12        69.57        13.81 
TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5261 
        0.26        16.37         9.50         0.07         2.86         3.02 
TCGA-CC-5263 TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MC TCGA-DD-A113 TCGA-DD-A114 
        4.24         0.10         0.07         0.13        79.73        37.74 
TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D 
       83.57        53.29       112.96         0.46        21.76        51.25 
TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EF 
       79.36        66.31        19.76        75.65         6.67        12.95 
TCGA-DD-A1EI TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A2 TCGA-DD-A3A3 
        6.02        55.66         5.59        19.73        70.06        17.59 
TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A8 TCGA-DD-A4NA TCGA-DD-A4ND 
       20.12       102.74       107.11         0.36        33.14        73.38 
TCGA-DD-A4NE TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK 
       21.67        14.07        14.24        10.78        15.06        39.75 
TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-ED-A5KG 
       56.25        29.56        61.45        93.67        12.26         0.20 
TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-ES-A2HS TCGA-ES-A2HT 
       10.85         7.76        11.74         1.97        23.01        14.40 
TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A4ZQ 
       19.07         0.20         6.35         0.13         0.03         0.39 
TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25X TCGA-G3-A25Y 
       51.02        53.79        28.27        30.71        58.49        14.86 
TCGA-G3-A3CG TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SJ 
       22.13        25.64         5.88        19.53        19.23        11.97 
TCGA-G3-A5SK TCGA-G3-A5SL TCGA-G3-A5SM 
        9.93         7.99         4.37 

  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
              0.10               0.03 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
             90.67             112.96 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
             13.64              19.07 
[1] "0.1 - 90.7 (13.6)"  "0.0 - 113.0 (19.1)"
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
  "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
  "21Q LOSS MUTATED"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-BC-A5W4 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-CC-5258         TCGA-CC-5260         TCGA-CC-5261 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-CC-5262         TCGA-CC-5263         TCGA-CC-A1HT 
  "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" 
        TCGA-CC-A3M9         TCGA-CC-A3MA         TCGA-CC-A3MB 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" 
        TCGA-CC-A3MC         TCGA-DD-A113         TCGA-DD-A114 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
  "21Q LOSS MUTATED"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" 
        TCGA-DD-A1EA         TCGA-DD-A1EB         TCGA-DD-A1EC 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-DD-A1ED         TCGA-DD-A1EE         TCGA-DD-A1EF 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-DD-A1EH         TCGA-DD-A1EI         TCGA-DD-A1EJ 
  "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" 
        TCGA-DD-A1EL         TCGA-DD-A39V         TCGA-DD-A39X 
  "21Q LOSS MUTATED"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-DD-A39Y         TCGA-DD-A39Z         TCGA-DD-A3A0 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" 
        TCGA-DD-A3A1         TCGA-DD-A3A2         TCGA-DD-A3A3 
  "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-DD-A3A4         TCGA-DD-A3A5         TCGA-DD-A3A6 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-DD-A3A7         TCGA-DD-A3A8         TCGA-DD-A3A9 
  "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" 
        TCGA-DD-A4NA         TCGA-DD-A4ND         TCGA-DD-A4NE 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-DD-A4NF         TCGA-DD-A4NG         TCGA-DD-A4NH 
"21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-DD-A4NI         TCGA-DD-A4NJ         TCGA-DD-A4NK 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-DD-A4NL         TCGA-DD-A4NN         TCGA-DD-A4NO 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-DD-A4NP         TCGA-DD-A4NQ         TCGA-ED-A459 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" 
        TCGA-ED-A5KG         TCGA-EP-A12J         TCGA-EP-A26S 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-EP-A2KA         TCGA-EP-A2KB         TCGA-EP-A2KC 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" 
        TCGA-EP-A3JL         TCGA-EP-A3RK         TCGA-ES-A2HS 
  "21Q LOSS MUTATED"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-ES-A2HT         TCGA-FV-A23B         TCGA-FV-A2QR 
"21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-FV-A3I0         TCGA-FV-A3R2         TCGA-FV-A3R3 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-FV-A495         TCGA-FV-A496         TCGA-FV-A4ZP 
"21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED"   "21Q LOSS MUTATED" 
        TCGA-FV-A4ZQ         TCGA-G3-A25S         TCGA-G3-A25T 
"21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-G3-A25U         TCGA-G3-A25V         TCGA-G3-A25W 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-G3-A25X         TCGA-G3-A25Y         TCGA-G3-A25Z 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" 
        TCGA-G3-A3CG         TCGA-G3-A3CH         TCGA-G3-A3CI 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK         TCGA-G3-A5SJ 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-G3-A5SK         TCGA-G3-A5SL         TCGA-G3-A5SM 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
  "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
  "21Q LOSS MUTATED"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-BC-A5W4 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-CC-5258         TCGA-CC-5260         TCGA-CC-5261 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-CC-5262         TCGA-CC-5263         TCGA-CC-A1HT 
  "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" 
        TCGA-CC-A3M9         TCGA-CC-A3MA         TCGA-CC-A3MB 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" 
        TCGA-CC-A3MC         TCGA-DD-A113         TCGA-DD-A114 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
  "21Q LOSS MUTATED"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" 
        TCGA-DD-A1EA         TCGA-DD-A1EB         TCGA-DD-A1EC 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-DD-A1ED         TCGA-DD-A1EE         TCGA-DD-A1EF 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-DD-A1EH         TCGA-DD-A1EI         TCGA-DD-A1EJ 
  "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" 
        TCGA-DD-A1EL         TCGA-DD-A39V         TCGA-DD-A39X 
  "21Q LOSS MUTATED"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-DD-A39Y         TCGA-DD-A39Z         TCGA-DD-A3A0 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" 
        TCGA-DD-A3A1         TCGA-DD-A3A2         TCGA-DD-A3A3 
  "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-DD-A3A4         TCGA-DD-A3A5         TCGA-DD-A3A6 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-DD-A3A7         TCGA-DD-A3A8         TCGA-DD-A3A9 
  "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" 
        TCGA-DD-A4NA         TCGA-DD-A4ND         TCGA-DD-A4NE 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-DD-A4NF         TCGA-DD-A4NG         TCGA-DD-A4NH 
"21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-DD-A4NI         TCGA-DD-A4NJ         TCGA-DD-A4NK 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-DD-A4NL         TCGA-DD-A4NN         TCGA-DD-A4NO 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-DD-A4NP         TCGA-DD-A4NQ         TCGA-ED-A459 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" 
        TCGA-ED-A5KG         TCGA-EP-A12J         TCGA-EP-A26S 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-EP-A2KA         TCGA-EP-A2KB         TCGA-EP-A2KC 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" 
        TCGA-EP-A3JL         TCGA-EP-A3RK         TCGA-ES-A2HS 
  "21Q LOSS MUTATED"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-ES-A2HT         TCGA-FV-A23B         TCGA-FV-A2QR 
"21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-FV-A3I0         TCGA-FV-A3R2         TCGA-FV-A3R3 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-FV-A495         TCGA-FV-A496         TCGA-FV-A4ZP 
"21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED"   "21Q LOSS MUTATED" 
        TCGA-FV-A4ZQ         TCGA-G3-A25S         TCGA-G3-A25T 
"21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-G3-A25U         TCGA-G3-A25V         TCGA-G3-A25W 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-G3-A25X         TCGA-G3-A25Y         TCGA-G3-A25Z 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" 
        TCGA-G3-A3CG         TCGA-G3-A3CH         TCGA-G3-A3CI 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK         TCGA-G3-A5SJ 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-G3-A5SK         TCGA-G3-A5SL         TCGA-G3-A5SM 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
  "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
  "21Q LOSS MUTATED"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-BC-A5W4 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-CC-5258         TCGA-CC-5260         TCGA-CC-5261 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-CC-5262         TCGA-CC-5263         TCGA-CC-A1HT 
  "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" 
        TCGA-CC-A3M9         TCGA-CC-A3MA         TCGA-CC-A3MB 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" 
        TCGA-CC-A3MC         TCGA-DD-A113         TCGA-DD-A114 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
  "21Q LOSS MUTATED"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" 
        TCGA-DD-A1EA         TCGA-DD-A1EB         TCGA-DD-A1EC 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-DD-A1ED         TCGA-DD-A1EE         TCGA-DD-A1EF 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-DD-A1EH         TCGA-DD-A1EI         TCGA-DD-A1EJ 
  "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" 
        TCGA-DD-A1EL         TCGA-DD-A39V         TCGA-DD-A39X 
  "21Q LOSS MUTATED"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-DD-A39Y         TCGA-DD-A39Z         TCGA-DD-A3A0 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" 
        TCGA-DD-A3A1         TCGA-DD-A3A2         TCGA-DD-A3A3 
  "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-DD-A3A4         TCGA-DD-A3A5         TCGA-DD-A3A6 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-DD-A3A7         TCGA-DD-A3A8         TCGA-DD-A3A9 
  "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" 
        TCGA-DD-A4NA         TCGA-DD-A4ND         TCGA-DD-A4NE 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-DD-A4NF         TCGA-DD-A4NG         TCGA-DD-A4NH 
"21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-DD-A4NI         TCGA-DD-A4NJ         TCGA-DD-A4NK 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-DD-A4NL         TCGA-DD-A4NN         TCGA-DD-A4NO 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-DD-A4NP         TCGA-DD-A4NQ         TCGA-ED-A459 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" 
        TCGA-ED-A5KG         TCGA-EP-A12J         TCGA-EP-A26S 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-EP-A2KA         TCGA-EP-A2KB         TCGA-EP-A2KC 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" 
        TCGA-EP-A3JL         TCGA-EP-A3RK         TCGA-ES-A2HS 
  "21Q LOSS MUTATED"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-ES-A2HT         TCGA-FV-A23B         TCGA-FV-A2QR 
"21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-FV-A3I0         TCGA-FV-A3R2         TCGA-FV-A3R3 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-FV-A495         TCGA-FV-A496         TCGA-FV-A4ZP 
"21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED"   "21Q LOSS MUTATED" 
        TCGA-FV-A4ZQ         TCGA-G3-A25S         TCGA-G3-A25T 
"21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-G3-A25U         TCGA-G3-A25V         TCGA-G3-A25W 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-G3-A25X         TCGA-G3-A25Y         TCGA-G3-A25Z 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" 
        TCGA-G3-A3CG         TCGA-G3-A3CH         TCGA-G3-A3CI 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK         TCGA-G3-A5SJ 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-G3-A5SK         TCGA-G3-A5SL         TCGA-G3-A5SM 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
[1] "hr=" "1.8"
D78V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  21Q LOSS MUTATED         8        4         1          8          1
  21Q LOSS WILD-TYPE      37       21         1         17          2
                    vv
clus                 STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  21Q LOSS MUTATED            2        1         1         1
  21Q LOSS WILD-TYPE          2        0         0         0
D78V3, multiclass
                    vv
clus                 T1 T2 T3 T4
  21Q LOSS MUTATED   10  5 12  2
  21Q LOSS WILD-TYPE 38 23 22  4
D78V4, multiclass
    clus
vv   21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  T1               10                 38
  T2                5                 23
  T3               12                 22
  T4                2                  4
D78V5, binary
                    cls
clus                  0  1
  21Q LOSS MUTATED   16  2
  21Q LOSS WILD-TYPE 58  1
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED     16    2
  21Q LOSS WILD-TYPE   58    1
   clus
vv  21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  0               16                 58
  1                2                  1
                    vv
clus                 M0 M1 MX
  21Q LOSS MUTATED   21  2  6
  21Q LOSS WILD-TYPE 69  0 19
D78V6, multiclass
    clus
vv   21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  M0               21                 69
  M1                2                  0
  MX                6                 19
D78V7, binary
                    cls
clus                  0  1
  21Q LOSS MUTATED    5 24
  21Q LOSS WILD-TYPE 39 49
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED      5   24
  21Q LOSS WILD-TYPE   39   49
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  FEMALE                5                 39
  MALE                 24                 49
                    vv
clus                 R0 R1 R2 RX
  21Q LOSS MUTATED   20  3  1  1
  21Q LOSS WILD-TYPE 73  7  0  7
D78V8, multiclass
    clus
vv   21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  R0               20                 73
  R1                3                  7
  R2                1                  0
  RX                1                  7

Clustering(79) Variable = 22Q LOSS MUTATION ANALYSIS
D79V1, survival
                    sevent
clus2                 0  1
  22Q LOSS MUTATED   11  8
  22Q LOSS WILD-TYPE 50 45
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                19                 95 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                 8                 45 
$`22Q LOSS MUTATED`
TCGA-BC-A10Q TCGA-BC-A10T TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A5W4 TCGA-CC-5260 
       37.32        27.52        13.81         0.26         9.50         2.86 
TCGA-CC-A1HT TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A39X TCGA-DD-A3A6 TCGA-DD-A4NJ 
        3.32        79.73        37.74        55.66       107.11        15.06 
TCGA-DD-A4NO TCGA-DD-A4NP TCGA-ED-A459 TCGA-EP-A2KB TCGA-FV-A4ZP TCGA-G3-A25S 
       61.45        93.67         0.23         1.97        60.36         1.22 
TCGA-G3-A25T 
       51.02 

$`22Q LOSS WILD-TYPE`
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10U TCGA-BC-A10W 
       48.99        27.91        10.13        46.78        27.52         2.99 
TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A216 
       25.32        23.34         1.12        69.57         5.03        44.42 
TCGA-BC-A3KG TCGA-CC-5258 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A3M9 
       16.37         0.07         3.02         3.39         4.24         0.10 
TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 
        0.07         0.10         0.13        83.57        53.29       112.96 
TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 
        7.33         2.60         0.46        21.76        51.25        90.67 
TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EF 
       79.36        66.31        19.76        75.65         6.67        12.95 
TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39Y 
       49.15         6.02        29.16        13.64        21.14         5.59 
TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 
       19.73        25.81         7.66        70.06        17.59        20.12 
TCGA-DD-A3A5 TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4ND 
      102.74        13.78         0.36        30.58        33.14        73.38 
TCGA-DD-A4NE TCGA-DD-A4NF TCGA-DD-A4NG TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NK 
       21.67        14.07        14.93        14.24        10.78        39.75 
TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NQ TCGA-ED-A5KG TCGA-EP-A12J TCGA-EP-A26S 
       56.25        29.56        12.26         0.20        10.85         7.76 
TCGA-EP-A2KA TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT 
       11.74         0.62         3.19         0.43        23.01        14.40 
TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 
       32.45        19.07         0.20         6.35         0.13         0.03 
TCGA-FV-A496 TCGA-FV-A4ZQ TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25X 
        0.33         0.39        53.79        28.27        30.71        58.49 
TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ 
       14.86        21.53        22.13        25.64         5.88        19.53 
TCGA-G3-A3CK TCGA-G3-A5SJ TCGA-G3-A5SK TCGA-G3-A5SL TCGA-G3-A5SM 
       19.23        11.97         9.93         7.99         4.37 

  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
              0.23               0.03 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
            107.11             112.96 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
             27.52              14.93 
[1] "0.2 - 107.1 (27.5)" "0.0 - 113.0 (14.9)"
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-BC-A5W4 
  "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" 
        TCGA-CC-5258         TCGA-CC-5260         TCGA-CC-5261 
"22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" 
        TCGA-CC-5262         TCGA-CC-5263         TCGA-CC-A1HT 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" 
        TCGA-CC-A3M9         TCGA-CC-A3MA         TCGA-CC-A3MB 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-CC-A3MC         TCGA-DD-A113         TCGA-DD-A114 
"22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED"   "22Q LOSS MUTATED" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-DD-A1EA         TCGA-DD-A1EB         TCGA-DD-A1EC 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-DD-A1ED         TCGA-DD-A1EE         TCGA-DD-A1EF 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-DD-A1EH         TCGA-DD-A1EI         TCGA-DD-A1EJ 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-DD-A1EL         TCGA-DD-A39V         TCGA-DD-A39X 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" 
        TCGA-DD-A39Y         TCGA-DD-A39Z         TCGA-DD-A3A0 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-DD-A3A1         TCGA-DD-A3A2         TCGA-DD-A3A3 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-DD-A3A4         TCGA-DD-A3A5         TCGA-DD-A3A6 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" 
        TCGA-DD-A3A7         TCGA-DD-A3A8         TCGA-DD-A3A9 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-DD-A4NA         TCGA-DD-A4ND         TCGA-DD-A4NE 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-DD-A4NF         TCGA-DD-A4NG         TCGA-DD-A4NH 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-DD-A4NI         TCGA-DD-A4NJ         TCGA-DD-A4NK 
"22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" 
        TCGA-DD-A4NL         TCGA-DD-A4NN         TCGA-DD-A4NO 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" 
        TCGA-DD-A4NP         TCGA-DD-A4NQ         TCGA-ED-A459 
  "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" 
        TCGA-ED-A5KG         TCGA-EP-A12J         TCGA-EP-A26S 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-EP-A2KA         TCGA-EP-A2KB         TCGA-EP-A2KC 
"22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" 
        TCGA-EP-A3JL         TCGA-EP-A3RK         TCGA-ES-A2HS 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-ES-A2HT         TCGA-FV-A23B         TCGA-FV-A2QR 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-FV-A3I0         TCGA-FV-A3R2         TCGA-FV-A3R3 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-FV-A495         TCGA-FV-A496         TCGA-FV-A4ZP 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" 
        TCGA-FV-A4ZQ         TCGA-G3-A25S         TCGA-G3-A25T 
"22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED"   "22Q LOSS MUTATED" 
        TCGA-G3-A25U         TCGA-G3-A25V         TCGA-G3-A25W 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-G3-A25X         TCGA-G3-A25Y         TCGA-G3-A25Z 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-G3-A3CG         TCGA-G3-A3CH         TCGA-G3-A3CI 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK         TCGA-G3-A5SJ 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-G3-A5SK         TCGA-G3-A5SL         TCGA-G3-A5SM 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-BC-A5W4 
  "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" 
        TCGA-CC-5258         TCGA-CC-5260         TCGA-CC-5261 
"22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" 
        TCGA-CC-5262         TCGA-CC-5263         TCGA-CC-A1HT 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" 
        TCGA-CC-A3M9         TCGA-CC-A3MA         TCGA-CC-A3MB 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-CC-A3MC         TCGA-DD-A113         TCGA-DD-A114 
"22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED"   "22Q LOSS MUTATED" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-DD-A1EA         TCGA-DD-A1EB         TCGA-DD-A1EC 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-DD-A1ED         TCGA-DD-A1EE         TCGA-DD-A1EF 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-DD-A1EH         TCGA-DD-A1EI         TCGA-DD-A1EJ 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-DD-A1EL         TCGA-DD-A39V         TCGA-DD-A39X 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" 
        TCGA-DD-A39Y         TCGA-DD-A39Z         TCGA-DD-A3A0 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-DD-A3A1         TCGA-DD-A3A2         TCGA-DD-A3A3 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-DD-A3A4         TCGA-DD-A3A5         TCGA-DD-A3A6 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" 
        TCGA-DD-A3A7         TCGA-DD-A3A8         TCGA-DD-A3A9 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-DD-A4NA         TCGA-DD-A4ND         TCGA-DD-A4NE 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-DD-A4NF         TCGA-DD-A4NG         TCGA-DD-A4NH 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-DD-A4NI         TCGA-DD-A4NJ         TCGA-DD-A4NK 
"22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" 
        TCGA-DD-A4NL         TCGA-DD-A4NN         TCGA-DD-A4NO 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" 
        TCGA-DD-A4NP         TCGA-DD-A4NQ         TCGA-ED-A459 
  "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" 
        TCGA-ED-A5KG         TCGA-EP-A12J         TCGA-EP-A26S 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-EP-A2KA         TCGA-EP-A2KB         TCGA-EP-A2KC 
"22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" 
        TCGA-EP-A3JL         TCGA-EP-A3RK         TCGA-ES-A2HS 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-ES-A2HT         TCGA-FV-A23B         TCGA-FV-A2QR 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-FV-A3I0         TCGA-FV-A3R2         TCGA-FV-A3R3 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-FV-A495         TCGA-FV-A496         TCGA-FV-A4ZP 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" 
        TCGA-FV-A4ZQ         TCGA-G3-A25S         TCGA-G3-A25T 
"22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED"   "22Q LOSS MUTATED" 
        TCGA-G3-A25U         TCGA-G3-A25V         TCGA-G3-A25W 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-G3-A25X         TCGA-G3-A25Y         TCGA-G3-A25Z 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-G3-A3CG         TCGA-G3-A3CH         TCGA-G3-A3CI 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK         TCGA-G3-A5SJ 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-G3-A5SK         TCGA-G3-A5SL         TCGA-G3-A5SM 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-BC-A5W4 
  "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" 
        TCGA-CC-5258         TCGA-CC-5260         TCGA-CC-5261 
"22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" 
        TCGA-CC-5262         TCGA-CC-5263         TCGA-CC-A1HT 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" 
        TCGA-CC-A3M9         TCGA-CC-A3MA         TCGA-CC-A3MB 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-CC-A3MC         TCGA-DD-A113         TCGA-DD-A114 
"22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED"   "22Q LOSS MUTATED" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-DD-A1EA         TCGA-DD-A1EB         TCGA-DD-A1EC 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-DD-A1ED         TCGA-DD-A1EE         TCGA-DD-A1EF 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-DD-A1EH         TCGA-DD-A1EI         TCGA-DD-A1EJ 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-DD-A1EL         TCGA-DD-A39V         TCGA-DD-A39X 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" 
        TCGA-DD-A39Y         TCGA-DD-A39Z         TCGA-DD-A3A0 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-DD-A3A1         TCGA-DD-A3A2         TCGA-DD-A3A3 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-DD-A3A4         TCGA-DD-A3A5         TCGA-DD-A3A6 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" 
        TCGA-DD-A3A7         TCGA-DD-A3A8         TCGA-DD-A3A9 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-DD-A4NA         TCGA-DD-A4ND         TCGA-DD-A4NE 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-DD-A4NF         TCGA-DD-A4NG         TCGA-DD-A4NH 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-DD-A4NI         TCGA-DD-A4NJ         TCGA-DD-A4NK 
"22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" 
        TCGA-DD-A4NL         TCGA-DD-A4NN         TCGA-DD-A4NO 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" 
        TCGA-DD-A4NP         TCGA-DD-A4NQ         TCGA-ED-A459 
  "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" 
        TCGA-ED-A5KG         TCGA-EP-A12J         TCGA-EP-A26S 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-EP-A2KA         TCGA-EP-A2KB         TCGA-EP-A2KC 
"22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" 
        TCGA-EP-A3JL         TCGA-EP-A3RK         TCGA-ES-A2HS 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-ES-A2HT         TCGA-FV-A23B         TCGA-FV-A2QR 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-FV-A3I0         TCGA-FV-A3R2         TCGA-FV-A3R3 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-FV-A495         TCGA-FV-A496         TCGA-FV-A4ZP 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" 
        TCGA-FV-A4ZQ         TCGA-G3-A25S         TCGA-G3-A25T 
"22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED"   "22Q LOSS MUTATED" 
        TCGA-G3-A25U         TCGA-G3-A25V         TCGA-G3-A25W 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-G3-A25X         TCGA-G3-A25Y         TCGA-G3-A25Z 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-G3-A3CG         TCGA-G3-A3CH         TCGA-G3-A3CI 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK         TCGA-G3-A5SJ 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-G3-A5SK         TCGA-G3-A5SL         TCGA-G3-A5SM 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
[1] "hr=" "1.6"
D79V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  22Q LOSS MUTATED         6        6         0          4          0
  22Q LOSS WILD-TYPE      39       19         2         21          3
                    vv
clus                 STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  22Q LOSS MUTATED            1        0         0         0
  22Q LOSS WILD-TYPE          3        1         1         1
D79V3, multiclass
                    vv
clus                 T1 T2 T3 T4
  22Q LOSS MUTATED    6  7  4  2
  22Q LOSS WILD-TYPE 42 21 30  4
D79V4, multiclass
    clus
vv   22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  T1                6                 42
  T2                7                 21
  T3                4                 30
  T4                2                  4
D79V5, binary
                    cls
clus                  0  1
  22Q LOSS MUTATED   11  0
  22Q LOSS WILD-TYPE 63  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED     11    0
  22Q LOSS WILD-TYPE   63    3
   clus
vv  22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  0               11                 63
  1                0                  3
                    vv
clus                 M0 M1 MX
  22Q LOSS MUTATED   17  0  3
  22Q LOSS WILD-TYPE 73  2 22
D79V6, multiclass
    clus
vv   22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  M0               17                 73
  M1                0                  2
  MX                3                 22
D79V7, binary
                    cls
clus                  0  1
  22Q LOSS MUTATED   10 10
  22Q LOSS WILD-TYPE 34 63
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED     10   10
  22Q LOSS WILD-TYPE   34   63
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  FEMALE               10                 34
  MALE                 10                 63
                    vv
clus                 R0 R1 R2 RX
  22Q LOSS MUTATED   12  5  0  2
  22Q LOSS WILD-TYPE 81  5  1  6
D79V8, multiclass
    clus
vv   22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  R0               12                 81
  R1                5                  5
  R2                0                  1
  RX                2                  6

Clustering(80) Variable = XQ LOSS MUTATION ANALYSIS
D80V1, survival
                   sevent
clus2                0  1
  XQ LOSS MUTATED    8  8
  XQ LOSS WILD-TYPE 53 45
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               16                98 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
                8                45 
$`XQ LOSS MUTATED`
TCGA-BC-A10R TCGA-BC-A112 TCGA-BC-A217 TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-CC-5263 
       10.13         5.03        13.81        16.37         9.50         4.24 
TCGA-CC-A3MA TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A11B TCGA-DD-A4NA 
        0.07        37.74        83.57        53.29         0.46        33.14 
TCGA-DD-A4NO TCGA-ED-A459 TCGA-FV-A2QR TCGA-FV-A3I0 
       61.45         0.23        19.07         0.20 

$`XQ LOSS WILD-TYPE`
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U 
       48.99        27.91        37.32        46.78        27.52        27.52 
TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A216 
        2.99        25.32        23.34         1.12        69.57        44.42 
TCGA-BC-A3KF TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-A1HT 
        0.26         0.07         2.86         3.02         3.39         3.32 
TCGA-CC-A3M9 TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A113 TCGA-DD-A118 TCGA-DD-A119 
        0.10         0.10         0.13        79.73       112.96         7.33 
TCGA-DD-A11A TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB 
        2.60        21.76        51.25        90.67        79.36        66.31 
TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EH TCGA-DD-A1EI 
       19.76        75.65         6.67        12.95        49.15         6.02 
TCGA-DD-A1EJ TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A39Z 
       29.16        13.64        21.14        55.66         5.59        19.73 
TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 
       25.81         7.66        70.06        17.59        20.12       102.74 
TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A3A9 TCGA-DD-A4ND TCGA-DD-A4NE 
      107.11        13.78         0.36        30.58        73.38        21.67 
TCGA-DD-A4NF TCGA-DD-A4NG TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK 
       14.07        14.93        14.24        10.78        15.06        39.75 
TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-ED-A5KG TCGA-EP-A12J 
       56.25        29.56        93.67        12.26         0.20        10.85 
TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK 
        7.76        11.74         1.97         0.62         3.19         0.43 
TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 
       23.01        14.40        32.45         6.35         0.13         0.03 
TCGA-FV-A496 TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25U 
        0.33        60.36         0.39         1.22        51.02        53.79 
TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG 
       28.27        30.71        58.49        14.86        21.53        22.13 
TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SJ TCGA-G3-A5SK 
       25.64         5.88        19.53        19.23        11.97         9.93 
TCGA-G3-A5SL TCGA-G3-A5SM 
        7.99         4.37 

  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
             0.07              0.03 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
            83.57            112.96 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
            11.97             18.41 
[1] "0.1 - 83.6 (12.0)"  "0.0 - 113.0 (18.4)"
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE"   "XQ LOSS MUTATED" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
  "XQ LOSS MUTATED" "XQ LOSS WILD-TYPE"   "XQ LOSS MUTATED" "XQ LOSS WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-BC-A5W4        TCGA-CC-5258        TCGA-CC-5260 
  "XQ LOSS MUTATED"   "XQ LOSS MUTATED" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-CC-5261        TCGA-CC-5262        TCGA-CC-5263        TCGA-CC-A1HT 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE"   "XQ LOSS MUTATED" "XQ LOSS WILD-TYPE" 
       TCGA-CC-A3M9        TCGA-CC-A3MA        TCGA-CC-A3MB        TCGA-CC-A3MC 
"XQ LOSS WILD-TYPE"   "XQ LOSS MUTATED" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DD-A113        TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116 
"XQ LOSS WILD-TYPE"   "XQ LOSS MUTATED"   "XQ LOSS MUTATED"   "XQ LOSS MUTATED" 
       TCGA-DD-A118        TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE"   "XQ LOSS MUTATED" 
       TCGA-DD-A11C        TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EA 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DD-A1EB        TCGA-DD-A1EC        TCGA-DD-A1ED        TCGA-DD-A1EE 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DD-A1EF        TCGA-DD-A1EH        TCGA-DD-A1EI        TCGA-DD-A1EJ 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DD-A1EL        TCGA-DD-A39V        TCGA-DD-A39X        TCGA-DD-A39Y 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DD-A39Z        TCGA-DD-A3A0        TCGA-DD-A3A1        TCGA-DD-A3A2 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DD-A3A3        TCGA-DD-A3A4        TCGA-DD-A3A5        TCGA-DD-A3A6 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DD-A3A7        TCGA-DD-A3A8        TCGA-DD-A3A9        TCGA-DD-A4NA 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE"   "XQ LOSS MUTATED" 
       TCGA-DD-A4ND        TCGA-DD-A4NE        TCGA-DD-A4NF        TCGA-DD-A4NG 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DD-A4NH        TCGA-DD-A4NI        TCGA-DD-A4NJ        TCGA-DD-A4NK 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DD-A4NL        TCGA-DD-A4NN        TCGA-DD-A4NO        TCGA-DD-A4NP 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE"   "XQ LOSS MUTATED" "XQ LOSS WILD-TYPE" 
       TCGA-DD-A4NQ        TCGA-ED-A459        TCGA-ED-A5KG        TCGA-EP-A12J 
"XQ LOSS WILD-TYPE"   "XQ LOSS MUTATED" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EP-A3JL        TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-FV-A23B        TCGA-FV-A2QR        TCGA-FV-A3I0        TCGA-FV-A3R2 
"XQ LOSS WILD-TYPE"   "XQ LOSS MUTATED"   "XQ LOSS MUTATED" "XQ LOSS WILD-TYPE" 
       TCGA-FV-A3R3        TCGA-FV-A495        TCGA-FV-A496        TCGA-FV-A4ZP 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-FV-A4ZQ        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-G3-A3CJ        TCGA-G3-A3CK        TCGA-G3-A5SJ        TCGA-G3-A5SK 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-G3-A5SL        TCGA-G3-A5SM 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE"   "XQ LOSS MUTATED" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
  "XQ LOSS MUTATED" "XQ LOSS WILD-TYPE"   "XQ LOSS MUTATED" "XQ LOSS WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-BC-A5W4        TCGA-CC-5258        TCGA-CC-5260 
  "XQ LOSS MUTATED"   "XQ LOSS MUTATED" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-CC-5261        TCGA-CC-5262        TCGA-CC-5263        TCGA-CC-A1HT 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE"   "XQ LOSS MUTATED" "XQ LOSS WILD-TYPE" 
       TCGA-CC-A3M9        TCGA-CC-A3MA        TCGA-CC-A3MB        TCGA-CC-A3MC 
"XQ LOSS WILD-TYPE"   "XQ LOSS MUTATED" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DD-A113        TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116 
"XQ LOSS WILD-TYPE"   "XQ LOSS MUTATED"   "XQ LOSS MUTATED"   "XQ LOSS MUTATED" 
       TCGA-DD-A118        TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE"   "XQ LOSS MUTATED" 
       TCGA-DD-A11C        TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EA 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DD-A1EB        TCGA-DD-A1EC        TCGA-DD-A1ED        TCGA-DD-A1EE 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DD-A1EF        TCGA-DD-A1EH        TCGA-DD-A1EI        TCGA-DD-A1EJ 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DD-A1EL        TCGA-DD-A39V        TCGA-DD-A39X        TCGA-DD-A39Y 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DD-A39Z        TCGA-DD-A3A0        TCGA-DD-A3A1        TCGA-DD-A3A2 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DD-A3A3        TCGA-DD-A3A4        TCGA-DD-A3A5        TCGA-DD-A3A6 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DD-A3A7        TCGA-DD-A3A8        TCGA-DD-A3A9        TCGA-DD-A4NA 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE"   "XQ LOSS MUTATED" 
       TCGA-DD-A4ND        TCGA-DD-A4NE        TCGA-DD-A4NF        TCGA-DD-A4NG 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DD-A4NH        TCGA-DD-A4NI        TCGA-DD-A4NJ        TCGA-DD-A4NK 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DD-A4NL        TCGA-DD-A4NN        TCGA-DD-A4NO        TCGA-DD-A4NP 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE"   "XQ LOSS MUTATED" "XQ LOSS WILD-TYPE" 
       TCGA-DD-A4NQ        TCGA-ED-A459        TCGA-ED-A5KG        TCGA-EP-A12J 
"XQ LOSS WILD-TYPE"   "XQ LOSS MUTATED" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EP-A3JL        TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-FV-A23B        TCGA-FV-A2QR        TCGA-FV-A3I0        TCGA-FV-A3R2 
"XQ LOSS WILD-TYPE"   "XQ LOSS MUTATED"   "XQ LOSS MUTATED" "XQ LOSS WILD-TYPE" 
       TCGA-FV-A3R3        TCGA-FV-A495        TCGA-FV-A496        TCGA-FV-A4ZP 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-FV-A4ZQ        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-G3-A3CJ        TCGA-G3-A3CK        TCGA-G3-A5SJ        TCGA-G3-A5SK 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-G3-A5SL        TCGA-G3-A5SM 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE"   "XQ LOSS MUTATED" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
  "XQ LOSS MUTATED" "XQ LOSS WILD-TYPE"   "XQ LOSS MUTATED" "XQ LOSS WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-BC-A5W4        TCGA-CC-5258        TCGA-CC-5260 
  "XQ LOSS MUTATED"   "XQ LOSS MUTATED" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-CC-5261        TCGA-CC-5262        TCGA-CC-5263        TCGA-CC-A1HT 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE"   "XQ LOSS MUTATED" "XQ LOSS WILD-TYPE" 
       TCGA-CC-A3M9        TCGA-CC-A3MA        TCGA-CC-A3MB        TCGA-CC-A3MC 
"XQ LOSS WILD-TYPE"   "XQ LOSS MUTATED" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DD-A113        TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116 
"XQ LOSS WILD-TYPE"   "XQ LOSS MUTATED"   "XQ LOSS MUTATED"   "XQ LOSS MUTATED" 
       TCGA-DD-A118        TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE"   "XQ LOSS MUTATED" 
       TCGA-DD-A11C        TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EA 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DD-A1EB        TCGA-DD-A1EC        TCGA-DD-A1ED        TCGA-DD-A1EE 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DD-A1EF        TCGA-DD-A1EH        TCGA-DD-A1EI        TCGA-DD-A1EJ 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DD-A1EL        TCGA-DD-A39V        TCGA-DD-A39X        TCGA-DD-A39Y 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DD-A39Z        TCGA-DD-A3A0        TCGA-DD-A3A1        TCGA-DD-A3A2 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DD-A3A3        TCGA-DD-A3A4        TCGA-DD-A3A5        TCGA-DD-A3A6 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DD-A3A7        TCGA-DD-A3A8        TCGA-DD-A3A9        TCGA-DD-A4NA 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE"   "XQ LOSS MUTATED" 
       TCGA-DD-A4ND        TCGA-DD-A4NE        TCGA-DD-A4NF        TCGA-DD-A4NG 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DD-A4NH        TCGA-DD-A4NI        TCGA-DD-A4NJ        TCGA-DD-A4NK 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DD-A4NL        TCGA-DD-A4NN        TCGA-DD-A4NO        TCGA-DD-A4NP 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE"   "XQ LOSS MUTATED" "XQ LOSS WILD-TYPE" 
       TCGA-DD-A4NQ        TCGA-ED-A459        TCGA-ED-A5KG        TCGA-EP-A12J 
"XQ LOSS WILD-TYPE"   "XQ LOSS MUTATED" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EP-A3JL        TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-FV-A23B        TCGA-FV-A2QR        TCGA-FV-A3I0        TCGA-FV-A3R2 
"XQ LOSS WILD-TYPE"   "XQ LOSS MUTATED"   "XQ LOSS MUTATED" "XQ LOSS WILD-TYPE" 
       TCGA-FV-A3R3        TCGA-FV-A495        TCGA-FV-A496        TCGA-FV-A4ZP 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-FV-A4ZQ        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-G3-A3CJ        TCGA-G3-A3CK        TCGA-G3-A5SJ        TCGA-G3-A5SK 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-G3-A5SL        TCGA-G3-A5SM 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
[1] "hr=" "1.3"
D80V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  XQ LOSS MUTATED         3        5         0          5          0          1
  XQ LOSS WILD-TYPE      42       20         2         20          3          3
                   vv
clus                STAGE IV STAGE IVA STAGE IVB
  XQ LOSS MUTATED          0         0         0
  XQ LOSS WILD-TYPE        1         1         1
D80V3, multiclass
                   vv
clus                T1 T2 T3 T4
  XQ LOSS MUTATED    3  6  7  0
  XQ LOSS WILD-TYPE 45 22 27  6
D80V4, multiclass
    clus
vv   XQ LOSS MUTATED XQ LOSS WILD-TYPE
  T1               3                45
  T2               6                22
  T3               7                27
  T4               0                 6
D80V5, binary
                   cls
clus                 0  1
  XQ LOSS MUTATED    9  1
  XQ LOSS WILD-TYPE 65  2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED      9    1
  XQ LOSS WILD-TYPE   65    2
   clus
vv  XQ LOSS MUTATED XQ LOSS WILD-TYPE
  0               9                65
  1               1                 2
                   vv
clus                M0 M1 MX
  XQ LOSS MUTATED   14  0  2
  XQ LOSS WILD-TYPE 76  2 23
D80V6, multiclass
    clus
vv   XQ LOSS MUTATED XQ LOSS WILD-TYPE
  M0              14                76
  M1               0                 2
  MX               2                23
D80V7, binary
                   cls
clus                 0  1
  XQ LOSS MUTATED    5 11
  XQ LOSS WILD-TYPE 39 62
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED      5   11
  XQ LOSS WILD-TYPE   39   62
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  FEMALE               5                39
  MALE                11                62
                   vv
clus                R0 R1 R2 RX
  XQ LOSS MUTATED   12  1  0  3
  XQ LOSS WILD-TYPE 81  9  1  5
D80V8, multiclass
    clus
vv   XQ LOSS MUTATED XQ LOSS WILD-TYPE
  R0              12                81
  R1               1                 9
  R2               0                 1
  RX               3                 5
> q(save="no")
