
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/8278984/transformed.cor.cli.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/LIHC-TP/8142945/LIHC-TP.merged_data.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/Append_Data/LIHC-TP/8142945/LIHC-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/LIHC-TP/8278984/transformed.cor.cli.txt"

nPatients in clinical file=157, in cluster file=199, common to both=149
[1]  80 149
[1] "1P GAIN MUTATION ANALYSIS"
[1] 3
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               20               129 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               20               129 
[1] "1Q GAIN MUTATION ANALYSIS"
[1] 3
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               85                64 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               85                64 
[1] "2P GAIN MUTATION ANALYSIS"
[1] 3
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               24               125 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               24               125 
[1] "2Q GAIN MUTATION ANALYSIS"
[1] 3
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               19               130 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               19               130 
[1] "3P GAIN MUTATION ANALYSIS"
[1] 3
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               13               136 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               13               136 
[1] "3Q GAIN MUTATION ANALYSIS"
[1] 3
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               14               135 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               14               135 
[1] "4P GAIN MUTATION ANALYSIS"
[1] 3
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               12               137 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               12               137 
[1] "4Q GAIN MUTATION ANALYSIS"
[1] 3
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                4               145 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                4               145 
[1] "5P GAIN MUTATION ANALYSIS"
[1] 3
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               58                91 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               58                91 
[1] "5Q GAIN MUTATION ANALYSIS"
[1] 3
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               44               105 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               44               105 
[1] "6P GAIN MUTATION ANALYSIS"
[1] 3
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               39               110 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               39               110 
[1] "6Q GAIN MUTATION ANALYSIS"
[1] 3
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               21               128 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               21               128 
[1] "7P GAIN MUTATION ANALYSIS"
[1] 3
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               47               102 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               47               102 
[1] "7Q GAIN MUTATION ANALYSIS"
[1] 3
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               48               101 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               48               101 
[1] "8P GAIN MUTATION ANALYSIS"
[1] 3
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               28               121 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               28               121 
[1] "8Q GAIN MUTATION ANALYSIS"
[1] 3
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               74                75 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               74                75 
[1] "9P GAIN MUTATION ANALYSIS"
[1] 3
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
                6               143 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
                6               143 
[1] "9Q GAIN MUTATION ANALYSIS"
[1] 3
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
                6               143 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
                6               143 
[1] "10P GAIN MUTATION ANALYSIS"
[1] 3
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                21                128 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                21                128 
[1] "10Q GAIN MUTATION ANALYSIS"
[1] 3
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                13                136 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                13                136 
[1] "11P GAIN MUTATION ANALYSIS"
[1] 3
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                10                139 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                10                139 
[1] "11Q GAIN MUTATION ANALYSIS"
[1] 3
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 9                140 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 9                140 
[1] "12P GAIN MUTATION ANALYSIS"
[1] 3
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                14                135 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                14                135 
[1] "12Q GAIN MUTATION ANALYSIS"
[1] 3
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                18                131 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                18                131 
[1] "13Q GAIN MUTATION ANALYSIS"
[1] 3
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                 8                141 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                 8                141 
[1] "14Q GAIN MUTATION ANALYSIS"
[1] 3
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                 8                141 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                 8                141 
[1] "15Q GAIN MUTATION ANALYSIS"
[1] 3
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                14                135 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                14                135 
[1] "16P GAIN MUTATION ANALYSIS"
[1] 3
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                12                137 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                12                137 
[1] "16Q GAIN MUTATION ANALYSIS"
[1] 3
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                 5                144 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                 5                144 
[1] "17P GAIN MUTATION ANALYSIS"
[1] 3
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                13                136 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                13                136 
[1] "17Q GAIN MUTATION ANALYSIS"
[1] 3
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                39                110 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                39                110 
[1] "18P GAIN MUTATION ANALYSIS"
[1] 3
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                10                139 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                10                139 
[1] "18Q GAIN MUTATION ANALYSIS"
[1] 3
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 9                140 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 9                140 
[1] "19P GAIN MUTATION ANALYSIS"
[1] 3
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                30                119 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                30                119 
[1] "19Q GAIN MUTATION ANALYSIS"
[1] 3
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                34                115 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                34                115 
[1] "20P GAIN MUTATION ANALYSIS"
[1] 3
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                43                106 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                43                106 
[1] "20Q GAIN MUTATION ANALYSIS"
[1] 3
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                45                104 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                45                104 
[1] "21Q GAIN MUTATION ANALYSIS"
[1] 3
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                13                136 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                13                136 
[1] "22Q GAIN MUTATION ANALYSIS"
[1] 3
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                19                130 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                19                130 
[1] "XQ GAIN MUTATION ANALYSIS"
[1] 3
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               28               121 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               28               121 
[1] "1P LOSS MUTATION ANALYSIS"
[1] 3
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               37               112 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               37               112 
[1] "1Q LOSS MUTATION ANALYSIS"
[1] 3
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               11               138 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               11               138 
[1] "2P LOSS MUTATION ANALYSIS"
[1] 3
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               11               138 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               11               138 
[1] "2Q LOSS MUTATION ANALYSIS"
[1] 3
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               13               136 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               13               136 
[1] "3P LOSS MUTATION ANALYSIS"
[1] 3
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               19               130 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               19               130 
[1] "3Q LOSS MUTATION ANALYSIS"
[1] 3
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               10               139 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               10               139 
[1] "4P LOSS MUTATION ANALYSIS"
[1] 3
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               31               118 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               31               118 
[1] "4Q LOSS MUTATION ANALYSIS"
[1] 3
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               48               101 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               48               101 
[1] "5P LOSS MUTATION ANALYSIS"
[1] 3
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               10               139 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               10               139 
[1] "5Q LOSS MUTATION ANALYSIS"
[1] 3
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               14               135 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               14               135 
[1] "6P LOSS MUTATION ANALYSIS"
[1] 3
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               17               132 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               17               132 
[1] "6Q LOSS MUTATION ANALYSIS"
[1] 3
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               46               103 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               46               103 
[1] "7P LOSS MUTATION ANALYSIS"
[1] 3
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
                8               141 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
                8               141 
[1] "7Q LOSS MUTATION ANALYSIS"
[1] 3
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
               11               138 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
               11               138 
[1] "8P LOSS MUTATION ANALYSIS"
[1] 3
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               74                75 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               74                75 
[1] "8Q LOSS MUTATION ANALYSIS"
[1] 3
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               15               134 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               15               134 
[1] "9P LOSS MUTATION ANALYSIS"
[1] 3
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               46               103 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               46               103 
[1] "9Q LOSS MUTATION ANALYSIS"
[1] 3
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               48               101 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               48               101 
[1] "10P LOSS MUTATION ANALYSIS"
[1] 3
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                17                132 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                17                132 
[1] "10Q LOSS MUTATION ANALYSIS"
[1] 3
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                30                119 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                30                119 
[1] "11P LOSS MUTATION ANALYSIS"
[1] 3
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                24                125 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                24                125 
[1] "11Q LOSS MUTATION ANALYSIS"
[1] 3
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                27                122 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                27                122 
[1] "12P LOSS MUTATION ANALYSIS"
[1] 3
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                27                122 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                27                122 
[1] "12Q LOSS MUTATION ANALYSIS"
[1] 3
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                16                133 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                16                133 
[1] "13Q LOSS MUTATION ANALYSIS"
[1] 3
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                52                 97 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                52                 97 
[1] "14Q LOSS MUTATION ANALYSIS"
[1] 3
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                45                104 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                45                104 
[1] "15Q LOSS MUTATION ANALYSIS"
[1] 3
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                29                120 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                29                120 
[1] "16P LOSS MUTATION ANALYSIS"
[1] 3
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                42                107 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                42                107 
[1] "16Q LOSS MUTATION ANALYSIS"
[1] 3
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                53                 96 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                53                 96 
[1] "17P LOSS MUTATION ANALYSIS"
[1] 3
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                75                 74 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                75                 74 
[1] "17Q LOSS MUTATION ANALYSIS"
[1] 3
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                19                130 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                19                130 
[1] "18P LOSS MUTATION ANALYSIS"
[1] 3
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                27                122 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                27                122 
[1] "18Q LOSS MUTATION ANALYSIS"
[1] 3
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                30                119 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                30                119 
[1] "19P LOSS MUTATION ANALYSIS"
[1] 3
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                16                133 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                16                133 
[1] "19Q LOSS MUTATION ANALYSIS"
[1] 3
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                11                138 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                11                138 
[1] "20P LOSS MUTATION ANALYSIS"
[1] 3
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                 8                141 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                 8                141 
[1] "20Q LOSS MUTATION ANALYSIS"
[1] 3
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 4                145 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 4                145 
[1] "21Q LOSS MUTATION ANALYSIS"
[1] 3
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                40                109 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                40                109 
[1] "22Q LOSS MUTATION ANALYSIS"
[1] 3
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                31                118 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                31                118 
[1] "XQ LOSS MUTATION ANALYSIS"
[1] 3
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               20               129 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               20               129 
[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] "GLEASON_SCORE"                         
[19] "PSA_VALUE"                             
[20] "DAYS_TO_PSA"                           
[21] "BATCHNUMBER"                           

Input Data has 21 rows and 149 columns.

[1] "Batch" "21"   
[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          421            8          680          289 
TCGA-BC-A69H TCGA-BC-A69I TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 
         120           16            2           NA           12           NA 
TCGA-CC-5263 TCGA-CC-5264 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB 
          NA           NA           NA            3            2            3 
TCGA-CC-A3MC TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 
           4         2425           NA           NA           NA         3437 
TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 
          NA           79           NA          662           NA           NA 
TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EF 
        2415         2017          602         2301          204           NA 
TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A1EL 
          NA         1495          183          887           NA           NA 
TCGA-DD-A39V TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 
          NA           NA           NA           NA           NA           NA 
TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 
          NA           NA           NA           NA           NA           NA 
TCGA-DD-A3A8 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NF 
          NA           NA         1008          391         2232          428 
TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN 
         433          561          458           NA         1711           NA 
TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV 
        1869         2849           NA           NA           NA         2018 
TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F 
         334           NA          230          334           44          843 
TCGA-DD-A73G TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X 
        3071          408          386          482          423          406 
TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XP TCGA-ED-A82E 
           7            6            6            6            6            6 
TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL 
         570          608          357          334           NA          303 
TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A2QR 
         363           NA           NA          987           NA           NA 
TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 
           6           NA           NA            4            1           10 
TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V 
        1836           12           37         1553         1636          860 
TCGA-G3-A25W TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CH 
         935         1779           NA          655          673          780 
TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SL 
         180          594          585          447          364          243 
TCGA-G3-A5SM TCGA-G3-A6UC TCGA-GJ-A6C0 TCGA-K7-A6G5 TCGA-LG-A6GG TCGA-MI-A75C 
         133          236           NA          122           15          291 
TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75I TCGA-NI-A4U2 TCGA-O8-A75V 
         155          433          265           NA          135 
Variable 1:'AGE':	nDistinctValues=50,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYSTODEATH':	nDistinctValues=62,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'DAYSTOLASTFOLLOWUP':	nDistinctValues=80,	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=18,	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=3,	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:'GLEASON_SCORE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 19:'PSA_VALUE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 20:'DAYS_TO_PSA':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 21:'BATCH.NUMBER':	nDistinctValues=14,	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 149 columns, 1 survival variables, and 7 non-survival variables.
AGE, nv=50, 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 
61 40 40  8 
[1] "table(vv)"
vv
T1 T2 T3 T4 
61 40 40  8 
$ClinVariableName
[1] "PATHOLOGY.T.STAGE"

$Table
vv
T1 T2 T3 T4 
61 40 40  8 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


T1 T2 T3 T4 
61 40 40  8 
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   12  8
  1P GAIN WILD-TYPE 72 55
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               20               127 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
                8                55 
$`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        37.78 
TCGA-DD-A11A TCGA-DD-A1EG TCGA-DD-A39Y TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-ED-A459 
        2.60        45.11         5.62        18.44        15.06        13.41 
TCGA-ED-A4XI TCGA-ED-A7PZ TCGA-EP-A12J TCGA-EP-A26S TCGA-ES-A2HT TCGA-G3-A25W 
       12.69         0.20        18.74        19.99        14.40        30.74 
TCGA-G3-A3CJ TCGA-G3-A5SJ 
       19.53        11.97 

$`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        13.84         0.26 
TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69H TCGA-BC-A69I TCGA-CC-5258 TCGA-CC-5260 
       22.36         9.50         3.95         0.53         0.07         2.86 
TCGA-CC-5261 TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB 
        0.39         4.24         3.32         0.10         0.07         0.10 
TCGA-CC-A3MC TCGA-DD-A113 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 
        0.13        79.73        83.57        53.33       113.00         7.33 
TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB 
        0.46        21.76        51.29        90.71        79.40        66.31 
TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EH TCGA-DD-A1EI 
       19.79        75.65         6.71        12.95        49.15         6.02 
TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39X TCGA-DD-A39Z 
       29.16        18.35        13.64        21.14        55.69        19.76 
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-A4NB 
      107.11        13.78         0.36        30.61        33.14        12.85 
TCGA-DD-A4ND TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN 
       73.38        14.07        14.24        39.78        56.25        29.56 
TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV 
       61.45        93.67        12.26         0.30        80.75        66.35 
TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F 
       10.98         9.30         7.56        10.98         1.45        27.72 
TCGA-DD-A73G TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PX 
      100.96        15.85        13.91        13.35         0.23         0.20 
TCGA-ED-A7PY TCGA-ED-A7XP TCGA-ED-A82E TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC 
        0.20         0.20         0.20        11.74        10.98         0.62 
TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-A3I0 
        9.96        11.93        22.85        32.45        19.10         0.20 
TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZP 
        8.12         6.38         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-A25X 
        0.39         1.22        51.06        53.79        28.27        58.49 
TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CK 
       14.86        21.53        22.13        25.64         5.92        19.23 
TCGA-G3-A5SI TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A6UC TCGA-GJ-A6C0 TCGA-K7-A6G5 
       14.70         7.99         4.37         7.76         1.02         4.01 
TCGA-LG-A6GG TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75I TCGA-NI-A4U2 
        0.49         9.57         5.10        14.24         8.71        58.88 
TCGA-O8-A75V 
        4.44 

  1P GAIN MUTATED 1P GAIN WILD-TYPE 
             0.20              0.03 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
            45.11            113.00 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
            16.75             13.84 
[1] "0.2 - 45.1 (16.8)"  "0.0 - 113.0 (13.8)"
       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-BC-A69H        TCGA-BC-A69I 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CC-5258        TCGA-CC-5260        TCGA-CC-5261        TCGA-CC-5262 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE"   "1P GAIN MUTATED" 
       TCGA-CC-5263        TCGA-CC-A1HT        TCGA-CC-A3M9        TCGA-CC-A3MA 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CC-A3MB        TCGA-CC-A3MC        TCGA-DD-A113        TCGA-DD-A114 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE"   "1P GAIN MUTATED" 
       TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118        TCGA-DD-A119 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C        TCGA-DD-A11D 
  "1P GAIN MUTATED" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB        TCGA-DD-A1EC 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EF        TCGA-DD-A1EG 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE"   "1P GAIN MUTATED" 
       TCGA-DD-A1EH        TCGA-DD-A1EI        TCGA-DD-A1EJ        TCGA-DD-A1EK 
"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-A4NB        TCGA-DD-A4ND        TCGA-DD-A4NF        TCGA-DD-A4NH 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DD-A4NI        TCGA-DD-A4NJ        TCGA-DD-A4NK        TCGA-DD-A4NL 
  "1P GAIN MUTATED"   "1P GAIN MUTATED" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DD-A4NN        TCGA-DD-A4NO        TCGA-DD-A4NP        TCGA-DD-A4NQ 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DD-A4NR        TCGA-DD-A4NS        TCGA-DD-A4NV        TCGA-DD-A73A 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DD-A73B        TCGA-DD-A73C        TCGA-DD-A73D        TCGA-DD-A73E 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DD-A73F        TCGA-DD-A73G        TCGA-ED-A459        TCGA-ED-A4XI 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE"   "1P GAIN MUTATED"   "1P GAIN MUTATED" 
       TCGA-ED-A5KG        TCGA-ED-A627        TCGA-ED-A66X        TCGA-ED-A66Y 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-ED-A7PX        TCGA-ED-A7PY        TCGA-ED-A7PZ        TCGA-ED-A7XP 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE"   "1P GAIN MUTATED" "1P GAIN WILD-TYPE" 
       TCGA-ED-A82E        TCGA-EP-A12J        TCGA-EP-A26S        TCGA-EP-A2KA 
"1P GAIN WILD-TYPE"   "1P GAIN MUTATED"   "1P GAIN MUTATED" "1P GAIN WILD-TYPE" 
       TCGA-EP-A2KB        TCGA-EP-A2KC        TCGA-EP-A3JL        TCGA-EP-A3RK 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-ES-A2HS        TCGA-ES-A2HT        TCGA-FV-A23B        TCGA-FV-A2QR 
"1P GAIN WILD-TYPE"   "1P GAIN MUTATED" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-FV-A3I0        TCGA-FV-A3I1        TCGA-FV-A3R2        TCGA-FV-A3R3 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-FV-A495        TCGA-FV-A496        TCGA-FV-A4ZP        TCGA-FV-A4ZQ 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U        TCGA-G3-A25V 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y        TCGA-G3-A25Z 
  "1P GAIN MUTATED" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI        TCGA-G3-A3CJ 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE"   "1P GAIN MUTATED" 
       TCGA-G3-A3CK        TCGA-G3-A5SI        TCGA-G3-A5SJ        TCGA-G3-A5SL 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE"   "1P GAIN MUTATED" "1P GAIN WILD-TYPE" 
       TCGA-G3-A5SM        TCGA-G3-A6UC        TCGA-GJ-A6C0        TCGA-K7-A6G5 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-LG-A6GG        TCGA-MI-A75C        TCGA-MI-A75E        TCGA-MI-A75G 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-MI-A75I        TCGA-NI-A4U2        TCGA-O8-A75V 
"1P GAIN WILD-TYPE" "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-BC-A69H        TCGA-BC-A69I 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CC-5258        TCGA-CC-5260        TCGA-CC-5261        TCGA-CC-5262 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE"   "1P GAIN MUTATED" 
       TCGA-CC-5263        TCGA-CC-A1HT        TCGA-CC-A3M9        TCGA-CC-A3MA 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CC-A3MB        TCGA-CC-A3MC        TCGA-DD-A113        TCGA-DD-A114 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE"   "1P GAIN MUTATED" 
       TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118        TCGA-DD-A119 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C        TCGA-DD-A11D 
  "1P GAIN MUTATED" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB        TCGA-DD-A1EC 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EF        TCGA-DD-A1EG 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE"   "1P GAIN MUTATED" 
       TCGA-DD-A1EH        TCGA-DD-A1EI        TCGA-DD-A1EJ        TCGA-DD-A1EK 
"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-A4NB        TCGA-DD-A4ND        TCGA-DD-A4NF        TCGA-DD-A4NH 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DD-A4NI        TCGA-DD-A4NJ        TCGA-DD-A4NK        TCGA-DD-A4NL 
  "1P GAIN MUTATED"   "1P GAIN MUTATED" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DD-A4NN        TCGA-DD-A4NO        TCGA-DD-A4NP        TCGA-DD-A4NQ 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DD-A4NR        TCGA-DD-A4NS        TCGA-DD-A4NV        TCGA-DD-A73A 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DD-A73B        TCGA-DD-A73C        TCGA-DD-A73D        TCGA-DD-A73E 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DD-A73F        TCGA-DD-A73G        TCGA-ED-A459        TCGA-ED-A4XI 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE"   "1P GAIN MUTATED"   "1P GAIN MUTATED" 
       TCGA-ED-A5KG        TCGA-ED-A627        TCGA-ED-A66X        TCGA-ED-A66Y 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-ED-A7PX        TCGA-ED-A7PY        TCGA-ED-A7PZ        TCGA-ED-A7XP 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE"   "1P GAIN MUTATED" "1P GAIN WILD-TYPE" 
       TCGA-ED-A82E        TCGA-EP-A12J        TCGA-EP-A26S        TCGA-EP-A2KA 
"1P GAIN WILD-TYPE"   "1P GAIN MUTATED"   "1P GAIN MUTATED" "1P GAIN WILD-TYPE" 
       TCGA-EP-A2KB        TCGA-EP-A2KC        TCGA-EP-A3JL        TCGA-EP-A3RK 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-ES-A2HS        TCGA-ES-A2HT        TCGA-FV-A23B        TCGA-FV-A2QR 
"1P GAIN WILD-TYPE"   "1P GAIN MUTATED" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-FV-A3I0        TCGA-FV-A3I1        TCGA-FV-A3R2        TCGA-FV-A3R3 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-FV-A495        TCGA-FV-A496        TCGA-FV-A4ZP        TCGA-FV-A4ZQ 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U        TCGA-G3-A25V 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y        TCGA-G3-A25Z 
  "1P GAIN MUTATED" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI        TCGA-G3-A3CJ 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE"   "1P GAIN MUTATED" 
       TCGA-G3-A3CK        TCGA-G3-A5SI        TCGA-G3-A5SJ        TCGA-G3-A5SL 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE"   "1P GAIN MUTATED" "1P GAIN WILD-TYPE" 
       TCGA-G3-A5SM        TCGA-G3-A6UC        TCGA-GJ-A6C0        TCGA-K7-A6G5 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-LG-A6GG        TCGA-MI-A75C        TCGA-MI-A75E        TCGA-MI-A75G 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-MI-A75I        TCGA-NI-A4U2        TCGA-O8-A75V 
"1P GAIN WILD-TYPE" "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-BC-A69H        TCGA-BC-A69I 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CC-5258        TCGA-CC-5260        TCGA-CC-5261        TCGA-CC-5262 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE"   "1P GAIN MUTATED" 
       TCGA-CC-5263        TCGA-CC-A1HT        TCGA-CC-A3M9        TCGA-CC-A3MA 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CC-A3MB        TCGA-CC-A3MC        TCGA-DD-A113        TCGA-DD-A114 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE"   "1P GAIN MUTATED" 
       TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118        TCGA-DD-A119 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C        TCGA-DD-A11D 
  "1P GAIN MUTATED" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB        TCGA-DD-A1EC 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EF        TCGA-DD-A1EG 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE"   "1P GAIN MUTATED" 
       TCGA-DD-A1EH        TCGA-DD-A1EI        TCGA-DD-A1EJ        TCGA-DD-A1EK 
"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-A4NB        TCGA-DD-A4ND        TCGA-DD-A4NF        TCGA-DD-A4NH 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DD-A4NI        TCGA-DD-A4NJ        TCGA-DD-A4NK        TCGA-DD-A4NL 
  "1P GAIN MUTATED"   "1P GAIN MUTATED" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DD-A4NN        TCGA-DD-A4NO        TCGA-DD-A4NP        TCGA-DD-A4NQ 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DD-A4NR        TCGA-DD-A4NS        TCGA-DD-A4NV        TCGA-DD-A73A 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DD-A73B        TCGA-DD-A73C        TCGA-DD-A73D        TCGA-DD-A73E 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DD-A73F        TCGA-DD-A73G        TCGA-ED-A459        TCGA-ED-A4XI 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE"   "1P GAIN MUTATED"   "1P GAIN MUTATED" 
       TCGA-ED-A5KG        TCGA-ED-A627        TCGA-ED-A66X        TCGA-ED-A66Y 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-ED-A7PX        TCGA-ED-A7PY        TCGA-ED-A7PZ        TCGA-ED-A7XP 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE"   "1P GAIN MUTATED" "1P GAIN WILD-TYPE" 
       TCGA-ED-A82E        TCGA-EP-A12J        TCGA-EP-A26S        TCGA-EP-A2KA 
"1P GAIN WILD-TYPE"   "1P GAIN MUTATED"   "1P GAIN MUTATED" "1P GAIN WILD-TYPE" 
       TCGA-EP-A2KB        TCGA-EP-A2KC        TCGA-EP-A3JL        TCGA-EP-A3RK 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-ES-A2HS        TCGA-ES-A2HT        TCGA-FV-A23B        TCGA-FV-A2QR 
"1P GAIN WILD-TYPE"   "1P GAIN MUTATED" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-FV-A3I0        TCGA-FV-A3I1        TCGA-FV-A3R2        TCGA-FV-A3R3 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-FV-A495        TCGA-FV-A496        TCGA-FV-A4ZP        TCGA-FV-A4ZQ 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U        TCGA-G3-A25V 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y        TCGA-G3-A25Z 
  "1P GAIN MUTATED" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI        TCGA-G3-A3CJ 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE"   "1P GAIN MUTATED" 
       TCGA-G3-A3CK        TCGA-G3-A5SI        TCGA-G3-A5SJ        TCGA-G3-A5SL 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE"   "1P GAIN MUTATED" "1P GAIN WILD-TYPE" 
       TCGA-G3-A5SM        TCGA-G3-A6UC        TCGA-GJ-A6C0        TCGA-K7-A6G5 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-LG-A6GG        TCGA-MI-A75C        TCGA-MI-A75E        TCGA-MI-A75G 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-MI-A75I        TCGA-NI-A4U2        TCGA-O8-A75V 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
[1] "hr=" "1.2"
D1V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  1P GAIN MUTATED         7        7         0          1          1          1
  1P GAIN WILD-TYPE      51       29         2         29          3          4
                   vv
clus                STAGE IV STAGE IVA STAGE IVB
  1P GAIN MUTATED          0         0         0
  1P GAIN WILD-TYPE        1         1         2
D1V3, multiclass
                   vv
clus                T1 T2 T3 T4
  1P GAIN MUTATED    7  9  2  2
  1P GAIN WILD-TYPE 54 31 38  6
D1V4, multiclass
    clus
vv   1P GAIN MUTATED 1P GAIN WILD-TYPE
  T1               7                54
  T2               9                31
  T3               2                38
  T4               2                 6
D1V5, binary
                   cls
clus                 0  1
  1P GAIN MUTATED    9  0
  1P GAIN WILD-TYPE 88  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED      9    0
  1P GAIN WILD-TYPE   88    3
   clus
vv  1P GAIN MUTATED 1P GAIN WILD-TYPE
  0               9                88
  1               0                 3
                   vv
clus                 M0  M1  MX
  1P GAIN MUTATED    14   0   6
  1P GAIN WILD-TYPE 101   3  25
D1V6, multiclass
    clus
vv   1P GAIN MUTATED 1P GAIN WILD-TYPE
  M0              14               101
  M1               0                 3
  MX               6                25
D1V7, binary
                   cls
clus                 0  1
  1P GAIN MUTATED    4 16
  1P GAIN WILD-TYPE 54 75
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED      4   16
  1P GAIN WILD-TYPE   54   75
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  FEMALE               4                54
  MALE                16                75
                   vv
clus                 R0  R1  R2  RX
  1P GAIN MUTATED    15   3   0   0
  1P GAIN WILD-TYPE 107   8   1  10
D1V8, multiclass
    clus
vv   1P GAIN MUTATED 1P GAIN WILD-TYPE
  R0              15               107
  R1               3                 8
  R2               0                 1
  RX               0                10

Clustering(2) Variable = 1Q GAIN MUTATION ANALYSIS
D2V1, survival
                   sevent
clus2                0  1
  1Q GAIN MUTATED   46 37
  1Q GAIN WILD-TYPE 38 26
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               83                64 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               37                26 
$`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-BC-A69H TCGA-BC-A69I TCGA-CC-5261 TCGA-CC-5262 
       44.42        22.36         3.95         0.53         0.39         3.39 
TCGA-CC-A3MA TCGA-CC-A3MC TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A118 TCGA-DD-A119 
        0.07         0.13        79.73        37.78       113.00         7.33 
TCGA-DD-A11A TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EE 
        2.60        21.76        51.29        90.71        79.40         6.71 
TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V 
       12.95        45.11        49.15        18.35        13.64        21.14 
TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A3 TCGA-DD-A3A7 TCGA-DD-A3A8 
        5.62        19.76        25.81        17.59        13.78         0.36 
TCGA-DD-A3A9 TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK 
       30.61        14.07        14.24        18.44        15.06        39.78 
TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A73D TCGA-DD-A73G 
       29.56        61.45        12.26         0.30        10.98       100.96 
TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PY TCGA-ED-A7PZ 
       13.41        12.69        13.35         0.23         0.20         0.20 
TCGA-ED-A7XP TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC 
        0.20        18.74        19.99        11.74        10.98         0.62 
TCGA-EP-A3JL TCGA-ES-A2HT TCGA-FV-A2QR TCGA-FV-A3I1 TCGA-FV-A3R3 TCGA-FV-A495 
        9.96        14.40        19.10         8.12         0.13         0.03 
TCGA-G3-A25S TCGA-G3-A25W TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG 
        1.22        30.74        58.49        14.86        21.53        22.13 
TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SL TCGA-G3-A5SM TCGA-LG-A6GG 
       19.53        19.23        14.70         7.99         4.37         0.49 
TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75I TCGA-O8-A75V 
        9.57         5.10        14.24         8.71         4.44 

$`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        13.84         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        53.33 
TCGA-DD-A11B TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EI TCGA-DD-A1EJ 
        0.46        66.31        19.79        75.65         6.02        29.16 
TCGA-DD-A39X TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 
       55.69         7.66        70.06        20.12       102.74       107.11 
TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NL TCGA-DD-A4NP TCGA-DD-A4NS 
       33.14        12.85        73.38        56.25        93.67        80.75 
TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73E TCGA-DD-A73F 
       66.35        10.98         9.30         7.56         1.45        27.72 
TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A7PX TCGA-ED-A82E TCGA-EP-A3RK TCGA-ES-A2HS 
       15.85        13.91         0.20         0.20        11.93        22.85 
TCGA-FV-A23B TCGA-FV-A3I0 TCGA-FV-A3R2 TCGA-FV-A496 TCGA-FV-A4ZP TCGA-FV-A4ZQ 
       32.45         0.20         6.38         0.33        60.36         0.39 
TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A5SJ 
       51.06        53.79        28.27        25.64         5.92        11.97 
TCGA-G3-A6UC TCGA-GJ-A6C0 TCGA-K7-A6G5 TCGA-NI-A4U2 
        7.76         1.02         4.01        58.88 

  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
             0.03              0.07 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
           113.00            107.11 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
            13.78             17.82 
[1] "0.0 - 113.0 (13.8)" "0.1 - 107.1 (17.8)"
       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-BC-A69H        TCGA-BC-A69I 
  "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED" 
       TCGA-CC-5258        TCGA-CC-5260        TCGA-CC-5261        TCGA-CC-5262 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED" 
       TCGA-CC-5263        TCGA-CC-A1HT        TCGA-CC-A3M9        TCGA-CC-A3MA 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" 
       TCGA-CC-A3MB        TCGA-CC-A3MC        TCGA-DD-A113        TCGA-DD-A114 
"1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED" 
       TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118        TCGA-DD-A119 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED" 
       TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C        TCGA-DD-A11D 
  "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED" 
       TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB        TCGA-DD-A1EC 
  "1Q GAIN MUTATED"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EF        TCGA-DD-A1EG 
"1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED" 
       TCGA-DD-A1EH        TCGA-DD-A1EI        TCGA-DD-A1EJ        TCGA-DD-A1EK 
  "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" 
       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-A4NB        TCGA-DD-A4ND        TCGA-DD-A4NF        TCGA-DD-A4NH 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED" 
       TCGA-DD-A4NI        TCGA-DD-A4NJ        TCGA-DD-A4NK        TCGA-DD-A4NL 
  "1Q GAIN MUTATED"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" 
       TCGA-DD-A4NN        TCGA-DD-A4NO        TCGA-DD-A4NP        TCGA-DD-A4NQ 
  "1Q GAIN MUTATED"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" 
       TCGA-DD-A4NR        TCGA-DD-A4NS        TCGA-DD-A4NV        TCGA-DD-A73A 
  "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-DD-A73B        TCGA-DD-A73C        TCGA-DD-A73D        TCGA-DD-A73E 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" 
       TCGA-DD-A73F        TCGA-DD-A73G        TCGA-ED-A459        TCGA-ED-A4XI 
"1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED" 
       TCGA-ED-A5KG        TCGA-ED-A627        TCGA-ED-A66X        TCGA-ED-A66Y 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED" 
       TCGA-ED-A7PX        TCGA-ED-A7PY        TCGA-ED-A7PZ        TCGA-ED-A7XP 
"1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED" 
       TCGA-ED-A82E        TCGA-EP-A12J        TCGA-EP-A26S        TCGA-EP-A2KA 
"1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED" 
       TCGA-EP-A2KB        TCGA-EP-A2KC        TCGA-EP-A3JL        TCGA-EP-A3RK 
  "1Q GAIN MUTATED"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" 
       TCGA-ES-A2HS        TCGA-ES-A2HT        TCGA-FV-A23B        TCGA-FV-A2QR 
"1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" 
       TCGA-FV-A3I0        TCGA-FV-A3I1        TCGA-FV-A3R2        TCGA-FV-A3R3 
"1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" 
       TCGA-FV-A495        TCGA-FV-A496        TCGA-FV-A4ZP        TCGA-FV-A4ZQ 
  "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U        TCGA-G3-A25V 
  "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y        TCGA-G3-A25Z 
  "1Q GAIN MUTATED"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED" 
       TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI        TCGA-G3-A3CJ 
  "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" 
       TCGA-G3-A3CK        TCGA-G3-A5SI        TCGA-G3-A5SJ        TCGA-G3-A5SL 
  "1Q GAIN MUTATED"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" 
       TCGA-G3-A5SM        TCGA-G3-A6UC        TCGA-GJ-A6C0        TCGA-K7-A6G5 
  "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-LG-A6GG        TCGA-MI-A75C        TCGA-MI-A75E        TCGA-MI-A75G 
  "1Q GAIN MUTATED"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED" 
       TCGA-MI-A75I        TCGA-NI-A4U2        TCGA-O8-A75V 
  "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE"   "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-BC-A69H        TCGA-BC-A69I 
  "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED" 
       TCGA-CC-5258        TCGA-CC-5260        TCGA-CC-5261        TCGA-CC-5262 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED" 
       TCGA-CC-5263        TCGA-CC-A1HT        TCGA-CC-A3M9        TCGA-CC-A3MA 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" 
       TCGA-CC-A3MB        TCGA-CC-A3MC        TCGA-DD-A113        TCGA-DD-A114 
"1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED" 
       TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118        TCGA-DD-A119 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED" 
       TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C        TCGA-DD-A11D 
  "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED" 
       TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB        TCGA-DD-A1EC 
  "1Q GAIN MUTATED"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EF        TCGA-DD-A1EG 
"1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED" 
       TCGA-DD-A1EH        TCGA-DD-A1EI        TCGA-DD-A1EJ        TCGA-DD-A1EK 
  "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" 
       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-A4NB        TCGA-DD-A4ND        TCGA-DD-A4NF        TCGA-DD-A4NH 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED" 
       TCGA-DD-A4NI        TCGA-DD-A4NJ        TCGA-DD-A4NK        TCGA-DD-A4NL 
  "1Q GAIN MUTATED"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" 
       TCGA-DD-A4NN        TCGA-DD-A4NO        TCGA-DD-A4NP        TCGA-DD-A4NQ 
  "1Q GAIN MUTATED"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" 
       TCGA-DD-A4NR        TCGA-DD-A4NS        TCGA-DD-A4NV        TCGA-DD-A73A 
  "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-DD-A73B        TCGA-DD-A73C        TCGA-DD-A73D        TCGA-DD-A73E 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" 
       TCGA-DD-A73F        TCGA-DD-A73G        TCGA-ED-A459        TCGA-ED-A4XI 
"1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED" 
       TCGA-ED-A5KG        TCGA-ED-A627        TCGA-ED-A66X        TCGA-ED-A66Y 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED" 
       TCGA-ED-A7PX        TCGA-ED-A7PY        TCGA-ED-A7PZ        TCGA-ED-A7XP 
"1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED" 
       TCGA-ED-A82E        TCGA-EP-A12J        TCGA-EP-A26S        TCGA-EP-A2KA 
"1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED" 
       TCGA-EP-A2KB        TCGA-EP-A2KC        TCGA-EP-A3JL        TCGA-EP-A3RK 
  "1Q GAIN MUTATED"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" 
       TCGA-ES-A2HS        TCGA-ES-A2HT        TCGA-FV-A23B        TCGA-FV-A2QR 
"1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" 
       TCGA-FV-A3I0        TCGA-FV-A3I1        TCGA-FV-A3R2        TCGA-FV-A3R3 
"1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" 
       TCGA-FV-A495        TCGA-FV-A496        TCGA-FV-A4ZP        TCGA-FV-A4ZQ 
  "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U        TCGA-G3-A25V 
  "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y        TCGA-G3-A25Z 
  "1Q GAIN MUTATED"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED" 
       TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI        TCGA-G3-A3CJ 
  "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" 
       TCGA-G3-A3CK        TCGA-G3-A5SI        TCGA-G3-A5SJ        TCGA-G3-A5SL 
  "1Q GAIN MUTATED"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" 
       TCGA-G3-A5SM        TCGA-G3-A6UC        TCGA-GJ-A6C0        TCGA-K7-A6G5 
  "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-LG-A6GG        TCGA-MI-A75C        TCGA-MI-A75E        TCGA-MI-A75G 
  "1Q GAIN MUTATED"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED" 
       TCGA-MI-A75I        TCGA-NI-A4U2        TCGA-O8-A75V 
  "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE"   "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-BC-A69H        TCGA-BC-A69I 
  "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED" 
       TCGA-CC-5258        TCGA-CC-5260        TCGA-CC-5261        TCGA-CC-5262 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED" 
       TCGA-CC-5263        TCGA-CC-A1HT        TCGA-CC-A3M9        TCGA-CC-A3MA 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" 
       TCGA-CC-A3MB        TCGA-CC-A3MC        TCGA-DD-A113        TCGA-DD-A114 
"1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED" 
       TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118        TCGA-DD-A119 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED" 
       TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C        TCGA-DD-A11D 
  "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED" 
       TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB        TCGA-DD-A1EC 
  "1Q GAIN MUTATED"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EF        TCGA-DD-A1EG 
"1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED" 
       TCGA-DD-A1EH        TCGA-DD-A1EI        TCGA-DD-A1EJ        TCGA-DD-A1EK 
  "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" 
       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-A4NB        TCGA-DD-A4ND        TCGA-DD-A4NF        TCGA-DD-A4NH 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED" 
       TCGA-DD-A4NI        TCGA-DD-A4NJ        TCGA-DD-A4NK        TCGA-DD-A4NL 
  "1Q GAIN MUTATED"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" 
       TCGA-DD-A4NN        TCGA-DD-A4NO        TCGA-DD-A4NP        TCGA-DD-A4NQ 
  "1Q GAIN MUTATED"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" 
       TCGA-DD-A4NR        TCGA-DD-A4NS        TCGA-DD-A4NV        TCGA-DD-A73A 
  "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-DD-A73B        TCGA-DD-A73C        TCGA-DD-A73D        TCGA-DD-A73E 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" 
       TCGA-DD-A73F        TCGA-DD-A73G        TCGA-ED-A459        TCGA-ED-A4XI 
"1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED" 
       TCGA-ED-A5KG        TCGA-ED-A627        TCGA-ED-A66X        TCGA-ED-A66Y 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED" 
       TCGA-ED-A7PX        TCGA-ED-A7PY        TCGA-ED-A7PZ        TCGA-ED-A7XP 
"1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED" 
       TCGA-ED-A82E        TCGA-EP-A12J        TCGA-EP-A26S        TCGA-EP-A2KA 
"1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED" 
       TCGA-EP-A2KB        TCGA-EP-A2KC        TCGA-EP-A3JL        TCGA-EP-A3RK 
  "1Q GAIN MUTATED"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" 
       TCGA-ES-A2HS        TCGA-ES-A2HT        TCGA-FV-A23B        TCGA-FV-A2QR 
"1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" 
       TCGA-FV-A3I0        TCGA-FV-A3I1        TCGA-FV-A3R2        TCGA-FV-A3R3 
"1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" 
       TCGA-FV-A495        TCGA-FV-A496        TCGA-FV-A4ZP        TCGA-FV-A4ZQ 
  "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U        TCGA-G3-A25V 
  "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y        TCGA-G3-A25Z 
  "1Q GAIN MUTATED"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED" 
       TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI        TCGA-G3-A3CJ 
  "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" 
       TCGA-G3-A3CK        TCGA-G3-A5SI        TCGA-G3-A5SJ        TCGA-G3-A5SL 
  "1Q GAIN MUTATED"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" 
       TCGA-G3-A5SM        TCGA-G3-A6UC        TCGA-GJ-A6C0        TCGA-K7-A6G5 
  "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-LG-A6GG        TCGA-MI-A75C        TCGA-MI-A75E        TCGA-MI-A75G 
  "1Q GAIN MUTATED"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED" 
       TCGA-MI-A75I        TCGA-NI-A4U2        TCGA-O8-A75V 
  "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" 
[1] "hr=" "1.6"
D2V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  1Q GAIN MUTATED        30       28         1         10          3          2
  1Q GAIN WILD-TYPE      28        8         1         20          1          3
                   vv
clus                STAGE IV STAGE IVA STAGE IVB
  1Q GAIN MUTATED          1         1         2
  1Q GAIN WILD-TYPE        0         0         0
D2V3, multiclass
                   vv
clus                T1 T2 T3 T4
  1Q GAIN MUTATED   31 31 17  6
  1Q GAIN WILD-TYPE 30  9 23  2
D2V4, multiclass
    clus
vv   1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  T1              31                30
  T2              31                 9
  T3              17                23
  T4               6                 2
D2V5, binary
                   cls
clus                 0  1
  1Q GAIN MUTATED   54  1
  1Q GAIN WILD-TYPE 43  2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED     54    1
  1Q GAIN WILD-TYPE   43    2
   clus
vv  1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  0              54                43
  1               1                 2
                   vv
clus                M0 M1 MX
  1Q GAIN MUTATED   63  3 19
  1Q GAIN WILD-TYPE 52  0 12
D2V6, multiclass
    clus
vv   1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  M0              63                52
  M1               3                 0
  MX              19                12
D2V7, binary
                   cls
clus                 0  1
  1Q GAIN MUTATED   29 56
  1Q GAIN WILD-TYPE 29 35
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED     29   56
  1Q GAIN WILD-TYPE   29   35
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  FEMALE              29                29
  MALE                56                35
                   vv
clus                R0 R1 R2 RX
  1Q GAIN MUTATED   71  6  1  4
  1Q GAIN WILD-TYPE 51  5  0  6
D2V8, multiclass
    clus
vv   1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  R0              71                51
  R1               6                 5
  R2               1                 0
  RX               4                 6

Clustering(3) Variable = 2P GAIN MUTATION ANALYSIS
D3V1, survival
                   sevent
clus2                0  1
  2P GAIN MUTATED   12 12
  2P GAIN WILD-TYPE 72 51
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               24               123 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               12                51 
$`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-A1EG TCGA-DD-A1EJ TCGA-DD-A1EL TCGA-DD-A39X 
       79.73        90.71        45.11        29.16        13.64        55.69 
TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A73B TCGA-DD-A73D TCGA-DD-A73E TCGA-ED-A7PY 
       30.61        33.14         9.30        10.98         1.45         0.20 
TCGA-ED-A82E TCGA-ES-A2HS TCGA-G3-A25T TCGA-G3-A25W TCGA-G3-A25Z TCGA-LG-A6GG 
        0.20        22.85        51.06        30.74        21.53         0.49 

$`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        13.84         0.26 
TCGA-BC-A3KG TCGA-BC-A69H TCGA-BC-A69I TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5261 
       22.36         3.95         0.53         0.07         2.86         0.39 
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-A118 TCGA-DD-A119 TCGA-DD-A11A 
       37.78        83.57        53.33       113.00         7.33         2.60 
TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC 
        0.46        21.76        51.29        79.40        66.31        19.79 
TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EK 
       75.65         6.71        12.95        49.15         6.02        18.35 
TCGA-DD-A39V TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 
       21.14         5.62        19.76        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-A4NB TCGA-DD-A4ND TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ 
       12.85        73.38        14.07        14.24        18.44        15.06 
TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ 
       39.78        56.25        29.56        61.45        93.67        12.26 
TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73C TCGA-DD-A73F 
        0.30        80.75        66.35        10.98         7.56        27.72 
TCGA-DD-A73G TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X 
      100.96        13.41        12.69        15.85        13.91        13.35 
TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PZ TCGA-ED-A7XP TCGA-EP-A12J TCGA-EP-A26S 
        0.23         0.20         0.20         0.20        18.74        19.99 
TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HT 
       11.74        10.98         0.62         9.96        11.93        14.40 
TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 
       32.45        19.10         0.20         8.12         6.38         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         5.92 
TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SL TCGA-G3-A5SM 
       19.53        19.23        14.70        11.97         7.99         4.37 
TCGA-G3-A6UC TCGA-GJ-A6C0 TCGA-K7-A6G5 TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G 
        7.76         1.02         4.01         9.57         5.10        14.24 
TCGA-MI-A75I TCGA-NI-A4U2 TCGA-O8-A75V 
        8.71        58.88         4.44 

  2P GAIN MUTATED 2P GAIN WILD-TYPE 
             0.10              0.03 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
            90.71            113.00 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
           25.185            13.840 
[1] "0.1 - 90.7 (25.2)"  "0.0 - 113.0 (13.8)"
       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-BC-A69H        TCGA-BC-A69I 
"2P GAIN WILD-TYPE"   "2P GAIN MUTATED" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-CC-5258        TCGA-CC-5260        TCGA-CC-5261        TCGA-CC-5262 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-CC-5263        TCGA-CC-A1HT        TCGA-CC-A3M9        TCGA-CC-A3MA 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE"   "2P GAIN MUTATED" "2P GAIN WILD-TYPE" 
       TCGA-CC-A3MB        TCGA-CC-A3MC        TCGA-DD-A113        TCGA-DD-A114 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE"   "2P GAIN MUTATED" "2P GAIN WILD-TYPE" 
       TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118        TCGA-DD-A119 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C        TCGA-DD-A11D 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB        TCGA-DD-A1EC 
  "2P GAIN MUTATED" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EF        TCGA-DD-A1EG 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE"   "2P GAIN MUTATED" 
       TCGA-DD-A1EH        TCGA-DD-A1EI        TCGA-DD-A1EJ        TCGA-DD-A1EK 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE"   "2P GAIN MUTATED" "2P GAIN WILD-TYPE" 
       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-A4NB        TCGA-DD-A4ND        TCGA-DD-A4NF        TCGA-DD-A4NH 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-DD-A4NI        TCGA-DD-A4NJ        TCGA-DD-A4NK        TCGA-DD-A4NL 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-DD-A4NN        TCGA-DD-A4NO        TCGA-DD-A4NP        TCGA-DD-A4NQ 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-DD-A4NR        TCGA-DD-A4NS        TCGA-DD-A4NV        TCGA-DD-A73A 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-DD-A73B        TCGA-DD-A73C        TCGA-DD-A73D        TCGA-DD-A73E 
  "2P GAIN MUTATED" "2P GAIN WILD-TYPE"   "2P GAIN MUTATED"   "2P GAIN MUTATED" 
       TCGA-DD-A73F        TCGA-DD-A73G        TCGA-ED-A459        TCGA-ED-A4XI 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-ED-A5KG        TCGA-ED-A627        TCGA-ED-A66X        TCGA-ED-A66Y 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-ED-A7PX        TCGA-ED-A7PY        TCGA-ED-A7PZ        TCGA-ED-A7XP 
"2P GAIN WILD-TYPE"   "2P GAIN MUTATED" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-ED-A82E        TCGA-EP-A12J        TCGA-EP-A26S        TCGA-EP-A2KA 
  "2P GAIN MUTATED" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-EP-A2KB        TCGA-EP-A2KC        TCGA-EP-A3JL        TCGA-EP-A3RK 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-ES-A2HS        TCGA-ES-A2HT        TCGA-FV-A23B        TCGA-FV-A2QR 
  "2P GAIN MUTATED" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-FV-A3I0        TCGA-FV-A3I1        TCGA-FV-A3R2        TCGA-FV-A3R3 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-FV-A495        TCGA-FV-A496        TCGA-FV-A4ZP        TCGA-FV-A4ZQ 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U        TCGA-G3-A25V 
"2P GAIN WILD-TYPE"   "2P GAIN MUTATED" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y        TCGA-G3-A25Z 
  "2P GAIN MUTATED" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE"   "2P GAIN MUTATED" 
       TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI        TCGA-G3-A3CJ 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-G3-A3CK        TCGA-G3-A5SI        TCGA-G3-A5SJ        TCGA-G3-A5SL 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-G3-A5SM        TCGA-G3-A6UC        TCGA-GJ-A6C0        TCGA-K7-A6G5 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-LG-A6GG        TCGA-MI-A75C        TCGA-MI-A75E        TCGA-MI-A75G 
  "2P GAIN MUTATED" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-MI-A75I        TCGA-NI-A4U2        TCGA-O8-A75V 
"2P GAIN WILD-TYPE" "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-BC-A69H        TCGA-BC-A69I 
"2P GAIN WILD-TYPE"   "2P GAIN MUTATED" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-CC-5258        TCGA-CC-5260        TCGA-CC-5261        TCGA-CC-5262 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-CC-5263        TCGA-CC-A1HT        TCGA-CC-A3M9        TCGA-CC-A3MA 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE"   "2P GAIN MUTATED" "2P GAIN WILD-TYPE" 
       TCGA-CC-A3MB        TCGA-CC-A3MC        TCGA-DD-A113        TCGA-DD-A114 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE"   "2P GAIN MUTATED" "2P GAIN WILD-TYPE" 
       TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118        TCGA-DD-A119 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C        TCGA-DD-A11D 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB        TCGA-DD-A1EC 
  "2P GAIN MUTATED" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EF        TCGA-DD-A1EG 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE"   "2P GAIN MUTATED" 
       TCGA-DD-A1EH        TCGA-DD-A1EI        TCGA-DD-A1EJ        TCGA-DD-A1EK 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE"   "2P GAIN MUTATED" "2P GAIN WILD-TYPE" 
       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-A4NB        TCGA-DD-A4ND        TCGA-DD-A4NF        TCGA-DD-A4NH 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-DD-A4NI        TCGA-DD-A4NJ        TCGA-DD-A4NK        TCGA-DD-A4NL 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-DD-A4NN        TCGA-DD-A4NO        TCGA-DD-A4NP        TCGA-DD-A4NQ 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-DD-A4NR        TCGA-DD-A4NS        TCGA-DD-A4NV        TCGA-DD-A73A 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-DD-A73B        TCGA-DD-A73C        TCGA-DD-A73D        TCGA-DD-A73E 
  "2P GAIN MUTATED" "2P GAIN WILD-TYPE"   "2P GAIN MUTATED"   "2P GAIN MUTATED" 
       TCGA-DD-A73F        TCGA-DD-A73G        TCGA-ED-A459        TCGA-ED-A4XI 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-ED-A5KG        TCGA-ED-A627        TCGA-ED-A66X        TCGA-ED-A66Y 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-ED-A7PX        TCGA-ED-A7PY        TCGA-ED-A7PZ        TCGA-ED-A7XP 
"2P GAIN WILD-TYPE"   "2P GAIN MUTATED" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-ED-A82E        TCGA-EP-A12J        TCGA-EP-A26S        TCGA-EP-A2KA 
  "2P GAIN MUTATED" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-EP-A2KB        TCGA-EP-A2KC        TCGA-EP-A3JL        TCGA-EP-A3RK 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-ES-A2HS        TCGA-ES-A2HT        TCGA-FV-A23B        TCGA-FV-A2QR 
  "2P GAIN MUTATED" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-FV-A3I0        TCGA-FV-A3I1        TCGA-FV-A3R2        TCGA-FV-A3R3 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-FV-A495        TCGA-FV-A496        TCGA-FV-A4ZP        TCGA-FV-A4ZQ 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U        TCGA-G3-A25V 
"2P GAIN WILD-TYPE"   "2P GAIN MUTATED" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y        TCGA-G3-A25Z 
  "2P GAIN MUTATED" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE"   "2P GAIN MUTATED" 
       TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI        TCGA-G3-A3CJ 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-G3-A3CK        TCGA-G3-A5SI        TCGA-G3-A5SJ        TCGA-G3-A5SL 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-G3-A5SM        TCGA-G3-A6UC        TCGA-GJ-A6C0        TCGA-K7-A6G5 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-LG-A6GG        TCGA-MI-A75C        TCGA-MI-A75E        TCGA-MI-A75G 
  "2P GAIN MUTATED" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-MI-A75I        TCGA-NI-A4U2        TCGA-O8-A75V 
"2P GAIN WILD-TYPE" "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-BC-A69H        TCGA-BC-A69I 
"2P GAIN WILD-TYPE"   "2P GAIN MUTATED" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-CC-5258        TCGA-CC-5260        TCGA-CC-5261        TCGA-CC-5262 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-CC-5263        TCGA-CC-A1HT        TCGA-CC-A3M9        TCGA-CC-A3MA 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE"   "2P GAIN MUTATED" "2P GAIN WILD-TYPE" 
       TCGA-CC-A3MB        TCGA-CC-A3MC        TCGA-DD-A113        TCGA-DD-A114 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE"   "2P GAIN MUTATED" "2P GAIN WILD-TYPE" 
       TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118        TCGA-DD-A119 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C        TCGA-DD-A11D 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB        TCGA-DD-A1EC 
  "2P GAIN MUTATED" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EF        TCGA-DD-A1EG 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE"   "2P GAIN MUTATED" 
       TCGA-DD-A1EH        TCGA-DD-A1EI        TCGA-DD-A1EJ        TCGA-DD-A1EK 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE"   "2P GAIN MUTATED" "2P GAIN WILD-TYPE" 
       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-A4NB        TCGA-DD-A4ND        TCGA-DD-A4NF        TCGA-DD-A4NH 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-DD-A4NI        TCGA-DD-A4NJ        TCGA-DD-A4NK        TCGA-DD-A4NL 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-DD-A4NN        TCGA-DD-A4NO        TCGA-DD-A4NP        TCGA-DD-A4NQ 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-DD-A4NR        TCGA-DD-A4NS        TCGA-DD-A4NV        TCGA-DD-A73A 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-DD-A73B        TCGA-DD-A73C        TCGA-DD-A73D        TCGA-DD-A73E 
  "2P GAIN MUTATED" "2P GAIN WILD-TYPE"   "2P GAIN MUTATED"   "2P GAIN MUTATED" 
       TCGA-DD-A73F        TCGA-DD-A73G        TCGA-ED-A459        TCGA-ED-A4XI 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-ED-A5KG        TCGA-ED-A627        TCGA-ED-A66X        TCGA-ED-A66Y 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-ED-A7PX        TCGA-ED-A7PY        TCGA-ED-A7PZ        TCGA-ED-A7XP 
"2P GAIN WILD-TYPE"   "2P GAIN MUTATED" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-ED-A82E        TCGA-EP-A12J        TCGA-EP-A26S        TCGA-EP-A2KA 
  "2P GAIN MUTATED" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-EP-A2KB        TCGA-EP-A2KC        TCGA-EP-A3JL        TCGA-EP-A3RK 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-ES-A2HS        TCGA-ES-A2HT        TCGA-FV-A23B        TCGA-FV-A2QR 
  "2P GAIN MUTATED" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-FV-A3I0        TCGA-FV-A3I1        TCGA-FV-A3R2        TCGA-FV-A3R3 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-FV-A495        TCGA-FV-A496        TCGA-FV-A4ZP        TCGA-FV-A4ZQ 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U        TCGA-G3-A25V 
"2P GAIN WILD-TYPE"   "2P GAIN MUTATED" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y        TCGA-G3-A25Z 
  "2P GAIN MUTATED" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE"   "2P GAIN MUTATED" 
       TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI        TCGA-G3-A3CJ 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-G3-A3CK        TCGA-G3-A5SI        TCGA-G3-A5SJ        TCGA-G3-A5SL 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-G3-A5SM        TCGA-G3-A6UC        TCGA-GJ-A6C0        TCGA-K7-A6G5 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-LG-A6GG        TCGA-MI-A75C        TCGA-MI-A75E        TCGA-MI-A75G 
  "2P GAIN MUTATED" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-MI-A75I        TCGA-NI-A4U2        TCGA-O8-A75V 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
[1] "hr=" "1"  
D3V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  2P GAIN MUTATED         7        5         0          5          1          2
  2P GAIN WILD-TYPE      51       31         2         25          3          3
                   vv
clus                STAGE IV STAGE IVA STAGE IVB
  2P GAIN MUTATED          0         0         1
  2P GAIN WILD-TYPE        1         1         1
D3V3, multiclass
                   vv
clus                T1 T2 T3 T4
  2P GAIN MUTATED    8  7  7  2
  2P GAIN WILD-TYPE 53 33 33  6
D3V4, multiclass
    clus
vv   2P GAIN MUTATED 2P GAIN WILD-TYPE
  T1               8                53
  T2               7                33
  T3               7                33
  T4               2                 6
D3V5, binary
                   cls
clus                 0  1
  2P GAIN MUTATED   13  2
  2P GAIN WILD-TYPE 84  1
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED     13    2
  2P GAIN WILD-TYPE   84    1
   clus
vv  2P GAIN MUTATED 2P GAIN WILD-TYPE
  0              13                84
  1               2                 1
                   vv
clus                M0 M1 MX
  2P GAIN MUTATED   18  1  5
  2P GAIN WILD-TYPE 97  2 26
D3V6, multiclass
    clus
vv   2P GAIN MUTATED 2P GAIN WILD-TYPE
  M0              18                97
  M1               1                 2
  MX               5                26
D3V7, binary
                   cls
clus                 0  1
  2P GAIN MUTATED   15  9
  2P GAIN WILD-TYPE 43 82
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED     15    9
  2P GAIN WILD-TYPE   43   82
        clus
vv       2P GAIN MUTATED 2P GAIN WILD-TYPE
  FEMALE              15                43
  MALE                 9                82
                   vv
clus                 R0  R1  R2  RX
  2P GAIN MUTATED    20   4   0   0
  2P GAIN WILD-TYPE 102   7   1  10
D3V8, multiclass
    clus
vv   2P GAIN MUTATED 2P GAIN WILD-TYPE
  R0              20               102
  R1               4                 7
  R2               0                 1
  RX               0                10

Clustering(4) Variable = 2Q GAIN MUTATION ANALYSIS
D4V1, survival
                   sevent
clus2                0  1
  2Q GAIN MUTATED    9 10
  2Q GAIN WILD-TYPE 75 53
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               19               128 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               10                53 
$`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        90.71        29.16 
TCGA-DD-A1EL TCGA-DD-A39X TCGA-DD-A3A9 TCGA-DD-A73D TCGA-DD-A73E TCGA-ED-A7PY 
       13.64        55.69        30.61        10.98         1.45         0.20 
TCGA-ED-A82E TCGA-ES-A2HS TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25W TCGA-G3-A25Z 
        0.20        22.85         1.22        51.06        30.74        21.53 
TCGA-LG-A6GG 
        0.49 

$`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        13.84 
TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69H TCGA-BC-A69I TCGA-CC-5258 
        0.26        22.36         9.50         3.95         0.53         0.07 
TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3M9 
        2.86         0.39         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        37.78        83.57        53.33 
TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D 
      113.00         7.33         2.60         0.46        21.76        51.29 
TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EF 
       79.40        66.31        19.79        75.65         6.71        12.95 
TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EK TCGA-DD-A39V TCGA-DD-A39Y 
       45.11        49.15         6.02        18.35        21.14         5.62 
TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 
       19.76        25.81         7.66        70.06        17.59        20.12 
TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A4NA TCGA-DD-A4NB 
      102.74       107.11        13.78         0.36        33.14        12.85 
TCGA-DD-A4ND TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK 
       73.38        14.07        14.24        18.44        15.06        39.78 
TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR 
       56.25        29.56        61.45        93.67        12.26         0.30 
TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73F 
       80.75        66.35        10.98         9.30         7.56        27.72 
TCGA-DD-A73G TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X 
      100.96        13.41        12.69        15.85        13.91        13.35 
TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PZ TCGA-ED-A7XP TCGA-EP-A12J TCGA-EP-A26S 
        0.23         0.20         0.20         0.20        18.74        19.99 
TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HT 
       11.74        10.98         0.62         9.96        11.93        14.40 
TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 
       32.45        19.10         0.20         8.12         6.38         0.13 
TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25U TCGA-G3-A25V 
        0.03         0.33        60.36         0.39        53.79        28.27 
TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A3CG TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ 
       58.49        14.86        22.13        25.64         5.92        19.53 
TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A6UC 
       19.23        14.70        11.97         7.99         4.37         7.76 
TCGA-GJ-A6C0 TCGA-K7-A6G5 TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75I 
        1.02         4.01         9.57         5.10        14.24         8.71 
TCGA-NI-A4U2 TCGA-O8-A75V 
       58.88         4.44 

  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
             0.20              0.03 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
            90.71            113.00 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
           22.850            13.875 
[1] "0.2 - 90.7 (22.9)"  "0.0 - 113.0 (13.9)"
       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-BC-A69H        TCGA-BC-A69I 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-CC-5258        TCGA-CC-5260        TCGA-CC-5261        TCGA-CC-5262 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-CC-5263        TCGA-CC-A1HT        TCGA-CC-A3M9        TCGA-CC-A3MA 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-CC-A3MB        TCGA-CC-A3MC        TCGA-DD-A113        TCGA-DD-A114 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" 
       TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118        TCGA-DD-A119 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C        TCGA-DD-A11D 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB        TCGA-DD-A1EC 
  "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EF        TCGA-DD-A1EG 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-DD-A1EH        TCGA-DD-A1EI        TCGA-DD-A1EJ        TCGA-DD-A1EK 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" 
       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-A4NB        TCGA-DD-A4ND        TCGA-DD-A4NF        TCGA-DD-A4NH 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-DD-A4NI        TCGA-DD-A4NJ        TCGA-DD-A4NK        TCGA-DD-A4NL 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-DD-A4NN        TCGA-DD-A4NO        TCGA-DD-A4NP        TCGA-DD-A4NQ 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-DD-A4NR        TCGA-DD-A4NS        TCGA-DD-A4NV        TCGA-DD-A73A 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-DD-A73B        TCGA-DD-A73C        TCGA-DD-A73D        TCGA-DD-A73E 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED"   "2Q GAIN MUTATED" 
       TCGA-DD-A73F        TCGA-DD-A73G        TCGA-ED-A459        TCGA-ED-A4XI 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-ED-A5KG        TCGA-ED-A627        TCGA-ED-A66X        TCGA-ED-A66Y 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-ED-A7PX        TCGA-ED-A7PY        TCGA-ED-A7PZ        TCGA-ED-A7XP 
"2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-ED-A82E        TCGA-EP-A12J        TCGA-EP-A26S        TCGA-EP-A2KA 
  "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-EP-A2KB        TCGA-EP-A2KC        TCGA-EP-A3JL        TCGA-EP-A3RK 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-ES-A2HS        TCGA-ES-A2HT        TCGA-FV-A23B        TCGA-FV-A2QR 
  "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-FV-A3I0        TCGA-FV-A3I1        TCGA-FV-A3R2        TCGA-FV-A3R3 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-FV-A495        TCGA-FV-A496        TCGA-FV-A4ZP        TCGA-FV-A4ZQ 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U        TCGA-G3-A25V 
  "2Q GAIN MUTATED"   "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y        TCGA-G3-A25Z 
  "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" 
       TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI        TCGA-G3-A3CJ 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-G3-A3CK        TCGA-G3-A5SI        TCGA-G3-A5SJ        TCGA-G3-A5SL 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-G3-A5SM        TCGA-G3-A6UC        TCGA-GJ-A6C0        TCGA-K7-A6G5 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-LG-A6GG        TCGA-MI-A75C        TCGA-MI-A75E        TCGA-MI-A75G 
  "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-MI-A75I        TCGA-NI-A4U2        TCGA-O8-A75V 
"2Q GAIN WILD-TYPE" "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-BC-A69H        TCGA-BC-A69I 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-CC-5258        TCGA-CC-5260        TCGA-CC-5261        TCGA-CC-5262 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-CC-5263        TCGA-CC-A1HT        TCGA-CC-A3M9        TCGA-CC-A3MA 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-CC-A3MB        TCGA-CC-A3MC        TCGA-DD-A113        TCGA-DD-A114 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" 
       TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118        TCGA-DD-A119 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C        TCGA-DD-A11D 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB        TCGA-DD-A1EC 
  "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EF        TCGA-DD-A1EG 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-DD-A1EH        TCGA-DD-A1EI        TCGA-DD-A1EJ        TCGA-DD-A1EK 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" 
       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-A4NB        TCGA-DD-A4ND        TCGA-DD-A4NF        TCGA-DD-A4NH 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-DD-A4NI        TCGA-DD-A4NJ        TCGA-DD-A4NK        TCGA-DD-A4NL 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-DD-A4NN        TCGA-DD-A4NO        TCGA-DD-A4NP        TCGA-DD-A4NQ 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-DD-A4NR        TCGA-DD-A4NS        TCGA-DD-A4NV        TCGA-DD-A73A 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-DD-A73B        TCGA-DD-A73C        TCGA-DD-A73D        TCGA-DD-A73E 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED"   "2Q GAIN MUTATED" 
       TCGA-DD-A73F        TCGA-DD-A73G        TCGA-ED-A459        TCGA-ED-A4XI 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-ED-A5KG        TCGA-ED-A627        TCGA-ED-A66X        TCGA-ED-A66Y 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-ED-A7PX        TCGA-ED-A7PY        TCGA-ED-A7PZ        TCGA-ED-A7XP 
"2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-ED-A82E        TCGA-EP-A12J        TCGA-EP-A26S        TCGA-EP-A2KA 
  "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-EP-A2KB        TCGA-EP-A2KC        TCGA-EP-A3JL        TCGA-EP-A3RK 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-ES-A2HS        TCGA-ES-A2HT        TCGA-FV-A23B        TCGA-FV-A2QR 
  "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-FV-A3I0        TCGA-FV-A3I1        TCGA-FV-A3R2        TCGA-FV-A3R3 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-FV-A495        TCGA-FV-A496        TCGA-FV-A4ZP        TCGA-FV-A4ZQ 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U        TCGA-G3-A25V 
  "2Q GAIN MUTATED"   "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y        TCGA-G3-A25Z 
  "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" 
       TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI        TCGA-G3-A3CJ 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-G3-A3CK        TCGA-G3-A5SI        TCGA-G3-A5SJ        TCGA-G3-A5SL 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-G3-A5SM        TCGA-G3-A6UC        TCGA-GJ-A6C0        TCGA-K7-A6G5 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-LG-A6GG        TCGA-MI-A75C        TCGA-MI-A75E        TCGA-MI-A75G 
  "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-MI-A75I        TCGA-NI-A4U2        TCGA-O8-A75V 
"2Q GAIN WILD-TYPE" "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-BC-A69H        TCGA-BC-A69I 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-CC-5258        TCGA-CC-5260        TCGA-CC-5261        TCGA-CC-5262 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-CC-5263        TCGA-CC-A1HT        TCGA-CC-A3M9        TCGA-CC-A3MA 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-CC-A3MB        TCGA-CC-A3MC        TCGA-DD-A113        TCGA-DD-A114 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" 
       TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118        TCGA-DD-A119 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C        TCGA-DD-A11D 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB        TCGA-DD-A1EC 
  "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EF        TCGA-DD-A1EG 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-DD-A1EH        TCGA-DD-A1EI        TCGA-DD-A1EJ        TCGA-DD-A1EK 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" 
       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-A4NB        TCGA-DD-A4ND        TCGA-DD-A4NF        TCGA-DD-A4NH 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-DD-A4NI        TCGA-DD-A4NJ        TCGA-DD-A4NK        TCGA-DD-A4NL 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-DD-A4NN        TCGA-DD-A4NO        TCGA-DD-A4NP        TCGA-DD-A4NQ 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-DD-A4NR        TCGA-DD-A4NS        TCGA-DD-A4NV        TCGA-DD-A73A 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-DD-A73B        TCGA-DD-A73C        TCGA-DD-A73D        TCGA-DD-A73E 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED"   "2Q GAIN MUTATED" 
       TCGA-DD-A73F        TCGA-DD-A73G        TCGA-ED-A459        TCGA-ED-A4XI 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-ED-A5KG        TCGA-ED-A627        TCGA-ED-A66X        TCGA-ED-A66Y 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-ED-A7PX        TCGA-ED-A7PY        TCGA-ED-A7PZ        TCGA-ED-A7XP 
"2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-ED-A82E        TCGA-EP-A12J        TCGA-EP-A26S        TCGA-EP-A2KA 
  "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-EP-A2KB        TCGA-EP-A2KC        TCGA-EP-A3JL        TCGA-EP-A3RK 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-ES-A2HS        TCGA-ES-A2HT        TCGA-FV-A23B        TCGA-FV-A2QR 
  "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-FV-A3I0        TCGA-FV-A3I1        TCGA-FV-A3R2        TCGA-FV-A3R3 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-FV-A495        TCGA-FV-A496        TCGA-FV-A4ZP        TCGA-FV-A4ZQ 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U        TCGA-G3-A25V 
  "2Q GAIN MUTATED"   "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y        TCGA-G3-A25Z 
  "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" 
       TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI        TCGA-G3-A3CJ 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-G3-A3CK        TCGA-G3-A5SI        TCGA-G3-A5SJ        TCGA-G3-A5SL 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-G3-A5SM        TCGA-G3-A6UC        TCGA-GJ-A6C0        TCGA-K7-A6G5 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-LG-A6GG        TCGA-MI-A75C        TCGA-MI-A75E        TCGA-MI-A75G 
  "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-MI-A75I        TCGA-NI-A4U2        TCGA-O8-A75V 
"2Q GAIN WILD-TYPE" "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         6        5         0          3          1          1
  2Q GAIN WILD-TYPE      52       31         2         27          3          4
                   vv
clus                STAGE IV STAGE IVA STAGE IVB
  2Q GAIN MUTATED          0         0         1
  2Q GAIN WILD-TYPE        1         1         1
D4V3, multiclass
                   vv
clus                T1 T2 T3 T4
  2Q GAIN MUTATED    7  6  5  1
  2Q GAIN WILD-TYPE 54 34 35  7
D4V4, multiclass
    clus
vv   2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  T1               7                54
  T2               6                34
  T3               5                35
  T4               1                 7
D4V5, binary
                   cls
clus                 0  1
  2Q GAIN MUTATED   11  1
  2Q GAIN WILD-TYPE 86  2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED     11    1
  2Q GAIN WILD-TYPE   86    2
   clus
vv  2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  0              11                86
  1               1                 2
                   vv
clus                 M0  M1  MX
  2Q GAIN MUTATED    14   1   4
  2Q GAIN WILD-TYPE 101   2  27
D4V6, multiclass
    clus
vv   2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  M0              14               101
  M1               1                 2
  MX               4                27
D4V7, binary
                   cls
clus                 0  1
  2Q GAIN MUTATED   13  6
  2Q GAIN WILD-TYPE 45 85
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED     13    6
  2Q GAIN WILD-TYPE   45   85
        clus
vv       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  FEMALE              13                45
  MALE                 6                85
                   vv
clus                 R0  R1  R2  RX
  2Q GAIN MUTATED    16   3   0   0
  2Q GAIN WILD-TYPE 106   8   1  10
D4V8, multiclass
    clus
vv   2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  R0              16               106
  R1               3                 8
  R2               0                 1
  RX               0                10

Clustering(5) Variable = 3P GAIN MUTATION ANALYSIS
D5V1, survival
                   sevent
clus2                0  1
  3P GAIN MUTATED    7  6
  3P GAIN WILD-TYPE 77 57
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               13               134 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
                6                57 
$`3P GAIN MUTATED`
TCGA-BC-A217 TCGA-BC-A69H TCGA-CC-A3M9 TCGA-DD-A114 TCGA-DD-A11C TCGA-DD-A1EF 
       13.84         3.95         0.10        37.78        21.76        12.95 
TCGA-DD-A1EJ TCGA-DD-A39Y TCGA-DD-A4NV TCGA-DD-A73E TCGA-ES-A2HS TCGA-FV-A3R2 
       29.16         5.62        66.35         1.45        22.85         6.38 
TCGA-MI-A75G 
       14.24 

$`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-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69I 
        5.03        44.42         0.26        22.36         9.50         0.53 
TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A1HT 
        0.07         2.86         0.39         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        53.33 
TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11D TCGA-DD-A1E9 
      113.00         7.33         2.60         0.46        51.29        90.71 
TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EG 
       79.40        66.31        19.79        75.65         6.71        45.11 
TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39X 
       49.15         6.02        18.35        13.64        21.14        55.69 
TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 
       19.76        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        30.61        33.14 
TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ 
       12.85        73.38        14.07        14.24        18.44        15.06 
TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ 
       39.78        56.25        29.56        61.45        93.67        12.26 
TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D 
        0.30        80.75        10.98         9.30         7.56        10.98 
TCGA-DD-A73F TCGA-DD-A73G TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 
       27.72       100.96        13.41        12.69        15.85        13.91 
TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XP 
       13.35         0.23         0.20         0.20         0.20         0.20 
TCGA-ED-A82E TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC 
        0.20        18.74        19.99        11.74        10.98         0.62 
TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-A3I0 
        9.96        11.93        14.40        32.45        19.10         0.20 
TCGA-FV-A3I1 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZP TCGA-FV-A4ZQ 
        8.12         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        51.06        53.79        28.27        30.74        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         5.92        19.53 
TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A6UC 
       19.23        14.70        11.97         7.99         4.37         7.76 
TCGA-GJ-A6C0 TCGA-K7-A6G5 TCGA-LG-A6GG TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75I 
        1.02         4.01         0.49         9.57         5.10         8.71 
TCGA-NI-A4U2 TCGA-O8-A75V 
       58.88         4.44 

  3P GAIN MUTATED 3P GAIN WILD-TYPE 
             0.10              0.03 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
            66.35            113.00 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
           13.840            14.155 
[1] "0.1 - 66.3 (13.8)"  "0.0 - 113.0 (14.2)"
       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 MUTATED" "3P GAIN WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-BC-A5W4        TCGA-BC-A69H        TCGA-BC-A69I 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"   "3P GAIN MUTATED" "3P GAIN WILD-TYPE" 
       TCGA-CC-5258        TCGA-CC-5260        TCGA-CC-5261        TCGA-CC-5262 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-CC-5263        TCGA-CC-A1HT        TCGA-CC-A3M9        TCGA-CC-A3MA 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"   "3P GAIN MUTATED" "3P GAIN WILD-TYPE" 
       TCGA-CC-A3MB        TCGA-CC-A3MC        TCGA-DD-A113        TCGA-DD-A114 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"   "3P GAIN MUTATED" 
       TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118        TCGA-DD-A119 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C        TCGA-DD-A11D 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"   "3P GAIN MUTATED" "3P GAIN WILD-TYPE" 
       TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB        TCGA-DD-A1EC 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EF        TCGA-DD-A1EG 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"   "3P GAIN MUTATED" "3P GAIN WILD-TYPE" 
       TCGA-DD-A1EH        TCGA-DD-A1EI        TCGA-DD-A1EJ        TCGA-DD-A1EK 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"   "3P GAIN MUTATED" "3P GAIN WILD-TYPE" 
       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-A4NB        TCGA-DD-A4ND        TCGA-DD-A4NF        TCGA-DD-A4NH 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DD-A4NI        TCGA-DD-A4NJ        TCGA-DD-A4NK        TCGA-DD-A4NL 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DD-A4NN        TCGA-DD-A4NO        TCGA-DD-A4NP        TCGA-DD-A4NQ 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DD-A4NR        TCGA-DD-A4NS        TCGA-DD-A4NV        TCGA-DD-A73A 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"   "3P GAIN MUTATED" "3P GAIN WILD-TYPE" 
       TCGA-DD-A73B        TCGA-DD-A73C        TCGA-DD-A73D        TCGA-DD-A73E 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"   "3P GAIN MUTATED" 
       TCGA-DD-A73F        TCGA-DD-A73G        TCGA-ED-A459        TCGA-ED-A4XI 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-ED-A5KG        TCGA-ED-A627        TCGA-ED-A66X        TCGA-ED-A66Y 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-ED-A7PX        TCGA-ED-A7PY        TCGA-ED-A7PZ        TCGA-ED-A7XP 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-ED-A82E        TCGA-EP-A12J        TCGA-EP-A26S        TCGA-EP-A2KA 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EP-A2KB        TCGA-EP-A2KC        TCGA-EP-A3JL        TCGA-EP-A3RK 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-ES-A2HS        TCGA-ES-A2HT        TCGA-FV-A23B        TCGA-FV-A2QR 
  "3P GAIN MUTATED" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-FV-A3I0        TCGA-FV-A3I1        TCGA-FV-A3R2        TCGA-FV-A3R3 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"   "3P GAIN MUTATED" "3P GAIN WILD-TYPE" 
       TCGA-FV-A495        TCGA-FV-A496        TCGA-FV-A4ZP        TCGA-FV-A4ZQ 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U        TCGA-G3-A25V 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y        TCGA-G3-A25Z 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI        TCGA-G3-A3CJ 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-G3-A3CK        TCGA-G3-A5SI        TCGA-G3-A5SJ        TCGA-G3-A5SL 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-G3-A5SM        TCGA-G3-A6UC        TCGA-GJ-A6C0        TCGA-K7-A6G5 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-LG-A6GG        TCGA-MI-A75C        TCGA-MI-A75E        TCGA-MI-A75G 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"   "3P GAIN MUTATED" 
       TCGA-MI-A75I        TCGA-NI-A4U2        TCGA-O8-A75V 
"3P GAIN WILD-TYPE" "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 MUTATED" "3P GAIN WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-BC-A5W4        TCGA-BC-A69H        TCGA-BC-A69I 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"   "3P GAIN MUTATED" "3P GAIN WILD-TYPE" 
       TCGA-CC-5258        TCGA-CC-5260        TCGA-CC-5261        TCGA-CC-5262 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-CC-5263        TCGA-CC-A1HT        TCGA-CC-A3M9        TCGA-CC-A3MA 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"   "3P GAIN MUTATED" "3P GAIN WILD-TYPE" 
       TCGA-CC-A3MB        TCGA-CC-A3MC        TCGA-DD-A113        TCGA-DD-A114 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"   "3P GAIN MUTATED" 
       TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118        TCGA-DD-A119 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C        TCGA-DD-A11D 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"   "3P GAIN MUTATED" "3P GAIN WILD-TYPE" 
       TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB        TCGA-DD-A1EC 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EF        TCGA-DD-A1EG 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"   "3P GAIN MUTATED" "3P GAIN WILD-TYPE" 
       TCGA-DD-A1EH        TCGA-DD-A1EI        TCGA-DD-A1EJ        TCGA-DD-A1EK 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"   "3P GAIN MUTATED" "3P GAIN WILD-TYPE" 
       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-A4NB        TCGA-DD-A4ND        TCGA-DD-A4NF        TCGA-DD-A4NH 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DD-A4NI        TCGA-DD-A4NJ        TCGA-DD-A4NK        TCGA-DD-A4NL 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DD-A4NN        TCGA-DD-A4NO        TCGA-DD-A4NP        TCGA-DD-A4NQ 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DD-A4NR        TCGA-DD-A4NS        TCGA-DD-A4NV        TCGA-DD-A73A 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"   "3P GAIN MUTATED" "3P GAIN WILD-TYPE" 
       TCGA-DD-A73B        TCGA-DD-A73C        TCGA-DD-A73D        TCGA-DD-A73E 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"   "3P GAIN MUTATED" 
       TCGA-DD-A73F        TCGA-DD-A73G        TCGA-ED-A459        TCGA-ED-A4XI 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-ED-A5KG        TCGA-ED-A627        TCGA-ED-A66X        TCGA-ED-A66Y 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-ED-A7PX        TCGA-ED-A7PY        TCGA-ED-A7PZ        TCGA-ED-A7XP 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-ED-A82E        TCGA-EP-A12J        TCGA-EP-A26S        TCGA-EP-A2KA 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EP-A2KB        TCGA-EP-A2KC        TCGA-EP-A3JL        TCGA-EP-A3RK 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-ES-A2HS        TCGA-ES-A2HT        TCGA-FV-A23B        TCGA-FV-A2QR 
  "3P GAIN MUTATED" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-FV-A3I0        TCGA-FV-A3I1        TCGA-FV-A3R2        TCGA-FV-A3R3 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"   "3P GAIN MUTATED" "3P GAIN WILD-TYPE" 
       TCGA-FV-A495        TCGA-FV-A496        TCGA-FV-A4ZP        TCGA-FV-A4ZQ 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U        TCGA-G3-A25V 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y        TCGA-G3-A25Z 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI        TCGA-G3-A3CJ 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-G3-A3CK        TCGA-G3-A5SI        TCGA-G3-A5SJ        TCGA-G3-A5SL 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-G3-A5SM        TCGA-G3-A6UC        TCGA-GJ-A6C0        TCGA-K7-A6G5 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-LG-A6GG        TCGA-MI-A75C        TCGA-MI-A75E        TCGA-MI-A75G 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"   "3P GAIN MUTATED" 
       TCGA-MI-A75I        TCGA-NI-A4U2        TCGA-O8-A75V 
"3P GAIN WILD-TYPE" "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 MUTATED" "3P GAIN WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-BC-A5W4        TCGA-BC-A69H        TCGA-BC-A69I 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"   "3P GAIN MUTATED" "3P GAIN WILD-TYPE" 
       TCGA-CC-5258        TCGA-CC-5260        TCGA-CC-5261        TCGA-CC-5262 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-CC-5263        TCGA-CC-A1HT        TCGA-CC-A3M9        TCGA-CC-A3MA 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"   "3P GAIN MUTATED" "3P GAIN WILD-TYPE" 
       TCGA-CC-A3MB        TCGA-CC-A3MC        TCGA-DD-A113        TCGA-DD-A114 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"   "3P GAIN MUTATED" 
       TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118        TCGA-DD-A119 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C        TCGA-DD-A11D 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"   "3P GAIN MUTATED" "3P GAIN WILD-TYPE" 
       TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB        TCGA-DD-A1EC 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EF        TCGA-DD-A1EG 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"   "3P GAIN MUTATED" "3P GAIN WILD-TYPE" 
       TCGA-DD-A1EH        TCGA-DD-A1EI        TCGA-DD-A1EJ        TCGA-DD-A1EK 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"   "3P GAIN MUTATED" "3P GAIN WILD-TYPE" 
       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-A4NB        TCGA-DD-A4ND        TCGA-DD-A4NF        TCGA-DD-A4NH 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DD-A4NI        TCGA-DD-A4NJ        TCGA-DD-A4NK        TCGA-DD-A4NL 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DD-A4NN        TCGA-DD-A4NO        TCGA-DD-A4NP        TCGA-DD-A4NQ 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DD-A4NR        TCGA-DD-A4NS        TCGA-DD-A4NV        TCGA-DD-A73A 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"   "3P GAIN MUTATED" "3P GAIN WILD-TYPE" 
       TCGA-DD-A73B        TCGA-DD-A73C        TCGA-DD-A73D        TCGA-DD-A73E 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"   "3P GAIN MUTATED" 
       TCGA-DD-A73F        TCGA-DD-A73G        TCGA-ED-A459        TCGA-ED-A4XI 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-ED-A5KG        TCGA-ED-A627        TCGA-ED-A66X        TCGA-ED-A66Y 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-ED-A7PX        TCGA-ED-A7PY        TCGA-ED-A7PZ        TCGA-ED-A7XP 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-ED-A82E        TCGA-EP-A12J        TCGA-EP-A26S        TCGA-EP-A2KA 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EP-A2KB        TCGA-EP-A2KC        TCGA-EP-A3JL        TCGA-EP-A3RK 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-ES-A2HS        TCGA-ES-A2HT        TCGA-FV-A23B        TCGA-FV-A2QR 
  "3P GAIN MUTATED" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-FV-A3I0        TCGA-FV-A3I1        TCGA-FV-A3R2        TCGA-FV-A3R3 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"   "3P GAIN MUTATED" "3P GAIN WILD-TYPE" 
       TCGA-FV-A495        TCGA-FV-A496        TCGA-FV-A4ZP        TCGA-FV-A4ZQ 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U        TCGA-G3-A25V 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y        TCGA-G3-A25Z 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI        TCGA-G3-A3CJ 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-G3-A3CK        TCGA-G3-A5SI        TCGA-G3-A5SJ        TCGA-G3-A5SL 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-G3-A5SM        TCGA-G3-A6UC        TCGA-GJ-A6C0        TCGA-K7-A6G5 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-LG-A6GG        TCGA-MI-A75C        TCGA-MI-A75E        TCGA-MI-A75G 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"   "3P GAIN MUTATED" 
       TCGA-MI-A75I        TCGA-NI-A4U2        TCGA-O8-A75V 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
[1] "hr=" "1.5"
D5V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  3P GAIN MUTATED         6        4         0          2          0          1
  3P GAIN WILD-TYPE      52       32         2         28          4          4
                   vv
clus                STAGE IV STAGE IVA STAGE IVB
  3P GAIN MUTATED          0         0         0
  3P GAIN WILD-TYPE        1         1         2
D5V3, multiclass
                   vv
clus                T1 T2 T3 T4
  3P GAIN MUTATED    7  4  2  0
  3P GAIN WILD-TYPE 54 36 38  8
D5V4, multiclass
    clus
vv   3P GAIN MUTATED 3P GAIN WILD-TYPE
  T1               7                54
  T2               4                36
  T3               2                38
  T4               0                 8
D5V5, binary
                   cls
clus                 0  1
  3P GAIN MUTATED    6  1
  3P GAIN WILD-TYPE 91  2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED      6    1
  3P GAIN WILD-TYPE   91    2
   clus
vv  3P GAIN MUTATED 3P GAIN WILD-TYPE
  0               6                91
  1               1                 2
                   vv
clus                 M0  M1  MX
  3P GAIN MUTATED    11   0   2
  3P GAIN WILD-TYPE 104   3  29
D5V6, multiclass
    clus
vv   3P GAIN MUTATED 3P GAIN WILD-TYPE
  M0              11               104
  M1               0                 3
  MX               2                29
D5V7, binary
                   cls
clus                 0  1
  3P GAIN MUTATED    3 10
  3P GAIN WILD-TYPE 55 81
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED      3   10
  3P GAIN WILD-TYPE   55   81
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  FEMALE               3                55
  MALE                10                81
                   vv
clus                 R0  R1  R2  RX
  3P GAIN MUTATED    12   0   0   1
  3P GAIN WILD-TYPE 110  11   1   9
D5V8, multiclass
    clus
vv   3P GAIN MUTATED 3P GAIN WILD-TYPE
  R0              12               110
  R1               0                11
  R2               0                 1
  RX               1                 9

Clustering(6) Variable = 3Q GAIN MUTATION ANALYSIS
D6V1, survival
                   sevent
clus2                0  1
  3Q GAIN MUTATED    7  7
  3Q GAIN WILD-TYPE 77 56
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               14               133 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
                7                56 
$`3Q GAIN MUTATED`
TCGA-BC-A10R TCGA-BC-A217 TCGA-BC-A69H TCGA-CC-A3M9 TCGA-DD-A114 TCGA-DD-A11C 
       10.13        13.84         3.95         0.10        37.78        21.76 
TCGA-DD-A1EF TCGA-DD-A1EJ TCGA-DD-A39Y TCGA-DD-A4NV TCGA-DD-A73E TCGA-ES-A2HS 
       12.95        29.16         5.62        66.35         1.45        22.85 
TCGA-FV-A3R2 TCGA-MI-A75G 
        6.38        14.24 

$`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-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69I TCGA-CC-5258 
       44.42         0.26        22.36         9.50         0.53         0.07 
TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3MA 
        2.86         0.39         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        53.33       113.00 
TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA 
        7.33         2.60         0.46        51.29        90.71        79.40 
TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EG TCGA-DD-A1EH 
       66.31        19.79        75.65         6.71        45.11        49.15 
TCGA-DD-A1EI TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39X TCGA-DD-A39Z 
        6.02        18.35        13.64        21.14        55.69        19.76 
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-A4NB 
      107.11        13.78         0.36        30.61        33.14        12.85 
TCGA-DD-A4ND TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK 
       73.38        14.07        14.24        18.44        15.06        39.78 
TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR 
       56.25        29.56        61.45        93.67        12.26         0.30 
TCGA-DD-A4NS TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73F 
       80.75        10.98         9.30         7.56        10.98        27.72 
TCGA-DD-A73G TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X 
      100.96        13.41        12.69        15.85        13.91        13.35 
TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XP TCGA-ED-A82E 
        0.23         0.20         0.20         0.20         0.20         0.20 
TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL 
       18.74        19.99        11.74        10.98         0.62         9.96 
TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3I1 
       11.93        14.40        32.45        19.10         0.20         8.12 
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 
       51.06        53.79        28.27        30.74        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         5.92        19.53        19.23 
TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A6UC TCGA-GJ-A6C0 
       14.70        11.97         7.99         4.37         7.76         1.02 
TCGA-K7-A6G5 TCGA-LG-A6GG TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75I TCGA-NI-A4U2 
        4.01         0.49         9.57         5.10         8.71        58.88 
TCGA-O8-A75V 
        4.44 

  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
             0.10              0.03 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
            66.35            113.00 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
           13.395            14.240 
[1] "0.1 - 66.3 (13.4)"  "0.0 - 113.0 (14.2)"
       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 MUTATED" "3Q GAIN WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-BC-A5W4        TCGA-BC-A69H        TCGA-BC-A69I 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" 
       TCGA-CC-5258        TCGA-CC-5260        TCGA-CC-5261        TCGA-CC-5262 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-CC-5263        TCGA-CC-A1HT        TCGA-CC-A3M9        TCGA-CC-A3MA 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" 
       TCGA-CC-A3MB        TCGA-CC-A3MC        TCGA-DD-A113        TCGA-DD-A114 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" 
       TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118        TCGA-DD-A119 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C        TCGA-DD-A11D 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" 
       TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB        TCGA-DD-A1EC 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EF        TCGA-DD-A1EG 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" 
       TCGA-DD-A1EH        TCGA-DD-A1EI        TCGA-DD-A1EJ        TCGA-DD-A1EK 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" 
       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-A4NB        TCGA-DD-A4ND        TCGA-DD-A4NF        TCGA-DD-A4NH 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-DD-A4NI        TCGA-DD-A4NJ        TCGA-DD-A4NK        TCGA-DD-A4NL 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-DD-A4NN        TCGA-DD-A4NO        TCGA-DD-A4NP        TCGA-DD-A4NQ 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-DD-A4NR        TCGA-DD-A4NS        TCGA-DD-A4NV        TCGA-DD-A73A 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" 
       TCGA-DD-A73B        TCGA-DD-A73C        TCGA-DD-A73D        TCGA-DD-A73E 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" 
       TCGA-DD-A73F        TCGA-DD-A73G        TCGA-ED-A459        TCGA-ED-A4XI 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-ED-A5KG        TCGA-ED-A627        TCGA-ED-A66X        TCGA-ED-A66Y 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-ED-A7PX        TCGA-ED-A7PY        TCGA-ED-A7PZ        TCGA-ED-A7XP 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-ED-A82E        TCGA-EP-A12J        TCGA-EP-A26S        TCGA-EP-A2KA 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-EP-A2KB        TCGA-EP-A2KC        TCGA-EP-A3JL        TCGA-EP-A3RK 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-ES-A2HS        TCGA-ES-A2HT        TCGA-FV-A23B        TCGA-FV-A2QR 
  "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-FV-A3I0        TCGA-FV-A3I1        TCGA-FV-A3R2        TCGA-FV-A3R3 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" 
       TCGA-FV-A495        TCGA-FV-A496        TCGA-FV-A4ZP        TCGA-FV-A4ZQ 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U        TCGA-G3-A25V 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y        TCGA-G3-A25Z 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI        TCGA-G3-A3CJ 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-G3-A3CK        TCGA-G3-A5SI        TCGA-G3-A5SJ        TCGA-G3-A5SL 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-G3-A5SM        TCGA-G3-A6UC        TCGA-GJ-A6C0        TCGA-K7-A6G5 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-LG-A6GG        TCGA-MI-A75C        TCGA-MI-A75E        TCGA-MI-A75G 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" 
       TCGA-MI-A75I        TCGA-NI-A4U2        TCGA-O8-A75V 
"3Q GAIN WILD-TYPE" "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 MUTATED" "3Q GAIN WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-BC-A5W4        TCGA-BC-A69H        TCGA-BC-A69I 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" 
       TCGA-CC-5258        TCGA-CC-5260        TCGA-CC-5261        TCGA-CC-5262 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-CC-5263        TCGA-CC-A1HT        TCGA-CC-A3M9        TCGA-CC-A3MA 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" 
       TCGA-CC-A3MB        TCGA-CC-A3MC        TCGA-DD-A113        TCGA-DD-A114 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" 
       TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118        TCGA-DD-A119 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C        TCGA-DD-A11D 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" 
       TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB        TCGA-DD-A1EC 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EF        TCGA-DD-A1EG 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" 
       TCGA-DD-A1EH        TCGA-DD-A1EI        TCGA-DD-A1EJ        TCGA-DD-A1EK 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" 
       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-A4NB        TCGA-DD-A4ND        TCGA-DD-A4NF        TCGA-DD-A4NH 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-DD-A4NI        TCGA-DD-A4NJ        TCGA-DD-A4NK        TCGA-DD-A4NL 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-DD-A4NN        TCGA-DD-A4NO        TCGA-DD-A4NP        TCGA-DD-A4NQ 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-DD-A4NR        TCGA-DD-A4NS        TCGA-DD-A4NV        TCGA-DD-A73A 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" 
       TCGA-DD-A73B        TCGA-DD-A73C        TCGA-DD-A73D        TCGA-DD-A73E 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" 
       TCGA-DD-A73F        TCGA-DD-A73G        TCGA-ED-A459        TCGA-ED-A4XI 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-ED-A5KG        TCGA-ED-A627        TCGA-ED-A66X        TCGA-ED-A66Y 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-ED-A7PX        TCGA-ED-A7PY        TCGA-ED-A7PZ        TCGA-ED-A7XP 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-ED-A82E        TCGA-EP-A12J        TCGA-EP-A26S        TCGA-EP-A2KA 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-EP-A2KB        TCGA-EP-A2KC        TCGA-EP-A3JL        TCGA-EP-A3RK 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-ES-A2HS        TCGA-ES-A2HT        TCGA-FV-A23B        TCGA-FV-A2QR 
  "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-FV-A3I0        TCGA-FV-A3I1        TCGA-FV-A3R2        TCGA-FV-A3R3 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" 
       TCGA-FV-A495        TCGA-FV-A496        TCGA-FV-A4ZP        TCGA-FV-A4ZQ 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U        TCGA-G3-A25V 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y        TCGA-G3-A25Z 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI        TCGA-G3-A3CJ 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-G3-A3CK        TCGA-G3-A5SI        TCGA-G3-A5SJ        TCGA-G3-A5SL 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-G3-A5SM        TCGA-G3-A6UC        TCGA-GJ-A6C0        TCGA-K7-A6G5 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-LG-A6GG        TCGA-MI-A75C        TCGA-MI-A75E        TCGA-MI-A75G 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" 
       TCGA-MI-A75I        TCGA-NI-A4U2        TCGA-O8-A75V 
"3Q GAIN WILD-TYPE" "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 MUTATED" "3Q GAIN WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-BC-A5W4        TCGA-BC-A69H        TCGA-BC-A69I 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" 
       TCGA-CC-5258        TCGA-CC-5260        TCGA-CC-5261        TCGA-CC-5262 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-CC-5263        TCGA-CC-A1HT        TCGA-CC-A3M9        TCGA-CC-A3MA 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" 
       TCGA-CC-A3MB        TCGA-CC-A3MC        TCGA-DD-A113        TCGA-DD-A114 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" 
       TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118        TCGA-DD-A119 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C        TCGA-DD-A11D 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" 
       TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB        TCGA-DD-A1EC 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EF        TCGA-DD-A1EG 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" 
       TCGA-DD-A1EH        TCGA-DD-A1EI        TCGA-DD-A1EJ        TCGA-DD-A1EK 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" 
       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-A4NB        TCGA-DD-A4ND        TCGA-DD-A4NF        TCGA-DD-A4NH 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-DD-A4NI        TCGA-DD-A4NJ        TCGA-DD-A4NK        TCGA-DD-A4NL 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-DD-A4NN        TCGA-DD-A4NO        TCGA-DD-A4NP        TCGA-DD-A4NQ 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-DD-A4NR        TCGA-DD-A4NS        TCGA-DD-A4NV        TCGA-DD-A73A 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" 
       TCGA-DD-A73B        TCGA-DD-A73C        TCGA-DD-A73D        TCGA-DD-A73E 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" 
       TCGA-DD-A73F        TCGA-DD-A73G        TCGA-ED-A459        TCGA-ED-A4XI 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-ED-A5KG        TCGA-ED-A627        TCGA-ED-A66X        TCGA-ED-A66Y 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-ED-A7PX        TCGA-ED-A7PY        TCGA-ED-A7PZ        TCGA-ED-A7XP 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-ED-A82E        TCGA-EP-A12J        TCGA-EP-A26S        TCGA-EP-A2KA 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-EP-A2KB        TCGA-EP-A2KC        TCGA-EP-A3JL        TCGA-EP-A3RK 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-ES-A2HS        TCGA-ES-A2HT        TCGA-FV-A23B        TCGA-FV-A2QR 
  "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-FV-A3I0        TCGA-FV-A3I1        TCGA-FV-A3R2        TCGA-FV-A3R3 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" 
       TCGA-FV-A495        TCGA-FV-A496        TCGA-FV-A4ZP        TCGA-FV-A4ZQ 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U        TCGA-G3-A25V 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y        TCGA-G3-A25Z 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI        TCGA-G3-A3CJ 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-G3-A3CK        TCGA-G3-A5SI        TCGA-G3-A5SJ        TCGA-G3-A5SL 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-G3-A5SM        TCGA-G3-A6UC        TCGA-GJ-A6C0        TCGA-K7-A6G5 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-LG-A6GG        TCGA-MI-A75C        TCGA-MI-A75E        TCGA-MI-A75G 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" 
       TCGA-MI-A75I        TCGA-NI-A4U2        TCGA-O8-A75V 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
[1] "hr=" "1.7"
D6V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  3Q GAIN MUTATED         6        4         0          2          0          1
  3Q GAIN WILD-TYPE      52       32         2         28          4          4
                   vv
clus                STAGE IV STAGE IVA STAGE IVB
  3Q GAIN MUTATED          0         0         0
  3Q GAIN WILD-TYPE        1         1         2
D6V3, multiclass
                   vv
clus                T1 T2 T3 T4
  3Q GAIN MUTATED    7  4  3  0
  3Q GAIN WILD-TYPE 54 36 37  8
D6V4, multiclass
    clus
vv   3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  T1               7                54
  T2               4                36
  T3               3                37
  T4               0                 8
D6V5, binary
                   cls
clus                 0  1
  3Q GAIN MUTATED    6  1
  3Q GAIN WILD-TYPE 91  2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED      6    1
  3Q GAIN WILD-TYPE   91    2
   clus
vv  3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  0               6                91
  1               1                 2
                   vv
clus                 M0  M1  MX
  3Q GAIN MUTATED    11   0   3
  3Q GAIN WILD-TYPE 104   3  28
D6V6, multiclass
    clus
vv   3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  M0              11               104
  M1               0                 3
  MX               3                28
D6V7, binary
                   cls
clus                 0  1
  3Q GAIN MUTATED    4 10
  3Q GAIN WILD-TYPE 54 81
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED      4   10
  3Q GAIN WILD-TYPE   54   81
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  FEMALE               4                54
  MALE                10                81
                   vv
clus                 R0  R1  R2  RX
  3Q GAIN MUTATED    13   0   0   1
  3Q GAIN WILD-TYPE 109  11   1   9
D6V8, multiclass
    clus
vv   3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  R0              13               109
  R1               0                11
  R2               0                 1
  RX               1                 9

Clustering(7) Variable = 4P GAIN MUTATION ANALYSIS
D7V1, survival
                   sevent
clus2                0  1
  4P GAIN MUTATED   10  2
  4P GAIN WILD-TYPE 74 61
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               12               135 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                2                61 
$`4P GAIN MUTATED`
TCGA-BC-A10R TCGA-CC-5261 TCGA-CC-A3M9 TCGA-CC-A3MB TCGA-DD-A118 TCGA-DD-A11A 
       10.13         0.39         0.10         0.10       113.00         2.60 
TCGA-DD-A1EC TCGA-DD-A1EH TCGA-DD-A73G TCGA-ED-A82E TCGA-G3-A3CG TCGA-LG-A6GG 
       19.79        49.15       100.96         0.20        22.13         0.49 

$`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-BC-A69H 
       44.42        13.84         0.26        22.36         9.50         3.95 
TCGA-BC-A69I TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A1HT 
        0.53         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        37.78        83.57        53.33 
TCGA-DD-A119 TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA 
        7.33         0.46        21.76        51.29        90.71        79.40 
TCGA-DD-A1EB TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EI 
       66.31        75.65         6.71        12.95        45.11         6.02 
TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39X TCGA-DD-A39Y 
       29.16        18.35        13.64        21.14        55.69         5.62 
TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 
       19.76        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        30.61        33.14 
TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ 
       12.85        73.38        14.07        14.24        18.44        15.06 
TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ 
       39.78        56.25        29.56        61.45        93.67        12.26 
TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C 
        0.30        80.75        66.35        10.98         9.30         7.56 
TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG 
       10.98         1.45        27.72        13.41        12.69        15.85 
TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ 
       13.91        13.35         0.23         0.20         0.20         0.20 
TCGA-ED-A7XP TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC 
        0.20        18.74        19.99        11.74        10.98         0.62 
TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QR 
        9.96        11.93        22.85        14.40        32.45        19.10 
TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 
        0.20         8.12         6.38         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        51.06        53.79        28.27 
TCGA-G3-A25W TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CH TCGA-G3-A3CI 
       30.74        58.49        14.86        21.53        25.64         5.92 
TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SL TCGA-G3-A5SM 
       19.53        19.23        14.70        11.97         7.99         4.37 
TCGA-G3-A6UC TCGA-GJ-A6C0 TCGA-K7-A6G5 TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G 
        7.76         1.02         4.01         9.57         5.10        14.24 
TCGA-MI-A75I TCGA-NI-A4U2 TCGA-O8-A75V 
        8.71        58.88         4.44 

  4P GAIN MUTATED 4P GAIN WILD-TYPE 
             0.10              0.03 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
           113.00            107.11 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
            6.365            14.240 
[1] "0.1 - 113.0 (6.4)"  "0.0 - 107.1 (14.2)"
       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-BC-A69H        TCGA-BC-A69I 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-CC-5258        TCGA-CC-5260        TCGA-CC-5261        TCGA-CC-5262 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE"   "4P GAIN MUTATED" "4P GAIN WILD-TYPE" 
       TCGA-CC-5263        TCGA-CC-A1HT        TCGA-CC-A3M9        TCGA-CC-A3MA 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE"   "4P GAIN MUTATED" "4P GAIN WILD-TYPE" 
       TCGA-CC-A3MB        TCGA-CC-A3MC        TCGA-DD-A113        TCGA-DD-A114 
  "4P GAIN MUTATED" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118        TCGA-DD-A119 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE"   "4P GAIN MUTATED" "4P GAIN WILD-TYPE" 
       TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C        TCGA-DD-A11D 
  "4P GAIN MUTATED" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB        TCGA-DD-A1EC 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE"   "4P GAIN MUTATED" 
       TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EF        TCGA-DD-A1EG 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DD-A1EH        TCGA-DD-A1EI        TCGA-DD-A1EJ        TCGA-DD-A1EK 
  "4P GAIN MUTATED" "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-A4NB        TCGA-DD-A4ND        TCGA-DD-A4NF        TCGA-DD-A4NH 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DD-A4NI        TCGA-DD-A4NJ        TCGA-DD-A4NK        TCGA-DD-A4NL 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DD-A4NN        TCGA-DD-A4NO        TCGA-DD-A4NP        TCGA-DD-A4NQ 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DD-A4NR        TCGA-DD-A4NS        TCGA-DD-A4NV        TCGA-DD-A73A 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DD-A73B        TCGA-DD-A73C        TCGA-DD-A73D        TCGA-DD-A73E 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DD-A73F        TCGA-DD-A73G        TCGA-ED-A459        TCGA-ED-A4XI 
"4P GAIN WILD-TYPE"   "4P GAIN MUTATED" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-ED-A5KG        TCGA-ED-A627        TCGA-ED-A66X        TCGA-ED-A66Y 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-ED-A7PX        TCGA-ED-A7PY        TCGA-ED-A7PZ        TCGA-ED-A7XP 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-ED-A82E        TCGA-EP-A12J        TCGA-EP-A26S        TCGA-EP-A2KA 
  "4P GAIN MUTATED" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EP-A2KB        TCGA-EP-A2KC        TCGA-EP-A3JL        TCGA-EP-A3RK 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-ES-A2HS        TCGA-ES-A2HT        TCGA-FV-A23B        TCGA-FV-A2QR 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-FV-A3I0        TCGA-FV-A3I1        TCGA-FV-A3R2        TCGA-FV-A3R3 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-FV-A495        TCGA-FV-A496        TCGA-FV-A4ZP        TCGA-FV-A4ZQ 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U        TCGA-G3-A25V 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y        TCGA-G3-A25Z 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI        TCGA-G3-A3CJ 
  "4P GAIN MUTATED" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-G3-A3CK        TCGA-G3-A5SI        TCGA-G3-A5SJ        TCGA-G3-A5SL 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-G3-A5SM        TCGA-G3-A6UC        TCGA-GJ-A6C0        TCGA-K7-A6G5 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-LG-A6GG        TCGA-MI-A75C        TCGA-MI-A75E        TCGA-MI-A75G 
  "4P GAIN MUTATED" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-MI-A75I        TCGA-NI-A4U2        TCGA-O8-A75V 
"4P GAIN WILD-TYPE" "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-BC-A69H        TCGA-BC-A69I 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-CC-5258        TCGA-CC-5260        TCGA-CC-5261        TCGA-CC-5262 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE"   "4P GAIN MUTATED" "4P GAIN WILD-TYPE" 
       TCGA-CC-5263        TCGA-CC-A1HT        TCGA-CC-A3M9        TCGA-CC-A3MA 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE"   "4P GAIN MUTATED" "4P GAIN WILD-TYPE" 
       TCGA-CC-A3MB        TCGA-CC-A3MC        TCGA-DD-A113        TCGA-DD-A114 
  "4P GAIN MUTATED" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118        TCGA-DD-A119 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE"   "4P GAIN MUTATED" "4P GAIN WILD-TYPE" 
       TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C        TCGA-DD-A11D 
  "4P GAIN MUTATED" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB        TCGA-DD-A1EC 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE"   "4P GAIN MUTATED" 
       TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EF        TCGA-DD-A1EG 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DD-A1EH        TCGA-DD-A1EI        TCGA-DD-A1EJ        TCGA-DD-A1EK 
  "4P GAIN MUTATED" "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-A4NB        TCGA-DD-A4ND        TCGA-DD-A4NF        TCGA-DD-A4NH 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DD-A4NI        TCGA-DD-A4NJ        TCGA-DD-A4NK        TCGA-DD-A4NL 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DD-A4NN        TCGA-DD-A4NO        TCGA-DD-A4NP        TCGA-DD-A4NQ 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DD-A4NR        TCGA-DD-A4NS        TCGA-DD-A4NV        TCGA-DD-A73A 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DD-A73B        TCGA-DD-A73C        TCGA-DD-A73D        TCGA-DD-A73E 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DD-A73F        TCGA-DD-A73G        TCGA-ED-A459        TCGA-ED-A4XI 
"4P GAIN WILD-TYPE"   "4P GAIN MUTATED" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-ED-A5KG        TCGA-ED-A627        TCGA-ED-A66X        TCGA-ED-A66Y 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-ED-A7PX        TCGA-ED-A7PY        TCGA-ED-A7PZ        TCGA-ED-A7XP 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-ED-A82E        TCGA-EP-A12J        TCGA-EP-A26S        TCGA-EP-A2KA 
  "4P GAIN MUTATED" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EP-A2KB        TCGA-EP-A2KC        TCGA-EP-A3JL        TCGA-EP-A3RK 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-ES-A2HS        TCGA-ES-A2HT        TCGA-FV-A23B        TCGA-FV-A2QR 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-FV-A3I0        TCGA-FV-A3I1        TCGA-FV-A3R2        TCGA-FV-A3R3 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-FV-A495        TCGA-FV-A496        TCGA-FV-A4ZP        TCGA-FV-A4ZQ 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U        TCGA-G3-A25V 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y        TCGA-G3-A25Z 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI        TCGA-G3-A3CJ 
  "4P GAIN MUTATED" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-G3-A3CK        TCGA-G3-A5SI        TCGA-G3-A5SJ        TCGA-G3-A5SL 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-G3-A5SM        TCGA-G3-A6UC        TCGA-GJ-A6C0        TCGA-K7-A6G5 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-LG-A6GG        TCGA-MI-A75C        TCGA-MI-A75E        TCGA-MI-A75G 
  "4P GAIN MUTATED" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-MI-A75I        TCGA-NI-A4U2        TCGA-O8-A75V 
"4P GAIN WILD-TYPE" "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-BC-A69H        TCGA-BC-A69I 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-CC-5258        TCGA-CC-5260        TCGA-CC-5261        TCGA-CC-5262 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE"   "4P GAIN MUTATED" "4P GAIN WILD-TYPE" 
       TCGA-CC-5263        TCGA-CC-A1HT        TCGA-CC-A3M9        TCGA-CC-A3MA 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE"   "4P GAIN MUTATED" "4P GAIN WILD-TYPE" 
       TCGA-CC-A3MB        TCGA-CC-A3MC        TCGA-DD-A113        TCGA-DD-A114 
  "4P GAIN MUTATED" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118        TCGA-DD-A119 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE"   "4P GAIN MUTATED" "4P GAIN WILD-TYPE" 
       TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C        TCGA-DD-A11D 
  "4P GAIN MUTATED" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB        TCGA-DD-A1EC 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE"   "4P GAIN MUTATED" 
       TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EF        TCGA-DD-A1EG 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DD-A1EH        TCGA-DD-A1EI        TCGA-DD-A1EJ        TCGA-DD-A1EK 
  "4P GAIN MUTATED" "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-A4NB        TCGA-DD-A4ND        TCGA-DD-A4NF        TCGA-DD-A4NH 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DD-A4NI        TCGA-DD-A4NJ        TCGA-DD-A4NK        TCGA-DD-A4NL 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DD-A4NN        TCGA-DD-A4NO        TCGA-DD-A4NP        TCGA-DD-A4NQ 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DD-A4NR        TCGA-DD-A4NS        TCGA-DD-A4NV        TCGA-DD-A73A 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DD-A73B        TCGA-DD-A73C        TCGA-DD-A73D        TCGA-DD-A73E 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DD-A73F        TCGA-DD-A73G        TCGA-ED-A459        TCGA-ED-A4XI 
"4P GAIN WILD-TYPE"   "4P GAIN MUTATED" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-ED-A5KG        TCGA-ED-A627        TCGA-ED-A66X        TCGA-ED-A66Y 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-ED-A7PX        TCGA-ED-A7PY        TCGA-ED-A7PZ        TCGA-ED-A7XP 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-ED-A82E        TCGA-EP-A12J        TCGA-EP-A26S        TCGA-EP-A2KA 
  "4P GAIN MUTATED" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EP-A2KB        TCGA-EP-A2KC        TCGA-EP-A3JL        TCGA-EP-A3RK 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-ES-A2HS        TCGA-ES-A2HT        TCGA-FV-A23B        TCGA-FV-A2QR 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-FV-A3I0        TCGA-FV-A3I1        TCGA-FV-A3R2        TCGA-FV-A3R3 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-FV-A495        TCGA-FV-A496        TCGA-FV-A4ZP        TCGA-FV-A4ZQ 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U        TCGA-G3-A25V 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y        TCGA-G3-A25Z 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI        TCGA-G3-A3CJ 
  "4P GAIN MUTATED" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-G3-A3CK        TCGA-G3-A5SI        TCGA-G3-A5SJ        TCGA-G3-A5SL 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-G3-A5SM        TCGA-G3-A6UC        TCGA-GJ-A6C0        TCGA-K7-A6G5 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-LG-A6GG        TCGA-MI-A75C        TCGA-MI-A75E        TCGA-MI-A75G 
  "4P GAIN MUTATED" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-MI-A75I        TCGA-NI-A4U2        TCGA-O8-A75V 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
[1] "hr=" "3.4"
D7V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  4P GAIN MUTATED         4        3         1          3          0          0
  4P GAIN WILD-TYPE      54       33         1         27          4          5
                   vv
clus                STAGE IV STAGE IVA STAGE IVB
  4P GAIN MUTATED          0         0         0
  4P GAIN WILD-TYPE        1         1         2
D7V3, multiclass
                   vv
clus                T1 T2 T3 T4
  4P GAIN MUTATED    4  3  5  0
  4P GAIN WILD-TYPE 57 37 35  8
D7V4, multiclass
    clus
vv   4P GAIN MUTATED 4P GAIN WILD-TYPE
  T1               4                57
  T2               3                37
  T3               5                35
  T4               0                 8
D7V5, binary
                   cls
clus                 0  1
  4P GAIN MUTATED   10  0
  4P GAIN WILD-TYPE 87  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED     10    0
  4P GAIN WILD-TYPE   87    3
   clus
vv  4P GAIN MUTATED 4P GAIN WILD-TYPE
  0              10                87
  1               0                 3
                   vv
clus                 M0  M1  MX
  4P GAIN MUTATED    11   0   1
  4P GAIN WILD-TYPE 104   3  30
D7V6, multiclass
    clus
vv   4P GAIN MUTATED 4P GAIN WILD-TYPE
  M0              11               104
  M1               0                 3
  MX               1                30
D7V7, binary
                   cls
clus                 0  1
  4P GAIN MUTATED    6  6
  4P GAIN WILD-TYPE 52 85
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED      6    6
  4P GAIN WILD-TYPE   52   85
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  FEMALE               6                52
  MALE                 6                85
                   vv
clus                 R0  R1  R2  RX
  4P GAIN MUTATED    10   1   0   1
  4P GAIN WILD-TYPE 112  10   1   9
D7V8, multiclass
    clus
vv   4P GAIN MUTATED 4P GAIN WILD-TYPE
  R0              10               112
  R1               1                10
  R2               0                 1
  RX               1                 9

Clustering(8) Variable = 4Q GAIN MUTATION ANALYSIS
D8V1, survival
                   sevent
clus2                0  1
  4Q GAIN MUTATED    3  1
  4Q GAIN WILD-TYPE 81 62
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                4               143 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                1                62 
$`4Q GAIN MUTATED`
TCGA-CC-5261 TCGA-DD-A1EC TCGA-ED-A82E TCGA-G3-A3CG 
        0.39        19.79         0.20        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        13.84         0.26        22.36         9.50 
TCGA-BC-A69H TCGA-BC-A69I TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5262 TCGA-CC-5263 
        3.95         0.53         0.07         2.86         3.39         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-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A 
       37.78        83.57        53.33       113.00         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        51.29        90.71        79.40        66.31 
TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI 
       75.65         6.71        12.95        45.11        49.15         6.02 
TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39X TCGA-DD-A39Y 
       29.16        18.35        13.64        21.14        55.69         5.62 
TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 
       19.76        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        30.61        33.14 
TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ 
       12.85        73.38        14.07        14.24        18.44        15.06 
TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ 
       39.78        56.25        29.56        61.45        93.67        12.26 
TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C 
        0.30        80.75        66.35        10.98         9.30         7.56 
TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G TCGA-ED-A459 TCGA-ED-A4XI 
       10.98         1.45        27.72       100.96        13.41        12.69 
TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY 
       15.85        13.91        13.35         0.23         0.20         0.20 
TCGA-ED-A7PZ TCGA-ED-A7XP TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB 
        0.20         0.20        18.74        19.99        11.74        10.98 
TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A23B 
        0.62         9.96        11.93        22.85        14.40        32.45 
TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 
       19.10         0.20         8.12         6.38         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        51.06        53.79 
TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CH 
       28.27        30.74        58.49        14.86        21.53        25.64 
TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SL 
        5.92        19.53        19.23        14.70        11.97         7.99 
TCGA-G3-A5SM TCGA-G3-A6UC TCGA-GJ-A6C0 TCGA-K7-A6G5 TCGA-LG-A6GG TCGA-MI-A75C 
        4.37         7.76         1.02         4.01         0.49         9.57 
TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75I TCGA-NI-A4U2 TCGA-O8-A75V 
        5.10        14.24         8.71        58.88         4.44 

  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
             0.20              0.03 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
            22.13            113.00 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
            10.09             14.07 
[1] "0.2 - 22.1 (10.1)"  "0.0 - 113.0 (14.1)"
       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-BC-A69H        TCGA-BC-A69I 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-CC-5258        TCGA-CC-5260        TCGA-CC-5261        TCGA-CC-5262 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE"   "4Q GAIN MUTATED" "4Q GAIN WILD-TYPE" 
       TCGA-CC-5263        TCGA-CC-A1HT        TCGA-CC-A3M9        TCGA-CC-A3MA 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-CC-A3MB        TCGA-CC-A3MC        TCGA-DD-A113        TCGA-DD-A114 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118        TCGA-DD-A119 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C        TCGA-DD-A11D 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB        TCGA-DD-A1EC 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE"   "4Q GAIN MUTATED" 
       TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EF        TCGA-DD-A1EG 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DD-A1EH        TCGA-DD-A1EI        TCGA-DD-A1EJ        TCGA-DD-A1EK 
"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-A4NB        TCGA-DD-A4ND        TCGA-DD-A4NF        TCGA-DD-A4NH 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DD-A4NI        TCGA-DD-A4NJ        TCGA-DD-A4NK        TCGA-DD-A4NL 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DD-A4NN        TCGA-DD-A4NO        TCGA-DD-A4NP        TCGA-DD-A4NQ 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DD-A4NR        TCGA-DD-A4NS        TCGA-DD-A4NV        TCGA-DD-A73A 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DD-A73B        TCGA-DD-A73C        TCGA-DD-A73D        TCGA-DD-A73E 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DD-A73F        TCGA-DD-A73G        TCGA-ED-A459        TCGA-ED-A4XI 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-ED-A5KG        TCGA-ED-A627        TCGA-ED-A66X        TCGA-ED-A66Y 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-ED-A7PX        TCGA-ED-A7PY        TCGA-ED-A7PZ        TCGA-ED-A7XP 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-ED-A82E        TCGA-EP-A12J        TCGA-EP-A26S        TCGA-EP-A2KA 
  "4Q GAIN MUTATED" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EP-A2KB        TCGA-EP-A2KC        TCGA-EP-A3JL        TCGA-EP-A3RK 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-ES-A2HS        TCGA-ES-A2HT        TCGA-FV-A23B        TCGA-FV-A2QR 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-FV-A3I0        TCGA-FV-A3I1        TCGA-FV-A3R2        TCGA-FV-A3R3 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-FV-A495        TCGA-FV-A496        TCGA-FV-A4ZP        TCGA-FV-A4ZQ 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U        TCGA-G3-A25V 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y        TCGA-G3-A25Z 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI        TCGA-G3-A3CJ 
  "4Q GAIN MUTATED" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-G3-A3CK        TCGA-G3-A5SI        TCGA-G3-A5SJ        TCGA-G3-A5SL 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-G3-A5SM        TCGA-G3-A6UC        TCGA-GJ-A6C0        TCGA-K7-A6G5 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-LG-A6GG        TCGA-MI-A75C        TCGA-MI-A75E        TCGA-MI-A75G 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-MI-A75I        TCGA-NI-A4U2        TCGA-O8-A75V 
"4Q GAIN WILD-TYPE" "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-BC-A69H        TCGA-BC-A69I 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-CC-5258        TCGA-CC-5260        TCGA-CC-5261        TCGA-CC-5262 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE"   "4Q GAIN MUTATED" "4Q GAIN WILD-TYPE" 
       TCGA-CC-5263        TCGA-CC-A1HT        TCGA-CC-A3M9        TCGA-CC-A3MA 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-CC-A3MB        TCGA-CC-A3MC        TCGA-DD-A113        TCGA-DD-A114 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118        TCGA-DD-A119 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C        TCGA-DD-A11D 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB        TCGA-DD-A1EC 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE"   "4Q GAIN MUTATED" 
       TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EF        TCGA-DD-A1EG 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DD-A1EH        TCGA-DD-A1EI        TCGA-DD-A1EJ        TCGA-DD-A1EK 
"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-A4NB        TCGA-DD-A4ND        TCGA-DD-A4NF        TCGA-DD-A4NH 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DD-A4NI        TCGA-DD-A4NJ        TCGA-DD-A4NK        TCGA-DD-A4NL 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DD-A4NN        TCGA-DD-A4NO        TCGA-DD-A4NP        TCGA-DD-A4NQ 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DD-A4NR        TCGA-DD-A4NS        TCGA-DD-A4NV        TCGA-DD-A73A 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DD-A73B        TCGA-DD-A73C        TCGA-DD-A73D        TCGA-DD-A73E 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DD-A73F        TCGA-DD-A73G        TCGA-ED-A459        TCGA-ED-A4XI 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-ED-A5KG        TCGA-ED-A627        TCGA-ED-A66X        TCGA-ED-A66Y 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-ED-A7PX        TCGA-ED-A7PY        TCGA-ED-A7PZ        TCGA-ED-A7XP 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-ED-A82E        TCGA-EP-A12J        TCGA-EP-A26S        TCGA-EP-A2KA 
  "4Q GAIN MUTATED" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EP-A2KB        TCGA-EP-A2KC        TCGA-EP-A3JL        TCGA-EP-A3RK 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-ES-A2HS        TCGA-ES-A2HT        TCGA-FV-A23B        TCGA-FV-A2QR 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-FV-A3I0        TCGA-FV-A3I1        TCGA-FV-A3R2        TCGA-FV-A3R3 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-FV-A495        TCGA-FV-A496        TCGA-FV-A4ZP        TCGA-FV-A4ZQ 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U        TCGA-G3-A25V 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y        TCGA-G3-A25Z 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI        TCGA-G3-A3CJ 
  "4Q GAIN MUTATED" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-G3-A3CK        TCGA-G3-A5SI        TCGA-G3-A5SJ        TCGA-G3-A5SL 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-G3-A5SM        TCGA-G3-A6UC        TCGA-GJ-A6C0        TCGA-K7-A6G5 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-LG-A6GG        TCGA-MI-A75C        TCGA-MI-A75E        TCGA-MI-A75G 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-MI-A75I        TCGA-NI-A4U2        TCGA-O8-A75V 
"4Q GAIN WILD-TYPE" "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-BC-A69H        TCGA-BC-A69I 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-CC-5258        TCGA-CC-5260        TCGA-CC-5261        TCGA-CC-5262 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE"   "4Q GAIN MUTATED" "4Q GAIN WILD-TYPE" 
       TCGA-CC-5263        TCGA-CC-A1HT        TCGA-CC-A3M9        TCGA-CC-A3MA 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-CC-A3MB        TCGA-CC-A3MC        TCGA-DD-A113        TCGA-DD-A114 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118        TCGA-DD-A119 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C        TCGA-DD-A11D 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB        TCGA-DD-A1EC 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE"   "4Q GAIN MUTATED" 
       TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EF        TCGA-DD-A1EG 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DD-A1EH        TCGA-DD-A1EI        TCGA-DD-A1EJ        TCGA-DD-A1EK 
"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-A4NB        TCGA-DD-A4ND        TCGA-DD-A4NF        TCGA-DD-A4NH 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DD-A4NI        TCGA-DD-A4NJ        TCGA-DD-A4NK        TCGA-DD-A4NL 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DD-A4NN        TCGA-DD-A4NO        TCGA-DD-A4NP        TCGA-DD-A4NQ 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DD-A4NR        TCGA-DD-A4NS        TCGA-DD-A4NV        TCGA-DD-A73A 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DD-A73B        TCGA-DD-A73C        TCGA-DD-A73D        TCGA-DD-A73E 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DD-A73F        TCGA-DD-A73G        TCGA-ED-A459        TCGA-ED-A4XI 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-ED-A5KG        TCGA-ED-A627        TCGA-ED-A66X        TCGA-ED-A66Y 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-ED-A7PX        TCGA-ED-A7PY        TCGA-ED-A7PZ        TCGA-ED-A7XP 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-ED-A82E        TCGA-EP-A12J        TCGA-EP-A26S        TCGA-EP-A2KA 
  "4Q GAIN MUTATED" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EP-A2KB        TCGA-EP-A2KC        TCGA-EP-A3JL        TCGA-EP-A3RK 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-ES-A2HS        TCGA-ES-A2HT        TCGA-FV-A23B        TCGA-FV-A2QR 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-FV-A3I0        TCGA-FV-A3I1        TCGA-FV-A3R2        TCGA-FV-A3R3 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-FV-A495        TCGA-FV-A496        TCGA-FV-A4ZP        TCGA-FV-A4ZQ 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U        TCGA-G3-A25V 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y        TCGA-G3-A25Z 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI        TCGA-G3-A3CJ 
  "4Q GAIN MUTATED" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-G3-A3CK        TCGA-G3-A5SI        TCGA-G3-A5SJ        TCGA-G3-A5SL 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-G3-A5SM        TCGA-G3-A6UC        TCGA-GJ-A6C0        TCGA-K7-A6G5 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-LG-A6GG        TCGA-MI-A75C        TCGA-MI-A75E        TCGA-MI-A75G 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-MI-A75I        TCGA-NI-A4U2        TCGA-O8-A75V 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
[1] "hr=" "1.3"
D8V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  4Q GAIN MUTATED         2        1         0          1          0          0
  4Q GAIN WILD-TYPE      56       35         2         29          4          5
                   vv
clus                STAGE IV STAGE IVA STAGE IVB
  4Q GAIN MUTATED          0         0         0
  4Q GAIN WILD-TYPE        1         1         2
D8V3, multiclass
                   vv
clus                T1 T2 T3 T4
  4Q GAIN MUTATED    2  1  1  0
  4Q GAIN WILD-TYPE 59 39 39  8
D8V4, multiclass
    clus
vv   4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  T1               2                59
  T2               1                39
  T3               1                39
  T4               0                 8
D8V5, binary
                   cls
clus                 0  1
  4Q GAIN MUTATED    4  0
  4Q GAIN WILD-TYPE 93  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED      4    0
  4Q GAIN WILD-TYPE   93    3
   clus
vv  4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  0               4                93
  1               0                 3
                   vv
clus                 M0  M1  MX
  4Q GAIN MUTATED     4   0   0
  4Q GAIN WILD-TYPE 111   3  31
D8V6, multiclass
    clus
vv   4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  M0               4               111
  M1               0                 3
  MX               0                31
D8V7, binary
                   cls
clus                 0  1
  4Q GAIN MUTATED    2  2
  4Q GAIN WILD-TYPE 56 89
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED      2    2
  4Q GAIN WILD-TYPE   56   89
        clus
vv       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  FEMALE               2                56
  MALE                 2                89
                   vv
clus                 R0  R1  R2  RX
  4Q GAIN MUTATED     2   1   0   1
  4Q GAIN WILD-TYPE 120  10   1   9
D8V8, multiclass
    clus
vv   4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  R0               2               120
  R1               1                10
  R2               0                 1
  RX               1                 9

Clustering(9) Variable = 5P GAIN MUTATION ANALYSIS
D9V1, survival
                   sevent
clus2                0  1
  5P GAIN MUTATED   31 26
  5P GAIN WILD-TYPE 53 37
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               57                90 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               26                37 
$`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        13.84        22.36 
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        53.33 
TCGA-DD-A118 TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EE 
      113.00        51.29        90.71        79.40        66.31         6.71 
TCGA-DD-A1EF TCGA-DD-A39V TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A3A1 TCGA-DD-A3A3 
       12.95        21.14        55.69         5.62         7.66        17.59 
TCGA-DD-A3A5 TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A4ND TCGA-DD-A4NK TCGA-DD-A4NO 
      102.74        13.78         0.36        73.38        39.78        61.45 
TCGA-DD-A4NV TCGA-DD-A73G TCGA-ED-A459 TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7XP 
       66.35       100.96        13.41        13.35         0.23         0.20 
TCGA-ED-A82E TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL TCGA-ES-A2HT TCGA-FV-A2QR 
        0.20        10.98         0.62         9.96        14.40        19.10 
TCGA-FV-A3I0 TCGA-FV-A495 TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25T TCGA-G3-A25W 
        0.20         0.03        60.36         0.39        51.06        30.74 
TCGA-G3-A25X TCGA-G3-A3CG TCGA-G3-A5SI TCGA-G3-A5SM TCGA-LG-A6GG TCGA-MI-A75G 
       58.49        22.13        14.70         4.37         0.49        14.24 
TCGA-MI-A75I TCGA-NI-A4U2 TCGA-O8-A75V 
        8.71        58.88         4.44 

$`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-BC-A69H TCGA-BC-A69I TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 
        3.95         0.53         0.07         2.86         0.39         3.39 
TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A119 TCGA-DD-A11A 
        0.10         0.07        79.73        37.78         7.33         2.60 
TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EG TCGA-DD-A1EH 
        0.46        21.76        19.79        75.65        45.11        49.15 
TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39Z TCGA-DD-A3A0 
        6.02        29.16        18.35        13.64        19.76        25.81 
TCGA-DD-A3A2 TCGA-DD-A3A4 TCGA-DD-A3A6 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB 
       70.06        20.12       107.11        30.61        33.14        12.85 
TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NL TCGA-DD-A4NN 
       14.07        14.24        18.44        15.06        56.25        29.56 
TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A73A TCGA-DD-A73B 
       93.67        12.26         0.30        80.75        10.98         9.30 
TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-ED-A4XI TCGA-ED-A5KG 
        7.56        10.98         1.45        27.72        12.69        15.85 
TCGA-ED-A627 TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-EP-A12J TCGA-EP-A26S 
       13.91         0.20         0.20         0.20        18.74        19.99 
TCGA-EP-A2KA TCGA-EP-A3RK TCGA-ES-A2HS TCGA-FV-A23B TCGA-FV-A3I1 TCGA-FV-A3R2 
       11.74        11.93        22.85        32.45         8.12         6.38 
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         5.92        19.53        19.23        11.97 
TCGA-G3-A5SL TCGA-G3-A6UC TCGA-GJ-A6C0 TCGA-K7-A6G5 TCGA-MI-A75C TCGA-MI-A75E 
        7.99         7.76         1.02         4.01         9.57         5.10 

  5P GAIN MUTATED 5P GAIN WILD-TYPE 
             0.03              0.07 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
           113.00            107.11 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
           13.840            14.155 
[1] "0.0 - 113.0 (13.8)" "0.1 - 107.1 (14.2)"
       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-BC-A69H        TCGA-BC-A69I 
  "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-CC-5258        TCGA-CC-5260        TCGA-CC-5261        TCGA-CC-5262 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-CC-5263        TCGA-CC-A1HT        TCGA-CC-A3M9        TCGA-CC-A3MA 
  "5P GAIN MUTATED"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-CC-A3MB        TCGA-CC-A3MC        TCGA-DD-A113        TCGA-DD-A114 
  "5P GAIN MUTATED"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118        TCGA-DD-A119 
  "5P GAIN MUTATED"   "5P GAIN MUTATED"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" 
       TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C        TCGA-DD-A11D 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" 
       TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB        TCGA-DD-A1EC 
  "5P GAIN MUTATED"   "5P GAIN MUTATED"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" 
       TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EF        TCGA-DD-A1EG 
"5P GAIN WILD-TYPE"   "5P GAIN MUTATED"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" 
       TCGA-DD-A1EH        TCGA-DD-A1EI        TCGA-DD-A1EJ        TCGA-DD-A1EK 
"5P GAIN WILD-TYPE" "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-A4NB        TCGA-DD-A4ND        TCGA-DD-A4NF        TCGA-DD-A4NH 
"5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-DD-A4NI        TCGA-DD-A4NJ        TCGA-DD-A4NK        TCGA-DD-A4NL 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" 
       TCGA-DD-A4NN        TCGA-DD-A4NO        TCGA-DD-A4NP        TCGA-DD-A4NQ 
"5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-DD-A4NR        TCGA-DD-A4NS        TCGA-DD-A4NV        TCGA-DD-A73A 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" 
       TCGA-DD-A73B        TCGA-DD-A73C        TCGA-DD-A73D        TCGA-DD-A73E 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-DD-A73F        TCGA-DD-A73G        TCGA-ED-A459        TCGA-ED-A4XI 
"5P GAIN WILD-TYPE"   "5P GAIN MUTATED"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" 
       TCGA-ED-A5KG        TCGA-ED-A627        TCGA-ED-A66X        TCGA-ED-A66Y 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED"   "5P GAIN MUTATED" 
       TCGA-ED-A7PX        TCGA-ED-A7PY        TCGA-ED-A7PZ        TCGA-ED-A7XP 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" 
       TCGA-ED-A82E        TCGA-EP-A12J        TCGA-EP-A26S        TCGA-EP-A2KA 
  "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-EP-A2KB        TCGA-EP-A2KC        TCGA-EP-A3JL        TCGA-EP-A3RK 
  "5P GAIN MUTATED"   "5P GAIN MUTATED"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" 
       TCGA-ES-A2HS        TCGA-ES-A2HT        TCGA-FV-A23B        TCGA-FV-A2QR 
"5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" 
       TCGA-FV-A3I0        TCGA-FV-A3I1        TCGA-FV-A3R2        TCGA-FV-A3R3 
  "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-FV-A495        TCGA-FV-A496        TCGA-FV-A4ZP        TCGA-FV-A4ZQ 
  "5P GAIN MUTATED" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED"   "5P GAIN MUTATED" 
       TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U        TCGA-G3-A25V 
"5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y        TCGA-G3-A25Z 
  "5P GAIN MUTATED"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI        TCGA-G3-A3CJ 
  "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-G3-A3CK        TCGA-G3-A5SI        TCGA-G3-A5SJ        TCGA-G3-A5SL 
"5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-G3-A5SM        TCGA-G3-A6UC        TCGA-GJ-A6C0        TCGA-K7-A6G5 
  "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-LG-A6GG        TCGA-MI-A75C        TCGA-MI-A75E        TCGA-MI-A75G 
  "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" 
       TCGA-MI-A75I        TCGA-NI-A4U2        TCGA-O8-A75V 
  "5P GAIN MUTATED"   "5P GAIN MUTATED"   "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-BC-A69H        TCGA-BC-A69I 
  "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-CC-5258        TCGA-CC-5260        TCGA-CC-5261        TCGA-CC-5262 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-CC-5263        TCGA-CC-A1HT        TCGA-CC-A3M9        TCGA-CC-A3MA 
  "5P GAIN MUTATED"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-CC-A3MB        TCGA-CC-A3MC        TCGA-DD-A113        TCGA-DD-A114 
  "5P GAIN MUTATED"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118        TCGA-DD-A119 
  "5P GAIN MUTATED"   "5P GAIN MUTATED"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" 
       TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C        TCGA-DD-A11D 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" 
       TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB        TCGA-DD-A1EC 
  "5P GAIN MUTATED"   "5P GAIN MUTATED"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" 
       TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EF        TCGA-DD-A1EG 
"5P GAIN WILD-TYPE"   "5P GAIN MUTATED"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" 
       TCGA-DD-A1EH        TCGA-DD-A1EI        TCGA-DD-A1EJ        TCGA-DD-A1EK 
"5P GAIN WILD-TYPE" "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-A4NB        TCGA-DD-A4ND        TCGA-DD-A4NF        TCGA-DD-A4NH 
"5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-DD-A4NI        TCGA-DD-A4NJ        TCGA-DD-A4NK        TCGA-DD-A4NL 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" 
       TCGA-DD-A4NN        TCGA-DD-A4NO        TCGA-DD-A4NP        TCGA-DD-A4NQ 
"5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-DD-A4NR        TCGA-DD-A4NS        TCGA-DD-A4NV        TCGA-DD-A73A 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" 
       TCGA-DD-A73B        TCGA-DD-A73C        TCGA-DD-A73D        TCGA-DD-A73E 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-DD-A73F        TCGA-DD-A73G        TCGA-ED-A459        TCGA-ED-A4XI 
"5P GAIN WILD-TYPE"   "5P GAIN MUTATED"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" 
       TCGA-ED-A5KG        TCGA-ED-A627        TCGA-ED-A66X        TCGA-ED-A66Y 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED"   "5P GAIN MUTATED" 
       TCGA-ED-A7PX        TCGA-ED-A7PY        TCGA-ED-A7PZ        TCGA-ED-A7XP 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" 
       TCGA-ED-A82E        TCGA-EP-A12J        TCGA-EP-A26S        TCGA-EP-A2KA 
  "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-EP-A2KB        TCGA-EP-A2KC        TCGA-EP-A3JL        TCGA-EP-A3RK 
  "5P GAIN MUTATED"   "5P GAIN MUTATED"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" 
       TCGA-ES-A2HS        TCGA-ES-A2HT        TCGA-FV-A23B        TCGA-FV-A2QR 
"5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" 
       TCGA-FV-A3I0        TCGA-FV-A3I1        TCGA-FV-A3R2        TCGA-FV-A3R3 
  "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-FV-A495        TCGA-FV-A496        TCGA-FV-A4ZP        TCGA-FV-A4ZQ 
  "5P GAIN MUTATED" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED"   "5P GAIN MUTATED" 
       TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U        TCGA-G3-A25V 
"5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y        TCGA-G3-A25Z 
  "5P GAIN MUTATED"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI        TCGA-G3-A3CJ 
  "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-G3-A3CK        TCGA-G3-A5SI        TCGA-G3-A5SJ        TCGA-G3-A5SL 
"5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-G3-A5SM        TCGA-G3-A6UC        TCGA-GJ-A6C0        TCGA-K7-A6G5 
  "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-LG-A6GG        TCGA-MI-A75C        TCGA-MI-A75E        TCGA-MI-A75G 
  "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" 
       TCGA-MI-A75I        TCGA-NI-A4U2        TCGA-O8-A75V 
  "5P GAIN MUTATED"   "5P GAIN MUTATED"   "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-BC-A69H        TCGA-BC-A69I 
  "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-CC-5258        TCGA-CC-5260        TCGA-CC-5261        TCGA-CC-5262 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-CC-5263        TCGA-CC-A1HT        TCGA-CC-A3M9        TCGA-CC-A3MA 
  "5P GAIN MUTATED"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-CC-A3MB        TCGA-CC-A3MC        TCGA-DD-A113        TCGA-DD-A114 
  "5P GAIN MUTATED"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118        TCGA-DD-A119 
  "5P GAIN MUTATED"   "5P GAIN MUTATED"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" 
       TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C        TCGA-DD-A11D 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" 
       TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB        TCGA-DD-A1EC 
  "5P GAIN MUTATED"   "5P GAIN MUTATED"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" 
       TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EF        TCGA-DD-A1EG 
"5P GAIN WILD-TYPE"   "5P GAIN MUTATED"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" 
       TCGA-DD-A1EH        TCGA-DD-A1EI        TCGA-DD-A1EJ        TCGA-DD-A1EK 
"5P GAIN WILD-TYPE" "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-A4NB        TCGA-DD-A4ND        TCGA-DD-A4NF        TCGA-DD-A4NH 
"5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-DD-A4NI        TCGA-DD-A4NJ        TCGA-DD-A4NK        TCGA-DD-A4NL 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" 
       TCGA-DD-A4NN        TCGA-DD-A4NO        TCGA-DD-A4NP        TCGA-DD-A4NQ 
"5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-DD-A4NR        TCGA-DD-A4NS        TCGA-DD-A4NV        TCGA-DD-A73A 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" 
       TCGA-DD-A73B        TCGA-DD-A73C        TCGA-DD-A73D        TCGA-DD-A73E 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-DD-A73F        TCGA-DD-A73G        TCGA-ED-A459        TCGA-ED-A4XI 
"5P GAIN WILD-TYPE"   "5P GAIN MUTATED"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" 
       TCGA-ED-A5KG        TCGA-ED-A627        TCGA-ED-A66X        TCGA-ED-A66Y 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED"   "5P GAIN MUTATED" 
       TCGA-ED-A7PX        TCGA-ED-A7PY        TCGA-ED-A7PZ        TCGA-ED-A7XP 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" 
       TCGA-ED-A82E        TCGA-EP-A12J        TCGA-EP-A26S        TCGA-EP-A2KA 
  "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-EP-A2KB        TCGA-EP-A2KC        TCGA-EP-A3JL        TCGA-EP-A3RK 
  "5P GAIN MUTATED"   "5P GAIN MUTATED"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" 
       TCGA-ES-A2HS        TCGA-ES-A2HT        TCGA-FV-A23B        TCGA-FV-A2QR 
"5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" 
       TCGA-FV-A3I0        TCGA-FV-A3I1        TCGA-FV-A3R2        TCGA-FV-A3R3 
  "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-FV-A495        TCGA-FV-A496        TCGA-FV-A4ZP        TCGA-FV-A4ZQ 
  "5P GAIN MUTATED" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED"   "5P GAIN MUTATED" 
       TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U        TCGA-G3-A25V 
"5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y        TCGA-G3-A25Z 
  "5P GAIN MUTATED"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI        TCGA-G3-A3CJ 
  "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-G3-A3CK        TCGA-G3-A5SI        TCGA-G3-A5SJ        TCGA-G3-A5SL 
"5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-G3-A5SM        TCGA-G3-A6UC        TCGA-GJ-A6C0        TCGA-K7-A6G5 
  "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-LG-A6GG        TCGA-MI-A75C        TCGA-MI-A75E        TCGA-MI-A75G 
  "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" 
       TCGA-MI-A75I        TCGA-NI-A4U2        TCGA-O8-A75V 
  "5P GAIN MUTATED"   "5P GAIN MUTATED"   "5P GAIN MUTATED" 
[1] "hr=" "1.2"
D9V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  5P GAIN MUTATED        18       15         1         17          2          0
  5P GAIN WILD-TYPE      40       21         1         13          2          5
                   vv
clus                STAGE IV STAGE IVA STAGE IVB
  5P GAIN MUTATED          0         0         0
  5P GAIN WILD-TYPE        1         1         2
D9V3, multiclass
                   vv
clus                T1 T2 T3 T4
  5P GAIN MUTATED   18 17 22  1
  5P GAIN WILD-TYPE 43 23 18  7
D9V4, multiclass
    clus
vv   5P GAIN MUTATED 5P GAIN WILD-TYPE
  T1              18                43
  T2              17                23
  T3              22                18
  T4               1                 7
D9V5, binary
                   cls
clus                 0  1
  5P GAIN MUTATED   37  0
  5P GAIN WILD-TYPE 60  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED     37    0
  5P GAIN WILD-TYPE   60    3
   clus
vv  5P GAIN MUTATED 5P GAIN WILD-TYPE
  0              37                60
  1               0                 3
                   vv
clus                M0 M1 MX
  5P GAIN MUTATED   47  0 11
  5P GAIN WILD-TYPE 68  3 20
D9V6, multiclass
    clus
vv   5P GAIN MUTATED 5P GAIN WILD-TYPE
  M0              47                68
  M1               0                 3
  MX              11                20
D9V7, binary
                   cls
clus                 0  1
  5P GAIN MUTATED   22 36
  5P GAIN WILD-TYPE 36 55
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED     22   36
  5P GAIN WILD-TYPE   36   55
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  FEMALE              22                36
  MALE                36                55
                   vv
clus                R0 R1 R2 RX
  5P GAIN MUTATED   48  5  0  3
  5P GAIN WILD-TYPE 74  6  1  7
D9V8, multiclass
    clus
vv   5P GAIN MUTATED 5P GAIN WILD-TYPE
  R0              48                74
  R1               5                 6
  R2               0                 1
  RX               3                 7

Clustering(10) Variable = 5Q GAIN MUTATION ANALYSIS
D10V1, survival
                   sevent
clus2                0  1
  5Q GAIN MUTATED   23 20
  5Q GAIN WILD-TYPE 61 43
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               43               104 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               20                43 
$`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 
       53.33       113.00        51.29        90.71        79.40         6.71 
TCGA-DD-A39V TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A3A1 TCGA-DD-A3A3 TCGA-DD-A3A5 
       21.14        55.69         5.62         7.66        17.59       102.74 
TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A4ND TCGA-DD-A4NK TCGA-DD-A4NO TCGA-DD-A4NV 
       13.78         0.36        73.38        39.78        61.45        66.35 
TCGA-DD-A73A TCGA-DD-A73G TCGA-ED-A459 TCGA-ED-A66Y TCGA-ED-A7XP TCGA-EP-A2KB 
       10.98       100.96        13.41         0.23         0.20        10.98 
TCGA-EP-A2KC TCGA-EP-A3JL TCGA-ES-A2HT TCGA-FV-A495 TCGA-FV-A4ZQ TCGA-G3-A25T 
        0.62         9.96        14.40         0.03         0.39        51.06 
TCGA-G3-A25W TCGA-G3-A3CG TCGA-G3-A5SM TCGA-LG-A6GG TCGA-MI-A75G TCGA-MI-A75I 
       30.74        22.13         4.37         0.49        14.24         8.71 
TCGA-O8-A75V 
        4.44 

$`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        13.84 
TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69H TCGA-BC-A69I TCGA-CC-5258 
        0.26        22.36         9.50         3.95         0.53         0.07 
TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3M9 
        2.86         0.39         3.39         4.24         3.32         0.10 
TCGA-CC-A3MA TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B 
        0.07        79.73        37.78         7.33         2.60         0.46 
TCGA-DD-A11C TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EF TCGA-DD-A1EG 
       21.76        66.31        19.79        75.65        12.95        45.11 
TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39Z 
       49.15         6.02        29.16        18.35        13.64        19.76 
TCGA-DD-A3A0 TCGA-DD-A3A2 TCGA-DD-A3A4 TCGA-DD-A3A6 TCGA-DD-A3A9 TCGA-DD-A4NA 
       25.81        70.06        20.12       107.11        30.61        33.14 
TCGA-DD-A4NB TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NL 
       12.85        14.07        14.24        18.44        15.06        56.25 
TCGA-DD-A4NN TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A73B 
       29.56        93.67        12.26         0.30        80.75         9.30 
TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-ED-A4XI TCGA-ED-A5KG 
        7.56        10.98         1.45        27.72        12.69        15.85 
TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A82E 
       13.91        13.35         0.20         0.20         0.20         0.20 
TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A3RK TCGA-ES-A2HS TCGA-FV-A23B 
       18.74        19.99        11.74        11.93        22.85        32.45 
TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A496 
       19.10         0.20         8.12         6.38         0.13         0.33 
TCGA-FV-A4ZP TCGA-G3-A25S TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25X TCGA-G3-A25Y 
       60.36         1.22        53.79        28.27        58.49        14.86 
TCGA-G3-A25Z TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI 
       21.53        25.64         5.92        19.53        19.23        14.70 
TCGA-G3-A5SJ TCGA-G3-A5SL TCGA-G3-A6UC TCGA-GJ-A6C0 TCGA-K7-A6G5 TCGA-MI-A75C 
       11.97         7.99         7.76         1.02         4.01         9.57 
TCGA-MI-A75E TCGA-NI-A4U2 
        5.10        58.88 

  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
             0.03              0.07 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
           113.00            107.11 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
           13.780            14.155 
[1] "0.0 - 113.0 (13.8)" "0.1 - 107.1 (14.2)"
       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-BC-A69H        TCGA-BC-A69I 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-CC-5258        TCGA-CC-5260        TCGA-CC-5261        TCGA-CC-5262 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-CC-5263        TCGA-CC-A1HT        TCGA-CC-A3M9        TCGA-CC-A3MA 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-CC-A3MB        TCGA-CC-A3MC        TCGA-DD-A113        TCGA-DD-A114 
  "5Q GAIN MUTATED"   "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118        TCGA-DD-A119 
  "5Q GAIN MUTATED"   "5Q GAIN MUTATED"   "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE" 
       TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C        TCGA-DD-A11D 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED" 
       TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB        TCGA-DD-A1EC 
  "5Q GAIN MUTATED"   "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EF        TCGA-DD-A1EG 
"5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-DD-A1EH        TCGA-DD-A1EI        TCGA-DD-A1EJ        TCGA-DD-A1EK 
"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-A4NB        TCGA-DD-A4ND        TCGA-DD-A4NF        TCGA-DD-A4NH 
"5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-DD-A4NI        TCGA-DD-A4NJ        TCGA-DD-A4NK        TCGA-DD-A4NL 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE" 
       TCGA-DD-A4NN        TCGA-DD-A4NO        TCGA-DD-A4NP        TCGA-DD-A4NQ 
"5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-DD-A4NR        TCGA-DD-A4NS        TCGA-DD-A4NV        TCGA-DD-A73A 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED"   "5Q GAIN MUTATED" 
       TCGA-DD-A73B        TCGA-DD-A73C        TCGA-DD-A73D        TCGA-DD-A73E 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-DD-A73F        TCGA-DD-A73G        TCGA-ED-A459        TCGA-ED-A4XI 
"5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED"   "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE" 
       TCGA-ED-A5KG        TCGA-ED-A627        TCGA-ED-A66X        TCGA-ED-A66Y 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED" 
       TCGA-ED-A7PX        TCGA-ED-A7PY        TCGA-ED-A7PZ        TCGA-ED-A7XP 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED" 
       TCGA-ED-A82E        TCGA-EP-A12J        TCGA-EP-A26S        TCGA-EP-A2KA 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-EP-A2KB        TCGA-EP-A2KC        TCGA-EP-A3JL        TCGA-EP-A3RK 
  "5Q GAIN MUTATED"   "5Q GAIN MUTATED"   "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE" 
       TCGA-ES-A2HS        TCGA-ES-A2HT        TCGA-FV-A23B        TCGA-FV-A2QR 
"5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-FV-A3I0        TCGA-FV-A3I1        TCGA-FV-A3R2        TCGA-FV-A3R3 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-FV-A495        TCGA-FV-A496        TCGA-FV-A4ZP        TCGA-FV-A4ZQ 
  "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED" 
       TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U        TCGA-G3-A25V 
"5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y        TCGA-G3-A25Z 
  "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI        TCGA-G3-A3CJ 
  "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-G3-A3CK        TCGA-G3-A5SI        TCGA-G3-A5SJ        TCGA-G3-A5SL 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-G3-A5SM        TCGA-G3-A6UC        TCGA-GJ-A6C0        TCGA-K7-A6G5 
  "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-LG-A6GG        TCGA-MI-A75C        TCGA-MI-A75E        TCGA-MI-A75G 
  "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED" 
       TCGA-MI-A75I        TCGA-NI-A4U2        TCGA-O8-A75V 
  "5Q GAIN MUTATED" "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-BC-A69H        TCGA-BC-A69I 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-CC-5258        TCGA-CC-5260        TCGA-CC-5261        TCGA-CC-5262 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-CC-5263        TCGA-CC-A1HT        TCGA-CC-A3M9        TCGA-CC-A3MA 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-CC-A3MB        TCGA-CC-A3MC        TCGA-DD-A113        TCGA-DD-A114 
  "5Q GAIN MUTATED"   "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118        TCGA-DD-A119 
  "5Q GAIN MUTATED"   "5Q GAIN MUTATED"   "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE" 
       TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C        TCGA-DD-A11D 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED" 
       TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB        TCGA-DD-A1EC 
  "5Q GAIN MUTATED"   "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EF        TCGA-DD-A1EG 
"5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-DD-A1EH        TCGA-DD-A1EI        TCGA-DD-A1EJ        TCGA-DD-A1EK 
"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-A4NB        TCGA-DD-A4ND        TCGA-DD-A4NF        TCGA-DD-A4NH 
"5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-DD-A4NI        TCGA-DD-A4NJ        TCGA-DD-A4NK        TCGA-DD-A4NL 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE" 
       TCGA-DD-A4NN        TCGA-DD-A4NO        TCGA-DD-A4NP        TCGA-DD-A4NQ 
"5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-DD-A4NR        TCGA-DD-A4NS        TCGA-DD-A4NV        TCGA-DD-A73A 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED"   "5Q GAIN MUTATED" 
       TCGA-DD-A73B        TCGA-DD-A73C        TCGA-DD-A73D        TCGA-DD-A73E 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-DD-A73F        TCGA-DD-A73G        TCGA-ED-A459        TCGA-ED-A4XI 
"5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED"   "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE" 
       TCGA-ED-A5KG        TCGA-ED-A627        TCGA-ED-A66X        TCGA-ED-A66Y 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED" 
       TCGA-ED-A7PX        TCGA-ED-A7PY        TCGA-ED-A7PZ        TCGA-ED-A7XP 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED" 
       TCGA-ED-A82E        TCGA-EP-A12J        TCGA-EP-A26S        TCGA-EP-A2KA 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-EP-A2KB        TCGA-EP-A2KC        TCGA-EP-A3JL        TCGA-EP-A3RK 
  "5Q GAIN MUTATED"   "5Q GAIN MUTATED"   "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE" 
       TCGA-ES-A2HS        TCGA-ES-A2HT        TCGA-FV-A23B        TCGA-FV-A2QR 
"5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-FV-A3I0        TCGA-FV-A3I1        TCGA-FV-A3R2        TCGA-FV-A3R3 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-FV-A495        TCGA-FV-A496        TCGA-FV-A4ZP        TCGA-FV-A4ZQ 
  "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED" 
       TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U        TCGA-G3-A25V 
"5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y        TCGA-G3-A25Z 
  "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI        TCGA-G3-A3CJ 
  "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-G3-A3CK        TCGA-G3-A5SI        TCGA-G3-A5SJ        TCGA-G3-A5SL 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-G3-A5SM        TCGA-G3-A6UC        TCGA-GJ-A6C0        TCGA-K7-A6G5 
  "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-LG-A6GG        TCGA-MI-A75C        TCGA-MI-A75E        TCGA-MI-A75G 
  "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED" 
       TCGA-MI-A75I        TCGA-NI-A4U2        TCGA-O8-A75V 
  "5Q GAIN MUTATED" "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-BC-A69H        TCGA-BC-A69I 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-CC-5258        TCGA-CC-5260        TCGA-CC-5261        TCGA-CC-5262 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-CC-5263        TCGA-CC-A1HT        TCGA-CC-A3M9        TCGA-CC-A3MA 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-CC-A3MB        TCGA-CC-A3MC        TCGA-DD-A113        TCGA-DD-A114 
  "5Q GAIN MUTATED"   "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118        TCGA-DD-A119 
  "5Q GAIN MUTATED"   "5Q GAIN MUTATED"   "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE" 
       TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C        TCGA-DD-A11D 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED" 
       TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB        TCGA-DD-A1EC 
  "5Q GAIN MUTATED"   "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EF        TCGA-DD-A1EG 
"5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-DD-A1EH        TCGA-DD-A1EI        TCGA-DD-A1EJ        TCGA-DD-A1EK 
"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-A4NB        TCGA-DD-A4ND        TCGA-DD-A4NF        TCGA-DD-A4NH 
"5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-DD-A4NI        TCGA-DD-A4NJ        TCGA-DD-A4NK        TCGA-DD-A4NL 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE" 
       TCGA-DD-A4NN        TCGA-DD-A4NO        TCGA-DD-A4NP        TCGA-DD-A4NQ 
"5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-DD-A4NR        TCGA-DD-A4NS        TCGA-DD-A4NV        TCGA-DD-A73A 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED"   "5Q GAIN MUTATED" 
       TCGA-DD-A73B        TCGA-DD-A73C        TCGA-DD-A73D        TCGA-DD-A73E 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-DD-A73F        TCGA-DD-A73G        TCGA-ED-A459        TCGA-ED-A4XI 
"5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED"   "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE" 
       TCGA-ED-A5KG        TCGA-ED-A627        TCGA-ED-A66X        TCGA-ED-A66Y 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED" 
       TCGA-ED-A7PX        TCGA-ED-A7PY        TCGA-ED-A7PZ        TCGA-ED-A7XP 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED" 
       TCGA-ED-A82E        TCGA-EP-A12J        TCGA-EP-A26S        TCGA-EP-A2KA 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-EP-A2KB        TCGA-EP-A2KC        TCGA-EP-A3JL        TCGA-EP-A3RK 
  "5Q GAIN MUTATED"   "5Q GAIN MUTATED"   "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE" 
       TCGA-ES-A2HS        TCGA-ES-A2HT        TCGA-FV-A23B        TCGA-FV-A2QR 
"5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-FV-A3I0        TCGA-FV-A3I1        TCGA-FV-A3R2        TCGA-FV-A3R3 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-FV-A495        TCGA-FV-A496        TCGA-FV-A4ZP        TCGA-FV-A4ZQ 
  "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED" 
       TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U        TCGA-G3-A25V 
"5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y        TCGA-G3-A25Z 
  "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI        TCGA-G3-A3CJ 
  "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-G3-A3CK        TCGA-G3-A5SI        TCGA-G3-A5SJ        TCGA-G3-A5SL 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-G3-A5SM        TCGA-G3-A6UC        TCGA-GJ-A6C0        TCGA-K7-A6G5 
  "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-LG-A6GG        TCGA-MI-A75C        TCGA-MI-A75E        TCGA-MI-A75G 
  "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED" 
       TCGA-MI-A75I        TCGA-NI-A4U2        TCGA-O8-A75V 
  "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED" 
[1] "hr=" "1.2"
D10V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  5Q GAIN MUTATED        16       10         1         11          2          0
  5Q GAIN WILD-TYPE      42       26         1         19          2          5
                   vv
clus                STAGE IV STAGE IVA STAGE IVB
  5Q GAIN MUTATED          0         0         0
  5Q GAIN WILD-TYPE        1         1         2
D10V3, multiclass
                   vv
clus                T1 T2 T3 T4
  5Q GAIN MUTATED   16 12 15  1
  5Q GAIN WILD-TYPE 45 28 25  7
D10V4, multiclass
    clus
vv   5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  T1              16                45
  T2              12                28
  T3              15                25
  T4               1                 7
D10V5, binary
                   cls
clus                 0  1
  5Q GAIN MUTATED   28  0
  5Q GAIN WILD-TYPE 69  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED     28    0
  5Q GAIN WILD-TYPE   69    3
   clus
vv  5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  0              28                69
  1               0                 3
                   vv
clus                M0 M1 MX
  5Q GAIN MUTATED   35  0  9
  5Q GAIN WILD-TYPE 80  3 22
D10V6, multiclass
    clus
vv   5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  M0              35                80
  M1               0                 3
  MX               9                22
D10V7, binary
                   cls
clus                 0  1
  5Q GAIN MUTATED   15 29
  5Q GAIN WILD-TYPE 43 62
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED     15   29
  5Q GAIN WILD-TYPE   43   62
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  FEMALE              15                43
  MALE                29                62
                   vv
clus                R0 R1 R2 RX
  5Q GAIN MUTATED   38  4  0  1
  5Q GAIN WILD-TYPE 84  7  1  9
D10V8, multiclass
    clus
vv   5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  R0              38                84
  R1               4                 7
  R2               0                 1
  RX               1                 9

Clustering(11) Variable = 6P GAIN MUTATION ANALYSIS
D11V1, survival
                   sevent
clus2                0  1
  6P GAIN MUTATED   21 17
  6P GAIN WILD-TYPE 63 46
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               38               109 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               17                46 
$`6P GAIN MUTATED`
TCGA-BC-A10U TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A69H TCGA-CC-5263 TCGA-CC-A3MC 
       27.52         0.26        22.36         3.95         4.24         0.13 
TCGA-DD-A114 TCGA-DD-A119 TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A39X TCGA-DD-A39Y 
       37.78         7.33        45.11        49.15        55.69         5.62 
TCGA-DD-A3A8 TCGA-DD-A3A9 TCGA-DD-A4NN TCGA-DD-A4NS TCGA-DD-A73B TCGA-DD-A73D 
        0.36        30.61        29.56        80.75         9.30        10.98 
TCGA-DD-A73E TCGA-ED-A66X TCGA-ED-A7PZ TCGA-ED-A82E TCGA-EP-A2KB TCGA-EP-A2KC 
        1.45        13.35         0.20         0.20        10.98         0.62 
TCGA-ES-A2HS TCGA-FV-A3I0 TCGA-FV-A3R2 TCGA-G3-A25S TCGA-G3-A25U TCGA-G3-A25X 
       22.85         0.20         6.38         1.22        53.79        58.49 
TCGA-G3-A3CG TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SL TCGA-G3-A6UC TCGA-LG-A6GG 
       22.13        19.23        14.70         7.99         7.76         0.49 
TCGA-MI-A75G TCGA-MI-A75I 
       14.24         8.71 

$`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-A217 TCGA-BC-A5W4 TCGA-BC-A69I TCGA-CC-5258 TCGA-CC-5260 
       44.42        13.84         9.50         0.53         0.07         2.86 
TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB 
        0.39         3.39         3.32         0.10         0.07         0.10 
TCGA-DD-A113 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A11A TCGA-DD-A11B 
       79.73        83.57        53.33       113.00         2.60         0.46 
TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC 
       21.76        51.29        90.71        79.40        66.31        19.79 
TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK 
       75.65         6.71        12.95         6.02        29.16        18.35 
TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 
       13.64        21.14        19.76        25.81         7.66        70.06 
TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A4NA 
       17.59        20.12       102.74       107.11        13.78        33.14 
TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ 
       12.85        73.38        14.07        14.24        18.44        15.06 
TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR 
       39.78        56.25        61.45        93.67        12.26         0.30 
TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73C TCGA-DD-A73F TCGA-DD-A73G TCGA-ED-A459 
       66.35        10.98         7.56        27.72       100.96        13.41 
TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY 
       12.69        15.85        13.91         0.23         0.20         0.20 
TCGA-ED-A7XP TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A3JL TCGA-EP-A3RK 
        0.20        18.74        19.99        11.74         9.96        11.93 
TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-A3I1 TCGA-FV-A3R3 TCGA-FV-A495 
       14.40        32.45        19.10         8.12         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        51.06        28.27        30.74 
TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A5SJ 
       14.86        21.53        25.64         5.92        19.53        11.97 
TCGA-G3-A5SM TCGA-GJ-A6C0 TCGA-K7-A6G5 TCGA-MI-A75C TCGA-MI-A75E TCGA-NI-A4U2 
        4.37         1.02         4.01         9.57         5.10        58.88 
TCGA-O8-A75V 
        4.44 

  6P GAIN MUTATED 6P GAIN WILD-TYPE 
             0.13              0.03 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
            80.75            113.00 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
            10.14             14.86 
[1] "0.1 - 80.8 (10.1)"  "0.0 - 113.0 (14.9)"
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" 
       TCGA-BC-A3KG        TCGA-BC-A5W4        TCGA-BC-A69H        TCGA-BC-A69I 
  "6P GAIN MUTATED" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" 
       TCGA-CC-5258        TCGA-CC-5260        TCGA-CC-5261        TCGA-CC-5262 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-CC-5263        TCGA-CC-A1HT        TCGA-CC-A3M9        TCGA-CC-A3MA 
  "6P GAIN MUTATED" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-CC-A3MB        TCGA-CC-A3MC        TCGA-DD-A113        TCGA-DD-A114 
"6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" 
       TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118        TCGA-DD-A119 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" 
       TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C        TCGA-DD-A11D 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB        TCGA-DD-A1EC 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EF        TCGA-DD-A1EG 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" 
       TCGA-DD-A1EH        TCGA-DD-A1EI        TCGA-DD-A1EJ        TCGA-DD-A1EK 
  "6P GAIN MUTATED" "6P GAIN WILD-TYPE" "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 MUTATED"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" 
       TCGA-DD-A4NB        TCGA-DD-A4ND        TCGA-DD-A4NF        TCGA-DD-A4NH 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-DD-A4NI        TCGA-DD-A4NJ        TCGA-DD-A4NK        TCGA-DD-A4NL 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-DD-A4NN        TCGA-DD-A4NO        TCGA-DD-A4NP        TCGA-DD-A4NQ 
  "6P GAIN MUTATED" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-DD-A4NR        TCGA-DD-A4NS        TCGA-DD-A4NV        TCGA-DD-A73A 
"6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-DD-A73B        TCGA-DD-A73C        TCGA-DD-A73D        TCGA-DD-A73E 
  "6P GAIN MUTATED" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED"   "6P GAIN MUTATED" 
       TCGA-DD-A73F        TCGA-DD-A73G        TCGA-ED-A459        TCGA-ED-A4XI 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-ED-A5KG        TCGA-ED-A627        TCGA-ED-A66X        TCGA-ED-A66Y 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" 
       TCGA-ED-A7PX        TCGA-ED-A7PY        TCGA-ED-A7PZ        TCGA-ED-A7XP 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" 
       TCGA-ED-A82E        TCGA-EP-A12J        TCGA-EP-A26S        TCGA-EP-A2KA 
  "6P GAIN MUTATED" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-EP-A2KB        TCGA-EP-A2KC        TCGA-EP-A3JL        TCGA-EP-A3RK 
  "6P GAIN MUTATED"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-ES-A2HS        TCGA-ES-A2HT        TCGA-FV-A23B        TCGA-FV-A2QR 
  "6P GAIN MUTATED" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-FV-A3I0        TCGA-FV-A3I1        TCGA-FV-A3R2        TCGA-FV-A3R3 
  "6P GAIN MUTATED" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" 
       TCGA-FV-A495        TCGA-FV-A496        TCGA-FV-A4ZP        TCGA-FV-A4ZQ 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U        TCGA-G3-A25V 
  "6P GAIN MUTATED" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" 
       TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y        TCGA-G3-A25Z 
"6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI        TCGA-G3-A3CJ 
  "6P GAIN MUTATED" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-G3-A3CK        TCGA-G3-A5SI        TCGA-G3-A5SJ        TCGA-G3-A5SL 
  "6P GAIN MUTATED"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" 
       TCGA-G3-A5SM        TCGA-G3-A6UC        TCGA-GJ-A6C0        TCGA-K7-A6G5 
"6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-LG-A6GG        TCGA-MI-A75C        TCGA-MI-A75E        TCGA-MI-A75G 
  "6P GAIN MUTATED" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" 
       TCGA-MI-A75I        TCGA-NI-A4U2        TCGA-O8-A75V 
  "6P GAIN MUTATED" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" 
       TCGA-BC-A3KG        TCGA-BC-A5W4        TCGA-BC-A69H        TCGA-BC-A69I 
  "6P GAIN MUTATED" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" 
       TCGA-CC-5258        TCGA-CC-5260        TCGA-CC-5261        TCGA-CC-5262 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-CC-5263        TCGA-CC-A1HT        TCGA-CC-A3M9        TCGA-CC-A3MA 
  "6P GAIN MUTATED" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-CC-A3MB        TCGA-CC-A3MC        TCGA-DD-A113        TCGA-DD-A114 
"6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" 
       TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118        TCGA-DD-A119 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" 
       TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C        TCGA-DD-A11D 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB        TCGA-DD-A1EC 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EF        TCGA-DD-A1EG 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" 
       TCGA-DD-A1EH        TCGA-DD-A1EI        TCGA-DD-A1EJ        TCGA-DD-A1EK 
  "6P GAIN MUTATED" "6P GAIN WILD-TYPE" "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 MUTATED"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" 
       TCGA-DD-A4NB        TCGA-DD-A4ND        TCGA-DD-A4NF        TCGA-DD-A4NH 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-DD-A4NI        TCGA-DD-A4NJ        TCGA-DD-A4NK        TCGA-DD-A4NL 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-DD-A4NN        TCGA-DD-A4NO        TCGA-DD-A4NP        TCGA-DD-A4NQ 
  "6P GAIN MUTATED" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-DD-A4NR        TCGA-DD-A4NS        TCGA-DD-A4NV        TCGA-DD-A73A 
"6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-DD-A73B        TCGA-DD-A73C        TCGA-DD-A73D        TCGA-DD-A73E 
  "6P GAIN MUTATED" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED"   "6P GAIN MUTATED" 
       TCGA-DD-A73F        TCGA-DD-A73G        TCGA-ED-A459        TCGA-ED-A4XI 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-ED-A5KG        TCGA-ED-A627        TCGA-ED-A66X        TCGA-ED-A66Y 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" 
       TCGA-ED-A7PX        TCGA-ED-A7PY        TCGA-ED-A7PZ        TCGA-ED-A7XP 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" 
       TCGA-ED-A82E        TCGA-EP-A12J        TCGA-EP-A26S        TCGA-EP-A2KA 
  "6P GAIN MUTATED" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-EP-A2KB        TCGA-EP-A2KC        TCGA-EP-A3JL        TCGA-EP-A3RK 
  "6P GAIN MUTATED"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-ES-A2HS        TCGA-ES-A2HT        TCGA-FV-A23B        TCGA-FV-A2QR 
  "6P GAIN MUTATED" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-FV-A3I0        TCGA-FV-A3I1        TCGA-FV-A3R2        TCGA-FV-A3R3 
  "6P GAIN MUTATED" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" 
       TCGA-FV-A495        TCGA-FV-A496        TCGA-FV-A4ZP        TCGA-FV-A4ZQ 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U        TCGA-G3-A25V 
  "6P GAIN MUTATED" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" 
       TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y        TCGA-G3-A25Z 
"6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI        TCGA-G3-A3CJ 
  "6P GAIN MUTATED" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-G3-A3CK        TCGA-G3-A5SI        TCGA-G3-A5SJ        TCGA-G3-A5SL 
  "6P GAIN MUTATED"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" 
       TCGA-G3-A5SM        TCGA-G3-A6UC        TCGA-GJ-A6C0        TCGA-K7-A6G5 
"6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-LG-A6GG        TCGA-MI-A75C        TCGA-MI-A75E        TCGA-MI-A75G 
  "6P GAIN MUTATED" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" 
       TCGA-MI-A75I        TCGA-NI-A4U2        TCGA-O8-A75V 
  "6P GAIN MUTATED" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" 
       TCGA-BC-A3KG        TCGA-BC-A5W4        TCGA-BC-A69H        TCGA-BC-A69I 
  "6P GAIN MUTATED" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" 
       TCGA-CC-5258        TCGA-CC-5260        TCGA-CC-5261        TCGA-CC-5262 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-CC-5263        TCGA-CC-A1HT        TCGA-CC-A3M9        TCGA-CC-A3MA 
  "6P GAIN MUTATED" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-CC-A3MB        TCGA-CC-A3MC        TCGA-DD-A113        TCGA-DD-A114 
"6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" 
       TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118        TCGA-DD-A119 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" 
       TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C        TCGA-DD-A11D 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB        TCGA-DD-A1EC 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EF        TCGA-DD-A1EG 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" 
       TCGA-DD-A1EH        TCGA-DD-A1EI        TCGA-DD-A1EJ        TCGA-DD-A1EK 
  "6P GAIN MUTATED" "6P GAIN WILD-TYPE" "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 MUTATED"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" 
       TCGA-DD-A4NB        TCGA-DD-A4ND        TCGA-DD-A4NF        TCGA-DD-A4NH 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-DD-A4NI        TCGA-DD-A4NJ        TCGA-DD-A4NK        TCGA-DD-A4NL 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-DD-A4NN        TCGA-DD-A4NO        TCGA-DD-A4NP        TCGA-DD-A4NQ 
  "6P GAIN MUTATED" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-DD-A4NR        TCGA-DD-A4NS        TCGA-DD-A4NV        TCGA-DD-A73A 
"6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-DD-A73B        TCGA-DD-A73C        TCGA-DD-A73D        TCGA-DD-A73E 
  "6P GAIN MUTATED" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED"   "6P GAIN MUTATED" 
       TCGA-DD-A73F        TCGA-DD-A73G        TCGA-ED-A459        TCGA-ED-A4XI 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-ED-A5KG        TCGA-ED-A627        TCGA-ED-A66X        TCGA-ED-A66Y 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" 
       TCGA-ED-A7PX        TCGA-ED-A7PY        TCGA-ED-A7PZ        TCGA-ED-A7XP 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" 
       TCGA-ED-A82E        TCGA-EP-A12J        TCGA-EP-A26S        TCGA-EP-A2KA 
  "6P GAIN MUTATED" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-EP-A2KB        TCGA-EP-A2KC        TCGA-EP-A3JL        TCGA-EP-A3RK 
  "6P GAIN MUTATED"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-ES-A2HS        TCGA-ES-A2HT        TCGA-FV-A23B        TCGA-FV-A2QR 
  "6P GAIN MUTATED" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-FV-A3I0        TCGA-FV-A3I1        TCGA-FV-A3R2        TCGA-FV-A3R3 
  "6P GAIN MUTATED" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" 
       TCGA-FV-A495        TCGA-FV-A496        TCGA-FV-A4ZP        TCGA-FV-A4ZQ 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U        TCGA-G3-A25V 
  "6P GAIN MUTATED" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" 
       TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y        TCGA-G3-A25Z 
"6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI        TCGA-G3-A3CJ 
  "6P GAIN MUTATED" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-G3-A3CK        TCGA-G3-A5SI        TCGA-G3-A5SJ        TCGA-G3-A5SL 
  "6P GAIN MUTATED"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" 
       TCGA-G3-A5SM        TCGA-G3-A6UC        TCGA-GJ-A6C0        TCGA-K7-A6G5 
"6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-LG-A6GG        TCGA-MI-A75C        TCGA-MI-A75E        TCGA-MI-A75G 
  "6P GAIN MUTATED" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" 
       TCGA-MI-A75I        TCGA-NI-A4U2        TCGA-O8-A75V 
  "6P GAIN MUTATED" "6P GAIN WILD-TYPE" "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        16       11         1          6          1          0
  6P GAIN WILD-TYPE      42       25         1         24          3          5
                   vv
clus                STAGE IV STAGE IVA STAGE IVB
  6P GAIN MUTATED          1         0         1
  6P GAIN WILD-TYPE        0         1         1
D11V3, multiclass
                   vv
clus                T1 T2 T3 T4
  6P GAIN MUTATED   16 13  9  1
  6P GAIN WILD-TYPE 45 27 31  7
D11V4, multiclass
    clus
vv   6P GAIN MUTATED 6P GAIN WILD-TYPE
  T1              16                45
  T2              13                27
  T3               9                31
  T4               1                 7
D11V5, binary
                   cls
clus                 0  1
  6P GAIN MUTATED   23  0
  6P GAIN WILD-TYPE 74  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED     23    0
  6P GAIN WILD-TYPE   74    3
   clus
vv  6P GAIN MUTATED 6P GAIN WILD-TYPE
  0              23                74
  1               0                 3
                   vv
clus                M0 M1 MX
  6P GAIN MUTATED   30  2  7
  6P GAIN WILD-TYPE 85  1 24
D11V6, multiclass
    clus
vv   6P GAIN MUTATED 6P GAIN WILD-TYPE
  M0              30                85
  M1               2                 1
  MX               7                24
D11V7, binary
                   cls
clus                 0  1
  6P GAIN MUTATED   13 26
  6P GAIN WILD-TYPE 45 65
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED     13   26
  6P GAIN WILD-TYPE   45   65
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  FEMALE              13                45
  MALE                26                65
                   vv
clus                R0 R1 R2 RX
  6P GAIN MUTATED   33  3  1  2
  6P GAIN WILD-TYPE 89  8  0  8
D11V8, multiclass
    clus
vv   6P GAIN MUTATED 6P GAIN WILD-TYPE
  R0              33                89
  R1               3                 8
  R2               1                 0
  RX               2                 8

Clustering(12) Variable = 6Q GAIN MUTATION ANALYSIS
D12V1, survival
                   sevent
clus2                0  1
  6Q GAIN MUTATED   12  8
  6Q GAIN WILD-TYPE 72 55
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               20               127 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
                8                55 
$`6Q GAIN MUTATED`
TCGA-BC-A3KG TCGA-BC-A69H TCGA-CC-5263 TCGA-CC-A3MC TCGA-DD-A114 TCGA-DD-A119 
       22.36         3.95         4.24         0.13        37.78         7.33 
TCGA-DD-A1EH TCGA-DD-A39Y TCGA-DD-A3A9 TCGA-DD-A73B TCGA-DD-A73D TCGA-ED-A66X 
       49.15         5.62        30.61         9.30        10.98        13.35 
TCGA-EP-A2KB TCGA-EP-A2KC TCGA-G3-A25U TCGA-G3-A3CG TCGA-G3-A3CK TCGA-G3-A5SI 
       10.98         0.62        53.79        22.13        19.23        14.70 
TCGA-LG-A6GG TCGA-MI-A75G 
        0.49        14.24 

$`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-BC-A69I 
        5.03        44.42        13.84         0.26         9.50         0.53 
TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-A1HT TCGA-CC-A3M9 
        0.07         2.86         0.39         3.39         3.32         0.10 
TCGA-CC-A3MA TCGA-CC-A3MB TCGA-DD-A113 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 
        0.07         0.10        79.73        83.57        53.33       113.00 
TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA 
        2.60         0.46        21.76        51.29        90.71        79.40 
TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EG 
       66.31        19.79        75.65         6.71        12.95        45.11 
TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39X 
        6.02        29.16        18.35        13.64        21.14        55.69 
TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 
       19.76        25.81         7.66        70.06        17.59        20.12 
TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A4NA TCGA-DD-A4NB 
      102.74       107.11        13.78         0.36        33.14        12.85 
TCGA-DD-A4ND TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK 
       73.38        14.07        14.24        18.44        15.06        39.78 
TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR 
       56.25        29.56        61.45        93.67        12.26         0.30 
TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73C TCGA-DD-A73E TCGA-DD-A73F 
       80.75        66.35        10.98         7.56         1.45        27.72 
TCGA-DD-A73G TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66Y 
      100.96        13.41        12.69        15.85        13.91         0.23 
TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XP TCGA-ED-A82E TCGA-EP-A12J 
        0.20         0.20         0.20         0.20         0.20        18.74 
TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT 
       19.99        11.74         9.96        11.93        22.85        14.40 
TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 
       32.45        19.10         0.20         8.12         6.38         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        51.06 
TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CH 
       28.27        30.74        58.49        14.86        21.53        25.64 
TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A5SJ TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A6UC 
        5.92        19.53        11.97         7.99         4.37         7.76 
TCGA-GJ-A6C0 TCGA-K7-A6G5 TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75I TCGA-NI-A4U2 
        1.02         4.01         9.57         5.10         8.71        58.88 
TCGA-O8-A75V 
        4.44 

  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
             0.13              0.03 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
            53.79            113.00 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
           12.165            14.240 
[1] "0.1 - 53.8 (12.2)"  "0.0 - 113.0 (14.2)"
       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-BC-A69H        TCGA-BC-A69I 
  "6Q GAIN MUTATED" "6Q GAIN WILD-TYPE"   "6Q GAIN MUTATED" "6Q GAIN WILD-TYPE" 
       TCGA-CC-5258        TCGA-CC-5260        TCGA-CC-5261        TCGA-CC-5262 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-CC-5263        TCGA-CC-A1HT        TCGA-CC-A3M9        TCGA-CC-A3MA 
  "6Q GAIN MUTATED" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-CC-A3MB        TCGA-CC-A3MC        TCGA-DD-A113        TCGA-DD-A114 
"6Q GAIN WILD-TYPE"   "6Q GAIN MUTATED" "6Q GAIN WILD-TYPE"   "6Q GAIN MUTATED" 
       TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118        TCGA-DD-A119 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE"   "6Q GAIN MUTATED" 
       TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C        TCGA-DD-A11D 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB        TCGA-DD-A1EC 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EF        TCGA-DD-A1EG 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-DD-A1EH        TCGA-DD-A1EI        TCGA-DD-A1EJ        TCGA-DD-A1EK 
  "6Q GAIN MUTATED" "6Q GAIN WILD-TYPE" "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-A4NB        TCGA-DD-A4ND        TCGA-DD-A4NF        TCGA-DD-A4NH 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-DD-A4NI        TCGA-DD-A4NJ        TCGA-DD-A4NK        TCGA-DD-A4NL 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-DD-A4NN        TCGA-DD-A4NO        TCGA-DD-A4NP        TCGA-DD-A4NQ 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-DD-A4NR        TCGA-DD-A4NS        TCGA-DD-A4NV        TCGA-DD-A73A 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-DD-A73B        TCGA-DD-A73C        TCGA-DD-A73D        TCGA-DD-A73E 
  "6Q GAIN MUTATED" "6Q GAIN WILD-TYPE"   "6Q GAIN MUTATED" "6Q GAIN WILD-TYPE" 
       TCGA-DD-A73F        TCGA-DD-A73G        TCGA-ED-A459        TCGA-ED-A4XI 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-ED-A5KG        TCGA-ED-A627        TCGA-ED-A66X        TCGA-ED-A66Y 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE"   "6Q GAIN MUTATED" "6Q GAIN WILD-TYPE" 
       TCGA-ED-A7PX        TCGA-ED-A7PY        TCGA-ED-A7PZ        TCGA-ED-A7XP 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-ED-A82E        TCGA-EP-A12J        TCGA-EP-A26S        TCGA-EP-A2KA 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-EP-A2KB        TCGA-EP-A2KC        TCGA-EP-A3JL        TCGA-EP-A3RK 
  "6Q GAIN MUTATED"   "6Q GAIN MUTATED" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-ES-A2HS        TCGA-ES-A2HT        TCGA-FV-A23B        TCGA-FV-A2QR 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-FV-A3I0        TCGA-FV-A3I1        TCGA-FV-A3R2        TCGA-FV-A3R3 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-FV-A495        TCGA-FV-A496        TCGA-FV-A4ZP        TCGA-FV-A4ZQ 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U        TCGA-G3-A25V 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE"   "6Q GAIN MUTATED" "6Q GAIN WILD-TYPE" 
       TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y        TCGA-G3-A25Z 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI        TCGA-G3-A3CJ 
  "6Q GAIN MUTATED" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-G3-A3CK        TCGA-G3-A5SI        TCGA-G3-A5SJ        TCGA-G3-A5SL 
  "6Q GAIN MUTATED"   "6Q GAIN MUTATED" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-G3-A5SM        TCGA-G3-A6UC        TCGA-GJ-A6C0        TCGA-K7-A6G5 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-LG-A6GG        TCGA-MI-A75C        TCGA-MI-A75E        TCGA-MI-A75G 
  "6Q GAIN MUTATED" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE"   "6Q GAIN MUTATED" 
       TCGA-MI-A75I        TCGA-NI-A4U2        TCGA-O8-A75V 
"6Q GAIN WILD-TYPE" "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-BC-A69H        TCGA-BC-A69I 
  "6Q GAIN MUTATED" "6Q GAIN WILD-TYPE"   "6Q GAIN MUTATED" "6Q GAIN WILD-TYPE" 
       TCGA-CC-5258        TCGA-CC-5260        TCGA-CC-5261        TCGA-CC-5262 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-CC-5263        TCGA-CC-A1HT        TCGA-CC-A3M9        TCGA-CC-A3MA 
  "6Q GAIN MUTATED" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-CC-A3MB        TCGA-CC-A3MC        TCGA-DD-A113        TCGA-DD-A114 
"6Q GAIN WILD-TYPE"   "6Q GAIN MUTATED" "6Q GAIN WILD-TYPE"   "6Q GAIN MUTATED" 
       TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118        TCGA-DD-A119 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE"   "6Q GAIN MUTATED" 
       TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C        TCGA-DD-A11D 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB        TCGA-DD-A1EC 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EF        TCGA-DD-A1EG 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-DD-A1EH        TCGA-DD-A1EI        TCGA-DD-A1EJ        TCGA-DD-A1EK 
  "6Q GAIN MUTATED" "6Q GAIN WILD-TYPE" "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-A4NB        TCGA-DD-A4ND        TCGA-DD-A4NF        TCGA-DD-A4NH 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-DD-A4NI        TCGA-DD-A4NJ        TCGA-DD-A4NK        TCGA-DD-A4NL 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-DD-A4NN        TCGA-DD-A4NO        TCGA-DD-A4NP        TCGA-DD-A4NQ 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-DD-A4NR        TCGA-DD-A4NS        TCGA-DD-A4NV        TCGA-DD-A73A 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-DD-A73B        TCGA-DD-A73C        TCGA-DD-A73D        TCGA-DD-A73E 
  "6Q GAIN MUTATED" "6Q GAIN WILD-TYPE"   "6Q GAIN MUTATED" "6Q GAIN WILD-TYPE" 
       TCGA-DD-A73F        TCGA-DD-A73G        TCGA-ED-A459        TCGA-ED-A4XI 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-ED-A5KG        TCGA-ED-A627        TCGA-ED-A66X        TCGA-ED-A66Y 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE"   "6Q GAIN MUTATED" "6Q GAIN WILD-TYPE" 
       TCGA-ED-A7PX        TCGA-ED-A7PY        TCGA-ED-A7PZ        TCGA-ED-A7XP 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-ED-A82E        TCGA-EP-A12J        TCGA-EP-A26S        TCGA-EP-A2KA 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-EP-A2KB        TCGA-EP-A2KC        TCGA-EP-A3JL        TCGA-EP-A3RK 
  "6Q GAIN MUTATED"   "6Q GAIN MUTATED" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-ES-A2HS        TCGA-ES-A2HT        TCGA-FV-A23B        TCGA-FV-A2QR 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-FV-A3I0        TCGA-FV-A3I1        TCGA-FV-A3R2        TCGA-FV-A3R3 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-FV-A495        TCGA-FV-A496        TCGA-FV-A4ZP        TCGA-FV-A4ZQ 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U        TCGA-G3-A25V 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE"   "6Q GAIN MUTATED" "6Q GAIN WILD-TYPE" 
       TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y        TCGA-G3-A25Z 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI        TCGA-G3-A3CJ 
  "6Q GAIN MUTATED" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-G3-A3CK        TCGA-G3-A5SI        TCGA-G3-A5SJ        TCGA-G3-A5SL 
  "6Q GAIN MUTATED"   "6Q GAIN MUTATED" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-G3-A5SM        TCGA-G3-A6UC        TCGA-GJ-A6C0        TCGA-K7-A6G5 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-LG-A6GG        TCGA-MI-A75C        TCGA-MI-A75E        TCGA-MI-A75G 
  "6Q GAIN MUTATED" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE"   "6Q GAIN MUTATED" 
       TCGA-MI-A75I        TCGA-NI-A4U2        TCGA-O8-A75V 
"6Q GAIN WILD-TYPE" "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-BC-A69H        TCGA-BC-A69I 
  "6Q GAIN MUTATED" "6Q GAIN WILD-TYPE"   "6Q GAIN MUTATED" "6Q GAIN WILD-TYPE" 
       TCGA-CC-5258        TCGA-CC-5260        TCGA-CC-5261        TCGA-CC-5262 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-CC-5263        TCGA-CC-A1HT        TCGA-CC-A3M9        TCGA-CC-A3MA 
  "6Q GAIN MUTATED" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-CC-A3MB        TCGA-CC-A3MC        TCGA-DD-A113        TCGA-DD-A114 
"6Q GAIN WILD-TYPE"   "6Q GAIN MUTATED" "6Q GAIN WILD-TYPE"   "6Q GAIN MUTATED" 
       TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118        TCGA-DD-A119 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE"   "6Q GAIN MUTATED" 
       TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C        TCGA-DD-A11D 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB        TCGA-DD-A1EC 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EF        TCGA-DD-A1EG 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-DD-A1EH        TCGA-DD-A1EI        TCGA-DD-A1EJ        TCGA-DD-A1EK 
  "6Q GAIN MUTATED" "6Q GAIN WILD-TYPE" "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-A4NB        TCGA-DD-A4ND        TCGA-DD-A4NF        TCGA-DD-A4NH 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-DD-A4NI        TCGA-DD-A4NJ        TCGA-DD-A4NK        TCGA-DD-A4NL 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-DD-A4NN        TCGA-DD-A4NO        TCGA-DD-A4NP        TCGA-DD-A4NQ 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-DD-A4NR        TCGA-DD-A4NS        TCGA-DD-A4NV        TCGA-DD-A73A 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-DD-A73B        TCGA-DD-A73C        TCGA-DD-A73D        TCGA-DD-A73E 
  "6Q GAIN MUTATED" "6Q GAIN WILD-TYPE"   "6Q GAIN MUTATED" "6Q GAIN WILD-TYPE" 
       TCGA-DD-A73F        TCGA-DD-A73G        TCGA-ED-A459        TCGA-ED-A4XI 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-ED-A5KG        TCGA-ED-A627        TCGA-ED-A66X        TCGA-ED-A66Y 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE"   "6Q GAIN MUTATED" "6Q GAIN WILD-TYPE" 
       TCGA-ED-A7PX        TCGA-ED-A7PY        TCGA-ED-A7PZ        TCGA-ED-A7XP 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-ED-A82E        TCGA-EP-A12J        TCGA-EP-A26S        TCGA-EP-A2KA 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-EP-A2KB        TCGA-EP-A2KC        TCGA-EP-A3JL        TCGA-EP-A3RK 
  "6Q GAIN MUTATED"   "6Q GAIN MUTATED" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-ES-A2HS        TCGA-ES-A2HT        TCGA-FV-A23B        TCGA-FV-A2QR 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-FV-A3I0        TCGA-FV-A3I1        TCGA-FV-A3R2        TCGA-FV-A3R3 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-FV-A495        TCGA-FV-A496        TCGA-FV-A4ZP        TCGA-FV-A4ZQ 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U        TCGA-G3-A25V 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE"   "6Q GAIN MUTATED" "6Q GAIN WILD-TYPE" 
       TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y        TCGA-G3-A25Z 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI        TCGA-G3-A3CJ 
  "6Q GAIN MUTATED" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-G3-A3CK        TCGA-G3-A5SI        TCGA-G3-A5SJ        TCGA-G3-A5SL 
  "6Q GAIN MUTATED"   "6Q GAIN MUTATED" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-G3-A5SM        TCGA-G3-A6UC        TCGA-GJ-A6C0        TCGA-K7-A6G5 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-LG-A6GG        TCGA-MI-A75C        TCGA-MI-A75E        TCGA-MI-A75G 
  "6Q GAIN MUTATED" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE"   "6Q GAIN MUTATED" 
       TCGA-MI-A75I        TCGA-NI-A4U2        TCGA-O8-A75V 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
[1] "hr=" "1.4"
D12V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  6Q GAIN MUTATED         7        7         1          4          0          0
  6Q GAIN WILD-TYPE      51       29         1         26          4          5
                   vv
clus                STAGE IV STAGE IVA STAGE IVB
  6Q GAIN MUTATED          1         0         1
  6Q GAIN WILD-TYPE        0         1         1
D12V3, multiclass
                   vv
clus                T1 T2 T3 T4
  6Q GAIN MUTATED    7  7  6  1
  6Q GAIN WILD-TYPE 54 33 34  7
D12V4, multiclass
    clus
vv   6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  T1               7                54
  T2               7                33
  T3               6                34
  T4               1                 7
D12V5, binary
                   cls
clus                 0  1
  6Q GAIN MUTATED   14  0
  6Q GAIN WILD-TYPE 83  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED     14    0
  6Q GAIN WILD-TYPE   83    3
   clus
vv  6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  0              14                83
  1               0                 3
                   vv
clus                M0 M1 MX
  6Q GAIN MUTATED   16  2  3
  6Q GAIN WILD-TYPE 99  1 28
D12V6, multiclass
    clus
vv   6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  M0              16                99
  M1               2                 1
  MX               3                28
D12V7, binary
                   cls
clus                 0  1
  6Q GAIN MUTATED    7 14
  6Q GAIN WILD-TYPE 51 77
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED      7   14
  6Q GAIN WILD-TYPE   51   77
        clus
vv       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  FEMALE               7                51
  MALE                14                77
                   vv
clus                 R0  R1  R2  RX
  6Q GAIN MUTATED    17   1   1   2
  6Q GAIN WILD-TYPE 105  10   0   8
D12V8, multiclass
    clus
vv   6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  R0              17               105
  R1               1                10
  R2               1                 0
  RX               2                 8

Clustering(13) Variable = 7P GAIN MUTATION ANALYSIS
D13V1, survival
                   sevent
clus2                0  1
  7P GAIN MUTATED   27 19
  7P GAIN WILD-TYPE 57 44
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               46               101 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               19                44 
$`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 
      113.00        51.29        90.71        19.79         6.71        29.16 
TCGA-DD-A39V TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A2 TCGA-DD-A3A7 TCGA-DD-A4NA 
       21.14         5.62        19.76        70.06        13.78        33.14 
TCGA-DD-A4ND TCGA-DD-A4NI TCGA-DD-A4NK TCGA-DD-A4NQ TCGA-DD-A4NV TCGA-DD-A73D 
       73.38        18.44        39.78        12.26        66.35        10.98 
TCGA-DD-A73E TCGA-DD-A73G TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY TCGA-EP-A2KC 
        1.45       100.96         0.23         0.20         0.20         0.62 
TCGA-EP-A3JL TCGA-ES-A2HS TCGA-FV-A3R2 TCGA-FV-A496 TCGA-FV-A4ZP TCGA-G3-A25S 
        9.96        22.85         6.38         0.33        60.36         1.22 
TCGA-G3-A25T TCGA-G3-A25V TCGA-G3-A25X TCGA-G3-A3CG TCGA-G3-A3CJ TCGA-G3-A5SL 
       51.06        28.27        58.49        22.13        19.53         7.99 
TCGA-G3-A5SM TCGA-G3-A6UC TCGA-LG-A6GG TCGA-MI-A75G 
        4.37         7.76         0.49        14.24 

$`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        13.84 
TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69H TCGA-BC-A69I TCGA-CC-5258 
        0.26        22.36         9.50         3.95         0.53         0.07 
TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA 
        0.39         3.39         4.24         3.32         0.10         0.07 
TCGA-CC-A3MC TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A119 TCGA-DD-A11A 
        0.13        37.78        83.57        53.33         7.33         2.60 
TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1ED TCGA-DD-A1EF 
        0.46        21.76        79.40        66.31        75.65        12.95 
TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39X 
       45.11        49.15         6.02        18.35        13.64        55.69 
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-A3A8 TCGA-DD-A3A9 TCGA-DD-A4NB TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NJ 
        0.36        30.61        12.85        14.07        14.24        15.06 
TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NR TCGA-DD-A4NS 
       56.25        29.56        61.45        93.67         0.30        80.75 
TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73F TCGA-ED-A459 TCGA-ED-A4XI 
       10.98         9.30         7.56        27.72        13.41        12.69 
TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A7PZ TCGA-ED-A7XP TCGA-ED-A82E 
       15.85        13.91        13.35         0.20         0.20         0.20 
TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A3RK TCGA-ES-A2HT 
       18.74        19.99        11.74        10.98        11.93        14.40 
TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R3 TCGA-FV-A495 
       32.45        19.10         0.20         8.12         0.13         0.03 
TCGA-FV-A4ZQ TCGA-G3-A25U TCGA-G3-A25W TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CH 
        0.39        53.79        30.74        14.86        21.53        25.64 
TCGA-G3-A3CI TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-GJ-A6C0 TCGA-K7-A6G5 
        5.92        19.23        14.70        11.97         1.02         4.01 
TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75I TCGA-NI-A4U2 TCGA-O8-A75V 
        9.57         5.10         8.71        58.88         4.44 

  7P GAIN MUTATED 7P GAIN WILD-TYPE 
             0.10              0.03 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
           113.00            107.11 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
           18.985            13.840 
[1] "0.1 - 113.0 (19.0)" "0.0 - 107.1 (13.8)"
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-BC-A5W4        TCGA-BC-A69H        TCGA-BC-A69I 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-CC-5258        TCGA-CC-5260        TCGA-CC-5261        TCGA-CC-5262 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-CC-5263        TCGA-CC-A1HT        TCGA-CC-A3M9        TCGA-CC-A3MA 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-CC-A3MB        TCGA-CC-A3MC        TCGA-DD-A113        TCGA-DD-A114 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118        TCGA-DD-A119 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C        TCGA-DD-A11D 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB        TCGA-DD-A1EC 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EF        TCGA-DD-A1EG 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-DD-A1EH        TCGA-DD-A1EI        TCGA-DD-A1EJ        TCGA-DD-A1EK 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       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-A4NB        TCGA-DD-A4ND        TCGA-DD-A4NF        TCGA-DD-A4NH 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-DD-A4NI        TCGA-DD-A4NJ        TCGA-DD-A4NK        TCGA-DD-A4NL 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-DD-A4NN        TCGA-DD-A4NO        TCGA-DD-A4NP        TCGA-DD-A4NQ 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       TCGA-DD-A4NR        TCGA-DD-A4NS        TCGA-DD-A4NV        TCGA-DD-A73A 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-DD-A73B        TCGA-DD-A73C        TCGA-DD-A73D        TCGA-DD-A73E 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-DD-A73F        TCGA-DD-A73G        TCGA-ED-A459        TCGA-ED-A4XI 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-ED-A5KG        TCGA-ED-A627        TCGA-ED-A66X        TCGA-ED-A66Y 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       TCGA-ED-A7PX        TCGA-ED-A7PY        TCGA-ED-A7PZ        TCGA-ED-A7XP 
  "7P GAIN MUTATED"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-ED-A82E        TCGA-EP-A12J        TCGA-EP-A26S        TCGA-EP-A2KA 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-EP-A2KB        TCGA-EP-A2KC        TCGA-EP-A3JL        TCGA-EP-A3RK 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-ES-A2HS        TCGA-ES-A2HT        TCGA-FV-A23B        TCGA-FV-A2QR 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-FV-A3I0        TCGA-FV-A3I1        TCGA-FV-A3R2        TCGA-FV-A3R3 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-FV-A495        TCGA-FV-A496        TCGA-FV-A4ZP        TCGA-FV-A4ZQ 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U        TCGA-G3-A25V 
  "7P GAIN MUTATED"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y        TCGA-G3-A25Z 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI        TCGA-G3-A3CJ 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       TCGA-G3-A3CK        TCGA-G3-A5SI        TCGA-G3-A5SJ        TCGA-G3-A5SL 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       TCGA-G3-A5SM        TCGA-G3-A6UC        TCGA-GJ-A6C0        TCGA-K7-A6G5 
  "7P GAIN MUTATED"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-LG-A6GG        TCGA-MI-A75C        TCGA-MI-A75E        TCGA-MI-A75G 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       TCGA-MI-A75I        TCGA-NI-A4U2        TCGA-O8-A75V 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-BC-A5W4        TCGA-BC-A69H        TCGA-BC-A69I 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-CC-5258        TCGA-CC-5260        TCGA-CC-5261        TCGA-CC-5262 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-CC-5263        TCGA-CC-A1HT        TCGA-CC-A3M9        TCGA-CC-A3MA 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-CC-A3MB        TCGA-CC-A3MC        TCGA-DD-A113        TCGA-DD-A114 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118        TCGA-DD-A119 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C        TCGA-DD-A11D 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB        TCGA-DD-A1EC 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EF        TCGA-DD-A1EG 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-DD-A1EH        TCGA-DD-A1EI        TCGA-DD-A1EJ        TCGA-DD-A1EK 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       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-A4NB        TCGA-DD-A4ND        TCGA-DD-A4NF        TCGA-DD-A4NH 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-DD-A4NI        TCGA-DD-A4NJ        TCGA-DD-A4NK        TCGA-DD-A4NL 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-DD-A4NN        TCGA-DD-A4NO        TCGA-DD-A4NP        TCGA-DD-A4NQ 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       TCGA-DD-A4NR        TCGA-DD-A4NS        TCGA-DD-A4NV        TCGA-DD-A73A 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-DD-A73B        TCGA-DD-A73C        TCGA-DD-A73D        TCGA-DD-A73E 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-DD-A73F        TCGA-DD-A73G        TCGA-ED-A459        TCGA-ED-A4XI 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-ED-A5KG        TCGA-ED-A627        TCGA-ED-A66X        TCGA-ED-A66Y 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       TCGA-ED-A7PX        TCGA-ED-A7PY        TCGA-ED-A7PZ        TCGA-ED-A7XP 
  "7P GAIN MUTATED"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-ED-A82E        TCGA-EP-A12J        TCGA-EP-A26S        TCGA-EP-A2KA 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-EP-A2KB        TCGA-EP-A2KC        TCGA-EP-A3JL        TCGA-EP-A3RK 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-ES-A2HS        TCGA-ES-A2HT        TCGA-FV-A23B        TCGA-FV-A2QR 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-FV-A3I0        TCGA-FV-A3I1        TCGA-FV-A3R2        TCGA-FV-A3R3 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-FV-A495        TCGA-FV-A496        TCGA-FV-A4ZP        TCGA-FV-A4ZQ 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U        TCGA-G3-A25V 
  "7P GAIN MUTATED"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y        TCGA-G3-A25Z 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI        TCGA-G3-A3CJ 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       TCGA-G3-A3CK        TCGA-G3-A5SI        TCGA-G3-A5SJ        TCGA-G3-A5SL 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       TCGA-G3-A5SM        TCGA-G3-A6UC        TCGA-GJ-A6C0        TCGA-K7-A6G5 
  "7P GAIN MUTATED"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-LG-A6GG        TCGA-MI-A75C        TCGA-MI-A75E        TCGA-MI-A75G 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       TCGA-MI-A75I        TCGA-NI-A4U2        TCGA-O8-A75V 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-BC-A5W4        TCGA-BC-A69H        TCGA-BC-A69I 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-CC-5258        TCGA-CC-5260        TCGA-CC-5261        TCGA-CC-5262 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-CC-5263        TCGA-CC-A1HT        TCGA-CC-A3M9        TCGA-CC-A3MA 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-CC-A3MB        TCGA-CC-A3MC        TCGA-DD-A113        TCGA-DD-A114 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118        TCGA-DD-A119 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C        TCGA-DD-A11D 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB        TCGA-DD-A1EC 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EF        TCGA-DD-A1EG 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-DD-A1EH        TCGA-DD-A1EI        TCGA-DD-A1EJ        TCGA-DD-A1EK 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       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-A4NB        TCGA-DD-A4ND        TCGA-DD-A4NF        TCGA-DD-A4NH 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-DD-A4NI        TCGA-DD-A4NJ        TCGA-DD-A4NK        TCGA-DD-A4NL 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-DD-A4NN        TCGA-DD-A4NO        TCGA-DD-A4NP        TCGA-DD-A4NQ 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       TCGA-DD-A4NR        TCGA-DD-A4NS        TCGA-DD-A4NV        TCGA-DD-A73A 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-DD-A73B        TCGA-DD-A73C        TCGA-DD-A73D        TCGA-DD-A73E 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-DD-A73F        TCGA-DD-A73G        TCGA-ED-A459        TCGA-ED-A4XI 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-ED-A5KG        TCGA-ED-A627        TCGA-ED-A66X        TCGA-ED-A66Y 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       TCGA-ED-A7PX        TCGA-ED-A7PY        TCGA-ED-A7PZ        TCGA-ED-A7XP 
  "7P GAIN MUTATED"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-ED-A82E        TCGA-EP-A12J        TCGA-EP-A26S        TCGA-EP-A2KA 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-EP-A2KB        TCGA-EP-A2KC        TCGA-EP-A3JL        TCGA-EP-A3RK 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-ES-A2HS        TCGA-ES-A2HT        TCGA-FV-A23B        TCGA-FV-A2QR 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-FV-A3I0        TCGA-FV-A3I1        TCGA-FV-A3R2        TCGA-FV-A3R3 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-FV-A495        TCGA-FV-A496        TCGA-FV-A4ZP        TCGA-FV-A4ZQ 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U        TCGA-G3-A25V 
  "7P GAIN MUTATED"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y        TCGA-G3-A25Z 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI        TCGA-G3-A3CJ 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       TCGA-G3-A3CK        TCGA-G3-A5SI        TCGA-G3-A5SJ        TCGA-G3-A5SL 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       TCGA-G3-A5SM        TCGA-G3-A6UC        TCGA-GJ-A6C0        TCGA-K7-A6G5 
  "7P GAIN MUTATED"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-LG-A6GG        TCGA-MI-A75C        TCGA-MI-A75E        TCGA-MI-A75G 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       TCGA-MI-A75I        TCGA-NI-A4U2        TCGA-O8-A75V 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
[1] "hr=" "1.3"
D13V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  7P GAIN MUTATED        16       14         0          9          2          3
  7P GAIN WILD-TYPE      42       22         2         21          2          2
                   vv
clus                STAGE IV STAGE IVA STAGE IVB
  7P GAIN MUTATED          0         0         0
  7P GAIN WILD-TYPE        1         1         2
D13V3, multiclass
                   vv
clus                T1 T2 T3 T4
  7P GAIN MUTATED   17 17 12  1
  7P GAIN WILD-TYPE 44 23 28  7
D13V4, multiclass
    clus
vv   7P GAIN MUTATED 7P GAIN WILD-TYPE
  T1              17                44
  T2              17                23
  T3              12                28
  T4               1                 7
D13V5, binary
                   cls
clus                 0  1
  7P GAIN MUTATED   26  2
  7P GAIN WILD-TYPE 71  1
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED     26    2
  7P GAIN WILD-TYPE   71    1
   clus
vv  7P GAIN MUTATED 7P GAIN WILD-TYPE
  0              26                71
  1               2                 1
                   vv
clus                M0 M1 MX
  7P GAIN MUTATED   39  0  8
  7P GAIN WILD-TYPE 76  3 23
D13V6, multiclass
    clus
vv   7P GAIN MUTATED 7P GAIN WILD-TYPE
  M0              39                76
  M1               0                 3
  MX               8                23
D13V7, binary
                   cls
clus                 0  1
  7P GAIN MUTATED   21 26
  7P GAIN WILD-TYPE 37 65
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED     21   26
  7P GAIN WILD-TYPE   37   65
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  FEMALE              21                37
  MALE                26                65
                   vv
clus                R0 R1 R2 RX
  7P GAIN MUTATED   39  5  0  2
  7P GAIN WILD-TYPE 83  6  1  8
D13V8, multiclass
    clus
vv   7P GAIN MUTATED 7P GAIN WILD-TYPE
  R0              39                83
  R1               5                 6
  R2               0                 1
  RX               2                 8

Clustering(14) Variable = 7Q GAIN MUTATION ANALYSIS
D14V1, survival
                   sevent
clus2                0  1
  7Q GAIN MUTATED   27 20
  7Q GAIN WILD-TYPE 57 43
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               47               100 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               20                43 
$`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       113.00         2.60        51.29        90.71        19.79 
TCGA-DD-A1EE TCGA-DD-A1EJ TCGA-DD-A39V TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A2 
        6.71        29.16        21.14         5.62        19.76        70.06 
TCGA-DD-A4NA TCGA-DD-A4NI TCGA-DD-A4NK TCGA-DD-A4NQ TCGA-DD-A4NV TCGA-DD-A73C 
       33.14        18.44        39.78        12.26        66.35         7.56 
TCGA-DD-A73E TCGA-DD-A73G TCGA-ED-A459 TCGA-ED-A66Y TCGA-ED-A7PY TCGA-EP-A26S 
        1.45       100.96        13.41         0.23         0.20        19.99 
TCGA-EP-A2KA TCGA-EP-A2KC TCGA-EP-A3JL TCGA-ES-A2HS TCGA-FV-A3I1 TCGA-FV-A3R2 
       11.74         0.62         9.96        22.85         8.12         6.38 
TCGA-G3-A25T TCGA-G3-A25V TCGA-G3-A25X TCGA-G3-A3CG TCGA-G3-A3CJ TCGA-G3-A5SL 
       51.06        28.27        58.49        22.13        19.53         7.99 
TCGA-G3-A5SM TCGA-G3-A6UC TCGA-LG-A6GG TCGA-MI-A75G TCGA-NI-A4U2 
        4.37         7.76         0.49        14.24        58.88 

$`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        13.84 
TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A69H TCGA-BC-A69I TCGA-CC-5258 TCGA-CC-5261 
        0.26        22.36         3.95         0.53         0.07         0.39 
TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3MA TCGA-CC-A3MC TCGA-DD-A113 
        3.39         4.24         3.32         0.07         0.13        79.73 
TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A119 TCGA-DD-A11B TCGA-DD-A11C 
       37.78        83.57        53.33         7.33         0.46        21.76 
TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1ED TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH 
       79.40        66.31        75.65        12.95        45.11        49.15 
TCGA-DD-A1EI TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39X TCGA-DD-A3A0 TCGA-DD-A3A1 
        6.02        18.35        13.64        55.69        25.81         7.66 
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-A4NB TCGA-DD-A4ND TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NJ 
       30.61        12.85        73.38        14.07        14.24        15.06 
TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NR TCGA-DD-A4NS 
       56.25        29.56        61.45        93.67         0.30        80.75 
TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73D TCGA-DD-A73F TCGA-ED-A4XI TCGA-ED-A5KG 
       10.98         9.30        10.98        27.72        12.69        15.85 
TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A7PX TCGA-ED-A7PZ TCGA-ED-A7XP TCGA-ED-A82E 
       13.91        13.35         0.20         0.20         0.20         0.20 
TCGA-EP-A12J TCGA-EP-A2KB TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QR 
       18.74        10.98        11.93        14.40        32.45        19.10 
TCGA-FV-A3I0 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZP TCGA-FV-A4ZQ 
        0.20         0.13         0.03         0.33        60.36         0.39 
TCGA-G3-A25S TCGA-G3-A25U TCGA-G3-A25W TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CH 
        1.22        53.79        30.74        14.86        21.53        25.64 
TCGA-G3-A3CI TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-GJ-A6C0 TCGA-K7-A6G5 
        5.92        19.23        14.70        11.97         1.02         4.01 
TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75I TCGA-O8-A75V 
        9.57         5.10         8.71         4.44 

  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
             0.10              0.03 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
           113.00            107.11 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
            14.24             13.99 
[1] "0.1 - 113.0 (14.2)" "0.0 - 107.1 (14.0)"
       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-BC-A69H        TCGA-BC-A69I 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-CC-5258        TCGA-CC-5260        TCGA-CC-5261        TCGA-CC-5262 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-CC-5263        TCGA-CC-A1HT        TCGA-CC-A3M9        TCGA-CC-A3MA 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-CC-A3MB        TCGA-CC-A3MC        TCGA-DD-A113        TCGA-DD-A114 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118        TCGA-DD-A119 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C        TCGA-DD-A11D 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB        TCGA-DD-A1EC 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EF        TCGA-DD-A1EG 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-DD-A1EH        TCGA-DD-A1EI        TCGA-DD-A1EJ        TCGA-DD-A1EK 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       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-A4NB        TCGA-DD-A4ND        TCGA-DD-A4NF        TCGA-DD-A4NH 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-DD-A4NI        TCGA-DD-A4NJ        TCGA-DD-A4NK        TCGA-DD-A4NL 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-DD-A4NN        TCGA-DD-A4NO        TCGA-DD-A4NP        TCGA-DD-A4NQ 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-DD-A4NR        TCGA-DD-A4NS        TCGA-DD-A4NV        TCGA-DD-A73A 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-DD-A73B        TCGA-DD-A73C        TCGA-DD-A73D        TCGA-DD-A73E 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-DD-A73F        TCGA-DD-A73G        TCGA-ED-A459        TCGA-ED-A4XI 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-ED-A5KG        TCGA-ED-A627        TCGA-ED-A66X        TCGA-ED-A66Y 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-ED-A7PX        TCGA-ED-A7PY        TCGA-ED-A7PZ        TCGA-ED-A7XP 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-ED-A82E        TCGA-EP-A12J        TCGA-EP-A26S        TCGA-EP-A2KA 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" 
       TCGA-EP-A2KB        TCGA-EP-A2KC        TCGA-EP-A3JL        TCGA-EP-A3RK 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-ES-A2HS        TCGA-ES-A2HT        TCGA-FV-A23B        TCGA-FV-A2QR 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-FV-A3I0        TCGA-FV-A3I1        TCGA-FV-A3R2        TCGA-FV-A3R3 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-FV-A495        TCGA-FV-A496        TCGA-FV-A4ZP        TCGA-FV-A4ZQ 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U        TCGA-G3-A25V 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y        TCGA-G3-A25Z 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI        TCGA-G3-A3CJ 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-G3-A3CK        TCGA-G3-A5SI        TCGA-G3-A5SJ        TCGA-G3-A5SL 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-G3-A5SM        TCGA-G3-A6UC        TCGA-GJ-A6C0        TCGA-K7-A6G5 
  "7Q GAIN MUTATED"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-LG-A6GG        TCGA-MI-A75C        TCGA-MI-A75E        TCGA-MI-A75G 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-MI-A75I        TCGA-NI-A4U2        TCGA-O8-A75V 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-BC-A5W4        TCGA-BC-A69H        TCGA-BC-A69I 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-CC-5258        TCGA-CC-5260        TCGA-CC-5261        TCGA-CC-5262 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-CC-5263        TCGA-CC-A1HT        TCGA-CC-A3M9        TCGA-CC-A3MA 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-CC-A3MB        TCGA-CC-A3MC        TCGA-DD-A113        TCGA-DD-A114 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118        TCGA-DD-A119 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C        TCGA-DD-A11D 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB        TCGA-DD-A1EC 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EF        TCGA-DD-A1EG 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-DD-A1EH        TCGA-DD-A1EI        TCGA-DD-A1EJ        TCGA-DD-A1EK 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       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-A4NB        TCGA-DD-A4ND        TCGA-DD-A4NF        TCGA-DD-A4NH 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-DD-A4NI        TCGA-DD-A4NJ        TCGA-DD-A4NK        TCGA-DD-A4NL 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-DD-A4NN        TCGA-DD-A4NO        TCGA-DD-A4NP        TCGA-DD-A4NQ 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-DD-A4NR        TCGA-DD-A4NS        TCGA-DD-A4NV        TCGA-DD-A73A 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-DD-A73B        TCGA-DD-A73C        TCGA-DD-A73D        TCGA-DD-A73E 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-DD-A73F        TCGA-DD-A73G        TCGA-ED-A459        TCGA-ED-A4XI 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-ED-A5KG        TCGA-ED-A627        TCGA-ED-A66X        TCGA-ED-A66Y 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-ED-A7PX        TCGA-ED-A7PY        TCGA-ED-A7PZ        TCGA-ED-A7XP 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-ED-A82E        TCGA-EP-A12J        TCGA-EP-A26S        TCGA-EP-A2KA 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" 
       TCGA-EP-A2KB        TCGA-EP-A2KC        TCGA-EP-A3JL        TCGA-EP-A3RK 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-ES-A2HS        TCGA-ES-A2HT        TCGA-FV-A23B        TCGA-FV-A2QR 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-FV-A3I0        TCGA-FV-A3I1        TCGA-FV-A3R2        TCGA-FV-A3R3 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-FV-A495        TCGA-FV-A496        TCGA-FV-A4ZP        TCGA-FV-A4ZQ 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U        TCGA-G3-A25V 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y        TCGA-G3-A25Z 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI        TCGA-G3-A3CJ 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-G3-A3CK        TCGA-G3-A5SI        TCGA-G3-A5SJ        TCGA-G3-A5SL 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-G3-A5SM        TCGA-G3-A6UC        TCGA-GJ-A6C0        TCGA-K7-A6G5 
  "7Q GAIN MUTATED"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-LG-A6GG        TCGA-MI-A75C        TCGA-MI-A75E        TCGA-MI-A75G 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-MI-A75I        TCGA-NI-A4U2        TCGA-O8-A75V 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-BC-A5W4        TCGA-BC-A69H        TCGA-BC-A69I 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-CC-5258        TCGA-CC-5260        TCGA-CC-5261        TCGA-CC-5262 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-CC-5263        TCGA-CC-A1HT        TCGA-CC-A3M9        TCGA-CC-A3MA 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-CC-A3MB        TCGA-CC-A3MC        TCGA-DD-A113        TCGA-DD-A114 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118        TCGA-DD-A119 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C        TCGA-DD-A11D 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB        TCGA-DD-A1EC 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EF        TCGA-DD-A1EG 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-DD-A1EH        TCGA-DD-A1EI        TCGA-DD-A1EJ        TCGA-DD-A1EK 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       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-A4NB        TCGA-DD-A4ND        TCGA-DD-A4NF        TCGA-DD-A4NH 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-DD-A4NI        TCGA-DD-A4NJ        TCGA-DD-A4NK        TCGA-DD-A4NL 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-DD-A4NN        TCGA-DD-A4NO        TCGA-DD-A4NP        TCGA-DD-A4NQ 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-DD-A4NR        TCGA-DD-A4NS        TCGA-DD-A4NV        TCGA-DD-A73A 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-DD-A73B        TCGA-DD-A73C        TCGA-DD-A73D        TCGA-DD-A73E 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-DD-A73F        TCGA-DD-A73G        TCGA-ED-A459        TCGA-ED-A4XI 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-ED-A5KG        TCGA-ED-A627        TCGA-ED-A66X        TCGA-ED-A66Y 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-ED-A7PX        TCGA-ED-A7PY        TCGA-ED-A7PZ        TCGA-ED-A7XP 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-ED-A82E        TCGA-EP-A12J        TCGA-EP-A26S        TCGA-EP-A2KA 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" 
       TCGA-EP-A2KB        TCGA-EP-A2KC        TCGA-EP-A3JL        TCGA-EP-A3RK 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-ES-A2HS        TCGA-ES-A2HT        TCGA-FV-A23B        TCGA-FV-A2QR 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-FV-A3I0        TCGA-FV-A3I1        TCGA-FV-A3R2        TCGA-FV-A3R3 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-FV-A495        TCGA-FV-A496        TCGA-FV-A4ZP        TCGA-FV-A4ZQ 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U        TCGA-G3-A25V 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y        TCGA-G3-A25Z 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI        TCGA-G3-A3CJ 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-G3-A3CK        TCGA-G3-A5SI        TCGA-G3-A5SJ        TCGA-G3-A5SL 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-G3-A5SM        TCGA-G3-A6UC        TCGA-GJ-A6C0        TCGA-K7-A6G5 
  "7Q GAIN MUTATED"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-LG-A6GG        TCGA-MI-A75C        TCGA-MI-A75E        TCGA-MI-A75G 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-MI-A75I        TCGA-NI-A4U2        TCGA-O8-A75V 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
[1] "hr=" "1.1"
D14V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  7Q GAIN MUTATED        15       13         0         13          1          3
  7Q GAIN WILD-TYPE      43       23         2         17          3          2
                   vv
clus                STAGE IV STAGE IVA STAGE IVB
  7Q GAIN MUTATED          0         0         0
  7Q GAIN WILD-TYPE        1         1         2
D14V3, multiclass
                   vv
clus                T1 T2 T3 T4
  7Q GAIN MUTATED   16 16 15  1
  7Q GAIN WILD-TYPE 45 24 25  7
D14V4, multiclass
    clus
vv   7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  T1              16                45
  T2              16                24
  T3              15                25
  T4               1                 7
D14V5, binary
                   cls
clus                 0  1
  7Q GAIN MUTATED   28  2
  7Q GAIN WILD-TYPE 69  1
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED     28    2
  7Q GAIN WILD-TYPE   69    1
   clus
vv  7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  0              28                69
  1               2                 1
                   vv
clus                M0 M1 MX
  7Q GAIN MUTATED   37  0 11
  7Q GAIN WILD-TYPE 78  3 20
D14V6, multiclass
    clus
vv   7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  M0              37                78
  M1               0                 3
  MX              11                20
D14V7, binary
                   cls
clus                 0  1
  7Q GAIN MUTATED   19 29
  7Q GAIN WILD-TYPE 39 62
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED     19   29
  7Q GAIN WILD-TYPE   39   62
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  FEMALE              19                39
  MALE                29                62
                   vv
clus                R0 R1 R2 RX
  7Q GAIN MUTATED   40  4  0  2
  7Q GAIN WILD-TYPE 82  7  1  8
D14V8, multiclass
    clus
vv   7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  R0              40                82
  R1               4                 7
  R2               0                 1
  RX               2                 8

Clustering(15) Variable = 8P GAIN MUTATION ANALYSIS
D15V1, survival
                   sevent
clus2                0  1
  8P GAIN MUTATED   15 12
  8P GAIN WILD-TYPE 69 51
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               27               120 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               12                51 
$`8P GAIN MUTATED`
TCGA-BC-4072 TCGA-BC-A10S TCGA-CC-5258 TCGA-CC-A1HT TCGA-CC-A3MB TCGA-DD-A119 
       48.99        46.78         0.07         3.32         0.10         7.33 
TCGA-DD-A11A TCGA-DD-A1E9 TCGA-DD-A1EC TCGA-DD-A1EF TCGA-DD-A1EI TCGA-DD-A39X 
        2.60        90.71        19.79        12.95         6.02        55.69 
TCGA-DD-A3A1 TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NQ TCGA-DD-A4NS TCGA-ED-A459 
        7.66        29.56        61.45        12.26        80.75        13.41 
TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7XP TCGA-ED-A82E TCGA-EP-A2KB TCGA-EP-A3JL 
       13.35         0.23         0.20         0.20        10.98         9.96 
TCGA-G3-A25X TCGA-G3-A25Z TCGA-G3-A5SL 
       58.49        21.53         7.99 

$`8P GAIN WILD-TYPE`
TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W 
       27.91        37.32        10.13        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-BC-A69H TCGA-BC-A69I 
       13.84         0.26        22.36         9.50         3.95         0.53 
TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A3M9 TCGA-CC-A3MA 
        2.86         0.39         3.39         4.24         0.10         0.07 
TCGA-CC-A3MC TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 
        0.13        79.73        37.78        83.57        53.33       113.00 
TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1ED 
        0.46        21.76        51.29        79.40        66.31        75.65 
TCGA-DD-A1EE TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A1EL 
        6.71        45.11        49.15        29.16        18.35        13.64 
TCGA-DD-A39V TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A2 TCGA-DD-A3A3 
       21.14         5.62        19.76        25.81        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        30.61 
TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NI 
       33.14        12.85        73.38        14.07        14.24        18.44 
TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NP TCGA-DD-A4NR TCGA-DD-A4NV 
       15.06        39.78        56.25        93.67         0.30        66.35 
TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F 
       10.98         9.30         7.56        10.98         1.45        27.72 
TCGA-DD-A73G TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A7PX TCGA-ED-A7PY 
      100.96        12.69        15.85        13.91         0.20         0.20 
TCGA-ED-A7PZ TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KC TCGA-EP-A3RK 
        0.20        18.74        19.99        11.74         0.62        11.93 
TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3I1 
       22.85        14.40        32.45        19.10         0.20         8.12 
TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZP TCGA-FV-A4ZQ 
        6.38         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-A25Y 
        1.22        51.06        53.79        28.27        30.74        14.86 
TCGA-G3-A3CG TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI 
       22.13        25.64         5.92        19.53        19.23        14.70 
TCGA-G3-A5SJ TCGA-G3-A5SM TCGA-G3-A6UC TCGA-GJ-A6C0 TCGA-K7-A6G5 TCGA-LG-A6GG 
       11.97         4.37         7.76         1.02         4.01         0.49 
TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75I TCGA-NI-A4U2 TCGA-O8-A75V 
        9.57         5.10        14.24         8.71        58.88         4.44 

  8P GAIN MUTATED 8P GAIN WILD-TYPE 
             0.07              0.03 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
            90.71            113.00 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
            12.26             14.55 
[1] "0.1 - 90.7 (12.3)"  "0.0 - 113.0 (14.6)"
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
  "8P GAIN MUTATED" "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-BC-A69H        TCGA-BC-A69I 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-CC-5258        TCGA-CC-5260        TCGA-CC-5261        TCGA-CC-5262 
  "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-CC-5263        TCGA-CC-A1HT        TCGA-CC-A3M9        TCGA-CC-A3MA 
"8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-CC-A3MB        TCGA-CC-A3MC        TCGA-DD-A113        TCGA-DD-A114 
  "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118        TCGA-DD-A119 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" 
       TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C        TCGA-DD-A11D 
  "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB        TCGA-DD-A1EC 
  "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" 
       TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EF        TCGA-DD-A1EG 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" 
       TCGA-DD-A1EH        TCGA-DD-A1EI        TCGA-DD-A1EJ        TCGA-DD-A1EK 
"8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "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 MUTATED" "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-A4NB        TCGA-DD-A4ND        TCGA-DD-A4NF        TCGA-DD-A4NH 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-DD-A4NI        TCGA-DD-A4NJ        TCGA-DD-A4NK        TCGA-DD-A4NL 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-DD-A4NN        TCGA-DD-A4NO        TCGA-DD-A4NP        TCGA-DD-A4NQ 
  "8P GAIN MUTATED"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" 
       TCGA-DD-A4NR        TCGA-DD-A4NS        TCGA-DD-A4NV        TCGA-DD-A73A 
"8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-DD-A73B        TCGA-DD-A73C        TCGA-DD-A73D        TCGA-DD-A73E 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-DD-A73F        TCGA-DD-A73G        TCGA-ED-A459        TCGA-ED-A4XI 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" 
       TCGA-ED-A5KG        TCGA-ED-A627        TCGA-ED-A66X        TCGA-ED-A66Y 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED"   "8P GAIN MUTATED" 
       TCGA-ED-A7PX        TCGA-ED-A7PY        TCGA-ED-A7PZ        TCGA-ED-A7XP 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" 
       TCGA-ED-A82E        TCGA-EP-A12J        TCGA-EP-A26S        TCGA-EP-A2KA 
  "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-EP-A2KB        TCGA-EP-A2KC        TCGA-EP-A3JL        TCGA-EP-A3RK 
  "8P GAIN MUTATED" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" 
       TCGA-ES-A2HS        TCGA-ES-A2HT        TCGA-FV-A23B        TCGA-FV-A2QR 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-FV-A3I0        TCGA-FV-A3I1        TCGA-FV-A3R2        TCGA-FV-A3R3 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-FV-A495        TCGA-FV-A496        TCGA-FV-A4ZP        TCGA-FV-A4ZQ 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U        TCGA-G3-A25V 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y        TCGA-G3-A25Z 
"8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" 
       TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI        TCGA-G3-A3CJ 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-G3-A3CK        TCGA-G3-A5SI        TCGA-G3-A5SJ        TCGA-G3-A5SL 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" 
       TCGA-G3-A5SM        TCGA-G3-A6UC        TCGA-GJ-A6C0        TCGA-K7-A6G5 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-LG-A6GG        TCGA-MI-A75C        TCGA-MI-A75E        TCGA-MI-A75G 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-MI-A75I        TCGA-NI-A4U2        TCGA-O8-A75V 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
  "8P GAIN MUTATED" "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-BC-A69H        TCGA-BC-A69I 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-CC-5258        TCGA-CC-5260        TCGA-CC-5261        TCGA-CC-5262 
  "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-CC-5263        TCGA-CC-A1HT        TCGA-CC-A3M9        TCGA-CC-A3MA 
"8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-CC-A3MB        TCGA-CC-A3MC        TCGA-DD-A113        TCGA-DD-A114 
  "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118        TCGA-DD-A119 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" 
       TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C        TCGA-DD-A11D 
  "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB        TCGA-DD-A1EC 
  "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" 
       TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EF        TCGA-DD-A1EG 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" 
       TCGA-DD-A1EH        TCGA-DD-A1EI        TCGA-DD-A1EJ        TCGA-DD-A1EK 
"8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "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 MUTATED" "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-A4NB        TCGA-DD-A4ND        TCGA-DD-A4NF        TCGA-DD-A4NH 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-DD-A4NI        TCGA-DD-A4NJ        TCGA-DD-A4NK        TCGA-DD-A4NL 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-DD-A4NN        TCGA-DD-A4NO        TCGA-DD-A4NP        TCGA-DD-A4NQ 
  "8P GAIN MUTATED"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" 
       TCGA-DD-A4NR        TCGA-DD-A4NS        TCGA-DD-A4NV        TCGA-DD-A73A 
"8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-DD-A73B        TCGA-DD-A73C        TCGA-DD-A73D        TCGA-DD-A73E 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-DD-A73F        TCGA-DD-A73G        TCGA-ED-A459        TCGA-ED-A4XI 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" 
       TCGA-ED-A5KG        TCGA-ED-A627        TCGA-ED-A66X        TCGA-ED-A66Y 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED"   "8P GAIN MUTATED" 
       TCGA-ED-A7PX        TCGA-ED-A7PY        TCGA-ED-A7PZ        TCGA-ED-A7XP 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" 
       TCGA-ED-A82E        TCGA-EP-A12J        TCGA-EP-A26S        TCGA-EP-A2KA 
  "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-EP-A2KB        TCGA-EP-A2KC        TCGA-EP-A3JL        TCGA-EP-A3RK 
  "8P GAIN MUTATED" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" 
       TCGA-ES-A2HS        TCGA-ES-A2HT        TCGA-FV-A23B        TCGA-FV-A2QR 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-FV-A3I0        TCGA-FV-A3I1        TCGA-FV-A3R2        TCGA-FV-A3R3 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-FV-A495        TCGA-FV-A496        TCGA-FV-A4ZP        TCGA-FV-A4ZQ 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U        TCGA-G3-A25V 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y        TCGA-G3-A25Z 
"8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" 
       TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI        TCGA-G3-A3CJ 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-G3-A3CK        TCGA-G3-A5SI        TCGA-G3-A5SJ        TCGA-G3-A5SL 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" 
       TCGA-G3-A5SM        TCGA-G3-A6UC        TCGA-GJ-A6C0        TCGA-K7-A6G5 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-LG-A6GG        TCGA-MI-A75C        TCGA-MI-A75E        TCGA-MI-A75G 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-MI-A75I        TCGA-NI-A4U2        TCGA-O8-A75V 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
  "8P GAIN MUTATED" "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-BC-A69H        TCGA-BC-A69I 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-CC-5258        TCGA-CC-5260        TCGA-CC-5261        TCGA-CC-5262 
  "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-CC-5263        TCGA-CC-A1HT        TCGA-CC-A3M9        TCGA-CC-A3MA 
"8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-CC-A3MB        TCGA-CC-A3MC        TCGA-DD-A113        TCGA-DD-A114 
  "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118        TCGA-DD-A119 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" 
       TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C        TCGA-DD-A11D 
  "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB        TCGA-DD-A1EC 
  "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" 
       TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EF        TCGA-DD-A1EG 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" 
       TCGA-DD-A1EH        TCGA-DD-A1EI        TCGA-DD-A1EJ        TCGA-DD-A1EK 
"8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "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 MUTATED" "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-A4NB        TCGA-DD-A4ND        TCGA-DD-A4NF        TCGA-DD-A4NH 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-DD-A4NI        TCGA-DD-A4NJ        TCGA-DD-A4NK        TCGA-DD-A4NL 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-DD-A4NN        TCGA-DD-A4NO        TCGA-DD-A4NP        TCGA-DD-A4NQ 
  "8P GAIN MUTATED"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" 
       TCGA-DD-A4NR        TCGA-DD-A4NS        TCGA-DD-A4NV        TCGA-DD-A73A 
"8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-DD-A73B        TCGA-DD-A73C        TCGA-DD-A73D        TCGA-DD-A73E 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-DD-A73F        TCGA-DD-A73G        TCGA-ED-A459        TCGA-ED-A4XI 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" 
       TCGA-ED-A5KG        TCGA-ED-A627        TCGA-ED-A66X        TCGA-ED-A66Y 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED"   "8P GAIN MUTATED" 
       TCGA-ED-A7PX        TCGA-ED-A7PY        TCGA-ED-A7PZ        TCGA-ED-A7XP 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" 
       TCGA-ED-A82E        TCGA-EP-A12J        TCGA-EP-A26S        TCGA-EP-A2KA 
  "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-EP-A2KB        TCGA-EP-A2KC        TCGA-EP-A3JL        TCGA-EP-A3RK 
  "8P GAIN MUTATED" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" 
       TCGA-ES-A2HS        TCGA-ES-A2HT        TCGA-FV-A23B        TCGA-FV-A2QR 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-FV-A3I0        TCGA-FV-A3I1        TCGA-FV-A3R2        TCGA-FV-A3R3 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-FV-A495        TCGA-FV-A496        TCGA-FV-A4ZP        TCGA-FV-A4ZQ 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U        TCGA-G3-A25V 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y        TCGA-G3-A25Z 
"8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" 
       TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI        TCGA-G3-A3CJ 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-G3-A3CK        TCGA-G3-A5SI        TCGA-G3-A5SJ        TCGA-G3-A5SL 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" 
       TCGA-G3-A5SM        TCGA-G3-A6UC        TCGA-GJ-A6C0        TCGA-K7-A6G5 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-LG-A6GG        TCGA-MI-A75C        TCGA-MI-A75E        TCGA-MI-A75G 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-MI-A75I        TCGA-NI-A4U2        TCGA-O8-A75V 
"8P GAIN WILD-TYPE" "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        12        5         0          9          0          0
  8P GAIN WILD-TYPE      46       31         2         21          4          5
                   vv
clus                STAGE IV STAGE IVA STAGE IVB
  8P GAIN MUTATED          1         0         0
  8P GAIN WILD-TYPE        0         1         2
D15V3, multiclass
                   vv
clus                T1 T2 T3 T4
  8P GAIN MUTATED   12  5 11  0
  8P GAIN WILD-TYPE 49 35 29  8
D15V4, multiclass
    clus
vv   8P GAIN MUTATED 8P GAIN WILD-TYPE
  T1              12                49
  T2               5                35
  T3              11                29
  T4               0                 8
D15V5, binary
                   cls
clus                 0  1
  8P GAIN MUTATED   23  0
  8P GAIN WILD-TYPE 74  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED     23    0
  8P GAIN WILD-TYPE   74    3
   clus
vv  8P GAIN MUTATED 8P GAIN WILD-TYPE
  0              23                74
  1               0                 3
                   vv
clus                M0 M1 MX
  8P GAIN MUTATED   24  1  3
  8P GAIN WILD-TYPE 91  2 28
D15V6, multiclass
    clus
vv   8P GAIN MUTATED 8P GAIN WILD-TYPE
  M0              24                91
  M1               1                 2
  MX               3                28
D15V7, binary
                   cls
clus                 0  1
  8P GAIN MUTATED   10 18
  8P GAIN WILD-TYPE 48 73
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED     10   18
  8P GAIN WILD-TYPE   48   73
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  FEMALE              10                48
  MALE                18                73
                   vv
clus                 R0  R1  R2  RX
  8P GAIN MUTATED    22   1   1   2
  8P GAIN WILD-TYPE 100  10   0   8
D15V8, multiclass
    clus
vv   8P GAIN MUTATED 8P GAIN WILD-TYPE
  R0              22               100
  R1               1                10
  R2               1                 0
  RX               2                 8

Clustering(16) Variable = 8Q GAIN MUTATION ANALYSIS
D16V1, survival
                   sevent
clus2                0  1
  8Q GAIN MUTATED   43 29
  8Q GAIN WILD-TYPE 41 34
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               72                75 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               29                34 
$`8Q GAIN MUTATED`
TCGA-BC-4072 TCGA-BC-A10S TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A3KF TCGA-BC-A69H 
       48.99        46.78        27.52         2.99         0.26         3.95 
TCGA-CC-5258 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A113 
        0.07         3.32         0.10         0.10         0.13        79.73 
TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11C TCGA-DD-A1E9 
       53.33       113.00         7.33         2.60        21.76        90.71 
TCGA-DD-A1EC TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EI TCGA-DD-A1EL 
       19.79         6.71        12.95        45.11         6.02        13.64 
TCGA-DD-A39V TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A1 TCGA-DD-A3A3 
       21.14        55.69         5.62        19.76         7.66        17.59 
TCGA-DD-A3A8 TCGA-DD-A4ND TCGA-DD-A4NF TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NN 
        0.36        73.38        14.07        18.44        15.06        29.56 
TCGA-DD-A4NO TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A73D TCGA-DD-A73G 
       61.45        12.26         0.30        80.75        10.98       100.96 
TCGA-ED-A459 TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PZ TCGA-ED-A7XP TCGA-ED-A82E 
       13.41        13.35         0.23         0.20         0.20         0.20 
TCGA-EP-A12J TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS 
       18.74        10.98         0.62         9.96        11.93        22.85 
TCGA-ES-A2HT TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A4ZP TCGA-G3-A25T TCGA-G3-A25W 
       14.40         8.12         6.38        60.36        51.06        30.74 
TCGA-G3-A25X TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CJ TCGA-G3-A5SI TCGA-G3-A5SJ 
       58.49        21.53        22.13        19.53        14.70        11.97 
TCGA-G3-A5SL TCGA-K7-A6G5 TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75I TCGA-O8-A75V 
        7.99         4.01         9.57         5.10         8.71         4.44 

$`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        13.84        22.36 
TCGA-BC-A5W4 TCGA-BC-A69I TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 
        9.50         0.53         2.86         0.39         3.39         4.24 
TCGA-CC-A3MA TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A11B TCGA-DD-A11D TCGA-DD-A1EA 
        0.07        37.78        83.57         0.46        51.29        79.40 
TCGA-DD-A1EB TCGA-DD-A1ED TCGA-DD-A1EH TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A3A0 
       66.31        75.65        49.15        29.16        18.35        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        30.61 
TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4NH TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NP 
       33.14        12.85        14.24        39.78        56.25        93.67 
TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73E TCGA-DD-A73F 
       66.35        10.98         9.30         7.56         1.45        27.72 
TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A7PX TCGA-ED-A7PY TCGA-EP-A26S 
       12.69        15.85        13.91         0.20         0.20        19.99 
TCGA-EP-A2KA TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3R3 TCGA-FV-A495 
       11.74        32.45        19.10         0.20         0.13         0.03 
TCGA-FV-A496 TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25Y 
        0.33         0.39         1.22        53.79        28.27        14.86 
TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CK TCGA-G3-A5SM TCGA-G3-A6UC TCGA-GJ-A6C0 
       25.64         5.92        19.23         4.37         7.76         1.02 
TCGA-LG-A6GG TCGA-MI-A75G TCGA-NI-A4U2 
        0.49        14.24        58.88 

  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
             0.07              0.03 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
           113.00            107.11 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
            13.15             15.85 
[1] "0.1 - 113.0 (13.1)" "0.0 - 107.1 (15.8)"
       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-BC-A69H        TCGA-BC-A69I 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-CC-5258        TCGA-CC-5260        TCGA-CC-5261        TCGA-CC-5262 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-CC-5263        TCGA-CC-A1HT        TCGA-CC-A3M9        TCGA-CC-A3MA 
"8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-CC-A3MB        TCGA-CC-A3MC        TCGA-DD-A113        TCGA-DD-A114 
  "8Q GAIN MUTATED"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118        TCGA-DD-A119 
"8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" 
       TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C        TCGA-DD-A11D 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB        TCGA-DD-A1EC 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
       TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EF        TCGA-DD-A1EG 
"8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" 
       TCGA-DD-A1EH        TCGA-DD-A1EI        TCGA-DD-A1EJ        TCGA-DD-A1EK 
"8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-DD-A1EL        TCGA-DD-A39V        TCGA-DD-A39X        TCGA-DD-A39Y 
  "8Q GAIN MUTATED"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" 
       TCGA-DD-A39Z        TCGA-DD-A3A0        TCGA-DD-A3A1        TCGA-DD-A3A2 
  "8Q GAIN MUTATED" "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-A4NB        TCGA-DD-A4ND        TCGA-DD-A4NF        TCGA-DD-A4NH 
"8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-DD-A4NI        TCGA-DD-A4NJ        TCGA-DD-A4NK        TCGA-DD-A4NL 
  "8Q GAIN MUTATED"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-DD-A4NN        TCGA-DD-A4NO        TCGA-DD-A4NP        TCGA-DD-A4NQ 
  "8Q GAIN MUTATED"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
       TCGA-DD-A4NR        TCGA-DD-A4NS        TCGA-DD-A4NV        TCGA-DD-A73A 
  "8Q GAIN MUTATED"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-DD-A73B        TCGA-DD-A73C        TCGA-DD-A73D        TCGA-DD-A73E 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-DD-A73F        TCGA-DD-A73G        TCGA-ED-A459        TCGA-ED-A4XI 
"8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-ED-A5KG        TCGA-ED-A627        TCGA-ED-A66X        TCGA-ED-A66Y 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" 
       TCGA-ED-A7PX        TCGA-ED-A7PY        TCGA-ED-A7PZ        TCGA-ED-A7XP 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" 
       TCGA-ED-A82E        TCGA-EP-A12J        TCGA-EP-A26S        TCGA-EP-A2KA 
  "8Q GAIN MUTATED"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-EP-A2KB        TCGA-EP-A2KC        TCGA-EP-A3JL        TCGA-EP-A3RK 
  "8Q GAIN MUTATED"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" 
       TCGA-ES-A2HS        TCGA-ES-A2HT        TCGA-FV-A23B        TCGA-FV-A2QR 
  "8Q GAIN MUTATED"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-FV-A3I0        TCGA-FV-A3I1        TCGA-FV-A3R2        TCGA-FV-A3R3 
"8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-FV-A495        TCGA-FV-A496        TCGA-FV-A4ZP        TCGA-FV-A4ZQ 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U        TCGA-G3-A25V 
"8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y        TCGA-G3-A25Z 
  "8Q GAIN MUTATED"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
       TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI        TCGA-G3-A3CJ 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
       TCGA-G3-A3CK        TCGA-G3-A5SI        TCGA-G3-A5SJ        TCGA-G3-A5SL 
"8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" 
       TCGA-G3-A5SM        TCGA-G3-A6UC        TCGA-GJ-A6C0        TCGA-K7-A6G5 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
       TCGA-LG-A6GG        TCGA-MI-A75C        TCGA-MI-A75E        TCGA-MI-A75G 
"8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-MI-A75I        TCGA-NI-A4U2        TCGA-O8-A75V 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
       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-BC-A69H        TCGA-BC-A69I 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-CC-5258        TCGA-CC-5260        TCGA-CC-5261        TCGA-CC-5262 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-CC-5263        TCGA-CC-A1HT        TCGA-CC-A3M9        TCGA-CC-A3MA 
"8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-CC-A3MB        TCGA-CC-A3MC        TCGA-DD-A113        TCGA-DD-A114 
  "8Q GAIN MUTATED"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118        TCGA-DD-A119 
"8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" 
       TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C        TCGA-DD-A11D 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB        TCGA-DD-A1EC 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
       TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EF        TCGA-DD-A1EG 
"8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" 
       TCGA-DD-A1EH        TCGA-DD-A1EI        TCGA-DD-A1EJ        TCGA-DD-A1EK 
"8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-DD-A1EL        TCGA-DD-A39V        TCGA-DD-A39X        TCGA-DD-A39Y 
  "8Q GAIN MUTATED"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" 
       TCGA-DD-A39Z        TCGA-DD-A3A0        TCGA-DD-A3A1        TCGA-DD-A3A2 
  "8Q GAIN MUTATED" "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-A4NB        TCGA-DD-A4ND        TCGA-DD-A4NF        TCGA-DD-A4NH 
"8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-DD-A4NI        TCGA-DD-A4NJ        TCGA-DD-A4NK        TCGA-DD-A4NL 
  "8Q GAIN MUTATED"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-DD-A4NN        TCGA-DD-A4NO        TCGA-DD-A4NP        TCGA-DD-A4NQ 
  "8Q GAIN MUTATED"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
       TCGA-DD-A4NR        TCGA-DD-A4NS        TCGA-DD-A4NV        TCGA-DD-A73A 
  "8Q GAIN MUTATED"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-DD-A73B        TCGA-DD-A73C        TCGA-DD-A73D        TCGA-DD-A73E 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-DD-A73F        TCGA-DD-A73G        TCGA-ED-A459        TCGA-ED-A4XI 
"8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-ED-A5KG        TCGA-ED-A627        TCGA-ED-A66X        TCGA-ED-A66Y 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" 
       TCGA-ED-A7PX        TCGA-ED-A7PY        TCGA-ED-A7PZ        TCGA-ED-A7XP 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" 
       TCGA-ED-A82E        TCGA-EP-A12J        TCGA-EP-A26S        TCGA-EP-A2KA 
  "8Q GAIN MUTATED"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-EP-A2KB        TCGA-EP-A2KC        TCGA-EP-A3JL        TCGA-EP-A3RK 
  "8Q GAIN MUTATED"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" 
       TCGA-ES-A2HS        TCGA-ES-A2HT        TCGA-FV-A23B        TCGA-FV-A2QR 
  "8Q GAIN MUTATED"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-FV-A3I0        TCGA-FV-A3I1        TCGA-FV-A3R2        TCGA-FV-A3R3 
"8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-FV-A495        TCGA-FV-A496        TCGA-FV-A4ZP        TCGA-FV-A4ZQ 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U        TCGA-G3-A25V 
"8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y        TCGA-G3-A25Z 
  "8Q GAIN MUTATED"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
       TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI        TCGA-G3-A3CJ 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
       TCGA-G3-A3CK        TCGA-G3-A5SI        TCGA-G3-A5SJ        TCGA-G3-A5SL 
"8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" 
       TCGA-G3-A5SM        TCGA-G3-A6UC        TCGA-GJ-A6C0        TCGA-K7-A6G5 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
       TCGA-LG-A6GG        TCGA-MI-A75C        TCGA-MI-A75E        TCGA-MI-A75G 
"8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-MI-A75I        TCGA-NI-A4U2        TCGA-O8-A75V 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
       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-BC-A69H        TCGA-BC-A69I 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-CC-5258        TCGA-CC-5260        TCGA-CC-5261        TCGA-CC-5262 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-CC-5263        TCGA-CC-A1HT        TCGA-CC-A3M9        TCGA-CC-A3MA 
"8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-CC-A3MB        TCGA-CC-A3MC        TCGA-DD-A113        TCGA-DD-A114 
  "8Q GAIN MUTATED"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118        TCGA-DD-A119 
"8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" 
       TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C        TCGA-DD-A11D 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB        TCGA-DD-A1EC 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
       TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EF        TCGA-DD-A1EG 
"8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" 
       TCGA-DD-A1EH        TCGA-DD-A1EI        TCGA-DD-A1EJ        TCGA-DD-A1EK 
"8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-DD-A1EL        TCGA-DD-A39V        TCGA-DD-A39X        TCGA-DD-A39Y 
  "8Q GAIN MUTATED"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" 
       TCGA-DD-A39Z        TCGA-DD-A3A0        TCGA-DD-A3A1        TCGA-DD-A3A2 
  "8Q GAIN MUTATED" "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-A4NB        TCGA-DD-A4ND        TCGA-DD-A4NF        TCGA-DD-A4NH 
"8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-DD-A4NI        TCGA-DD-A4NJ        TCGA-DD-A4NK        TCGA-DD-A4NL 
  "8Q GAIN MUTATED"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-DD-A4NN        TCGA-DD-A4NO        TCGA-DD-A4NP        TCGA-DD-A4NQ 
  "8Q GAIN MUTATED"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
       TCGA-DD-A4NR        TCGA-DD-A4NS        TCGA-DD-A4NV        TCGA-DD-A73A 
  "8Q GAIN MUTATED"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-DD-A73B        TCGA-DD-A73C        TCGA-DD-A73D        TCGA-DD-A73E 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-DD-A73F        TCGA-DD-A73G        TCGA-ED-A459        TCGA-ED-A4XI 
"8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-ED-A5KG        TCGA-ED-A627        TCGA-ED-A66X        TCGA-ED-A66Y 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" 
       TCGA-ED-A7PX        TCGA-ED-A7PY        TCGA-ED-A7PZ        TCGA-ED-A7XP 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" 
       TCGA-ED-A82E        TCGA-EP-A12J        TCGA-EP-A26S        TCGA-EP-A2KA 
  "8Q GAIN MUTATED"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-EP-A2KB        TCGA-EP-A2KC        TCGA-EP-A3JL        TCGA-EP-A3RK 
  "8Q GAIN MUTATED"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" 
       TCGA-ES-A2HS        TCGA-ES-A2HT        TCGA-FV-A23B        TCGA-FV-A2QR 
  "8Q GAIN MUTATED"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-FV-A3I0        TCGA-FV-A3I1        TCGA-FV-A3R2        TCGA-FV-A3R3 
"8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-FV-A495        TCGA-FV-A496        TCGA-FV-A4ZP        TCGA-FV-A4ZQ 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U        TCGA-G3-A25V 
"8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y        TCGA-G3-A25Z 
  "8Q GAIN MUTATED"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
       TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI        TCGA-G3-A3CJ 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
       TCGA-G3-A3CK        TCGA-G3-A5SI        TCGA-G3-A5SJ        TCGA-G3-A5SL 
"8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" 
       TCGA-G3-A5SM        TCGA-G3-A6UC        TCGA-GJ-A6C0        TCGA-K7-A6G5 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
       TCGA-LG-A6GG        TCGA-MI-A75C        TCGA-MI-A75E        TCGA-MI-A75G 
"8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-MI-A75I        TCGA-NI-A4U2        TCGA-O8-A75V 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
[1] "hr=" "1"  
D16V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  8Q GAIN MUTATED        31       19         0         16          1          1
  8Q GAIN WILD-TYPE      27       17         2         14          3          4
                   vv
clus                STAGE IV STAGE IVA STAGE IVB
  8Q GAIN MUTATED          1         1         0
  8Q GAIN WILD-TYPE        0         0         2
D16V3, multiclass
                   vv
clus                T1 T2 T3 T4
  8Q GAIN MUTATED   32 21 19  2
  8Q GAIN WILD-TYPE 29 19 21  6
D16V4, multiclass
    clus
vv   8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  T1              32                29
  T2              21                19
  T3              19                21
  T4               2                 6
D16V5, binary
                   cls
clus                 0  1
  8Q GAIN MUTATED   48  1
  8Q GAIN WILD-TYPE 49  2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED     48    1
  8Q GAIN WILD-TYPE   49    2
   clus
vv  8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  0              48                49
  1               1                 2
                   vv
clus                M0 M1 MX
  8Q GAIN MUTATED   56  1 17
  8Q GAIN WILD-TYPE 59  2 14
D16V6, multiclass
    clus
vv   8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  M0              56                59
  M1               1                 2
  MX              17                14
D16V7, binary
                   cls
clus                 0  1
  8Q GAIN MUTATED   22 52
  8Q GAIN WILD-TYPE 36 39
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED     22   52
  8Q GAIN WILD-TYPE   36   39
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  FEMALE              22                36
  MALE                52                39
                   vv
clus                R0 R1 R2 RX
  8Q GAIN MUTATED   60  6  1  4
  8Q GAIN WILD-TYPE 62  5  0  6
D16V8, multiclass
    clus
vv   8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  R0              60                62
  R1               6                 5
  R2               1                 0
  RX               4                 6

Clustering(17) Variable = 9P GAIN MUTATION ANALYSIS
D17V1, survival
                   sevent
clus2                0  1
  9P GAIN MUTATED    3  2
  9P GAIN WILD-TYPE 81 61
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
                5               142 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
                2                61 
$`9P GAIN MUTATED`
TCGA-DD-A3A7 TCGA-DD-A4NV TCGA-ED-A66Y TCGA-EP-A2KB TCGA-G3-A25U 
       13.78        66.35         0.23        10.98        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        13.84         0.26        22.36         9.50 
TCGA-BC-A69H TCGA-BC-A69I TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 
        3.95         0.53         0.07         2.86         0.39         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        37.78        83.57        53.33       113.00         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        51.29        90.71        79.40 
TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EG 
       66.31        19.79        75.65         6.71        12.95        45.11 
TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V 
       49.15         6.02        29.16        18.35        13.64        21.14 
TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 
       55.69         5.62        19.76        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        30.61 
TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NI 
       33.14        12.85        73.38        14.07        14.24        18.44 
TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP 
       15.06        39.78        56.25        29.56        61.45        93.67 
TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C 
       12.26         0.30        80.75        10.98         9.30         7.56 
TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G TCGA-ED-A459 TCGA-ED-A4XI 
       10.98         1.45        27.72       100.96        13.41        12.69 
TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ 
       15.85        13.91        13.35         0.20         0.20         0.20 
TCGA-ED-A7XP TCGA-ED-A82E TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KC 
        0.20         0.20        18.74        19.99        11.74         0.62 
TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QR 
        9.96        11.93        22.85        14.40        32.45        19.10 
TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 
        0.20         8.12         6.38         0.13         0.03         0.33 
TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25V TCGA-G3-A25W 
       60.36         0.39         1.22        51.06        28.27        30.74 
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         5.92 
TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SL TCGA-G3-A5SM 
       19.53        19.23        14.70        11.97         7.99         4.37 
TCGA-G3-A6UC TCGA-GJ-A6C0 TCGA-K7-A6G5 TCGA-LG-A6GG TCGA-MI-A75C TCGA-MI-A75E 
        7.76         1.02         4.01         0.49         9.57         5.10 
TCGA-MI-A75G TCGA-MI-A75I TCGA-NI-A4U2 TCGA-O8-A75V 
       14.24         8.71        58.88         4.44 

  9P GAIN MUTATED 9P GAIN WILD-TYPE 
             0.23              0.03 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
            66.35            113.00 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
           13.780            14.155 
[1] "0.2 - 66.3 (13.8)"  "0.0 - 113.0 (14.2)"
       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-BC-A69H        TCGA-BC-A69I 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-CC-5258        TCGA-CC-5260        TCGA-CC-5261        TCGA-CC-5262 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-CC-5263        TCGA-CC-A1HT        TCGA-CC-A3M9        TCGA-CC-A3MA 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-CC-A3MB        TCGA-CC-A3MC        TCGA-DD-A113        TCGA-DD-A114 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118        TCGA-DD-A119 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C        TCGA-DD-A11D 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB        TCGA-DD-A1EC 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EF        TCGA-DD-A1EG 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DD-A1EH        TCGA-DD-A1EI        TCGA-DD-A1EJ        TCGA-DD-A1EK 
"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-A4NB        TCGA-DD-A4ND        TCGA-DD-A4NF        TCGA-DD-A4NH 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DD-A4NI        TCGA-DD-A4NJ        TCGA-DD-A4NK        TCGA-DD-A4NL 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DD-A4NN        TCGA-DD-A4NO        TCGA-DD-A4NP        TCGA-DD-A4NQ 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DD-A4NR        TCGA-DD-A4NS        TCGA-DD-A4NV        TCGA-DD-A73A 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE"   "9P GAIN MUTATED" "9P GAIN WILD-TYPE" 
       TCGA-DD-A73B        TCGA-DD-A73C        TCGA-DD-A73D        TCGA-DD-A73E 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DD-A73F        TCGA-DD-A73G        TCGA-ED-A459        TCGA-ED-A4XI 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-ED-A5KG        TCGA-ED-A627        TCGA-ED-A66X        TCGA-ED-A66Y 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE"   "9P GAIN MUTATED" 
       TCGA-ED-A7PX        TCGA-ED-A7PY        TCGA-ED-A7PZ        TCGA-ED-A7XP 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-ED-A82E        TCGA-EP-A12J        TCGA-EP-A26S        TCGA-EP-A2KA 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EP-A2KB        TCGA-EP-A2KC        TCGA-EP-A3JL        TCGA-EP-A3RK 
  "9P GAIN MUTATED" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-ES-A2HS        TCGA-ES-A2HT        TCGA-FV-A23B        TCGA-FV-A2QR 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-FV-A3I0        TCGA-FV-A3I1        TCGA-FV-A3R2        TCGA-FV-A3R3 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-FV-A495        TCGA-FV-A496        TCGA-FV-A4ZP        TCGA-FV-A4ZQ 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U        TCGA-G3-A25V 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE"   "9P GAIN MUTATED" "9P GAIN WILD-TYPE" 
       TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y        TCGA-G3-A25Z 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI        TCGA-G3-A3CJ 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-G3-A3CK        TCGA-G3-A5SI        TCGA-G3-A5SJ        TCGA-G3-A5SL 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-G3-A5SM        TCGA-G3-A6UC        TCGA-GJ-A6C0        TCGA-K7-A6G5 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-LG-A6GG        TCGA-MI-A75C        TCGA-MI-A75E        TCGA-MI-A75G 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-MI-A75I        TCGA-NI-A4U2        TCGA-O8-A75V 
"9P GAIN WILD-TYPE" "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-BC-A69H        TCGA-BC-A69I 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-CC-5258        TCGA-CC-5260        TCGA-CC-5261        TCGA-CC-5262 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-CC-5263        TCGA-CC-A1HT        TCGA-CC-A3M9        TCGA-CC-A3MA 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-CC-A3MB        TCGA-CC-A3MC        TCGA-DD-A113        TCGA-DD-A114 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118        TCGA-DD-A119 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C        TCGA-DD-A11D 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB        TCGA-DD-A1EC 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EF        TCGA-DD-A1EG 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DD-A1EH        TCGA-DD-A1EI        TCGA-DD-A1EJ        TCGA-DD-A1EK 
"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-A4NB        TCGA-DD-A4ND        TCGA-DD-A4NF        TCGA-DD-A4NH 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DD-A4NI        TCGA-DD-A4NJ        TCGA-DD-A4NK        TCGA-DD-A4NL 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DD-A4NN        TCGA-DD-A4NO        TCGA-DD-A4NP        TCGA-DD-A4NQ 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DD-A4NR        TCGA-DD-A4NS        TCGA-DD-A4NV        TCGA-DD-A73A 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE"   "9P GAIN MUTATED" "9P GAIN WILD-TYPE" 
       TCGA-DD-A73B        TCGA-DD-A73C        TCGA-DD-A73D        TCGA-DD-A73E 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DD-A73F        TCGA-DD-A73G        TCGA-ED-A459        TCGA-ED-A4XI 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-ED-A5KG        TCGA-ED-A627        TCGA-ED-A66X        TCGA-ED-A66Y 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE"   "9P GAIN MUTATED" 
       TCGA-ED-A7PX        TCGA-ED-A7PY        TCGA-ED-A7PZ        TCGA-ED-A7XP 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-ED-A82E        TCGA-EP-A12J        TCGA-EP-A26S        TCGA-EP-A2KA 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EP-A2KB        TCGA-EP-A2KC        TCGA-EP-A3JL        TCGA-EP-A3RK 
  "9P GAIN MUTATED" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-ES-A2HS        TCGA-ES-A2HT        TCGA-FV-A23B        TCGA-FV-A2QR 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-FV-A3I0        TCGA-FV-A3I1        TCGA-FV-A3R2        TCGA-FV-A3R3 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-FV-A495        TCGA-FV-A496        TCGA-FV-A4ZP        TCGA-FV-A4ZQ 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U        TCGA-G3-A25V 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE"   "9P GAIN MUTATED" "9P GAIN WILD-TYPE" 
       TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y        TCGA-G3-A25Z 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI        TCGA-G3-A3CJ 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-G3-A3CK        TCGA-G3-A5SI        TCGA-G3-A5SJ        TCGA-G3-A5SL 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-G3-A5SM        TCGA-G3-A6UC        TCGA-GJ-A6C0        TCGA-K7-A6G5 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-LG-A6GG        TCGA-MI-A75C        TCGA-MI-A75E        TCGA-MI-A75G 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-MI-A75I        TCGA-NI-A4U2        TCGA-O8-A75V 
"9P GAIN WILD-TYPE" "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-BC-A69H        TCGA-BC-A69I 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-CC-5258        TCGA-CC-5260        TCGA-CC-5261        TCGA-CC-5262 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-CC-5263        TCGA-CC-A1HT        TCGA-CC-A3M9        TCGA-CC-A3MA 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-CC-A3MB        TCGA-CC-A3MC        TCGA-DD-A113        TCGA-DD-A114 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118        TCGA-DD-A119 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C        TCGA-DD-A11D 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB        TCGA-DD-A1EC 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EF        TCGA-DD-A1EG 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DD-A1EH        TCGA-DD-A1EI        TCGA-DD-A1EJ        TCGA-DD-A1EK 
"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-A4NB        TCGA-DD-A4ND        TCGA-DD-A4NF        TCGA-DD-A4NH 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DD-A4NI        TCGA-DD-A4NJ        TCGA-DD-A4NK        TCGA-DD-A4NL 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DD-A4NN        TCGA-DD-A4NO        TCGA-DD-A4NP        TCGA-DD-A4NQ 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DD-A4NR        TCGA-DD-A4NS        TCGA-DD-A4NV        TCGA-DD-A73A 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE"   "9P GAIN MUTATED" "9P GAIN WILD-TYPE" 
       TCGA-DD-A73B        TCGA-DD-A73C        TCGA-DD-A73D        TCGA-DD-A73E 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DD-A73F        TCGA-DD-A73G        TCGA-ED-A459        TCGA-ED-A4XI 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-ED-A5KG        TCGA-ED-A627        TCGA-ED-A66X        TCGA-ED-A66Y 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE"   "9P GAIN MUTATED" 
       TCGA-ED-A7PX        TCGA-ED-A7PY        TCGA-ED-A7PZ        TCGA-ED-A7XP 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-ED-A82E        TCGA-EP-A12J        TCGA-EP-A26S        TCGA-EP-A2KA 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EP-A2KB        TCGA-EP-A2KC        TCGA-EP-A3JL        TCGA-EP-A3RK 
  "9P GAIN MUTATED" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-ES-A2HS        TCGA-ES-A2HT        TCGA-FV-A23B        TCGA-FV-A2QR 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-FV-A3I0        TCGA-FV-A3I1        TCGA-FV-A3R2        TCGA-FV-A3R3 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-FV-A495        TCGA-FV-A496        TCGA-FV-A4ZP        TCGA-FV-A4ZQ 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U        TCGA-G3-A25V 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE"   "9P GAIN MUTATED" "9P GAIN WILD-TYPE" 
       TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y        TCGA-G3-A25Z 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI        TCGA-G3-A3CJ 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-G3-A3CK        TCGA-G3-A5SI        TCGA-G3-A5SJ        TCGA-G3-A5SL 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-G3-A5SM        TCGA-G3-A6UC        TCGA-GJ-A6C0        TCGA-K7-A6G5 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-LG-A6GG        TCGA-MI-A75C        TCGA-MI-A75E        TCGA-MI-A75G 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-MI-A75I        TCGA-NI-A4U2        TCGA-O8-A75V 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
[1] "hr=" "1.2"
D17V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  9P GAIN MUTATED         2        0         0          3          1          0
  9P GAIN WILD-TYPE      56       36         2         27          3          5
                   vv
clus                STAGE IV STAGE IVA STAGE IVB
  9P GAIN MUTATED          0         0         0
  9P GAIN WILD-TYPE        1         1         2
D17V3, multiclass
                   vv
clus                T1 T2 T3 T4
  9P GAIN MUTATED    2  0  4  0
  9P GAIN WILD-TYPE 59 40 36  8
D17V4, multiclass
    clus
vv   9P GAIN MUTATED 9P GAIN WILD-TYPE
  T1               2                59
  T2               0                40
  T3               4                36
  T4               0                 8
D17V5, binary
                   cls
clus                 0  1
  9P GAIN MUTATED    5  0
  9P GAIN WILD-TYPE 92  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED      5    0
  9P GAIN WILD-TYPE   92    3
   clus
vv  9P GAIN MUTATED 9P GAIN WILD-TYPE
  0               5                92
  1               0                 3
                   vv
clus                 M0  M1  MX
  9P GAIN MUTATED     5   0   1
  9P GAIN WILD-TYPE 110   3  30
D17V6, multiclass
    clus
vv   9P GAIN MUTATED 9P GAIN WILD-TYPE
  M0               5               110
  M1               0                 3
  MX               1                30
D17V7, binary
                   cls
clus                 0  1
  9P GAIN MUTATED    3  3
  9P GAIN WILD-TYPE 55 88
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED      3    3
  9P GAIN WILD-TYPE   55   88
        clus
vv       9P GAIN MUTATED 9P GAIN WILD-TYPE
  FEMALE               3                55
  MALE                 3                88
                   vv
clus                 R0  R1  R2  RX
  9P GAIN MUTATED     5   0   0   1
  9P GAIN WILD-TYPE 117  11   1   9
D17V8, multiclass
    clus
vv   9P GAIN MUTATED 9P GAIN WILD-TYPE
  R0               5               117
  R1               0                11
  R2               0                 1
  RX               1                 9

Clustering(18) Variable = 9Q GAIN MUTATION ANALYSIS
D18V1, survival
                   sevent
clus2                0  1
  9Q GAIN MUTATED    3  2
  9Q GAIN WILD-TYPE 81 61
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
                5               142 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
                2                61 
$`9Q GAIN MUTATED`
TCGA-DD-A3A6 TCGA-DD-A4NV TCGA-ED-A66Y TCGA-EP-A2KB TCGA-G3-A25U 
      107.11        66.35         0.23        10.98        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        13.84         0.26        22.36         9.50 
TCGA-BC-A69H TCGA-BC-A69I TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 
        3.95         0.53         0.07         2.86         0.39         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        37.78        83.57        53.33       113.00         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        51.29        90.71        79.40 
TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EG 
       66.31        19.79        75.65         6.71        12.95        45.11 
TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V 
       49.15         6.02        29.16        18.35        13.64        21.14 
TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 
       55.69         5.62        19.76        25.81         7.66        70.06 
TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A3A9 
       17.59        20.12       102.74        13.78         0.36        30.61 
TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NI 
       33.14        12.85        73.38        14.07        14.24        18.44 
TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP 
       15.06        39.78        56.25        29.56        61.45        93.67 
TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C 
       12.26         0.30        80.75        10.98         9.30         7.56 
TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G TCGA-ED-A459 TCGA-ED-A4XI 
       10.98         1.45        27.72       100.96        13.41        12.69 
TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ 
       15.85        13.91        13.35         0.20         0.20         0.20 
TCGA-ED-A7XP TCGA-ED-A82E TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KC 
        0.20         0.20        18.74        19.99        11.74         0.62 
TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QR 
        9.96        11.93        22.85        14.40        32.45        19.10 
TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 
        0.20         8.12         6.38         0.13         0.03         0.33 
TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25V TCGA-G3-A25W 
       60.36         0.39         1.22        51.06        28.27        30.74 
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         5.92 
TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SL TCGA-G3-A5SM 
       19.53        19.23        14.70        11.97         7.99         4.37 
TCGA-G3-A6UC TCGA-GJ-A6C0 TCGA-K7-A6G5 TCGA-LG-A6GG TCGA-MI-A75C TCGA-MI-A75E 
        7.76         1.02         4.01         0.49         9.57         5.10 
TCGA-MI-A75G TCGA-MI-A75I TCGA-NI-A4U2 TCGA-O8-A75V 
       14.24         8.71        58.88         4.44 

  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
             0.23              0.03 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
           107.11            113.00 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
            53.79             13.99 
[1] "0.2 - 107.1 (53.8)" "0.0 - 113.0 (14.0)"
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-BC-A5W4        TCGA-BC-A69H        TCGA-BC-A69I 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-CC-5258        TCGA-CC-5260        TCGA-CC-5261        TCGA-CC-5262 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-CC-5263        TCGA-CC-A1HT        TCGA-CC-A3M9        TCGA-CC-A3MA 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-CC-A3MB        TCGA-CC-A3MC        TCGA-DD-A113        TCGA-DD-A114 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118        TCGA-DD-A119 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C        TCGA-DD-A11D 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB        TCGA-DD-A1EC 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EF        TCGA-DD-A1EG 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-DD-A1EH        TCGA-DD-A1EI        TCGA-DD-A1EJ        TCGA-DD-A1EK 
"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-A4NB        TCGA-DD-A4ND        TCGA-DD-A4NF        TCGA-DD-A4NH 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-DD-A4NI        TCGA-DD-A4NJ        TCGA-DD-A4NK        TCGA-DD-A4NL 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-DD-A4NN        TCGA-DD-A4NO        TCGA-DD-A4NP        TCGA-DD-A4NQ 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-DD-A4NR        TCGA-DD-A4NS        TCGA-DD-A4NV        TCGA-DD-A73A 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE"   "9Q GAIN MUTATED" "9Q GAIN WILD-TYPE" 
       TCGA-DD-A73B        TCGA-DD-A73C        TCGA-DD-A73D        TCGA-DD-A73E 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-DD-A73F        TCGA-DD-A73G        TCGA-ED-A459        TCGA-ED-A4XI 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-ED-A5KG        TCGA-ED-A627        TCGA-ED-A66X        TCGA-ED-A66Y 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE"   "9Q GAIN MUTATED" 
       TCGA-ED-A7PX        TCGA-ED-A7PY        TCGA-ED-A7PZ        TCGA-ED-A7XP 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-ED-A82E        TCGA-EP-A12J        TCGA-EP-A26S        TCGA-EP-A2KA 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EP-A2KB        TCGA-EP-A2KC        TCGA-EP-A3JL        TCGA-EP-A3RK 
  "9Q GAIN MUTATED" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-ES-A2HS        TCGA-ES-A2HT        TCGA-FV-A23B        TCGA-FV-A2QR 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-FV-A3I0        TCGA-FV-A3I1        TCGA-FV-A3R2        TCGA-FV-A3R3 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-FV-A495        TCGA-FV-A496        TCGA-FV-A4ZP        TCGA-FV-A4ZQ 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U        TCGA-G3-A25V 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE"   "9Q GAIN MUTATED" "9Q GAIN WILD-TYPE" 
       TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y        TCGA-G3-A25Z 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI        TCGA-G3-A3CJ 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-G3-A3CK        TCGA-G3-A5SI        TCGA-G3-A5SJ        TCGA-G3-A5SL 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-G3-A5SM        TCGA-G3-A6UC        TCGA-GJ-A6C0        TCGA-K7-A6G5 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-LG-A6GG        TCGA-MI-A75C        TCGA-MI-A75E        TCGA-MI-A75G 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-MI-A75I        TCGA-NI-A4U2        TCGA-O8-A75V 
"9Q GAIN WILD-TYPE" "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-BC-A69H        TCGA-BC-A69I 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-CC-5258        TCGA-CC-5260        TCGA-CC-5261        TCGA-CC-5262 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-CC-5263        TCGA-CC-A1HT        TCGA-CC-A3M9        TCGA-CC-A3MA 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-CC-A3MB        TCGA-CC-A3MC        TCGA-DD-A113        TCGA-DD-A114 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118        TCGA-DD-A119 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C        TCGA-DD-A11D 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB        TCGA-DD-A1EC 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EF        TCGA-DD-A1EG 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-DD-A1EH        TCGA-DD-A1EI        TCGA-DD-A1EJ        TCGA-DD-A1EK 
"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-A4NB        TCGA-DD-A4ND        TCGA-DD-A4NF        TCGA-DD-A4NH 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-DD-A4NI        TCGA-DD-A4NJ        TCGA-DD-A4NK        TCGA-DD-A4NL 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-DD-A4NN        TCGA-DD-A4NO        TCGA-DD-A4NP        TCGA-DD-A4NQ 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-DD-A4NR        TCGA-DD-A4NS        TCGA-DD-A4NV        TCGA-DD-A73A 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE"   "9Q GAIN MUTATED" "9Q GAIN WILD-TYPE" 
       TCGA-DD-A73B        TCGA-DD-A73C        TCGA-DD-A73D        TCGA-DD-A73E 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-DD-A73F        TCGA-DD-A73G        TCGA-ED-A459        TCGA-ED-A4XI 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-ED-A5KG        TCGA-ED-A627        TCGA-ED-A66X        TCGA-ED-A66Y 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE"   "9Q GAIN MUTATED" 
       TCGA-ED-A7PX        TCGA-ED-A7PY        TCGA-ED-A7PZ        TCGA-ED-A7XP 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-ED-A82E        TCGA-EP-A12J        TCGA-EP-A26S        TCGA-EP-A2KA 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EP-A2KB        TCGA-EP-A2KC        TCGA-EP-A3JL        TCGA-EP-A3RK 
  "9Q GAIN MUTATED" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-ES-A2HS        TCGA-ES-A2HT        TCGA-FV-A23B        TCGA-FV-A2QR 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-FV-A3I0        TCGA-FV-A3I1        TCGA-FV-A3R2        TCGA-FV-A3R3 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-FV-A495        TCGA-FV-A496        TCGA-FV-A4ZP        TCGA-FV-A4ZQ 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U        TCGA-G3-A25V 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE"   "9Q GAIN MUTATED" "9Q GAIN WILD-TYPE" 
       TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y        TCGA-G3-A25Z 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI        TCGA-G3-A3CJ 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-G3-A3CK        TCGA-G3-A5SI        TCGA-G3-A5SJ        TCGA-G3-A5SL 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-G3-A5SM        TCGA-G3-A6UC        TCGA-GJ-A6C0        TCGA-K7-A6G5 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-LG-A6GG        TCGA-MI-A75C        TCGA-MI-A75E        TCGA-MI-A75G 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-MI-A75I        TCGA-NI-A4U2        TCGA-O8-A75V 
"9Q GAIN WILD-TYPE" "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-BC-A69H        TCGA-BC-A69I 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-CC-5258        TCGA-CC-5260        TCGA-CC-5261        TCGA-CC-5262 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-CC-5263        TCGA-CC-A1HT        TCGA-CC-A3M9        TCGA-CC-A3MA 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-CC-A3MB        TCGA-CC-A3MC        TCGA-DD-A113        TCGA-DD-A114 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118        TCGA-DD-A119 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C        TCGA-DD-A11D 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB        TCGA-DD-A1EC 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EF        TCGA-DD-A1EG 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-DD-A1EH        TCGA-DD-A1EI        TCGA-DD-A1EJ        TCGA-DD-A1EK 
"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-A4NB        TCGA-DD-A4ND        TCGA-DD-A4NF        TCGA-DD-A4NH 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-DD-A4NI        TCGA-DD-A4NJ        TCGA-DD-A4NK        TCGA-DD-A4NL 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-DD-A4NN        TCGA-DD-A4NO        TCGA-DD-A4NP        TCGA-DD-A4NQ 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-DD-A4NR        TCGA-DD-A4NS        TCGA-DD-A4NV        TCGA-DD-A73A 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE"   "9Q GAIN MUTATED" "9Q GAIN WILD-TYPE" 
       TCGA-DD-A73B        TCGA-DD-A73C        TCGA-DD-A73D        TCGA-DD-A73E 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-DD-A73F        TCGA-DD-A73G        TCGA-ED-A459        TCGA-ED-A4XI 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-ED-A5KG        TCGA-ED-A627        TCGA-ED-A66X        TCGA-ED-A66Y 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE"   "9Q GAIN MUTATED" 
       TCGA-ED-A7PX        TCGA-ED-A7PY        TCGA-ED-A7PZ        TCGA-ED-A7XP 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-ED-A82E        TCGA-EP-A12J        TCGA-EP-A26S        TCGA-EP-A2KA 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EP-A2KB        TCGA-EP-A2KC        TCGA-EP-A3JL        TCGA-EP-A3RK 
  "9Q GAIN MUTATED" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-ES-A2HS        TCGA-ES-A2HT        TCGA-FV-A23B        TCGA-FV-A2QR 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-FV-A3I0        TCGA-FV-A3I1        TCGA-FV-A3R2        TCGA-FV-A3R3 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-FV-A495        TCGA-FV-A496        TCGA-FV-A4ZP        TCGA-FV-A4ZQ 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U        TCGA-G3-A25V 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE"   "9Q GAIN MUTATED" "9Q GAIN WILD-TYPE" 
       TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y        TCGA-G3-A25Z 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI        TCGA-G3-A3CJ 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-G3-A3CK        TCGA-G3-A5SI        TCGA-G3-A5SJ        TCGA-G3-A5SL 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-G3-A5SM        TCGA-G3-A6UC        TCGA-GJ-A6C0        TCGA-K7-A6G5 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-LG-A6GG        TCGA-MI-A75C        TCGA-MI-A75E        TCGA-MI-A75G 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-MI-A75I        TCGA-NI-A4U2        TCGA-O8-A75V 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
[1] "hr=" "2.5"
D18V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  9Q GAIN MUTATED         2        1         0          3          0          0
  9Q GAIN WILD-TYPE      56       35         2         27          4          5
                   vv
clus                STAGE IV STAGE IVA STAGE IVB
  9Q GAIN MUTATED          0         0         0
  9Q GAIN WILD-TYPE        1         1         2
D18V3, multiclass
                   vv
clus                T1 T2 T3 T4
  9Q GAIN MUTATED    2  1  3  0
  9Q GAIN WILD-TYPE 59 39 37  8
D18V4, multiclass
    clus
vv   9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  T1               2                59
  T2               1                39
  T3               3                37
  T4               0                 8
D18V5, binary
                   cls
clus                 0  1
  9Q GAIN MUTATED    5  0
  9Q GAIN WILD-TYPE 92  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED      5    0
  9Q GAIN WILD-TYPE   92    3
   clus
vv  9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  0               5                92
  1               0                 3
                   vv
clus                 M0  M1  MX
  9Q GAIN MUTATED     5   0   1
  9Q GAIN WILD-TYPE 110   3  30
D18V6, multiclass
    clus
vv   9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  M0               5               110
  M1               0                 3
  MX               1                30
D18V7, binary
                   cls
clus                 0  1
  9Q GAIN MUTATED    4  2
  9Q GAIN WILD-TYPE 54 89
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED      4    2
  9Q GAIN WILD-TYPE   54   89
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  FEMALE               4                54
  MALE                 2                89
                   vv
clus                 R0  R1  R2  RX
  9Q GAIN MUTATED     5   0   0   1
  9Q GAIN WILD-TYPE 117  11   1   9
D18V8, multiclass
    clus
vv   9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  R0               5               117
  R1               0                11
  R2               0                 1
  RX               1                 9

Clustering(19) Variable = 10P GAIN MUTATION ANALYSIS
D19V1, survival
                    sevent
clus2                 0  1
  10P GAIN MUTATED   13  7
  10P GAIN WILD-TYPE 71 56
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                20                127 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                 7                 56 
$`10P GAIN MUTATED`
TCGA-BC-A10Q TCGA-BC-A10R TCGA-CC-A3MB TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A1EL 
       37.32        10.13         0.10        79.73        37.78        13.64 
TCGA-DD-A3A9 TCGA-DD-A4NV TCGA-DD-A73D TCGA-DD-A73G TCGA-ED-A459 TCGA-ED-A66X 
       30.61        66.35        10.98       100.96        13.41        13.35 
TCGA-ED-A66Y TCGA-ED-A82E TCGA-EP-A2KB TCGA-ES-A2HS TCGA-FV-A4ZQ TCGA-G3-A5SJ 
        0.23         0.20        10.98        22.85         0.39        11.97 
TCGA-G3-A5SL TCGA-G3-A5SM 
        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-BC-A69H TCGA-BC-A69I 
       13.84         0.26        22.36         9.50         3.95         0.53 
TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A1HT 
        0.07         2.86         0.39         3.39         4.24         3.32 
TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MC TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 
        0.10         0.07         0.13        83.57        53.33       113.00 
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        51.29        90.71 
TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EF 
       79.40        66.31        19.79        75.65         6.71        12.95 
TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A39V 
       45.11        49.15         6.02        29.16        18.35        21.14 
TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 
       55.69         5.62        19.76        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-A4NB TCGA-DD-A4ND TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NI 
       33.14        12.85        73.38        14.07        14.24        18.44 
TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP 
       15.06        39.78        56.25        29.56        61.45        93.67 
TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C 
       12.26         0.30        80.75        10.98         9.30         7.56 
TCGA-DD-A73E TCGA-DD-A73F TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A7PX 
        1.45        27.72        12.69        15.85        13.91         0.20 
TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XP TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA 
        0.20         0.20         0.20        18.74        19.99        11.74 
TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QR 
        0.62         9.96        11.93        14.40        32.45        19.10 
TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 
        0.20         8.12         6.38         0.13         0.03         0.33 
TCGA-FV-A4ZP TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W 
       60.36         1.22        51.06        53.79        28.27        30.74 
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         5.92 
TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A6UC TCGA-GJ-A6C0 TCGA-K7-A6G5 
       19.53        19.23        14.70         7.76         1.02         4.01 
TCGA-LG-A6GG TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75I TCGA-NI-A4U2 
        0.49         9.57         5.10        14.24         8.71        58.88 
TCGA-O8-A75V 
        4.44 

  10P GAIN MUTATED 10P GAIN WILD-TYPE 
              0.10               0.03 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
            100.96             113.00 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
             12.66              14.40 
[1] "0.1 - 101.0 (12.7)" "0.0 - 113.0 (14.4)"
        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-BC-A69H         TCGA-BC-A69I         TCGA-CC-5258 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-CC-5260         TCGA-CC-5261         TCGA-CC-5262 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-CC-5263         TCGA-CC-A1HT         TCGA-CC-A3M9 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-CC-A3MA         TCGA-CC-A3MB         TCGA-CC-A3MC 
"10P GAIN WILD-TYPE"   "10P GAIN MUTATED" "10P GAIN WILD-TYPE" 
        TCGA-DD-A113         TCGA-DD-A114         TCGA-DD-A115 
  "10P GAIN MUTATED"   "10P GAIN MUTATED" "10P GAIN WILD-TYPE" 
        TCGA-DD-A116         TCGA-DD-A118         TCGA-DD-A119 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-DD-A11A         TCGA-DD-A11B         TCGA-DD-A11C 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-DD-A11D         TCGA-DD-A1E9         TCGA-DD-A1EA 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-DD-A1EB         TCGA-DD-A1EC         TCGA-DD-A1ED 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-DD-A1EE         TCGA-DD-A1EF         TCGA-DD-A1EG 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-DD-A1EH         TCGA-DD-A1EI         TCGA-DD-A1EJ 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-DD-A1EK         TCGA-DD-A1EL         TCGA-DD-A39V 
"10P GAIN WILD-TYPE"   "10P GAIN MUTATED" "10P GAIN WILD-TYPE" 
        TCGA-DD-A39X         TCGA-DD-A39Y         TCGA-DD-A39Z 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-DD-A3A0         TCGA-DD-A3A1         TCGA-DD-A3A2 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-DD-A3A3         TCGA-DD-A3A4         TCGA-DD-A3A5 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-DD-A3A6         TCGA-DD-A3A7         TCGA-DD-A3A8 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-DD-A3A9         TCGA-DD-A4NA         TCGA-DD-A4NB 
  "10P GAIN MUTATED" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-DD-A4ND         TCGA-DD-A4NF         TCGA-DD-A4NH 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "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-DD-A4NR 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-DD-A4NS         TCGA-DD-A4NV         TCGA-DD-A73A 
"10P GAIN WILD-TYPE"   "10P GAIN MUTATED" "10P GAIN WILD-TYPE" 
        TCGA-DD-A73B         TCGA-DD-A73C         TCGA-DD-A73D 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE"   "10P GAIN MUTATED" 
        TCGA-DD-A73E         TCGA-DD-A73F         TCGA-DD-A73G 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE"   "10P GAIN MUTATED" 
        TCGA-ED-A459         TCGA-ED-A4XI         TCGA-ED-A5KG 
  "10P GAIN MUTATED" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-ED-A627         TCGA-ED-A66X         TCGA-ED-A66Y 
"10P GAIN WILD-TYPE"   "10P GAIN MUTATED"   "10P GAIN MUTATED" 
        TCGA-ED-A7PX         TCGA-ED-A7PY         TCGA-ED-A7PZ 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-ED-A7XP         TCGA-ED-A82E         TCGA-EP-A12J 
"10P GAIN WILD-TYPE"   "10P GAIN MUTATED" "10P GAIN WILD-TYPE" 
        TCGA-EP-A26S         TCGA-EP-A2KA         TCGA-EP-A2KB 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE"   "10P GAIN MUTATED" 
        TCGA-EP-A2KC         TCGA-EP-A3JL         TCGA-EP-A3RK 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-ES-A2HS         TCGA-ES-A2HT         TCGA-FV-A23B 
  "10P GAIN MUTATED" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-FV-A2QR         TCGA-FV-A3I0         TCGA-FV-A3I1 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-FV-A3R2         TCGA-FV-A3R3         TCGA-FV-A495 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-FV-A496         TCGA-FV-A4ZP         TCGA-FV-A4ZQ 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE"   "10P GAIN MUTATED" 
        TCGA-G3-A25S         TCGA-G3-A25T         TCGA-G3-A25U 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-G3-A25V         TCGA-G3-A25W         TCGA-G3-A25X 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-G3-A25Y         TCGA-G3-A25Z         TCGA-G3-A3CG 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-G3-A3CH         TCGA-G3-A3CI         TCGA-G3-A3CJ 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-G3-A3CK         TCGA-G3-A5SI         TCGA-G3-A5SJ 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE"   "10P GAIN MUTATED" 
        TCGA-G3-A5SL         TCGA-G3-A5SM         TCGA-G3-A6UC 
  "10P GAIN MUTATED"   "10P GAIN MUTATED" "10P GAIN WILD-TYPE" 
        TCGA-GJ-A6C0         TCGA-K7-A6G5         TCGA-LG-A6GG 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-MI-A75C         TCGA-MI-A75E         TCGA-MI-A75G 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-MI-A75I         TCGA-NI-A4U2         TCGA-O8-A75V 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE"   "10P GAIN MUTATED" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
  "10P GAIN MUTATED" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-BC-A5W4 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BC-A69H         TCGA-BC-A69I         TCGA-CC-5258 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-CC-5260         TCGA-CC-5261         TCGA-CC-5262 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-CC-5263         TCGA-CC-A1HT         TCGA-CC-A3M9 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-CC-A3MA         TCGA-CC-A3MB         TCGA-CC-A3MC 
"10P GAIN WILD-TYPE"   "10P GAIN MUTATED" "10P GAIN WILD-TYPE" 
        TCGA-DD-A113         TCGA-DD-A114         TCGA-DD-A115 
  "10P GAIN MUTATED"   "10P GAIN MUTATED" "10P GAIN WILD-TYPE" 
        TCGA-DD-A116         TCGA-DD-A118         TCGA-DD-A119 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-DD-A11A         TCGA-DD-A11B         TCGA-DD-A11C 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-DD-A11D         TCGA-DD-A1E9         TCGA-DD-A1EA 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-DD-A1EB         TCGA-DD-A1EC         TCGA-DD-A1ED 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-DD-A1EE         TCGA-DD-A1EF         TCGA-DD-A1EG 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-DD-A1EH         TCGA-DD-A1EI         TCGA-DD-A1EJ 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-DD-A1EK         TCGA-DD-A1EL         TCGA-DD-A39V 
"10P GAIN WILD-TYPE"   "10P GAIN MUTATED" "10P GAIN WILD-TYPE" 
        TCGA-DD-A39X         TCGA-DD-A39Y         TCGA-DD-A39Z 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-DD-A3A0         TCGA-DD-A3A1         TCGA-DD-A3A2 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-DD-A3A3         TCGA-DD-A3A4         TCGA-DD-A3A5 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-DD-A3A6         TCGA-DD-A3A7         TCGA-DD-A3A8 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-DD-A3A9         TCGA-DD-A4NA         TCGA-DD-A4NB 
  "10P GAIN MUTATED" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-DD-A4ND         TCGA-DD-A4NF         TCGA-DD-A4NH 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "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-DD-A4NR 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-DD-A4NS         TCGA-DD-A4NV         TCGA-DD-A73A 
"10P GAIN WILD-TYPE"   "10P GAIN MUTATED" "10P GAIN WILD-TYPE" 
        TCGA-DD-A73B         TCGA-DD-A73C         TCGA-DD-A73D 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE"   "10P GAIN MUTATED" 
        TCGA-DD-A73E         TCGA-DD-A73F         TCGA-DD-A73G 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE"   "10P GAIN MUTATED" 
        TCGA-ED-A459         TCGA-ED-A4XI         TCGA-ED-A5KG 
  "10P GAIN MUTATED" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-ED-A627         TCGA-ED-A66X         TCGA-ED-A66Y 
"10P GAIN WILD-TYPE"   "10P GAIN MUTATED"   "10P GAIN MUTATED" 
        TCGA-ED-A7PX         TCGA-ED-A7PY         TCGA-ED-A7PZ 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-ED-A7XP         TCGA-ED-A82E         TCGA-EP-A12J 
"10P GAIN WILD-TYPE"   "10P GAIN MUTATED" "10P GAIN WILD-TYPE" 
        TCGA-EP-A26S         TCGA-EP-A2KA         TCGA-EP-A2KB 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE"   "10P GAIN MUTATED" 
        TCGA-EP-A2KC         TCGA-EP-A3JL         TCGA-EP-A3RK 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-ES-A2HS         TCGA-ES-A2HT         TCGA-FV-A23B 
  "10P GAIN MUTATED" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-FV-A2QR         TCGA-FV-A3I0         TCGA-FV-A3I1 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-FV-A3R2         TCGA-FV-A3R3         TCGA-FV-A495 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-FV-A496         TCGA-FV-A4ZP         TCGA-FV-A4ZQ 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE"   "10P GAIN MUTATED" 
        TCGA-G3-A25S         TCGA-G3-A25T         TCGA-G3-A25U 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-G3-A25V         TCGA-G3-A25W         TCGA-G3-A25X 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-G3-A25Y         TCGA-G3-A25Z         TCGA-G3-A3CG 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-G3-A3CH         TCGA-G3-A3CI         TCGA-G3-A3CJ 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-G3-A3CK         TCGA-G3-A5SI         TCGA-G3-A5SJ 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE"   "10P GAIN MUTATED" 
        TCGA-G3-A5SL         TCGA-G3-A5SM         TCGA-G3-A6UC 
  "10P GAIN MUTATED"   "10P GAIN MUTATED" "10P GAIN WILD-TYPE" 
        TCGA-GJ-A6C0         TCGA-K7-A6G5         TCGA-LG-A6GG 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-MI-A75C         TCGA-MI-A75E         TCGA-MI-A75G 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-MI-A75I         TCGA-NI-A4U2         TCGA-O8-A75V 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE"   "10P GAIN MUTATED" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
  "10P GAIN MUTATED" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-BC-A5W4 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BC-A69H         TCGA-BC-A69I         TCGA-CC-5258 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-CC-5260         TCGA-CC-5261         TCGA-CC-5262 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-CC-5263         TCGA-CC-A1HT         TCGA-CC-A3M9 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-CC-A3MA         TCGA-CC-A3MB         TCGA-CC-A3MC 
"10P GAIN WILD-TYPE"   "10P GAIN MUTATED" "10P GAIN WILD-TYPE" 
        TCGA-DD-A113         TCGA-DD-A114         TCGA-DD-A115 
  "10P GAIN MUTATED"   "10P GAIN MUTATED" "10P GAIN WILD-TYPE" 
        TCGA-DD-A116         TCGA-DD-A118         TCGA-DD-A119 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-DD-A11A         TCGA-DD-A11B         TCGA-DD-A11C 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-DD-A11D         TCGA-DD-A1E9         TCGA-DD-A1EA 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-DD-A1EB         TCGA-DD-A1EC         TCGA-DD-A1ED 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-DD-A1EE         TCGA-DD-A1EF         TCGA-DD-A1EG 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-DD-A1EH         TCGA-DD-A1EI         TCGA-DD-A1EJ 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-DD-A1EK         TCGA-DD-A1EL         TCGA-DD-A39V 
"10P GAIN WILD-TYPE"   "10P GAIN MUTATED" "10P GAIN WILD-TYPE" 
        TCGA-DD-A39X         TCGA-DD-A39Y         TCGA-DD-A39Z 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-DD-A3A0         TCGA-DD-A3A1         TCGA-DD-A3A2 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-DD-A3A3         TCGA-DD-A3A4         TCGA-DD-A3A5 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-DD-A3A6         TCGA-DD-A3A7         TCGA-DD-A3A8 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-DD-A3A9         TCGA-DD-A4NA         TCGA-DD-A4NB 
  "10P GAIN MUTATED" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-DD-A4ND         TCGA-DD-A4NF         TCGA-DD-A4NH 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "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-DD-A4NR 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-DD-A4NS         TCGA-DD-A4NV         TCGA-DD-A73A 
"10P GAIN WILD-TYPE"   "10P GAIN MUTATED" "10P GAIN WILD-TYPE" 
        TCGA-DD-A73B         TCGA-DD-A73C         TCGA-DD-A73D 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE"   "10P GAIN MUTATED" 
        TCGA-DD-A73E         TCGA-DD-A73F         TCGA-DD-A73G 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE"   "10P GAIN MUTATED" 
        TCGA-ED-A459         TCGA-ED-A4XI         TCGA-ED-A5KG 
  "10P GAIN MUTATED" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-ED-A627         TCGA-ED-A66X         TCGA-ED-A66Y 
"10P GAIN WILD-TYPE"   "10P GAIN MUTATED"   "10P GAIN MUTATED" 
        TCGA-ED-A7PX         TCGA-ED-A7PY         TCGA-ED-A7PZ 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-ED-A7XP         TCGA-ED-A82E         TCGA-EP-A12J 
"10P GAIN WILD-TYPE"   "10P GAIN MUTATED" "10P GAIN WILD-TYPE" 
        TCGA-EP-A26S         TCGA-EP-A2KA         TCGA-EP-A2KB 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE"   "10P GAIN MUTATED" 
        TCGA-EP-A2KC         TCGA-EP-A3JL         TCGA-EP-A3RK 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-ES-A2HS         TCGA-ES-A2HT         TCGA-FV-A23B 
  "10P GAIN MUTATED" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-FV-A2QR         TCGA-FV-A3I0         TCGA-FV-A3I1 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-FV-A3R2         TCGA-FV-A3R3         TCGA-FV-A495 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-FV-A496         TCGA-FV-A4ZP         TCGA-FV-A4ZQ 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE"   "10P GAIN MUTATED" 
        TCGA-G3-A25S         TCGA-G3-A25T         TCGA-G3-A25U 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-G3-A25V         TCGA-G3-A25W         TCGA-G3-A25X 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-G3-A25Y         TCGA-G3-A25Z         TCGA-G3-A3CG 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-G3-A3CH         TCGA-G3-A3CI         TCGA-G3-A3CJ 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-G3-A3CK         TCGA-G3-A5SI         TCGA-G3-A5SJ 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE"   "10P GAIN MUTATED" 
        TCGA-G3-A5SL         TCGA-G3-A5SM         TCGA-G3-A6UC 
  "10P GAIN MUTATED"   "10P GAIN MUTATED" "10P GAIN WILD-TYPE" 
        TCGA-GJ-A6C0         TCGA-K7-A6G5         TCGA-LG-A6GG 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-MI-A75C         TCGA-MI-A75E         TCGA-MI-A75G 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-MI-A75I         TCGA-NI-A4U2         TCGA-O8-A75V 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
[1] "hr=" "1.2"
D19V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  10P GAIN MUTATED         5        6         0          7          0
  10P GAIN WILD-TYPE      53       30         2         23          4
                    vv
clus                 STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  10P GAIN MUTATED            0        0         0         1
  10P GAIN WILD-TYPE          5        1         1         1
D19V3, multiclass
                    vv
clus                 T1 T2 T3 T4
  10P GAIN MUTATED    5  7  8  1
  10P GAIN WILD-TYPE 56 33 32  7
D19V4, multiclass
    clus
vv   10P GAIN MUTATED 10P GAIN WILD-TYPE
  T1                5                 56
  T2                7                 33
  T3                8                 32
  T4                1                  7
D19V5, binary
                    cls
clus                  0  1
  10P GAIN MUTATED   11  0
  10P GAIN WILD-TYPE 86  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED     11    0
  10P GAIN WILD-TYPE   86    3
   clus
vv  10P GAIN MUTATED 10P GAIN WILD-TYPE
  0               11                 86
  1                0                  3
                    vv
clus                  M0  M1  MX
  10P GAIN MUTATED    15   1   5
  10P GAIN WILD-TYPE 100   2  26
D19V6, multiclass
    clus
vv   10P GAIN MUTATED 10P GAIN WILD-TYPE
  M0               15                100
  M1                1                  2
  MX                5                 26
D19V7, binary
                    cls
clus                  0  1
  10P GAIN MUTATED    9 12
  10P GAIN WILD-TYPE 49 79
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED      9   12
  10P GAIN WILD-TYPE   49   79
        clus
vv       10P GAIN MUTATED 10P GAIN WILD-TYPE
  FEMALE                9                 49
  MALE                 12                 79
                    vv
clus                  R0  R1  R2  RX
  10P GAIN MUTATED    19   1   0   1
  10P GAIN WILD-TYPE 103  10   1   9
D19V8, multiclass
    clus
vv   10P GAIN MUTATED 10P GAIN WILD-TYPE
  R0               19                103
  R1                1                 10
  R2                0                  1
  RX                1                  9

Clustering(20) Variable = 10Q GAIN MUTATION ANALYSIS
D20V1, survival
                    sevent
clus2                 0  1
  10Q GAIN MUTATED    9  4
  10Q GAIN WILD-TYPE 75 59
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                13                134 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                 4                 59 
$`10Q GAIN MUTATED`
TCGA-DD-A113 TCGA-DD-A39Z TCGA-DD-A3A9 TCGA-DD-A4NV TCGA-DD-A73G TCGA-ED-A66X 
       79.73        19.76        30.61        66.35       100.96        13.35 
TCGA-ED-A66Y TCGA-ED-A82E TCGA-EP-A2KB TCGA-ES-A2HS TCGA-FV-A4ZQ TCGA-G3-A5SL 
        0.23         0.20        10.98        22.85         0.39         7.99 
TCGA-G3-A5SM 
        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        13.84         0.26        22.36         9.50 
TCGA-BC-A69H TCGA-BC-A69I TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 
        3.95         0.53         0.07         2.86         0.39         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-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A 
       37.78        83.57        53.33       113.00         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        51.29        90.71        79.40        66.31 
TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH 
       19.79        75.65         6.71        12.95        45.11        49.15 
TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39X 
        6.02        29.16        18.35        13.64        21.14        55.69 
TCGA-DD-A39Y TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 
        5.62        25.81         7.66        70.06        17.59        20.12 
TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A4NA TCGA-DD-A4NB 
      102.74       107.11        13.78         0.36        33.14        12.85 
TCGA-DD-A4ND TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK 
       73.38        14.07        14.24        18.44        15.06        39.78 
TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR 
       56.25        29.56        61.45        93.67        12.26         0.30 
TCGA-DD-A4NS TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E 
       80.75        10.98         9.30         7.56        10.98         1.45 
TCGA-DD-A73F TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A7PX 
       27.72        13.41        12.69        15.85        13.91         0.20 
TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XP TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA 
        0.20         0.20         0.20        18.74        19.99        11.74 
TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QR 
        0.62         9.96        11.93        14.40        32.45        19.10 
TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 
        0.20         8.12         6.38         0.13         0.03         0.33 
TCGA-FV-A4ZP TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W 
       60.36         1.22        51.06        53.79        28.27        30.74 
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         5.92 
TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A6UC TCGA-GJ-A6C0 
       19.53        19.23        14.70        11.97         7.76         1.02 
TCGA-K7-A6G5 TCGA-LG-A6GG TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75I 
        4.01         0.49         9.57         5.10        14.24         8.71 
TCGA-NI-A4U2 TCGA-O8-A75V 
       58.88         4.44 

  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
              0.20               0.03 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
            100.96             113.00 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
            13.350             14.155 
[1] "0.2 - 101.0 (13.3)" "0.0 - 113.0 (14.2)"
        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-BC-A69H         TCGA-BC-A69I         TCGA-CC-5258 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CC-5260         TCGA-CC-5261         TCGA-CC-5262 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CC-5263         TCGA-CC-A1HT         TCGA-CC-A3M9 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CC-A3MA         TCGA-CC-A3MB         TCGA-CC-A3MC 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DD-A113         TCGA-DD-A114         TCGA-DD-A115 
  "10Q GAIN MUTATED" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DD-A116         TCGA-DD-A118         TCGA-DD-A119 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DD-A11A         TCGA-DD-A11B         TCGA-DD-A11C 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DD-A11D         TCGA-DD-A1E9         TCGA-DD-A1EA 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DD-A1EB         TCGA-DD-A1EC         TCGA-DD-A1ED 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DD-A1EE         TCGA-DD-A1EF         TCGA-DD-A1EG 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DD-A1EH         TCGA-DD-A1EI         TCGA-DD-A1EJ 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DD-A1EK         TCGA-DD-A1EL         TCGA-DD-A39V 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DD-A39X         TCGA-DD-A39Y         TCGA-DD-A39Z 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE"   "10Q GAIN MUTATED" 
        TCGA-DD-A3A0         TCGA-DD-A3A1         TCGA-DD-A3A2 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DD-A3A3         TCGA-DD-A3A4         TCGA-DD-A3A5 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DD-A3A6         TCGA-DD-A3A7         TCGA-DD-A3A8 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DD-A3A9         TCGA-DD-A4NA         TCGA-DD-A4NB 
  "10Q GAIN MUTATED" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DD-A4ND         TCGA-DD-A4NF         TCGA-DD-A4NH 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "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-DD-A4NR 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DD-A4NS         TCGA-DD-A4NV         TCGA-DD-A73A 
"10Q GAIN WILD-TYPE"   "10Q GAIN MUTATED" "10Q GAIN WILD-TYPE" 
        TCGA-DD-A73B         TCGA-DD-A73C         TCGA-DD-A73D 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DD-A73E         TCGA-DD-A73F         TCGA-DD-A73G 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE"   "10Q GAIN MUTATED" 
        TCGA-ED-A459         TCGA-ED-A4XI         TCGA-ED-A5KG 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-ED-A627         TCGA-ED-A66X         TCGA-ED-A66Y 
"10Q GAIN WILD-TYPE"   "10Q GAIN MUTATED"   "10Q GAIN MUTATED" 
        TCGA-ED-A7PX         TCGA-ED-A7PY         TCGA-ED-A7PZ 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-ED-A7XP         TCGA-ED-A82E         TCGA-EP-A12J 
"10Q GAIN WILD-TYPE"   "10Q GAIN MUTATED" "10Q GAIN WILD-TYPE" 
        TCGA-EP-A26S         TCGA-EP-A2KA         TCGA-EP-A2KB 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE"   "10Q GAIN MUTATED" 
        TCGA-EP-A2KC         TCGA-EP-A3JL         TCGA-EP-A3RK 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-ES-A2HS         TCGA-ES-A2HT         TCGA-FV-A23B 
  "10Q GAIN MUTATED" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-FV-A2QR         TCGA-FV-A3I0         TCGA-FV-A3I1 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-FV-A3R2         TCGA-FV-A3R3         TCGA-FV-A495 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-FV-A496         TCGA-FV-A4ZP         TCGA-FV-A4ZQ 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE"   "10Q GAIN MUTATED" 
        TCGA-G3-A25S         TCGA-G3-A25T         TCGA-G3-A25U 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-G3-A25V         TCGA-G3-A25W         TCGA-G3-A25X 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-G3-A25Y         TCGA-G3-A25Z         TCGA-G3-A3CG 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-G3-A3CH         TCGA-G3-A3CI         TCGA-G3-A3CJ 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-G3-A3CK         TCGA-G3-A5SI         TCGA-G3-A5SJ 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-G3-A5SL         TCGA-G3-A5SM         TCGA-G3-A6UC 
  "10Q GAIN MUTATED"   "10Q GAIN MUTATED" "10Q GAIN WILD-TYPE" 
        TCGA-GJ-A6C0         TCGA-K7-A6G5         TCGA-LG-A6GG 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-MI-A75C         TCGA-MI-A75E         TCGA-MI-A75G 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-MI-A75I         TCGA-NI-A4U2         TCGA-O8-A75V 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        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-BC-A69H         TCGA-BC-A69I         TCGA-CC-5258 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CC-5260         TCGA-CC-5261         TCGA-CC-5262 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CC-5263         TCGA-CC-A1HT         TCGA-CC-A3M9 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CC-A3MA         TCGA-CC-A3MB         TCGA-CC-A3MC 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DD-A113         TCGA-DD-A114         TCGA-DD-A115 
  "10Q GAIN MUTATED" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DD-A116         TCGA-DD-A118         TCGA-DD-A119 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DD-A11A         TCGA-DD-A11B         TCGA-DD-A11C 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DD-A11D         TCGA-DD-A1E9         TCGA-DD-A1EA 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DD-A1EB         TCGA-DD-A1EC         TCGA-DD-A1ED 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DD-A1EE         TCGA-DD-A1EF         TCGA-DD-A1EG 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DD-A1EH         TCGA-DD-A1EI         TCGA-DD-A1EJ 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DD-A1EK         TCGA-DD-A1EL         TCGA-DD-A39V 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DD-A39X         TCGA-DD-A39Y         TCGA-DD-A39Z 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE"   "10Q GAIN MUTATED" 
        TCGA-DD-A3A0         TCGA-DD-A3A1         TCGA-DD-A3A2 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DD-A3A3         TCGA-DD-A3A4         TCGA-DD-A3A5 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DD-A3A6         TCGA-DD-A3A7         TCGA-DD-A3A8 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DD-A3A9         TCGA-DD-A4NA         TCGA-DD-A4NB 
  "10Q GAIN MUTATED" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DD-A4ND         TCGA-DD-A4NF         TCGA-DD-A4NH 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "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-DD-A4NR 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DD-A4NS         TCGA-DD-A4NV         TCGA-DD-A73A 
"10Q GAIN WILD-TYPE"   "10Q GAIN MUTATED" "10Q GAIN WILD-TYPE" 
        TCGA-DD-A73B         TCGA-DD-A73C         TCGA-DD-A73D 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DD-A73E         TCGA-DD-A73F         TCGA-DD-A73G 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE"   "10Q GAIN MUTATED" 
        TCGA-ED-A459         TCGA-ED-A4XI         TCGA-ED-A5KG 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-ED-A627         TCGA-ED-A66X         TCGA-ED-A66Y 
"10Q GAIN WILD-TYPE"   "10Q GAIN MUTATED"   "10Q GAIN MUTATED" 
        TCGA-ED-A7PX         TCGA-ED-A7PY         TCGA-ED-A7PZ 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-ED-A7XP         TCGA-ED-A82E         TCGA-EP-A12J 
"10Q GAIN WILD-TYPE"   "10Q GAIN MUTATED" "10Q GAIN WILD-TYPE" 
        TCGA-EP-A26S         TCGA-EP-A2KA         TCGA-EP-A2KB 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE"   "10Q GAIN MUTATED" 
        TCGA-EP-A2KC         TCGA-EP-A3JL         TCGA-EP-A3RK 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-ES-A2HS         TCGA-ES-A2HT         TCGA-FV-A23B 
  "10Q GAIN MUTATED" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-FV-A2QR         TCGA-FV-A3I0         TCGA-FV-A3I1 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-FV-A3R2         TCGA-FV-A3R3         TCGA-FV-A495 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-FV-A496         TCGA-FV-A4ZP         TCGA-FV-A4ZQ 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE"   "10Q GAIN MUTATED" 
        TCGA-G3-A25S         TCGA-G3-A25T         TCGA-G3-A25U 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-G3-A25V         TCGA-G3-A25W         TCGA-G3-A25X 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-G3-A25Y         TCGA-G3-A25Z         TCGA-G3-A3CG 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-G3-A3CH         TCGA-G3-A3CI         TCGA-G3-A3CJ 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-G3-A3CK         TCGA-G3-A5SI         TCGA-G3-A5SJ 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-G3-A5SL         TCGA-G3-A5SM         TCGA-G3-A6UC 
  "10Q GAIN MUTATED"   "10Q GAIN MUTATED" "10Q GAIN WILD-TYPE" 
        TCGA-GJ-A6C0         TCGA-K7-A6G5         TCGA-LG-A6GG 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-MI-A75C         TCGA-MI-A75E         TCGA-MI-A75G 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-MI-A75I         TCGA-NI-A4U2         TCGA-O8-A75V 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        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-BC-A69H         TCGA-BC-A69I         TCGA-CC-5258 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CC-5260         TCGA-CC-5261         TCGA-CC-5262 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CC-5263         TCGA-CC-A1HT         TCGA-CC-A3M9 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CC-A3MA         TCGA-CC-A3MB         TCGA-CC-A3MC 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DD-A113         TCGA-DD-A114         TCGA-DD-A115 
  "10Q GAIN MUTATED" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DD-A116         TCGA-DD-A118         TCGA-DD-A119 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DD-A11A         TCGA-DD-A11B         TCGA-DD-A11C 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DD-A11D         TCGA-DD-A1E9         TCGA-DD-A1EA 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DD-A1EB         TCGA-DD-A1EC         TCGA-DD-A1ED 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DD-A1EE         TCGA-DD-A1EF         TCGA-DD-A1EG 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DD-A1EH         TCGA-DD-A1EI         TCGA-DD-A1EJ 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DD-A1EK         TCGA-DD-A1EL         TCGA-DD-A39V 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DD-A39X         TCGA-DD-A39Y         TCGA-DD-A39Z 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE"   "10Q GAIN MUTATED" 
        TCGA-DD-A3A0         TCGA-DD-A3A1         TCGA-DD-A3A2 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DD-A3A3         TCGA-DD-A3A4         TCGA-DD-A3A5 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DD-A3A6         TCGA-DD-A3A7         TCGA-DD-A3A8 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DD-A3A9         TCGA-DD-A4NA         TCGA-DD-A4NB 
  "10Q GAIN MUTATED" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DD-A4ND         TCGA-DD-A4NF         TCGA-DD-A4NH 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "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-DD-A4NR 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DD-A4NS         TCGA-DD-A4NV         TCGA-DD-A73A 
"10Q GAIN WILD-TYPE"   "10Q GAIN MUTATED" "10Q GAIN WILD-TYPE" 
        TCGA-DD-A73B         TCGA-DD-A73C         TCGA-DD-A73D 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DD-A73E         TCGA-DD-A73F         TCGA-DD-A73G 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE"   "10Q GAIN MUTATED" 
        TCGA-ED-A459         TCGA-ED-A4XI         TCGA-ED-A5KG 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-ED-A627         TCGA-ED-A66X         TCGA-ED-A66Y 
"10Q GAIN WILD-TYPE"   "10Q GAIN MUTATED"   "10Q GAIN MUTATED" 
        TCGA-ED-A7PX         TCGA-ED-A7PY         TCGA-ED-A7PZ 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-ED-A7XP         TCGA-ED-A82E         TCGA-EP-A12J 
"10Q GAIN WILD-TYPE"   "10Q GAIN MUTATED" "10Q GAIN WILD-TYPE" 
        TCGA-EP-A26S         TCGA-EP-A2KA         TCGA-EP-A2KB 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE"   "10Q GAIN MUTATED" 
        TCGA-EP-A2KC         TCGA-EP-A3JL         TCGA-EP-A3RK 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-ES-A2HS         TCGA-ES-A2HT         TCGA-FV-A23B 
  "10Q GAIN MUTATED" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-FV-A2QR         TCGA-FV-A3I0         TCGA-FV-A3I1 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-FV-A3R2         TCGA-FV-A3R3         TCGA-FV-A495 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-FV-A496         TCGA-FV-A4ZP         TCGA-FV-A4ZQ 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE"   "10Q GAIN MUTATED" 
        TCGA-G3-A25S         TCGA-G3-A25T         TCGA-G3-A25U 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-G3-A25V         TCGA-G3-A25W         TCGA-G3-A25X 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-G3-A25Y         TCGA-G3-A25Z         TCGA-G3-A3CG 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-G3-A3CH         TCGA-G3-A3CI         TCGA-G3-A3CJ 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-G3-A3CK         TCGA-G3-A5SI         TCGA-G3-A5SJ 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-G3-A5SL         TCGA-G3-A5SM         TCGA-G3-A6UC 
  "10Q GAIN MUTATED"   "10Q GAIN MUTATED" "10Q GAIN WILD-TYPE" 
        TCGA-GJ-A6C0         TCGA-K7-A6G5         TCGA-LG-A6GG 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-MI-A75C         TCGA-MI-A75E         TCGA-MI-A75G 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-MI-A75I         TCGA-NI-A4U2         TCGA-O8-A75V 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
[1] "hr=" "1.5"
D20V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  10Q GAIN MUTATED         4        3         0          5          0
  10Q GAIN WILD-TYPE      54       33         2         25          4
                    vv
clus                 STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  10Q GAIN MUTATED            0        0         0         1
  10Q GAIN WILD-TYPE          5        1         1         1
D20V3, multiclass
                    vv
clus                 T1 T2 T3 T4
  10Q GAIN MUTATED    4  3  5  1
  10Q GAIN WILD-TYPE 57 37 35  7
D20V4, multiclass
    clus
vv   10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  T1                4                 57
  T2                3                 37
  T3                5                 35
  T4                1                  7
D20V5, binary
                    cls
clus                  0  1
  10Q GAIN MUTATED    7  0
  10Q GAIN WILD-TYPE 90  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED      7    0
  10Q GAIN WILD-TYPE   90    3
   clus
vv  10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  0                7                 90
  1                0                  3
                    vv
clus                  M0  M1  MX
  10Q GAIN MUTATED    10   1   2
  10Q GAIN WILD-TYPE 105   2  29
D20V6, multiclass
    clus
vv   10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  M0               10                105
  M1                1                  2
  MX                2                 29
D20V7, binary
                    cls
clus                  0  1
  10Q GAIN MUTATED    7  6
  10Q GAIN WILD-TYPE 51 85
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED      7    6
  10Q GAIN WILD-TYPE   51   85
        clus
vv       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  FEMALE                7                 51
  MALE                  6                 85
                    vv
clus                  R0  R1  R2  RX
  10Q GAIN MUTATED    13   0   0   0
  10Q GAIN WILD-TYPE 109  11   1  10
D20V8, multiclass
    clus
vv   10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  R0               13                109
  R1                0                 11
  R2                0                  1
  RX                0                 10

Clustering(21) Variable = 11P GAIN MUTATION ANALYSIS
D21V1, survival
                    sevent
clus2                 0  1
  11P GAIN MUTATED    8  2
  11P GAIN WILD-TYPE 76 61
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                10                137 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 2                 61 
$`11P GAIN MUTATED`
TCGA-BC-A69H TCGA-CC-A3M9 TCGA-DD-A119 TCGA-DD-A39Y TCGA-DD-A4NV TCGA-ED-A66Y 
        3.95         0.10         7.33         5.62        66.35         0.23 
TCGA-ED-A82E TCGA-FV-A4ZQ TCGA-G3-A3CG TCGA-LG-A6GG 
        0.20         0.39        22.13         0.49 

$`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        13.84         0.26        22.36         9.50 
TCGA-BC-A69I TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 
        0.53         0.07         2.86         0.39         3.39         4.24 
TCGA-CC-A1HT TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A113 TCGA-DD-A114 
        3.32         0.07         0.10         0.13        79.73        37.78 
TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C 
       83.57        53.33       113.00         2.60         0.46        21.76 
TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED 
       51.29        90.71        79.40        66.31        19.79        75.65 
TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ 
        6.71        12.95        45.11        49.15         6.02        29.16 
TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39X TCGA-DD-A39Z TCGA-DD-A3A0 
       18.35        13.64        21.14        55.69        19.76        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-A4NB TCGA-DD-A4ND 
       13.78         0.36        30.61        33.14        12.85        73.38 
TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL 
       14.07        14.24        18.44        15.06        39.78        56.25 
TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS 
       29.56        61.45        93.67        12.26         0.30        80.75 
TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F 
       10.98         9.30         7.56        10.98         1.45        27.72 
TCGA-DD-A73G TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X 
      100.96        13.41        12.69        15.85        13.91        13.35 
TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XP TCGA-EP-A12J TCGA-EP-A26S 
        0.20         0.20         0.20         0.20        18.74        19.99 
TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS 
       11.74        10.98         0.62         9.96        11.93        22.85 
TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R2 
       14.40        32.45        19.10         0.20         8.12         6.38 
TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZP TCGA-G3-A25S TCGA-G3-A25T 
        0.13         0.03         0.33        60.36         1.22        51.06 
TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A25Z 
       53.79        28.27        30.74        58.49        14.86        21.53 
TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ 
       25.64         5.92        19.53        19.23        14.70        11.97 
TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A6UC TCGA-GJ-A6C0 TCGA-K7-A6G5 TCGA-MI-A75C 
        7.99         4.37         7.76         1.02         4.01         9.57 
TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75I TCGA-NI-A4U2 TCGA-O8-A75V 
        5.10        14.24         8.71        58.88         4.44 

  11P GAIN MUTATED 11P GAIN WILD-TYPE 
              0.10               0.03 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
             66.35             113.00 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
              2.22              14.40 
[1] "0.1 - 66.3 (2.2)"   "0.0 - 113.0 (14.4)"
        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-BC-A69H         TCGA-BC-A69I         TCGA-CC-5258 
  "11P GAIN MUTATED" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-CC-5260         TCGA-CC-5261         TCGA-CC-5262 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-CC-5263         TCGA-CC-A1HT         TCGA-CC-A3M9 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE"   "11P GAIN MUTATED" 
        TCGA-CC-A3MA         TCGA-CC-A3MB         TCGA-CC-A3MC 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DD-A113         TCGA-DD-A114         TCGA-DD-A115 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DD-A116         TCGA-DD-A118         TCGA-DD-A119 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE"   "11P GAIN MUTATED" 
        TCGA-DD-A11A         TCGA-DD-A11B         TCGA-DD-A11C 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DD-A11D         TCGA-DD-A1E9         TCGA-DD-A1EA 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DD-A1EB         TCGA-DD-A1EC         TCGA-DD-A1ED 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DD-A1EE         TCGA-DD-A1EF         TCGA-DD-A1EG 
"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-A1EK         TCGA-DD-A1EL         TCGA-DD-A39V 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DD-A39X         TCGA-DD-A39Y         TCGA-DD-A39Z 
"11P GAIN WILD-TYPE"   "11P GAIN MUTATED" "11P GAIN WILD-TYPE" 
        TCGA-DD-A3A0         TCGA-DD-A3A1         TCGA-DD-A3A2 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DD-A3A3         TCGA-DD-A3A4         TCGA-DD-A3A5 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DD-A3A6         TCGA-DD-A3A7         TCGA-DD-A3A8 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DD-A3A9         TCGA-DD-A4NA         TCGA-DD-A4NB 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DD-A4ND         TCGA-DD-A4NF         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-DD-A4NR 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DD-A4NS         TCGA-DD-A4NV         TCGA-DD-A73A 
"11P GAIN WILD-TYPE"   "11P GAIN MUTATED" "11P GAIN WILD-TYPE" 
        TCGA-DD-A73B         TCGA-DD-A73C         TCGA-DD-A73D 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DD-A73E         TCGA-DD-A73F         TCGA-DD-A73G 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-ED-A459         TCGA-ED-A4XI         TCGA-ED-A5KG 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-ED-A627         TCGA-ED-A66X         TCGA-ED-A66Y 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE"   "11P GAIN MUTATED" 
        TCGA-ED-A7PX         TCGA-ED-A7PY         TCGA-ED-A7PZ 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-ED-A7XP         TCGA-ED-A82E         TCGA-EP-A12J 
"11P GAIN WILD-TYPE"   "11P GAIN MUTATED" "11P GAIN WILD-TYPE" 
        TCGA-EP-A26S         TCGA-EP-A2KA         TCGA-EP-A2KB 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-EP-A2KC         TCGA-EP-A3JL         TCGA-EP-A3RK 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-ES-A2HS         TCGA-ES-A2HT         TCGA-FV-A23B 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-FV-A2QR         TCGA-FV-A3I0         TCGA-FV-A3I1 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-FV-A3R2         TCGA-FV-A3R3         TCGA-FV-A495 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-FV-A496         TCGA-FV-A4ZP         TCGA-FV-A4ZQ 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE"   "11P GAIN MUTATED" 
        TCGA-G3-A25S         TCGA-G3-A25T         TCGA-G3-A25U 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-G3-A25V         TCGA-G3-A25W         TCGA-G3-A25X 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-G3-A25Y         TCGA-G3-A25Z         TCGA-G3-A3CG 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE"   "11P GAIN MUTATED" 
        TCGA-G3-A3CH         TCGA-G3-A3CI         TCGA-G3-A3CJ 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-G3-A3CK         TCGA-G3-A5SI         TCGA-G3-A5SJ 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-G3-A5SL         TCGA-G3-A5SM         TCGA-G3-A6UC 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-GJ-A6C0         TCGA-K7-A6G5         TCGA-LG-A6GG 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE"   "11P GAIN MUTATED" 
        TCGA-MI-A75C         TCGA-MI-A75E         TCGA-MI-A75G 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-MI-A75I         TCGA-NI-A4U2         TCGA-O8-A75V 
"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-BC-A69H         TCGA-BC-A69I         TCGA-CC-5258 
  "11P GAIN MUTATED" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-CC-5260         TCGA-CC-5261         TCGA-CC-5262 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-CC-5263         TCGA-CC-A1HT         TCGA-CC-A3M9 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE"   "11P GAIN MUTATED" 
        TCGA-CC-A3MA         TCGA-CC-A3MB         TCGA-CC-A3MC 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DD-A113         TCGA-DD-A114         TCGA-DD-A115 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DD-A116         TCGA-DD-A118         TCGA-DD-A119 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE"   "11P GAIN MUTATED" 
        TCGA-DD-A11A         TCGA-DD-A11B         TCGA-DD-A11C 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DD-A11D         TCGA-DD-A1E9         TCGA-DD-A1EA 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DD-A1EB         TCGA-DD-A1EC         TCGA-DD-A1ED 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DD-A1EE         TCGA-DD-A1EF         TCGA-DD-A1EG 
"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-A1EK         TCGA-DD-A1EL         TCGA-DD-A39V 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DD-A39X         TCGA-DD-A39Y         TCGA-DD-A39Z 
"11P GAIN WILD-TYPE"   "11P GAIN MUTATED" "11P GAIN WILD-TYPE" 
        TCGA-DD-A3A0         TCGA-DD-A3A1         TCGA-DD-A3A2 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DD-A3A3         TCGA-DD-A3A4         TCGA-DD-A3A5 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DD-A3A6         TCGA-DD-A3A7         TCGA-DD-A3A8 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DD-A3A9         TCGA-DD-A4NA         TCGA-DD-A4NB 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DD-A4ND         TCGA-DD-A4NF         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-DD-A4NR 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DD-A4NS         TCGA-DD-A4NV         TCGA-DD-A73A 
"11P GAIN WILD-TYPE"   "11P GAIN MUTATED" "11P GAIN WILD-TYPE" 
        TCGA-DD-A73B         TCGA-DD-A73C         TCGA-DD-A73D 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DD-A73E         TCGA-DD-A73F         TCGA-DD-A73G 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-ED-A459         TCGA-ED-A4XI         TCGA-ED-A5KG 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-ED-A627         TCGA-ED-A66X         TCGA-ED-A66Y 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE"   "11P GAIN MUTATED" 
        TCGA-ED-A7PX         TCGA-ED-A7PY         TCGA-ED-A7PZ 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-ED-A7XP         TCGA-ED-A82E         TCGA-EP-A12J 
"11P GAIN WILD-TYPE"   "11P GAIN MUTATED" "11P GAIN WILD-TYPE" 
        TCGA-EP-A26S         TCGA-EP-A2KA         TCGA-EP-A2KB 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-EP-A2KC         TCGA-EP-A3JL         TCGA-EP-A3RK 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-ES-A2HS         TCGA-ES-A2HT         TCGA-FV-A23B 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-FV-A2QR         TCGA-FV-A3I0         TCGA-FV-A3I1 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-FV-A3R2         TCGA-FV-A3R3         TCGA-FV-A495 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-FV-A496         TCGA-FV-A4ZP         TCGA-FV-A4ZQ 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE"   "11P GAIN MUTATED" 
        TCGA-G3-A25S         TCGA-G3-A25T         TCGA-G3-A25U 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-G3-A25V         TCGA-G3-A25W         TCGA-G3-A25X 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-G3-A25Y         TCGA-G3-A25Z         TCGA-G3-A3CG 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE"   "11P GAIN MUTATED" 
        TCGA-G3-A3CH         TCGA-G3-A3CI         TCGA-G3-A3CJ 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-G3-A3CK         TCGA-G3-A5SI         TCGA-G3-A5SJ 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-G3-A5SL         TCGA-G3-A5SM         TCGA-G3-A6UC 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-GJ-A6C0         TCGA-K7-A6G5         TCGA-LG-A6GG 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE"   "11P GAIN MUTATED" 
        TCGA-MI-A75C         TCGA-MI-A75E         TCGA-MI-A75G 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-MI-A75I         TCGA-NI-A4U2         TCGA-O8-A75V 
"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-BC-A69H         TCGA-BC-A69I         TCGA-CC-5258 
  "11P GAIN MUTATED" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-CC-5260         TCGA-CC-5261         TCGA-CC-5262 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-CC-5263         TCGA-CC-A1HT         TCGA-CC-A3M9 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE"   "11P GAIN MUTATED" 
        TCGA-CC-A3MA         TCGA-CC-A3MB         TCGA-CC-A3MC 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DD-A113         TCGA-DD-A114         TCGA-DD-A115 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DD-A116         TCGA-DD-A118         TCGA-DD-A119 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE"   "11P GAIN MUTATED" 
        TCGA-DD-A11A         TCGA-DD-A11B         TCGA-DD-A11C 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DD-A11D         TCGA-DD-A1E9         TCGA-DD-A1EA 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DD-A1EB         TCGA-DD-A1EC         TCGA-DD-A1ED 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DD-A1EE         TCGA-DD-A1EF         TCGA-DD-A1EG 
"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-A1EK         TCGA-DD-A1EL         TCGA-DD-A39V 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DD-A39X         TCGA-DD-A39Y         TCGA-DD-A39Z 
"11P GAIN WILD-TYPE"   "11P GAIN MUTATED" "11P GAIN WILD-TYPE" 
        TCGA-DD-A3A0         TCGA-DD-A3A1         TCGA-DD-A3A2 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DD-A3A3         TCGA-DD-A3A4         TCGA-DD-A3A5 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DD-A3A6         TCGA-DD-A3A7         TCGA-DD-A3A8 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DD-A3A9         TCGA-DD-A4NA         TCGA-DD-A4NB 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DD-A4ND         TCGA-DD-A4NF         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-DD-A4NR 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DD-A4NS         TCGA-DD-A4NV         TCGA-DD-A73A 
"11P GAIN WILD-TYPE"   "11P GAIN MUTATED" "11P GAIN WILD-TYPE" 
        TCGA-DD-A73B         TCGA-DD-A73C         TCGA-DD-A73D 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DD-A73E         TCGA-DD-A73F         TCGA-DD-A73G 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-ED-A459         TCGA-ED-A4XI         TCGA-ED-A5KG 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-ED-A627         TCGA-ED-A66X         TCGA-ED-A66Y 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE"   "11P GAIN MUTATED" 
        TCGA-ED-A7PX         TCGA-ED-A7PY         TCGA-ED-A7PZ 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-ED-A7XP         TCGA-ED-A82E         TCGA-EP-A12J 
"11P GAIN WILD-TYPE"   "11P GAIN MUTATED" "11P GAIN WILD-TYPE" 
        TCGA-EP-A26S         TCGA-EP-A2KA         TCGA-EP-A2KB 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-EP-A2KC         TCGA-EP-A3JL         TCGA-EP-A3RK 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-ES-A2HS         TCGA-ES-A2HT         TCGA-FV-A23B 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-FV-A2QR         TCGA-FV-A3I0         TCGA-FV-A3I1 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-FV-A3R2         TCGA-FV-A3R3         TCGA-FV-A495 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-FV-A496         TCGA-FV-A4ZP         TCGA-FV-A4ZQ 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE"   "11P GAIN MUTATED" 
        TCGA-G3-A25S         TCGA-G3-A25T         TCGA-G3-A25U 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-G3-A25V         TCGA-G3-A25W         TCGA-G3-A25X 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-G3-A25Y         TCGA-G3-A25Z         TCGA-G3-A3CG 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE"   "11P GAIN MUTATED" 
        TCGA-G3-A3CH         TCGA-G3-A3CI         TCGA-G3-A3CJ 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-G3-A3CK         TCGA-G3-A5SI         TCGA-G3-A5SJ 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-G3-A5SL         TCGA-G3-A5SM         TCGA-G3-A6UC 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-GJ-A6C0         TCGA-K7-A6G5         TCGA-LG-A6GG 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE"   "11P GAIN MUTATED" 
        TCGA-MI-A75C         TCGA-MI-A75E         TCGA-MI-A75G 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-MI-A75I         TCGA-NI-A4U2         TCGA-O8-A75V 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
[1] "hr=" "1.1"
D21V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  11P GAIN MUTATED         3        2         0          4          0
  11P GAIN WILD-TYPE      55       34         2         26          4
                    vv
clus                 STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  11P GAIN MUTATED            0        1         0         0
  11P GAIN WILD-TYPE          5        0         1         2
D21V3, multiclass
                    vv
clus                 T1 T2 T3 T4
  11P GAIN MUTATED    3  2  5  0
  11P GAIN WILD-TYPE 58 38 35  8
D21V4, multiclass
    clus
vv   11P GAIN MUTATED 11P GAIN WILD-TYPE
  T1                3                 58
  T2                2                 38
  T3                5                 35
  T4                0                  8
D21V5, binary
                    cls
clus                  0  1
  11P GAIN MUTATED    6  0
  11P GAIN WILD-TYPE 91  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED      6    0
  11P GAIN WILD-TYPE   91    3
   clus
vv  11P GAIN MUTATED 11P GAIN WILD-TYPE
  0                6                 91
  1                0                  3
                    vv
clus                  M0  M1  MX
  11P GAIN MUTATED     9   1   0
  11P GAIN WILD-TYPE 106   2  31
D21V6, multiclass
    clus
vv   11P GAIN MUTATED 11P GAIN WILD-TYPE
  M0                9                106
  M1                1                  2
  MX                0                 31
D21V7, binary
                    cls
clus                  0  1
  11P GAIN MUTATED    3  7
  11P GAIN WILD-TYPE 55 84
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED      3    7
  11P GAIN WILD-TYPE   55   84
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  FEMALE                3                 55
  MALE                  7                 84
                    vv
clus                  R0  R1  R2  RX
  11P GAIN MUTATED     8   1   1   0
  11P GAIN WILD-TYPE 114  10   0  10
D21V8, multiclass
    clus
vv   11P GAIN MUTATED 11P GAIN WILD-TYPE
  R0                8                114
  R1                1                 10
  R2                1                  0
  RX                0                 10

Clustering(22) Variable = 11Q GAIN MUTATION ANALYSIS
D22V1, survival
                    sevent
clus2                 0  1
  11Q GAIN MUTATED    6  3
  11Q GAIN WILD-TYPE 78 60
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 9                138 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 3                 60 
$`11Q GAIN MUTATED`
TCGA-BC-A69I TCGA-DD-A119 TCGA-DD-A39Y TCGA-DD-A3A0 TCGA-DD-A4NV TCGA-ED-A66Y 
        0.53         7.33         5.62        25.81        66.35         0.23 
TCGA-ED-A82E TCGA-G3-A3CG TCGA-LG-A6GG 
        0.20        22.13         0.49 

$`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        13.84         0.26        22.36         9.50 
TCGA-BC-A69H TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 
        3.95         0.07         2.86         0.39         3.39         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-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A11A TCGA-DD-A11B 
       37.78        83.57        53.33       113.00         2.60         0.46 
TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC 
       21.76        51.29        90.71        79.40        66.31        19.79 
TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI 
       75.65         6.71        12.95        45.11        49.15         6.02 
TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39X TCGA-DD-A39Z 
       29.16        18.35        13.64        21.14        55.69        19.76 
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-A4NB TCGA-DD-A4ND 
       13.78         0.36        30.61        33.14        12.85        73.38 
TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL 
       14.07        14.24        18.44        15.06        39.78        56.25 
TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS 
       29.56        61.45        93.67        12.26         0.30        80.75 
TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F 
       10.98         9.30         7.56        10.98         1.45        27.72 
TCGA-DD-A73G TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X 
      100.96        13.41        12.69        15.85        13.91        13.35 
TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XP TCGA-EP-A12J TCGA-EP-A26S 
        0.20         0.20         0.20         0.20        18.74        19.99 
TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS 
       11.74        10.98         0.62         9.96        11.93        22.85 
TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R2 
       14.40        32.45        19.10         0.20         8.12         6.38 
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 
       51.06        53.79        28.27        30.74        58.49        14.86 
TCGA-G3-A25Z TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI 
       21.53        25.64         5.92        19.53        19.23        14.70 
TCGA-G3-A5SJ TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A6UC TCGA-GJ-A6C0 TCGA-K7-A6G5 
       11.97         7.99         4.37         7.76         1.02         4.01 
TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75I TCGA-NI-A4U2 TCGA-O8-A75V 
        9.57         5.10        14.24         8.71        58.88         4.44 

  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
              0.20               0.03 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
             66.35             113.00 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
              5.62              14.24 
[1] "0.2 - 66.3 (5.6)"   "0.0 - 113.0 (14.2)"
        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-BC-A69H         TCGA-BC-A69I         TCGA-CC-5258 
"11Q GAIN WILD-TYPE"   "11Q GAIN MUTATED" "11Q GAIN WILD-TYPE" 
        TCGA-CC-5260         TCGA-CC-5261         TCGA-CC-5262 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-CC-5263         TCGA-CC-A1HT         TCGA-CC-A3M9 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-CC-A3MA         TCGA-CC-A3MB         TCGA-CC-A3MC 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DD-A113         TCGA-DD-A114         TCGA-DD-A115 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DD-A116         TCGA-DD-A118         TCGA-DD-A119 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE"   "11Q GAIN MUTATED" 
        TCGA-DD-A11A         TCGA-DD-A11B         TCGA-DD-A11C 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DD-A11D         TCGA-DD-A1E9         TCGA-DD-A1EA 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DD-A1EB         TCGA-DD-A1EC         TCGA-DD-A1ED 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DD-A1EE         TCGA-DD-A1EF         TCGA-DD-A1EG 
"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-A1EK         TCGA-DD-A1EL         TCGA-DD-A39V 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DD-A39X         TCGA-DD-A39Y         TCGA-DD-A39Z 
"11Q GAIN WILD-TYPE"   "11Q GAIN MUTATED" "11Q GAIN WILD-TYPE" 
        TCGA-DD-A3A0         TCGA-DD-A3A1         TCGA-DD-A3A2 
  "11Q GAIN MUTATED" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DD-A3A3         TCGA-DD-A3A4         TCGA-DD-A3A5 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DD-A3A6         TCGA-DD-A3A7         TCGA-DD-A3A8 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DD-A3A9         TCGA-DD-A4NA         TCGA-DD-A4NB 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DD-A4ND         TCGA-DD-A4NF         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-DD-A4NR 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DD-A4NS         TCGA-DD-A4NV         TCGA-DD-A73A 
"11Q GAIN WILD-TYPE"   "11Q GAIN MUTATED" "11Q GAIN WILD-TYPE" 
        TCGA-DD-A73B         TCGA-DD-A73C         TCGA-DD-A73D 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DD-A73E         TCGA-DD-A73F         TCGA-DD-A73G 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-ED-A459         TCGA-ED-A4XI         TCGA-ED-A5KG 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-ED-A627         TCGA-ED-A66X         TCGA-ED-A66Y 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE"   "11Q GAIN MUTATED" 
        TCGA-ED-A7PX         TCGA-ED-A7PY         TCGA-ED-A7PZ 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-ED-A7XP         TCGA-ED-A82E         TCGA-EP-A12J 
"11Q GAIN WILD-TYPE"   "11Q GAIN MUTATED" "11Q GAIN WILD-TYPE" 
        TCGA-EP-A26S         TCGA-EP-A2KA         TCGA-EP-A2KB 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EP-A2KC         TCGA-EP-A3JL         TCGA-EP-A3RK 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-ES-A2HS         TCGA-ES-A2HT         TCGA-FV-A23B 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-FV-A2QR         TCGA-FV-A3I0         TCGA-FV-A3I1 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-FV-A3R2         TCGA-FV-A3R3         TCGA-FV-A495 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-FV-A496         TCGA-FV-A4ZP         TCGA-FV-A4ZQ 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-G3-A25S         TCGA-G3-A25T         TCGA-G3-A25U 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-G3-A25V         TCGA-G3-A25W         TCGA-G3-A25X 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-G3-A25Y         TCGA-G3-A25Z         TCGA-G3-A3CG 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE"   "11Q GAIN MUTATED" 
        TCGA-G3-A3CH         TCGA-G3-A3CI         TCGA-G3-A3CJ 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-G3-A3CK         TCGA-G3-A5SI         TCGA-G3-A5SJ 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-G3-A5SL         TCGA-G3-A5SM         TCGA-G3-A6UC 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-GJ-A6C0         TCGA-K7-A6G5         TCGA-LG-A6GG 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE"   "11Q GAIN MUTATED" 
        TCGA-MI-A75C         TCGA-MI-A75E         TCGA-MI-A75G 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-MI-A75I         TCGA-NI-A4U2         TCGA-O8-A75V 
"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-BC-A69H         TCGA-BC-A69I         TCGA-CC-5258 
"11Q GAIN WILD-TYPE"   "11Q GAIN MUTATED" "11Q GAIN WILD-TYPE" 
        TCGA-CC-5260         TCGA-CC-5261         TCGA-CC-5262 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-CC-5263         TCGA-CC-A1HT         TCGA-CC-A3M9 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-CC-A3MA         TCGA-CC-A3MB         TCGA-CC-A3MC 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DD-A113         TCGA-DD-A114         TCGA-DD-A115 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DD-A116         TCGA-DD-A118         TCGA-DD-A119 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE"   "11Q GAIN MUTATED" 
        TCGA-DD-A11A         TCGA-DD-A11B         TCGA-DD-A11C 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DD-A11D         TCGA-DD-A1E9         TCGA-DD-A1EA 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DD-A1EB         TCGA-DD-A1EC         TCGA-DD-A1ED 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DD-A1EE         TCGA-DD-A1EF         TCGA-DD-A1EG 
"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-A1EK         TCGA-DD-A1EL         TCGA-DD-A39V 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DD-A39X         TCGA-DD-A39Y         TCGA-DD-A39Z 
"11Q GAIN WILD-TYPE"   "11Q GAIN MUTATED" "11Q GAIN WILD-TYPE" 
        TCGA-DD-A3A0         TCGA-DD-A3A1         TCGA-DD-A3A2 
  "11Q GAIN MUTATED" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DD-A3A3         TCGA-DD-A3A4         TCGA-DD-A3A5 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DD-A3A6         TCGA-DD-A3A7         TCGA-DD-A3A8 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DD-A3A9         TCGA-DD-A4NA         TCGA-DD-A4NB 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DD-A4ND         TCGA-DD-A4NF         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-DD-A4NR 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DD-A4NS         TCGA-DD-A4NV         TCGA-DD-A73A 
"11Q GAIN WILD-TYPE"   "11Q GAIN MUTATED" "11Q GAIN WILD-TYPE" 
        TCGA-DD-A73B         TCGA-DD-A73C         TCGA-DD-A73D 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DD-A73E         TCGA-DD-A73F         TCGA-DD-A73G 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-ED-A459         TCGA-ED-A4XI         TCGA-ED-A5KG 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-ED-A627         TCGA-ED-A66X         TCGA-ED-A66Y 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE"   "11Q GAIN MUTATED" 
        TCGA-ED-A7PX         TCGA-ED-A7PY         TCGA-ED-A7PZ 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-ED-A7XP         TCGA-ED-A82E         TCGA-EP-A12J 
"11Q GAIN WILD-TYPE"   "11Q GAIN MUTATED" "11Q GAIN WILD-TYPE" 
        TCGA-EP-A26S         TCGA-EP-A2KA         TCGA-EP-A2KB 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EP-A2KC         TCGA-EP-A3JL         TCGA-EP-A3RK 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-ES-A2HS         TCGA-ES-A2HT         TCGA-FV-A23B 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-FV-A2QR         TCGA-FV-A3I0         TCGA-FV-A3I1 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-FV-A3R2         TCGA-FV-A3R3         TCGA-FV-A495 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-FV-A496         TCGA-FV-A4ZP         TCGA-FV-A4ZQ 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-G3-A25S         TCGA-G3-A25T         TCGA-G3-A25U 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-G3-A25V         TCGA-G3-A25W         TCGA-G3-A25X 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-G3-A25Y         TCGA-G3-A25Z         TCGA-G3-A3CG 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE"   "11Q GAIN MUTATED" 
        TCGA-G3-A3CH         TCGA-G3-A3CI         TCGA-G3-A3CJ 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-G3-A3CK         TCGA-G3-A5SI         TCGA-G3-A5SJ 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-G3-A5SL         TCGA-G3-A5SM         TCGA-G3-A6UC 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-GJ-A6C0         TCGA-K7-A6G5         TCGA-LG-A6GG 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE"   "11Q GAIN MUTATED" 
        TCGA-MI-A75C         TCGA-MI-A75E         TCGA-MI-A75G 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-MI-A75I         TCGA-NI-A4U2         TCGA-O8-A75V 
"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-BC-A69H         TCGA-BC-A69I         TCGA-CC-5258 
"11Q GAIN WILD-TYPE"   "11Q GAIN MUTATED" "11Q GAIN WILD-TYPE" 
        TCGA-CC-5260         TCGA-CC-5261         TCGA-CC-5262 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-CC-5263         TCGA-CC-A1HT         TCGA-CC-A3M9 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-CC-A3MA         TCGA-CC-A3MB         TCGA-CC-A3MC 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DD-A113         TCGA-DD-A114         TCGA-DD-A115 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DD-A116         TCGA-DD-A118         TCGA-DD-A119 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE"   "11Q GAIN MUTATED" 
        TCGA-DD-A11A         TCGA-DD-A11B         TCGA-DD-A11C 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DD-A11D         TCGA-DD-A1E9         TCGA-DD-A1EA 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DD-A1EB         TCGA-DD-A1EC         TCGA-DD-A1ED 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DD-A1EE         TCGA-DD-A1EF         TCGA-DD-A1EG 
"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-A1EK         TCGA-DD-A1EL         TCGA-DD-A39V 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DD-A39X         TCGA-DD-A39Y         TCGA-DD-A39Z 
"11Q GAIN WILD-TYPE"   "11Q GAIN MUTATED" "11Q GAIN WILD-TYPE" 
        TCGA-DD-A3A0         TCGA-DD-A3A1         TCGA-DD-A3A2 
  "11Q GAIN MUTATED" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DD-A3A3         TCGA-DD-A3A4         TCGA-DD-A3A5 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DD-A3A6         TCGA-DD-A3A7         TCGA-DD-A3A8 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DD-A3A9         TCGA-DD-A4NA         TCGA-DD-A4NB 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DD-A4ND         TCGA-DD-A4NF         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-DD-A4NR 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DD-A4NS         TCGA-DD-A4NV         TCGA-DD-A73A 
"11Q GAIN WILD-TYPE"   "11Q GAIN MUTATED" "11Q GAIN WILD-TYPE" 
        TCGA-DD-A73B         TCGA-DD-A73C         TCGA-DD-A73D 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DD-A73E         TCGA-DD-A73F         TCGA-DD-A73G 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-ED-A459         TCGA-ED-A4XI         TCGA-ED-A5KG 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-ED-A627         TCGA-ED-A66X         TCGA-ED-A66Y 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE"   "11Q GAIN MUTATED" 
        TCGA-ED-A7PX         TCGA-ED-A7PY         TCGA-ED-A7PZ 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-ED-A7XP         TCGA-ED-A82E         TCGA-EP-A12J 
"11Q GAIN WILD-TYPE"   "11Q GAIN MUTATED" "11Q GAIN WILD-TYPE" 
        TCGA-EP-A26S         TCGA-EP-A2KA         TCGA-EP-A2KB 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EP-A2KC         TCGA-EP-A3JL         TCGA-EP-A3RK 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-ES-A2HS         TCGA-ES-A2HT         TCGA-FV-A23B 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-FV-A2QR         TCGA-FV-A3I0         TCGA-FV-A3I1 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-FV-A3R2         TCGA-FV-A3R3         TCGA-FV-A495 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-FV-A496         TCGA-FV-A4ZP         TCGA-FV-A4ZQ 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-G3-A25S         TCGA-G3-A25T         TCGA-G3-A25U 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-G3-A25V         TCGA-G3-A25W         TCGA-G3-A25X 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-G3-A25Y         TCGA-G3-A25Z         TCGA-G3-A3CG 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE"   "11Q GAIN MUTATED" 
        TCGA-G3-A3CH         TCGA-G3-A3CI         TCGA-G3-A3CJ 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-G3-A3CK         TCGA-G3-A5SI         TCGA-G3-A5SJ 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-G3-A5SL         TCGA-G3-A5SM         TCGA-G3-A6UC 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-GJ-A6C0         TCGA-K7-A6G5         TCGA-LG-A6GG 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE"   "11Q GAIN MUTATED" 
        TCGA-MI-A75C         TCGA-MI-A75E         TCGA-MI-A75G 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-MI-A75I         TCGA-NI-A4U2         TCGA-O8-A75V 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
[1] "hr=" "1.4"
D22V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  11Q GAIN MUTATED         4        1         0          3          0
  11Q GAIN WILD-TYPE      54       35         2         27          4
                    vv
clus                 STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  11Q GAIN MUTATED            0        1         0         0
  11Q GAIN WILD-TYPE          5        0         1         2
D22V3, multiclass
                    vv
clus                 T1 T2 T3 T4
  11Q GAIN MUTATED    4  1  4  0
  11Q GAIN WILD-TYPE 57 39 36  8
D22V4, multiclass
    clus
vv   11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  T1                4                 57
  T2                1                 39
  T3                4                 36
  T4                0                  8
D22V5, binary
                    cls
clus                  0  1
  11Q GAIN MUTATED    6  0
  11Q GAIN WILD-TYPE 91  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED      6    0
  11Q GAIN WILD-TYPE   91    3
   clus
vv  11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  0                6                 91
  1                0                  3
                    vv
clus                  M0  M1  MX
  11Q GAIN MUTATED     8   1   0
  11Q GAIN WILD-TYPE 107   2  31
D22V6, multiclass
    clus
vv   11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  M0                8                107
  M1                1                  2
  MX                0                 31
D22V7, binary
                    cls
clus                  0  1
  11Q GAIN MUTATED    3  6
  11Q GAIN WILD-TYPE 55 85
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED      3    6
  11Q GAIN WILD-TYPE   55   85
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  FEMALE                3                 55
  MALE                  6                 85
                    vv
clus                  R0  R1  R2  RX
  11Q GAIN MUTATED     7   1   1   0
  11Q GAIN WILD-TYPE 115  10   0  10
D22V8, multiclass
    clus
vv   11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  R0                7                115
  R1                1                 10
  R2                1                  0
  RX                0                 10

Clustering(23) Variable = 12P GAIN MUTATION ANALYSIS
D23V1, survival
                    sevent
clus2                 0  1
  12P GAIN MUTATED   10  3
  12P GAIN WILD-TYPE 74 60
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                13                134 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                 3                 60 
$`12P GAIN MUTATED`
TCGA-DD-A11A TCGA-DD-A1EF TCGA-DD-A3A7 TCGA-DD-A4NR TCGA-DD-A73G TCGA-ED-A66Y 
        2.60        12.95        13.78         0.30       100.96         0.23 
TCGA-ED-A7PX TCGA-ED-A7PZ TCGA-ED-A82E TCGA-EP-A3JL TCGA-FV-A3I0 TCGA-G3-A25T 
        0.20         0.20         0.20         9.96         0.20        51.06 
TCGA-MI-A75C 
        9.57 

$`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        13.84         0.26        22.36         9.50 
TCGA-BC-A69H TCGA-BC-A69I TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 
        3.95         0.53         0.07         2.86         0.39         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        37.78        83.57        53.33       113.00         7.33 
TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB 
        0.46        21.76        51.29        90.71        79.40        66.31 
TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI 
       19.79        75.65         6.71        45.11        49.15         6.02 
TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39X TCGA-DD-A39Y 
       29.16        18.35        13.64        21.14        55.69         5.62 
TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 
       19.76        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-A4NB 
      102.74       107.11         0.36        30.61        33.14        12.85 
TCGA-DD-A4ND TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK 
       73.38        14.07        14.24        18.44        15.06        39.78 
TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NS 
       56.25        29.56        61.45        93.67        12.26        80.75 
TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E 
       66.35        10.98         9.30         7.56        10.98         1.45 
TCGA-DD-A73F TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X 
       27.72        13.41        12.69        15.85        13.91        13.35 
TCGA-ED-A7PY TCGA-ED-A7XP TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB 
        0.20         0.20        18.74        19.99        11.74        10.98 
TCGA-EP-A2KC TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QR 
        0.62        11.93        22.85        14.40        32.45        19.10 
TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZP 
        8.12         6.38         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-A25X 
        0.39         1.22        53.79        28.27        30.74        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         5.92        19.53 
TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A6UC 
       19.23        14.70        11.97         7.99         4.37         7.76 
TCGA-GJ-A6C0 TCGA-K7-A6G5 TCGA-LG-A6GG TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75I 
        1.02         4.01         0.49         5.10        14.24         8.71 
TCGA-NI-A4U2 TCGA-O8-A75V 
       58.88         4.44 

  12P GAIN MUTATED 12P GAIN WILD-TYPE 
              0.20               0.03 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
            100.96             113.00 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
              2.60              14.78 
[1] "0.2 - 101.0 (2.6)"  "0.0 - 113.0 (14.8)"
        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-BC-A69H         TCGA-BC-A69I         TCGA-CC-5258 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-CC-5260         TCGA-CC-5261         TCGA-CC-5262 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-CC-5263         TCGA-CC-A1HT         TCGA-CC-A3M9 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-CC-A3MA         TCGA-CC-A3MB         TCGA-CC-A3MC 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-DD-A113         TCGA-DD-A114         TCGA-DD-A115 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-DD-A116         TCGA-DD-A118         TCGA-DD-A119 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-DD-A11A         TCGA-DD-A11B         TCGA-DD-A11C 
  "12P GAIN MUTATED" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-DD-A11D         TCGA-DD-A1E9         TCGA-DD-A1EA 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-DD-A1EB         TCGA-DD-A1EC         TCGA-DD-A1ED 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-DD-A1EE         TCGA-DD-A1EF         TCGA-DD-A1EG 
"12P GAIN WILD-TYPE"   "12P GAIN MUTATED" "12P GAIN WILD-TYPE" 
        TCGA-DD-A1EH         TCGA-DD-A1EI         TCGA-DD-A1EJ 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-DD-A1EK         TCGA-DD-A1EL         TCGA-DD-A39V 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-DD-A39X         TCGA-DD-A39Y         TCGA-DD-A39Z 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-DD-A3A0         TCGA-DD-A3A1         TCGA-DD-A3A2 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-DD-A3A3         TCGA-DD-A3A4         TCGA-DD-A3A5 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-DD-A3A6         TCGA-DD-A3A7         TCGA-DD-A3A8 
"12P GAIN WILD-TYPE"   "12P GAIN MUTATED" "12P GAIN WILD-TYPE" 
        TCGA-DD-A3A9         TCGA-DD-A4NA         TCGA-DD-A4NB 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-DD-A4ND         TCGA-DD-A4NF         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-DD-A4NR 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE"   "12P GAIN MUTATED" 
        TCGA-DD-A4NS         TCGA-DD-A4NV         TCGA-DD-A73A 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-DD-A73B         TCGA-DD-A73C         TCGA-DD-A73D 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-DD-A73E         TCGA-DD-A73F         TCGA-DD-A73G 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE"   "12P GAIN MUTATED" 
        TCGA-ED-A459         TCGA-ED-A4XI         TCGA-ED-A5KG 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-ED-A627         TCGA-ED-A66X         TCGA-ED-A66Y 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE"   "12P GAIN MUTATED" 
        TCGA-ED-A7PX         TCGA-ED-A7PY         TCGA-ED-A7PZ 
  "12P GAIN MUTATED" "12P GAIN WILD-TYPE"   "12P GAIN MUTATED" 
        TCGA-ED-A7XP         TCGA-ED-A82E         TCGA-EP-A12J 
"12P GAIN WILD-TYPE"   "12P GAIN MUTATED" "12P GAIN WILD-TYPE" 
        TCGA-EP-A26S         TCGA-EP-A2KA         TCGA-EP-A2KB 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-EP-A2KC         TCGA-EP-A3JL         TCGA-EP-A3RK 
"12P GAIN WILD-TYPE"   "12P GAIN MUTATED" "12P GAIN WILD-TYPE" 
        TCGA-ES-A2HS         TCGA-ES-A2HT         TCGA-FV-A23B 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-FV-A2QR         TCGA-FV-A3I0         TCGA-FV-A3I1 
"12P GAIN WILD-TYPE"   "12P GAIN MUTATED" "12P GAIN WILD-TYPE" 
        TCGA-FV-A3R2         TCGA-FV-A3R3         TCGA-FV-A495 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-FV-A496         TCGA-FV-A4ZP         TCGA-FV-A4ZQ 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-G3-A25S         TCGA-G3-A25T         TCGA-G3-A25U 
"12P GAIN WILD-TYPE"   "12P GAIN MUTATED" "12P GAIN WILD-TYPE" 
        TCGA-G3-A25V         TCGA-G3-A25W         TCGA-G3-A25X 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-G3-A25Y         TCGA-G3-A25Z         TCGA-G3-A3CG 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-G3-A3CH         TCGA-G3-A3CI         TCGA-G3-A3CJ 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-G3-A3CK         TCGA-G3-A5SI         TCGA-G3-A5SJ 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-G3-A5SL         TCGA-G3-A5SM         TCGA-G3-A6UC 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-GJ-A6C0         TCGA-K7-A6G5         TCGA-LG-A6GG 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-MI-A75C         TCGA-MI-A75E         TCGA-MI-A75G 
  "12P GAIN MUTATED" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-MI-A75I         TCGA-NI-A4U2         TCGA-O8-A75V 
"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-BC-A69H         TCGA-BC-A69I         TCGA-CC-5258 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-CC-5260         TCGA-CC-5261         TCGA-CC-5262 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-CC-5263         TCGA-CC-A1HT         TCGA-CC-A3M9 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-CC-A3MA         TCGA-CC-A3MB         TCGA-CC-A3MC 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-DD-A113         TCGA-DD-A114         TCGA-DD-A115 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-DD-A116         TCGA-DD-A118         TCGA-DD-A119 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-DD-A11A         TCGA-DD-A11B         TCGA-DD-A11C 
  "12P GAIN MUTATED" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-DD-A11D         TCGA-DD-A1E9         TCGA-DD-A1EA 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-DD-A1EB         TCGA-DD-A1EC         TCGA-DD-A1ED 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-DD-A1EE         TCGA-DD-A1EF         TCGA-DD-A1EG 
"12P GAIN WILD-TYPE"   "12P GAIN MUTATED" "12P GAIN WILD-TYPE" 
        TCGA-DD-A1EH         TCGA-DD-A1EI         TCGA-DD-A1EJ 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-DD-A1EK         TCGA-DD-A1EL         TCGA-DD-A39V 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-DD-A39X         TCGA-DD-A39Y         TCGA-DD-A39Z 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-DD-A3A0         TCGA-DD-A3A1         TCGA-DD-A3A2 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-DD-A3A3         TCGA-DD-A3A4         TCGA-DD-A3A5 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-DD-A3A6         TCGA-DD-A3A7         TCGA-DD-A3A8 
"12P GAIN WILD-TYPE"   "12P GAIN MUTATED" "12P GAIN WILD-TYPE" 
        TCGA-DD-A3A9         TCGA-DD-A4NA         TCGA-DD-A4NB 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-DD-A4ND         TCGA-DD-A4NF         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-DD-A4NR 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE"   "12P GAIN MUTATED" 
        TCGA-DD-A4NS         TCGA-DD-A4NV         TCGA-DD-A73A 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-DD-A73B         TCGA-DD-A73C         TCGA-DD-A73D 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-DD-A73E         TCGA-DD-A73F         TCGA-DD-A73G 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE"   "12P GAIN MUTATED" 
        TCGA-ED-A459         TCGA-ED-A4XI         TCGA-ED-A5KG 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-ED-A627         TCGA-ED-A66X         TCGA-ED-A66Y 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE"   "12P GAIN MUTATED" 
        TCGA-ED-A7PX         TCGA-ED-A7PY         TCGA-ED-A7PZ 
  "12P GAIN MUTATED" "12P GAIN WILD-TYPE"   "12P GAIN MUTATED" 
        TCGA-ED-A7XP         TCGA-ED-A82E         TCGA-EP-A12J 
"12P GAIN WILD-TYPE"   "12P GAIN MUTATED" "12P GAIN WILD-TYPE" 
        TCGA-EP-A26S         TCGA-EP-A2KA         TCGA-EP-A2KB 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-EP-A2KC         TCGA-EP-A3JL         TCGA-EP-A3RK 
"12P GAIN WILD-TYPE"   "12P GAIN MUTATED" "12P GAIN WILD-TYPE" 
        TCGA-ES-A2HS         TCGA-ES-A2HT         TCGA-FV-A23B 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-FV-A2QR         TCGA-FV-A3I0         TCGA-FV-A3I1 
"12P GAIN WILD-TYPE"   "12P GAIN MUTATED" "12P GAIN WILD-TYPE" 
        TCGA-FV-A3R2         TCGA-FV-A3R3         TCGA-FV-A495 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-FV-A496         TCGA-FV-A4ZP         TCGA-FV-A4ZQ 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-G3-A25S         TCGA-G3-A25T         TCGA-G3-A25U 
"12P GAIN WILD-TYPE"   "12P GAIN MUTATED" "12P GAIN WILD-TYPE" 
        TCGA-G3-A25V         TCGA-G3-A25W         TCGA-G3-A25X 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-G3-A25Y         TCGA-G3-A25Z         TCGA-G3-A3CG 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-G3-A3CH         TCGA-G3-A3CI         TCGA-G3-A3CJ 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-G3-A3CK         TCGA-G3-A5SI         TCGA-G3-A5SJ 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-G3-A5SL         TCGA-G3-A5SM         TCGA-G3-A6UC 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-GJ-A6C0         TCGA-K7-A6G5         TCGA-LG-A6GG 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-MI-A75C         TCGA-MI-A75E         TCGA-MI-A75G 
  "12P GAIN MUTATED" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-MI-A75I         TCGA-NI-A4U2         TCGA-O8-A75V 
"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-BC-A69H         TCGA-BC-A69I         TCGA-CC-5258 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-CC-5260         TCGA-CC-5261         TCGA-CC-5262 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-CC-5263         TCGA-CC-A1HT         TCGA-CC-A3M9 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-CC-A3MA         TCGA-CC-A3MB         TCGA-CC-A3MC 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-DD-A113         TCGA-DD-A114         TCGA-DD-A115 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-DD-A116         TCGA-DD-A118         TCGA-DD-A119 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-DD-A11A         TCGA-DD-A11B         TCGA-DD-A11C 
  "12P GAIN MUTATED" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-DD-A11D         TCGA-DD-A1E9         TCGA-DD-A1EA 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-DD-A1EB         TCGA-DD-A1EC         TCGA-DD-A1ED 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-DD-A1EE         TCGA-DD-A1EF         TCGA-DD-A1EG 
"12P GAIN WILD-TYPE"   "12P GAIN MUTATED" "12P GAIN WILD-TYPE" 
        TCGA-DD-A1EH         TCGA-DD-A1EI         TCGA-DD-A1EJ 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-DD-A1EK         TCGA-DD-A1EL         TCGA-DD-A39V 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-DD-A39X         TCGA-DD-A39Y         TCGA-DD-A39Z 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-DD-A3A0         TCGA-DD-A3A1         TCGA-DD-A3A2 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-DD-A3A3         TCGA-DD-A3A4         TCGA-DD-A3A5 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-DD-A3A6         TCGA-DD-A3A7         TCGA-DD-A3A8 
"12P GAIN WILD-TYPE"   "12P GAIN MUTATED" "12P GAIN WILD-TYPE" 
        TCGA-DD-A3A9         TCGA-DD-A4NA         TCGA-DD-A4NB 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-DD-A4ND         TCGA-DD-A4NF         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-DD-A4NR 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE"   "12P GAIN MUTATED" 
        TCGA-DD-A4NS         TCGA-DD-A4NV         TCGA-DD-A73A 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-DD-A73B         TCGA-DD-A73C         TCGA-DD-A73D 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-DD-A73E         TCGA-DD-A73F         TCGA-DD-A73G 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE"   "12P GAIN MUTATED" 
        TCGA-ED-A459         TCGA-ED-A4XI         TCGA-ED-A5KG 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-ED-A627         TCGA-ED-A66X         TCGA-ED-A66Y 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE"   "12P GAIN MUTATED" 
        TCGA-ED-A7PX         TCGA-ED-A7PY         TCGA-ED-A7PZ 
  "12P GAIN MUTATED" "12P GAIN WILD-TYPE"   "12P GAIN MUTATED" 
        TCGA-ED-A7XP         TCGA-ED-A82E         TCGA-EP-A12J 
"12P GAIN WILD-TYPE"   "12P GAIN MUTATED" "12P GAIN WILD-TYPE" 
        TCGA-EP-A26S         TCGA-EP-A2KA         TCGA-EP-A2KB 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-EP-A2KC         TCGA-EP-A3JL         TCGA-EP-A3RK 
"12P GAIN WILD-TYPE"   "12P GAIN MUTATED" "12P GAIN WILD-TYPE" 
        TCGA-ES-A2HS         TCGA-ES-A2HT         TCGA-FV-A23B 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-FV-A2QR         TCGA-FV-A3I0         TCGA-FV-A3I1 
"12P GAIN WILD-TYPE"   "12P GAIN MUTATED" "12P GAIN WILD-TYPE" 
        TCGA-FV-A3R2         TCGA-FV-A3R3         TCGA-FV-A495 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-FV-A496         TCGA-FV-A4ZP         TCGA-FV-A4ZQ 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-G3-A25S         TCGA-G3-A25T         TCGA-G3-A25U 
"12P GAIN WILD-TYPE"   "12P GAIN MUTATED" "12P GAIN WILD-TYPE" 
        TCGA-G3-A25V         TCGA-G3-A25W         TCGA-G3-A25X 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-G3-A25Y         TCGA-G3-A25Z         TCGA-G3-A3CG 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-G3-A3CH         TCGA-G3-A3CI         TCGA-G3-A3CJ 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-G3-A3CK         TCGA-G3-A5SI         TCGA-G3-A5SJ 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-G3-A5SL         TCGA-G3-A5SM         TCGA-G3-A6UC 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-GJ-A6C0         TCGA-K7-A6G5         TCGA-LG-A6GG 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-MI-A75C         TCGA-MI-A75E         TCGA-MI-A75G 
  "12P GAIN MUTATED" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-MI-A75I         TCGA-NI-A4U2         TCGA-O8-A75V 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
[1] "hr=" "1.1"
D23V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  12P GAIN MUTATED         6        3         0          4          1
  12P GAIN WILD-TYPE      52       33         2         26          3
                    vv
clus                 STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  12P GAIN MUTATED            0        0         0         0
  12P GAIN WILD-TYPE          5        1         1         2
D23V3, multiclass
                    vv
clus                 T1 T2 T3 T4
  12P GAIN MUTATED    6  3  5  0
  12P GAIN WILD-TYPE 55 37 35  8
D23V4, multiclass
    clus
vv   12P GAIN MUTATED 12P GAIN WILD-TYPE
  T1                6                 55
  T2                3                 37
  T3                5                 35
  T4                0                  8
D23V5, binary
                    cls
clus                  0  1
  12P GAIN MUTATED   10  0
  12P GAIN WILD-TYPE 87  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED     10    0
  12P GAIN WILD-TYPE   87    3
   clus
vv  12P GAIN MUTATED 12P GAIN WILD-TYPE
  0               10                 87
  1                0                  3
                    vv
clus                  M0  M1  MX
  12P GAIN MUTATED    13   0   1
  12P GAIN WILD-TYPE 102   3  30
D23V6, multiclass
    clus
vv   12P GAIN MUTATED 12P GAIN WILD-TYPE
  M0               13                102
  M1                0                  3
  MX                1                 30
D23V7, binary
                    cls
clus                  0  1
  12P GAIN MUTATED    8  6
  12P GAIN WILD-TYPE 50 85
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED      8    6
  12P GAIN WILD-TYPE   50   85
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  FEMALE                8                 50
  MALE                  6                 85
                    vv
clus                  R0  R1  R2  RX
  12P GAIN MUTATED    12   0   0   1
  12P GAIN WILD-TYPE 110  11   1   9
D23V8, multiclass
    clus
vv   12P GAIN MUTATED 12P GAIN WILD-TYPE
  R0               12                110
  R1                0                 11
  R2                0                  1
  RX                1                  9

Clustering(24) Variable = 12Q GAIN MUTATION ANALYSIS
D24V1, survival
                    sevent
clus2                 0  1
  12Q GAIN MUTATED   13  4
  12Q GAIN WILD-TYPE 71 59
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                17                130 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                 4                 59 
$`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-DD-A4NR TCGA-DD-A73G TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PZ 
       14.24         0.30       100.96         0.23         0.20         0.20 
TCGA-ED-A82E TCGA-EP-A3JL TCGA-FV-A3I0 TCGA-G3-A25T TCGA-MI-A75C 
        0.20         9.96         0.20        51.06         9.57 

$`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-BC-A69H 
        5.03        44.42        13.84        22.36         9.50         3.95 
TCGA-BC-A69I TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 
        0.53         0.07         2.86         0.39         3.39         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-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11B 
       37.78        83.57        53.33       113.00         7.33         0.46 
TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC 
       21.76        51.29        90.71        79.40        66.31        19.79 
TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EK 
       75.65         6.71        45.11        49.15         6.02        18.35 
TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A0 
       13.64        21.14        55.69         5.62        19.76        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-A4NB TCGA-DD-A4NF TCGA-DD-A4NI 
        0.36        30.61        33.14        12.85        14.07        18.44 
TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP 
       15.06        39.78        56.25        29.56        61.45        93.67 
TCGA-DD-A4NQ TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C 
       12.26        80.75        66.35        10.98         9.30         7.56 
TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG 
       10.98         1.45        27.72        13.41        12.69        15.85 
TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A7PY TCGA-ED-A7XP TCGA-EP-A12J TCGA-EP-A26S 
       13.91        13.35         0.20         0.20        18.74        19.99 
TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT 
       11.74        10.98         0.62        11.93        22.85        14.40 
TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 
       32.45        19.10         8.12         6.38         0.13         0.03 
TCGA-FV-A496 TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25U TCGA-G3-A25V 
        0.33        60.36         0.39         1.22        53.79        28.27 
TCGA-G3-A25W TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CH 
       30.74        58.49        14.86        21.53        22.13        25.64 
TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SL 
        5.92        19.53        19.23        14.70        11.97         7.99 
TCGA-G3-A5SM TCGA-G3-A6UC TCGA-GJ-A6C0 TCGA-K7-A6G5 TCGA-LG-A6GG TCGA-MI-A75E 
        4.37         7.76         1.02         4.01         0.49         5.10 
TCGA-MI-A75G TCGA-MI-A75I TCGA-NI-A4U2 TCGA-O8-A75V 
       14.24         8.71        58.88         4.44 

  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
              0.20               0.03 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
            100.96             113.00 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
              9.57              14.78 
[1] "0.2 - 101.0 (9.6)"  "0.0 - 113.0 (14.8)"
        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-BC-A69H         TCGA-BC-A69I         TCGA-CC-5258 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-CC-5260         TCGA-CC-5261         TCGA-CC-5262 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-CC-5263         TCGA-CC-A1HT         TCGA-CC-A3M9 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-CC-A3MA         TCGA-CC-A3MB         TCGA-CC-A3MC 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DD-A113         TCGA-DD-A114         TCGA-DD-A115 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DD-A116         TCGA-DD-A118         TCGA-DD-A119 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DD-A11A         TCGA-DD-A11B         TCGA-DD-A11C 
  "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DD-A11D         TCGA-DD-A1E9         TCGA-DD-A1EA 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DD-A1EB         TCGA-DD-A1EC         TCGA-DD-A1ED 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DD-A1EE         TCGA-DD-A1EF         TCGA-DD-A1EG 
"12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" 
        TCGA-DD-A1EH         TCGA-DD-A1EI         TCGA-DD-A1EJ 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" 
        TCGA-DD-A1EK         TCGA-DD-A1EL         TCGA-DD-A39V 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DD-A39X         TCGA-DD-A39Y         TCGA-DD-A39Z 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DD-A3A0         TCGA-DD-A3A1         TCGA-DD-A3A2 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DD-A3A3         TCGA-DD-A3A4         TCGA-DD-A3A5 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DD-A3A6         TCGA-DD-A3A7         TCGA-DD-A3A8 
"12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" 
        TCGA-DD-A3A9         TCGA-DD-A4NA         TCGA-DD-A4NB 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DD-A4ND         TCGA-DD-A4NF         TCGA-DD-A4NH 
  "12Q GAIN MUTATED" "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-DD-A4NR 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" 
        TCGA-DD-A4NS         TCGA-DD-A4NV         TCGA-DD-A73A 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DD-A73B         TCGA-DD-A73C         TCGA-DD-A73D 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DD-A73E         TCGA-DD-A73F         TCGA-DD-A73G 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" 
        TCGA-ED-A459         TCGA-ED-A4XI         TCGA-ED-A5KG 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-ED-A627         TCGA-ED-A66X         TCGA-ED-A66Y 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" 
        TCGA-ED-A7PX         TCGA-ED-A7PY         TCGA-ED-A7PZ 
  "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" 
        TCGA-ED-A7XP         TCGA-ED-A82E         TCGA-EP-A12J 
"12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" 
        TCGA-EP-A26S         TCGA-EP-A2KA         TCGA-EP-A2KB 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EP-A2KC         TCGA-EP-A3JL         TCGA-EP-A3RK 
"12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" 
        TCGA-ES-A2HS         TCGA-ES-A2HT         TCGA-FV-A23B 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-FV-A2QR         TCGA-FV-A3I0         TCGA-FV-A3I1 
"12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" 
        TCGA-FV-A3R2         TCGA-FV-A3R3         TCGA-FV-A495 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-FV-A496         TCGA-FV-A4ZP         TCGA-FV-A4ZQ 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-G3-A25S         TCGA-G3-A25T         TCGA-G3-A25U 
"12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" 
        TCGA-G3-A25V         TCGA-G3-A25W         TCGA-G3-A25X 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-G3-A25Y         TCGA-G3-A25Z         TCGA-G3-A3CG 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-G3-A3CH         TCGA-G3-A3CI         TCGA-G3-A3CJ 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-G3-A3CK         TCGA-G3-A5SI         TCGA-G3-A5SJ 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-G3-A5SL         TCGA-G3-A5SM         TCGA-G3-A6UC 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-GJ-A6C0         TCGA-K7-A6G5         TCGA-LG-A6GG 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-MI-A75C         TCGA-MI-A75E         TCGA-MI-A75G 
  "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-MI-A75I         TCGA-NI-A4U2         TCGA-O8-A75V 
"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-BC-A69H         TCGA-BC-A69I         TCGA-CC-5258 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-CC-5260         TCGA-CC-5261         TCGA-CC-5262 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-CC-5263         TCGA-CC-A1HT         TCGA-CC-A3M9 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-CC-A3MA         TCGA-CC-A3MB         TCGA-CC-A3MC 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DD-A113         TCGA-DD-A114         TCGA-DD-A115 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DD-A116         TCGA-DD-A118         TCGA-DD-A119 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DD-A11A         TCGA-DD-A11B         TCGA-DD-A11C 
  "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DD-A11D         TCGA-DD-A1E9         TCGA-DD-A1EA 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DD-A1EB         TCGA-DD-A1EC         TCGA-DD-A1ED 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DD-A1EE         TCGA-DD-A1EF         TCGA-DD-A1EG 
"12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" 
        TCGA-DD-A1EH         TCGA-DD-A1EI         TCGA-DD-A1EJ 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" 
        TCGA-DD-A1EK         TCGA-DD-A1EL         TCGA-DD-A39V 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DD-A39X         TCGA-DD-A39Y         TCGA-DD-A39Z 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DD-A3A0         TCGA-DD-A3A1         TCGA-DD-A3A2 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DD-A3A3         TCGA-DD-A3A4         TCGA-DD-A3A5 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DD-A3A6         TCGA-DD-A3A7         TCGA-DD-A3A8 
"12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" 
        TCGA-DD-A3A9         TCGA-DD-A4NA         TCGA-DD-A4NB 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DD-A4ND         TCGA-DD-A4NF         TCGA-DD-A4NH 
  "12Q GAIN MUTATED" "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-DD-A4NR 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" 
        TCGA-DD-A4NS         TCGA-DD-A4NV         TCGA-DD-A73A 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DD-A73B         TCGA-DD-A73C         TCGA-DD-A73D 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DD-A73E         TCGA-DD-A73F         TCGA-DD-A73G 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" 
        TCGA-ED-A459         TCGA-ED-A4XI         TCGA-ED-A5KG 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-ED-A627         TCGA-ED-A66X         TCGA-ED-A66Y 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" 
        TCGA-ED-A7PX         TCGA-ED-A7PY         TCGA-ED-A7PZ 
  "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" 
        TCGA-ED-A7XP         TCGA-ED-A82E         TCGA-EP-A12J 
"12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" 
        TCGA-EP-A26S         TCGA-EP-A2KA         TCGA-EP-A2KB 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EP-A2KC         TCGA-EP-A3JL         TCGA-EP-A3RK 
"12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" 
        TCGA-ES-A2HS         TCGA-ES-A2HT         TCGA-FV-A23B 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-FV-A2QR         TCGA-FV-A3I0         TCGA-FV-A3I1 
"12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" 
        TCGA-FV-A3R2         TCGA-FV-A3R3         TCGA-FV-A495 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-FV-A496         TCGA-FV-A4ZP         TCGA-FV-A4ZQ 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-G3-A25S         TCGA-G3-A25T         TCGA-G3-A25U 
"12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" 
        TCGA-G3-A25V         TCGA-G3-A25W         TCGA-G3-A25X 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-G3-A25Y         TCGA-G3-A25Z         TCGA-G3-A3CG 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-G3-A3CH         TCGA-G3-A3CI         TCGA-G3-A3CJ 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-G3-A3CK         TCGA-G3-A5SI         TCGA-G3-A5SJ 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-G3-A5SL         TCGA-G3-A5SM         TCGA-G3-A6UC 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-GJ-A6C0         TCGA-K7-A6G5         TCGA-LG-A6GG 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-MI-A75C         TCGA-MI-A75E         TCGA-MI-A75G 
  "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-MI-A75I         TCGA-NI-A4U2         TCGA-O8-A75V 
"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-BC-A69H         TCGA-BC-A69I         TCGA-CC-5258 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-CC-5260         TCGA-CC-5261         TCGA-CC-5262 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-CC-5263         TCGA-CC-A1HT         TCGA-CC-A3M9 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-CC-A3MA         TCGA-CC-A3MB         TCGA-CC-A3MC 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DD-A113         TCGA-DD-A114         TCGA-DD-A115 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DD-A116         TCGA-DD-A118         TCGA-DD-A119 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DD-A11A         TCGA-DD-A11B         TCGA-DD-A11C 
  "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DD-A11D         TCGA-DD-A1E9         TCGA-DD-A1EA 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DD-A1EB         TCGA-DD-A1EC         TCGA-DD-A1ED 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DD-A1EE         TCGA-DD-A1EF         TCGA-DD-A1EG 
"12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" 
        TCGA-DD-A1EH         TCGA-DD-A1EI         TCGA-DD-A1EJ 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" 
        TCGA-DD-A1EK         TCGA-DD-A1EL         TCGA-DD-A39V 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DD-A39X         TCGA-DD-A39Y         TCGA-DD-A39Z 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DD-A3A0         TCGA-DD-A3A1         TCGA-DD-A3A2 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DD-A3A3         TCGA-DD-A3A4         TCGA-DD-A3A5 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DD-A3A6         TCGA-DD-A3A7         TCGA-DD-A3A8 
"12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" 
        TCGA-DD-A3A9         TCGA-DD-A4NA         TCGA-DD-A4NB 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DD-A4ND         TCGA-DD-A4NF         TCGA-DD-A4NH 
  "12Q GAIN MUTATED" "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-DD-A4NR 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" 
        TCGA-DD-A4NS         TCGA-DD-A4NV         TCGA-DD-A73A 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DD-A73B         TCGA-DD-A73C         TCGA-DD-A73D 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DD-A73E         TCGA-DD-A73F         TCGA-DD-A73G 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" 
        TCGA-ED-A459         TCGA-ED-A4XI         TCGA-ED-A5KG 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-ED-A627         TCGA-ED-A66X         TCGA-ED-A66Y 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" 
        TCGA-ED-A7PX         TCGA-ED-A7PY         TCGA-ED-A7PZ 
  "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" 
        TCGA-ED-A7XP         TCGA-ED-A82E         TCGA-EP-A12J 
"12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" 
        TCGA-EP-A26S         TCGA-EP-A2KA         TCGA-EP-A2KB 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EP-A2KC         TCGA-EP-A3JL         TCGA-EP-A3RK 
"12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" 
        TCGA-ES-A2HS         TCGA-ES-A2HT         TCGA-FV-A23B 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-FV-A2QR         TCGA-FV-A3I0         TCGA-FV-A3I1 
"12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" 
        TCGA-FV-A3R2         TCGA-FV-A3R3         TCGA-FV-A495 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-FV-A496         TCGA-FV-A4ZP         TCGA-FV-A4ZQ 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-G3-A25S         TCGA-G3-A25T         TCGA-G3-A25U 
"12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" 
        TCGA-G3-A25V         TCGA-G3-A25W         TCGA-G3-A25X 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-G3-A25Y         TCGA-G3-A25Z         TCGA-G3-A3CG 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-G3-A3CH         TCGA-G3-A3CI         TCGA-G3-A3CJ 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-G3-A3CK         TCGA-G3-A5SI         TCGA-G3-A5SJ 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-G3-A5SL         TCGA-G3-A5SM         TCGA-G3-A6UC 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-GJ-A6C0         TCGA-K7-A6G5         TCGA-LG-A6GG 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-MI-A75C         TCGA-MI-A75E         TCGA-MI-A75G 
  "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-MI-A75I         TCGA-NI-A4U2         TCGA-O8-A75V 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
[1] "hr=" "1.4"
D24V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  12Q GAIN MUTATED         8        3         0          4          2
  12Q GAIN WILD-TYPE      50       33         2         26          2
                    vv
clus                 STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  12Q GAIN MUTATED            1        0         0         0
  12Q GAIN WILD-TYPE          4        1         1         2
D24V3, multiclass
                    vv
clus                 T1 T2 T3 T4
  12Q GAIN MUTATED    9  3  6  0
  12Q GAIN WILD-TYPE 52 37 34  8
D24V4, multiclass
    clus
vv   12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  T1                9                 52
  T2                3                 37
  T3                6                 34
  T4                0                  8
D24V5, binary
                    cls
clus                  0  1
  12Q GAIN MUTATED   12  1
  12Q GAIN WILD-TYPE 85  2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED     12    1
  12Q GAIN WILD-TYPE   85    2
   clus
vv  12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  0               12                 85
  1                1                  2
                    vv
clus                 M0 M1 MX
  12Q GAIN MUTATED   17  0  1
  12Q GAIN WILD-TYPE 98  3 30
D24V6, multiclass
    clus
vv   12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  M0               17                 98
  M1                0                  3
  MX                1                 30
D24V7, binary
                    cls
clus                  0  1
  12Q GAIN MUTATED   12  6
  12Q GAIN WILD-TYPE 46 85
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED     12    6
  12Q GAIN WILD-TYPE   46   85
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  FEMALE               12                 46
  MALE                  6                 85
                    vv
clus                  R0  R1  R2  RX
  12Q GAIN MUTATED    16   0   0   1
  12Q GAIN WILD-TYPE 106  11   1   9
D24V8, multiclass
    clus
vv   12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  R0               16                106
  R1                0                 11
  R2                0                  1
  RX                1                  9

Clustering(25) Variable = 13Q GAIN MUTATION ANALYSIS
D25V1, survival
                    sevent
clus2                 0  1
  13Q GAIN MUTATED    3  5
  13Q GAIN WILD-TYPE 81 58
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                 8                139 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                 5                 58 
$`13Q GAIN MUTATED`
TCGA-BC-A3KF TCGA-CC-5263 TCGA-DD-A1EG TCGA-DD-A1EJ TCGA-DD-A3A7 TCGA-ED-A66Y 
        0.26         4.24        45.11        29.16        13.78         0.23 
TCGA-EP-A3JL TCGA-FV-A23B 
        9.96        32.45 

$`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-BC-A69H 
        5.03        44.42        13.84        22.36         9.50         3.95 
TCGA-BC-A69I TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-A1HT 
        0.53         0.07         2.86         0.39         3.39         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        37.78 
TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B 
       83.57        53.33       113.00         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        51.29        90.71        79.40        66.31        19.79 
TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EK 
       75.65         6.71        12.95        49.15         6.02        18.35 
TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A0 
       13.64        21.14        55.69         5.62        19.76        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-A4NB TCGA-DD-A4ND TCGA-DD-A4NF 
        0.36        30.61        33.14        12.85        73.38        14.07 
TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN 
       14.24        18.44        15.06        39.78        56.25        29.56 
TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV 
       61.45        93.67        12.26         0.30        80.75        66.35 
TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F 
       10.98         9.30         7.56        10.98         1.45        27.72 
TCGA-DD-A73G TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X 
      100.96        13.41        12.69        15.85        13.91        13.35 
TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XP TCGA-ED-A82E TCGA-EP-A12J 
        0.20         0.20         0.20         0.20         0.20        18.74 
TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3RK TCGA-ES-A2HS 
       19.99        11.74        10.98         0.62        11.93        22.85 
TCGA-ES-A2HT TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 
       14.40        19.10         0.20         8.12         6.38         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        51.06 
TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A25Z 
       53.79        28.27        30.74        58.49        14.86        21.53 
TCGA-G3-A3CG TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI 
       22.13        25.64         5.92        19.53        19.23        14.70 
TCGA-G3-A5SJ TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A6UC TCGA-GJ-A6C0 TCGA-K7-A6G5 
       11.97         7.99         4.37         7.76         1.02         4.01 
TCGA-LG-A6GG TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75I TCGA-NI-A4U2 
        0.49         9.57         5.10        14.24         8.71        58.88 
TCGA-O8-A75V 
        4.44 

  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
              0.23               0.03 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
             45.11             113.00 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
             11.87              14.24 
[1] "0.2 - 45.1 (11.9)"  "0.0 - 113.0 (14.2)"
        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-BC-A69H         TCGA-BC-A69I         TCGA-CC-5258 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-CC-5260         TCGA-CC-5261         TCGA-CC-5262 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-CC-5263         TCGA-CC-A1HT         TCGA-CC-A3M9 
  "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-CC-A3MA         TCGA-CC-A3MB         TCGA-CC-A3MC 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DD-A113         TCGA-DD-A114         TCGA-DD-A115 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DD-A116         TCGA-DD-A118         TCGA-DD-A119 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DD-A11A         TCGA-DD-A11B         TCGA-DD-A11C 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DD-A11D         TCGA-DD-A1E9         TCGA-DD-A1EA 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DD-A1EB         TCGA-DD-A1EC         TCGA-DD-A1ED 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DD-A1EE         TCGA-DD-A1EF         TCGA-DD-A1EG 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" 
        TCGA-DD-A1EH         TCGA-DD-A1EI         TCGA-DD-A1EJ 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" 
        TCGA-DD-A1EK         TCGA-DD-A1EL         TCGA-DD-A39V 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DD-A39X         TCGA-DD-A39Y         TCGA-DD-A39Z 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DD-A3A0         TCGA-DD-A3A1         TCGA-DD-A3A2 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DD-A3A3         TCGA-DD-A3A4         TCGA-DD-A3A5 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DD-A3A6         TCGA-DD-A3A7         TCGA-DD-A3A8 
"13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" 
        TCGA-DD-A3A9         TCGA-DD-A4NA         TCGA-DD-A4NB 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DD-A4ND         TCGA-DD-A4NF         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 WILD-TYPE" "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-DD-A4NR 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DD-A4NS         TCGA-DD-A4NV         TCGA-DD-A73A 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DD-A73B         TCGA-DD-A73C         TCGA-DD-A73D 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DD-A73E         TCGA-DD-A73F         TCGA-DD-A73G 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-ED-A459         TCGA-ED-A4XI         TCGA-ED-A5KG 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-ED-A627         TCGA-ED-A66X         TCGA-ED-A66Y 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" 
        TCGA-ED-A7PX         TCGA-ED-A7PY         TCGA-ED-A7PZ 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-ED-A7XP         TCGA-ED-A82E         TCGA-EP-A12J 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EP-A26S         TCGA-EP-A2KA         TCGA-EP-A2KB 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EP-A2KC         TCGA-EP-A3JL         TCGA-EP-A3RK 
"13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" 
        TCGA-ES-A2HS         TCGA-ES-A2HT         TCGA-FV-A23B 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" 
        TCGA-FV-A2QR         TCGA-FV-A3I0         TCGA-FV-A3I1 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-FV-A3R2         TCGA-FV-A3R3         TCGA-FV-A495 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-FV-A496         TCGA-FV-A4ZP         TCGA-FV-A4ZQ 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-G3-A25S         TCGA-G3-A25T         TCGA-G3-A25U 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-G3-A25V         TCGA-G3-A25W         TCGA-G3-A25X 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-G3-A25Y         TCGA-G3-A25Z         TCGA-G3-A3CG 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-G3-A3CH         TCGA-G3-A3CI         TCGA-G3-A3CJ 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-G3-A3CK         TCGA-G3-A5SI         TCGA-G3-A5SJ 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-G3-A5SL         TCGA-G3-A5SM         TCGA-G3-A6UC 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-GJ-A6C0         TCGA-K7-A6G5         TCGA-LG-A6GG 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-MI-A75C         TCGA-MI-A75E         TCGA-MI-A75G 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-MI-A75I         TCGA-NI-A4U2         TCGA-O8-A75V 
"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-BC-A69H         TCGA-BC-A69I         TCGA-CC-5258 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-CC-5260         TCGA-CC-5261         TCGA-CC-5262 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-CC-5263         TCGA-CC-A1HT         TCGA-CC-A3M9 
  "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-CC-A3MA         TCGA-CC-A3MB         TCGA-CC-A3MC 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DD-A113         TCGA-DD-A114         TCGA-DD-A115 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DD-A116         TCGA-DD-A118         TCGA-DD-A119 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DD-A11A         TCGA-DD-A11B         TCGA-DD-A11C 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DD-A11D         TCGA-DD-A1E9         TCGA-DD-A1EA 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DD-A1EB         TCGA-DD-A1EC         TCGA-DD-A1ED 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DD-A1EE         TCGA-DD-A1EF         TCGA-DD-A1EG 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" 
        TCGA-DD-A1EH         TCGA-DD-A1EI         TCGA-DD-A1EJ 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" 
        TCGA-DD-A1EK         TCGA-DD-A1EL         TCGA-DD-A39V 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DD-A39X         TCGA-DD-A39Y         TCGA-DD-A39Z 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DD-A3A0         TCGA-DD-A3A1         TCGA-DD-A3A2 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DD-A3A3         TCGA-DD-A3A4         TCGA-DD-A3A5 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DD-A3A6         TCGA-DD-A3A7         TCGA-DD-A3A8 
"13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" 
        TCGA-DD-A3A9         TCGA-DD-A4NA         TCGA-DD-A4NB 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DD-A4ND         TCGA-DD-A4NF         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 WILD-TYPE" "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-DD-A4NR 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DD-A4NS         TCGA-DD-A4NV         TCGA-DD-A73A 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DD-A73B         TCGA-DD-A73C         TCGA-DD-A73D 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DD-A73E         TCGA-DD-A73F         TCGA-DD-A73G 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-ED-A459         TCGA-ED-A4XI         TCGA-ED-A5KG 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-ED-A627         TCGA-ED-A66X         TCGA-ED-A66Y 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" 
        TCGA-ED-A7PX         TCGA-ED-A7PY         TCGA-ED-A7PZ 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-ED-A7XP         TCGA-ED-A82E         TCGA-EP-A12J 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EP-A26S         TCGA-EP-A2KA         TCGA-EP-A2KB 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EP-A2KC         TCGA-EP-A3JL         TCGA-EP-A3RK 
"13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" 
        TCGA-ES-A2HS         TCGA-ES-A2HT         TCGA-FV-A23B 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" 
        TCGA-FV-A2QR         TCGA-FV-A3I0         TCGA-FV-A3I1 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-FV-A3R2         TCGA-FV-A3R3         TCGA-FV-A495 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-FV-A496         TCGA-FV-A4ZP         TCGA-FV-A4ZQ 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-G3-A25S         TCGA-G3-A25T         TCGA-G3-A25U 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-G3-A25V         TCGA-G3-A25W         TCGA-G3-A25X 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-G3-A25Y         TCGA-G3-A25Z         TCGA-G3-A3CG 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-G3-A3CH         TCGA-G3-A3CI         TCGA-G3-A3CJ 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-G3-A3CK         TCGA-G3-A5SI         TCGA-G3-A5SJ 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-G3-A5SL         TCGA-G3-A5SM         TCGA-G3-A6UC 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-GJ-A6C0         TCGA-K7-A6G5         TCGA-LG-A6GG 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-MI-A75C         TCGA-MI-A75E         TCGA-MI-A75G 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-MI-A75I         TCGA-NI-A4U2         TCGA-O8-A75V 
"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-BC-A69H         TCGA-BC-A69I         TCGA-CC-5258 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-CC-5260         TCGA-CC-5261         TCGA-CC-5262 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-CC-5263         TCGA-CC-A1HT         TCGA-CC-A3M9 
  "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-CC-A3MA         TCGA-CC-A3MB         TCGA-CC-A3MC 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DD-A113         TCGA-DD-A114         TCGA-DD-A115 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DD-A116         TCGA-DD-A118         TCGA-DD-A119 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DD-A11A         TCGA-DD-A11B         TCGA-DD-A11C 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DD-A11D         TCGA-DD-A1E9         TCGA-DD-A1EA 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DD-A1EB         TCGA-DD-A1EC         TCGA-DD-A1ED 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DD-A1EE         TCGA-DD-A1EF         TCGA-DD-A1EG 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" 
        TCGA-DD-A1EH         TCGA-DD-A1EI         TCGA-DD-A1EJ 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" 
        TCGA-DD-A1EK         TCGA-DD-A1EL         TCGA-DD-A39V 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DD-A39X         TCGA-DD-A39Y         TCGA-DD-A39Z 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DD-A3A0         TCGA-DD-A3A1         TCGA-DD-A3A2 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DD-A3A3         TCGA-DD-A3A4         TCGA-DD-A3A5 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DD-A3A6         TCGA-DD-A3A7         TCGA-DD-A3A8 
"13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" 
        TCGA-DD-A3A9         TCGA-DD-A4NA         TCGA-DD-A4NB 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DD-A4ND         TCGA-DD-A4NF         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 WILD-TYPE" "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-DD-A4NR 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DD-A4NS         TCGA-DD-A4NV         TCGA-DD-A73A 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DD-A73B         TCGA-DD-A73C         TCGA-DD-A73D 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DD-A73E         TCGA-DD-A73F         TCGA-DD-A73G 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-ED-A459         TCGA-ED-A4XI         TCGA-ED-A5KG 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-ED-A627         TCGA-ED-A66X         TCGA-ED-A66Y 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" 
        TCGA-ED-A7PX         TCGA-ED-A7PY         TCGA-ED-A7PZ 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-ED-A7XP         TCGA-ED-A82E         TCGA-EP-A12J 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EP-A26S         TCGA-EP-A2KA         TCGA-EP-A2KB 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EP-A2KC         TCGA-EP-A3JL         TCGA-EP-A3RK 
"13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" 
        TCGA-ES-A2HS         TCGA-ES-A2HT         TCGA-FV-A23B 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" 
        TCGA-FV-A2QR         TCGA-FV-A3I0         TCGA-FV-A3I1 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-FV-A3R2         TCGA-FV-A3R3         TCGA-FV-A495 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-FV-A496         TCGA-FV-A4ZP         TCGA-FV-A4ZQ 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-G3-A25S         TCGA-G3-A25T         TCGA-G3-A25U 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-G3-A25V         TCGA-G3-A25W         TCGA-G3-A25X 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-G3-A25Y         TCGA-G3-A25Z         TCGA-G3-A3CG 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-G3-A3CH         TCGA-G3-A3CI         TCGA-G3-A3CJ 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-G3-A3CK         TCGA-G3-A5SI         TCGA-G3-A5SJ 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-G3-A5SL         TCGA-G3-A5SM         TCGA-G3-A6UC 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-GJ-A6C0         TCGA-K7-A6G5         TCGA-LG-A6GG 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-MI-A75C         TCGA-MI-A75E         TCGA-MI-A75G 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-MI-A75I         TCGA-NI-A4U2         TCGA-O8-A75V 
"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         3        1         0          2          1
  13Q GAIN WILD-TYPE      55       35         2         28          3
                    vv
clus                 STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  13Q GAIN MUTATED            1        0         0         0
  13Q GAIN WILD-TYPE          4        1         1         2
D25V3, multiclass
                    vv
clus                 T1 T2 T3 T4
  13Q GAIN MUTATED    4  1  3  0
  13Q GAIN WILD-TYPE 57 39 37  8
D25V4, multiclass
    clus
vv   13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  T1                4                 57
  T2                1                 39
  T3                3                 37
  T4                0                  8
D25V5, binary
                    cls
clus                  0  1
  13Q GAIN MUTATED    5  1
  13Q GAIN WILD-TYPE 92  2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED      5    1
  13Q GAIN WILD-TYPE   92    2
   clus
vv  13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  0                5                 92
  1                1                  2
                    vv
clus                  M0  M1  MX
  13Q GAIN MUTATED     7   0   1
  13Q GAIN WILD-TYPE 108   3  30
D25V6, multiclass
    clus
vv   13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  M0                7                108
  M1                0                  3
  MX                1                 30
D25V7, binary
                    cls
clus                  0  1
  13Q GAIN MUTATED    4  4
  13Q GAIN WILD-TYPE 54 87
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED      4    4
  13Q GAIN WILD-TYPE   54   87
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  FEMALE                4                 54
  MALE                  4                 87
                    vv
clus                  R0  R1  R2  RX
  13Q GAIN MUTATED     6   0   0   1
  13Q GAIN WILD-TYPE 116  11   1   9
D25V8, multiclass
    clus
vv   13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  R0                6                116
  R1                0                 11
  R2                0                  1
  RX                1                  9

Clustering(26) Variable = 14Q GAIN MUTATION ANALYSIS
D26V1, survival
                    sevent
clus2                 0  1
  14Q GAIN MUTATED    5  3
  14Q GAIN WILD-TYPE 79 60
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                 8                139 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                 3                 60 
$`14Q GAIN MUTATED`
TCGA-CC-A3M9 TCGA-DD-A114 TCGA-DD-A119 TCGA-DD-A4ND TCGA-ED-A66Y TCGA-ES-A2HS 
        0.10        37.78         7.33        73.38         0.23        22.85 
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        13.84         0.26        22.36         9.50 
TCGA-BC-A69H TCGA-BC-A69I TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 
        3.95         0.53         0.07         2.86         0.39         3.39 
TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A113 
        4.24         3.32         0.07         0.10         0.13        79.73 
TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C 
       83.57        53.33       113.00         2.60         0.46        21.76 
TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED 
       51.29        90.71        79.40        66.31        19.79        75.65 
TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ 
        6.71        12.95        45.11        49.15         6.02        29.16 
TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A39Z 
       18.35        13.64        21.14        55.69         5.62        19.76 
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-A4NB 
      107.11        13.78         0.36        30.61        33.14        12.85 
TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL 
       14.07        14.24        18.44        15.06        39.78        56.25 
TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS 
       29.56        61.45        93.67        12.26         0.30        80.75 
TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E 
       66.35        10.98         9.30         7.56        10.98         1.45 
TCGA-DD-A73F TCGA-DD-A73G TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 
       27.72       100.96        13.41        12.69        15.85        13.91 
TCGA-ED-A66X TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XP TCGA-ED-A82E 
       13.35         0.20         0.20         0.20         0.20         0.20 
TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL 
       18.74        19.99        11.74        10.98         0.62         9.96 
TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-A3I1 TCGA-FV-A3R2 
       11.93        14.40        32.45        19.10         8.12         6.38 
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 
       51.06        53.79        28.27        30.74        58.49        14.86 
TCGA-G3-A25Z TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI 
       21.53        25.64         5.92        19.53        19.23        14.70 
TCGA-G3-A5SJ TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A6UC TCGA-GJ-A6C0 TCGA-K7-A6G5 
       11.97         7.99         4.37         7.76         1.02         4.01 
TCGA-LG-A6GG TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75I TCGA-NI-A4U2 
        0.49         9.57         5.10        14.24         8.71        58.88 
TCGA-O8-A75V 
        4.44 

  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
              0.10               0.03 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
             73.38             113.00 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
             14.73              14.07 
[1] "0.1 - 73.4 (14.7)"  "0.0 - 113.0 (14.1)"
        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-BC-A69H         TCGA-BC-A69I         TCGA-CC-5258 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CC-5260         TCGA-CC-5261         TCGA-CC-5262 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CC-5263         TCGA-CC-A1HT         TCGA-CC-A3M9 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE"   "14Q GAIN MUTATED" 
        TCGA-CC-A3MA         TCGA-CC-A3MB         TCGA-CC-A3MC 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DD-A113         TCGA-DD-A114         TCGA-DD-A115 
"14Q GAIN WILD-TYPE"   "14Q GAIN MUTATED" "14Q GAIN WILD-TYPE" 
        TCGA-DD-A116         TCGA-DD-A118         TCGA-DD-A119 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE"   "14Q GAIN MUTATED" 
        TCGA-DD-A11A         TCGA-DD-A11B         TCGA-DD-A11C 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DD-A11D         TCGA-DD-A1E9         TCGA-DD-A1EA 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DD-A1EB         TCGA-DD-A1EC         TCGA-DD-A1ED 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DD-A1EE         TCGA-DD-A1EF         TCGA-DD-A1EG 
"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-A1EK         TCGA-DD-A1EL         TCGA-DD-A39V 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DD-A39X         TCGA-DD-A39Y         TCGA-DD-A39Z 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DD-A3A0         TCGA-DD-A3A1         TCGA-DD-A3A2 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DD-A3A3         TCGA-DD-A3A4         TCGA-DD-A3A5 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DD-A3A6         TCGA-DD-A3A7         TCGA-DD-A3A8 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DD-A3A9         TCGA-DD-A4NA         TCGA-DD-A4NB 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DD-A4ND         TCGA-DD-A4NF         TCGA-DD-A4NH 
  "14Q GAIN MUTATED" "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-DD-A4NR 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DD-A4NS         TCGA-DD-A4NV         TCGA-DD-A73A 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DD-A73B         TCGA-DD-A73C         TCGA-DD-A73D 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DD-A73E         TCGA-DD-A73F         TCGA-DD-A73G 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-ED-A459         TCGA-ED-A4XI         TCGA-ED-A5KG 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-ED-A627         TCGA-ED-A66X         TCGA-ED-A66Y 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE"   "14Q GAIN MUTATED" 
        TCGA-ED-A7PX         TCGA-ED-A7PY         TCGA-ED-A7PZ 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-ED-A7XP         TCGA-ED-A82E         TCGA-EP-A12J 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EP-A26S         TCGA-EP-A2KA         TCGA-EP-A2KB 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EP-A2KC         TCGA-EP-A3JL         TCGA-EP-A3RK 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-ES-A2HS         TCGA-ES-A2HT         TCGA-FV-A23B 
  "14Q GAIN MUTATED" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-FV-A2QR         TCGA-FV-A3I0         TCGA-FV-A3I1 
"14Q GAIN WILD-TYPE"   "14Q GAIN MUTATED" "14Q GAIN WILD-TYPE" 
        TCGA-FV-A3R2         TCGA-FV-A3R3         TCGA-FV-A495 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-FV-A496         TCGA-FV-A4ZP         TCGA-FV-A4ZQ 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-G3-A25S         TCGA-G3-A25T         TCGA-G3-A25U 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-G3-A25V         TCGA-G3-A25W         TCGA-G3-A25X 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-G3-A25Y         TCGA-G3-A25Z         TCGA-G3-A3CG 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE"   "14Q GAIN MUTATED" 
        TCGA-G3-A3CH         TCGA-G3-A3CI         TCGA-G3-A3CJ 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-G3-A3CK         TCGA-G3-A5SI         TCGA-G3-A5SJ 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-G3-A5SL         TCGA-G3-A5SM         TCGA-G3-A6UC 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-GJ-A6C0         TCGA-K7-A6G5         TCGA-LG-A6GG 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-MI-A75C         TCGA-MI-A75E         TCGA-MI-A75G 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-MI-A75I         TCGA-NI-A4U2         TCGA-O8-A75V 
"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-BC-A69H         TCGA-BC-A69I         TCGA-CC-5258 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CC-5260         TCGA-CC-5261         TCGA-CC-5262 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CC-5263         TCGA-CC-A1HT         TCGA-CC-A3M9 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE"   "14Q GAIN MUTATED" 
        TCGA-CC-A3MA         TCGA-CC-A3MB         TCGA-CC-A3MC 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DD-A113         TCGA-DD-A114         TCGA-DD-A115 
"14Q GAIN WILD-TYPE"   "14Q GAIN MUTATED" "14Q GAIN WILD-TYPE" 
        TCGA-DD-A116         TCGA-DD-A118         TCGA-DD-A119 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE"   "14Q GAIN MUTATED" 
        TCGA-DD-A11A         TCGA-DD-A11B         TCGA-DD-A11C 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DD-A11D         TCGA-DD-A1E9         TCGA-DD-A1EA 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DD-A1EB         TCGA-DD-A1EC         TCGA-DD-A1ED 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DD-A1EE         TCGA-DD-A1EF         TCGA-DD-A1EG 
"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-A1EK         TCGA-DD-A1EL         TCGA-DD-A39V 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DD-A39X         TCGA-DD-A39Y         TCGA-DD-A39Z 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DD-A3A0         TCGA-DD-A3A1         TCGA-DD-A3A2 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DD-A3A3         TCGA-DD-A3A4         TCGA-DD-A3A5 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DD-A3A6         TCGA-DD-A3A7         TCGA-DD-A3A8 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DD-A3A9         TCGA-DD-A4NA         TCGA-DD-A4NB 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DD-A4ND         TCGA-DD-A4NF         TCGA-DD-A4NH 
  "14Q GAIN MUTATED" "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-DD-A4NR 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DD-A4NS         TCGA-DD-A4NV         TCGA-DD-A73A 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DD-A73B         TCGA-DD-A73C         TCGA-DD-A73D 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DD-A73E         TCGA-DD-A73F         TCGA-DD-A73G 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-ED-A459         TCGA-ED-A4XI         TCGA-ED-A5KG 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-ED-A627         TCGA-ED-A66X         TCGA-ED-A66Y 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE"   "14Q GAIN MUTATED" 
        TCGA-ED-A7PX         TCGA-ED-A7PY         TCGA-ED-A7PZ 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-ED-A7XP         TCGA-ED-A82E         TCGA-EP-A12J 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EP-A26S         TCGA-EP-A2KA         TCGA-EP-A2KB 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EP-A2KC         TCGA-EP-A3JL         TCGA-EP-A3RK 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-ES-A2HS         TCGA-ES-A2HT         TCGA-FV-A23B 
  "14Q GAIN MUTATED" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-FV-A2QR         TCGA-FV-A3I0         TCGA-FV-A3I1 
"14Q GAIN WILD-TYPE"   "14Q GAIN MUTATED" "14Q GAIN WILD-TYPE" 
        TCGA-FV-A3R2         TCGA-FV-A3R3         TCGA-FV-A495 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-FV-A496         TCGA-FV-A4ZP         TCGA-FV-A4ZQ 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-G3-A25S         TCGA-G3-A25T         TCGA-G3-A25U 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-G3-A25V         TCGA-G3-A25W         TCGA-G3-A25X 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-G3-A25Y         TCGA-G3-A25Z         TCGA-G3-A3CG 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE"   "14Q GAIN MUTATED" 
        TCGA-G3-A3CH         TCGA-G3-A3CI         TCGA-G3-A3CJ 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-G3-A3CK         TCGA-G3-A5SI         TCGA-G3-A5SJ 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-G3-A5SL         TCGA-G3-A5SM         TCGA-G3-A6UC 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-GJ-A6C0         TCGA-K7-A6G5         TCGA-LG-A6GG 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-MI-A75C         TCGA-MI-A75E         TCGA-MI-A75G 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-MI-A75I         TCGA-NI-A4U2         TCGA-O8-A75V 
"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-BC-A69H         TCGA-BC-A69I         TCGA-CC-5258 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CC-5260         TCGA-CC-5261         TCGA-CC-5262 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CC-5263         TCGA-CC-A1HT         TCGA-CC-A3M9 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE"   "14Q GAIN MUTATED" 
        TCGA-CC-A3MA         TCGA-CC-A3MB         TCGA-CC-A3MC 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DD-A113         TCGA-DD-A114         TCGA-DD-A115 
"14Q GAIN WILD-TYPE"   "14Q GAIN MUTATED" "14Q GAIN WILD-TYPE" 
        TCGA-DD-A116         TCGA-DD-A118         TCGA-DD-A119 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE"   "14Q GAIN MUTATED" 
        TCGA-DD-A11A         TCGA-DD-A11B         TCGA-DD-A11C 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DD-A11D         TCGA-DD-A1E9         TCGA-DD-A1EA 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DD-A1EB         TCGA-DD-A1EC         TCGA-DD-A1ED 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DD-A1EE         TCGA-DD-A1EF         TCGA-DD-A1EG 
"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-A1EK         TCGA-DD-A1EL         TCGA-DD-A39V 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DD-A39X         TCGA-DD-A39Y         TCGA-DD-A39Z 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DD-A3A0         TCGA-DD-A3A1         TCGA-DD-A3A2 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DD-A3A3         TCGA-DD-A3A4         TCGA-DD-A3A5 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DD-A3A6         TCGA-DD-A3A7         TCGA-DD-A3A8 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DD-A3A9         TCGA-DD-A4NA         TCGA-DD-A4NB 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DD-A4ND         TCGA-DD-A4NF         TCGA-DD-A4NH 
  "14Q GAIN MUTATED" "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-DD-A4NR 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DD-A4NS         TCGA-DD-A4NV         TCGA-DD-A73A 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DD-A73B         TCGA-DD-A73C         TCGA-DD-A73D 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DD-A73E         TCGA-DD-A73F         TCGA-DD-A73G 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-ED-A459         TCGA-ED-A4XI         TCGA-ED-A5KG 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-ED-A627         TCGA-ED-A66X         TCGA-ED-A66Y 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE"   "14Q GAIN MUTATED" 
        TCGA-ED-A7PX         TCGA-ED-A7PY         TCGA-ED-A7PZ 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-ED-A7XP         TCGA-ED-A82E         TCGA-EP-A12J 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EP-A26S         TCGA-EP-A2KA         TCGA-EP-A2KB 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EP-A2KC         TCGA-EP-A3JL         TCGA-EP-A3RK 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-ES-A2HS         TCGA-ES-A2HT         TCGA-FV-A23B 
  "14Q GAIN MUTATED" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-FV-A2QR         TCGA-FV-A3I0         TCGA-FV-A3I1 
"14Q GAIN WILD-TYPE"   "14Q GAIN MUTATED" "14Q GAIN WILD-TYPE" 
        TCGA-FV-A3R2         TCGA-FV-A3R3         TCGA-FV-A495 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-FV-A496         TCGA-FV-A4ZP         TCGA-FV-A4ZQ 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-G3-A25S         TCGA-G3-A25T         TCGA-G3-A25U 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-G3-A25V         TCGA-G3-A25W         TCGA-G3-A25X 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-G3-A25Y         TCGA-G3-A25Z         TCGA-G3-A3CG 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE"   "14Q GAIN MUTATED" 
        TCGA-G3-A3CH         TCGA-G3-A3CI         TCGA-G3-A3CJ 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-G3-A3CK         TCGA-G3-A5SI         TCGA-G3-A5SJ 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-G3-A5SL         TCGA-G3-A5SM         TCGA-G3-A6UC 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-GJ-A6C0         TCGA-K7-A6G5         TCGA-LG-A6GG 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-MI-A75C         TCGA-MI-A75E         TCGA-MI-A75G 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-MI-A75I         TCGA-NI-A4U2         TCGA-O8-A75V 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
[1] "hr=" "1.1"
D26V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  14Q GAIN MUTATED         3        2         0          2          0
  14Q GAIN WILD-TYPE      55       34         2         28          4
                    vv
clus                 STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  14Q GAIN MUTATED            0        1         0         0
  14Q GAIN WILD-TYPE          5        0         1         2
D26V3, multiclass
                    vv
clus                 T1 T2 T3 T4
  14Q GAIN MUTATED    3  2  3  0
  14Q GAIN WILD-TYPE 58 38 37  8
D26V4, multiclass
    clus
vv   14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  T1                3                 58
  T2                2                 38
  T3                3                 37
  T4                0                  8
D26V5, binary
                    cls
clus                  0  1
  14Q GAIN MUTATED    5  0
  14Q GAIN WILD-TYPE 92  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED      5    0
  14Q GAIN WILD-TYPE   92    3
   clus
vv  14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  0                5                 92
  1                0                  3
                    vv
clus                  M0  M1  MX
  14Q GAIN MUTATED     6   1   1
  14Q GAIN WILD-TYPE 109   2  30
D26V6, multiclass
    clus
vv   14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  M0                6                109
  M1                1                  2
  MX                1                 30
D26V7, binary
                    cls
clus                  0  1
  14Q GAIN MUTATED    3  5
  14Q GAIN WILD-TYPE 55 86
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED      3    5
  14Q GAIN WILD-TYPE   55   86
        clus
vv       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  FEMALE                3                 55
  MALE                  5                 86
                    vv
clus                  R0  R1  R2  RX
  14Q GAIN MUTATED     6   1   1   0
  14Q GAIN WILD-TYPE 116  10   0  10
D26V8, multiclass
    clus
vv   14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  R0                6                116
  R1                1                 10
  R2                1                  0
  RX                0                 10

Clustering(27) Variable = 15Q GAIN MUTATION ANALYSIS
D27V1, survival
                    sevent
clus2                 0  1
  15Q GAIN MUTATED   11  3
  15Q GAIN WILD-TYPE 73 60
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                14                133 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                 3                 60 
$`15Q GAIN MUTATED`
TCGA-BC-A10Q TCGA-BC-A10Y TCGA-BC-A3KG TCGA-CC-A3M9 TCGA-DD-A4NI TCGA-DD-A4NV 
       37.32        23.34        22.36         0.10        18.44        66.35 
TCGA-DD-A73G TCGA-ED-A66X TCGA-ES-A2HS TCGA-FV-A4ZQ TCGA-G3-A25T TCGA-G3-A25X 
      100.96        13.35        22.85         0.39        51.06        58.49 
TCGA-G3-A6UC TCGA-MI-A75G 
        7.76        14.24 

$`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-BC-A69H TCGA-BC-A69I TCGA-CC-5258 
       13.84         0.26         9.50         3.95         0.53         0.07 
TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3MA 
        2.86         0.39         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        37.78        83.57        53.33 
TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D 
      113.00         7.33         2.60         0.46        21.76        51.29 
TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE 
       90.71        79.40        66.31        19.79        75.65         6.71 
TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK 
       12.95        45.11        49.15         6.02        29.16        18.35 
TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A0 
       13.64        21.14        55.69         5.62        19.76        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-A4NB TCGA-DD-A4ND 
       13.78         0.36        30.61        33.14        12.85        73.38 
TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN 
       14.07        14.24        15.06        39.78        56.25        29.56 
TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A73A 
       61.45        93.67        12.26         0.30        80.75        10.98 
TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-ED-A459 
        9.30         7.56        10.98         1.45        27.72        13.41 
TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY 
       12.69        15.85        13.91         0.23         0.20         0.20 
TCGA-ED-A7PZ TCGA-ED-A7XP TCGA-ED-A82E TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA 
        0.20         0.20         0.20        18.74        19.99        11.74 
TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A23B 
       10.98         0.62         9.96        11.93        14.40        32.45 
TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 
       19.10         0.20         8.12         6.38         0.13         0.03 
TCGA-FV-A496 TCGA-FV-A4ZP TCGA-G3-A25S TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W 
        0.33        60.36         1.22        53.79        28.27        30.74 
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         5.92        19.53 
TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SL TCGA-G3-A5SM TCGA-GJ-A6C0 
       19.23        14.70        11.97         7.99         4.37         1.02 
TCGA-K7-A6G5 TCGA-LG-A6GG TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75I TCGA-NI-A4U2 
        4.01         0.49         9.57         5.10         8.71        58.88 
TCGA-O8-A75V 
        4.44 

  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
              0.10               0.03 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
            100.96             113.00 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
            22.605             13.780 
[1] "0.1 - 101.0 (22.6)" "0.0 - 113.0 (13.8)"
        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-BC-A69H         TCGA-BC-A69I         TCGA-CC-5258 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-CC-5260         TCGA-CC-5261         TCGA-CC-5262 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-CC-5263         TCGA-CC-A1HT         TCGA-CC-A3M9 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" 
        TCGA-CC-A3MA         TCGA-CC-A3MB         TCGA-CC-A3MC 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-DD-A113         TCGA-DD-A114         TCGA-DD-A115 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-DD-A116         TCGA-DD-A118         TCGA-DD-A119 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-DD-A11A         TCGA-DD-A11B         TCGA-DD-A11C 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-DD-A11D         TCGA-DD-A1E9         TCGA-DD-A1EA 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-DD-A1EB         TCGA-DD-A1EC         TCGA-DD-A1ED 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-DD-A1EE         TCGA-DD-A1EF         TCGA-DD-A1EG 
"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-A1EK         TCGA-DD-A1EL         TCGA-DD-A39V 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-DD-A39X         TCGA-DD-A39Y         TCGA-DD-A39Z 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-DD-A3A0         TCGA-DD-A3A1         TCGA-DD-A3A2 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-DD-A3A3         TCGA-DD-A3A4         TCGA-DD-A3A5 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-DD-A3A6         TCGA-DD-A3A7         TCGA-DD-A3A8 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-DD-A3A9         TCGA-DD-A4NA         TCGA-DD-A4NB 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-DD-A4ND         TCGA-DD-A4NF         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-DD-A4NR 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-DD-A4NS         TCGA-DD-A4NV         TCGA-DD-A73A 
"15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" "15Q GAIN WILD-TYPE" 
        TCGA-DD-A73B         TCGA-DD-A73C         TCGA-DD-A73D 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-DD-A73E         TCGA-DD-A73F         TCGA-DD-A73G 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" 
        TCGA-ED-A459         TCGA-ED-A4XI         TCGA-ED-A5KG 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-ED-A627         TCGA-ED-A66X         TCGA-ED-A66Y 
"15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" "15Q GAIN WILD-TYPE" 
        TCGA-ED-A7PX         TCGA-ED-A7PY         TCGA-ED-A7PZ 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-ED-A7XP         TCGA-ED-A82E         TCGA-EP-A12J 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EP-A26S         TCGA-EP-A2KA         TCGA-EP-A2KB 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EP-A2KC         TCGA-EP-A3JL         TCGA-EP-A3RK 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-ES-A2HS         TCGA-ES-A2HT         TCGA-FV-A23B 
  "15Q GAIN MUTATED" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-FV-A2QR         TCGA-FV-A3I0         TCGA-FV-A3I1 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-FV-A3R2         TCGA-FV-A3R3         TCGA-FV-A495 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-FV-A496         TCGA-FV-A4ZP         TCGA-FV-A4ZQ 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" 
        TCGA-G3-A25S         TCGA-G3-A25T         TCGA-G3-A25U 
"15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" "15Q GAIN WILD-TYPE" 
        TCGA-G3-A25V         TCGA-G3-A25W         TCGA-G3-A25X 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" 
        TCGA-G3-A25Y         TCGA-G3-A25Z         TCGA-G3-A3CG 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-G3-A3CH         TCGA-G3-A3CI         TCGA-G3-A3CJ 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-G3-A3CK         TCGA-G3-A5SI         TCGA-G3-A5SJ 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-G3-A5SL         TCGA-G3-A5SM         TCGA-G3-A6UC 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" 
        TCGA-GJ-A6C0         TCGA-K7-A6G5         TCGA-LG-A6GG 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-MI-A75C         TCGA-MI-A75E         TCGA-MI-A75G 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" 
        TCGA-MI-A75I         TCGA-NI-A4U2         TCGA-O8-A75V 
"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-BC-A69H         TCGA-BC-A69I         TCGA-CC-5258 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-CC-5260         TCGA-CC-5261         TCGA-CC-5262 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-CC-5263         TCGA-CC-A1HT         TCGA-CC-A3M9 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" 
        TCGA-CC-A3MA         TCGA-CC-A3MB         TCGA-CC-A3MC 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-DD-A113         TCGA-DD-A114         TCGA-DD-A115 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-DD-A116         TCGA-DD-A118         TCGA-DD-A119 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-DD-A11A         TCGA-DD-A11B         TCGA-DD-A11C 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-DD-A11D         TCGA-DD-A1E9         TCGA-DD-A1EA 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-DD-A1EB         TCGA-DD-A1EC         TCGA-DD-A1ED 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-DD-A1EE         TCGA-DD-A1EF         TCGA-DD-A1EG 
"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-A1EK         TCGA-DD-A1EL         TCGA-DD-A39V 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-DD-A39X         TCGA-DD-A39Y         TCGA-DD-A39Z 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-DD-A3A0         TCGA-DD-A3A1         TCGA-DD-A3A2 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-DD-A3A3         TCGA-DD-A3A4         TCGA-DD-A3A5 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-DD-A3A6         TCGA-DD-A3A7         TCGA-DD-A3A8 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-DD-A3A9         TCGA-DD-A4NA         TCGA-DD-A4NB 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-DD-A4ND         TCGA-DD-A4NF         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-DD-A4NR 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-DD-A4NS         TCGA-DD-A4NV         TCGA-DD-A73A 
"15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" "15Q GAIN WILD-TYPE" 
        TCGA-DD-A73B         TCGA-DD-A73C         TCGA-DD-A73D 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-DD-A73E         TCGA-DD-A73F         TCGA-DD-A73G 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" 
        TCGA-ED-A459         TCGA-ED-A4XI         TCGA-ED-A5KG 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-ED-A627         TCGA-ED-A66X         TCGA-ED-A66Y 
"15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" "15Q GAIN WILD-TYPE" 
        TCGA-ED-A7PX         TCGA-ED-A7PY         TCGA-ED-A7PZ 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-ED-A7XP         TCGA-ED-A82E         TCGA-EP-A12J 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EP-A26S         TCGA-EP-A2KA         TCGA-EP-A2KB 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EP-A2KC         TCGA-EP-A3JL         TCGA-EP-A3RK 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-ES-A2HS         TCGA-ES-A2HT         TCGA-FV-A23B 
  "15Q GAIN MUTATED" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-FV-A2QR         TCGA-FV-A3I0         TCGA-FV-A3I1 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-FV-A3R2         TCGA-FV-A3R3         TCGA-FV-A495 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-FV-A496         TCGA-FV-A4ZP         TCGA-FV-A4ZQ 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" 
        TCGA-G3-A25S         TCGA-G3-A25T         TCGA-G3-A25U 
"15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" "15Q GAIN WILD-TYPE" 
        TCGA-G3-A25V         TCGA-G3-A25W         TCGA-G3-A25X 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" 
        TCGA-G3-A25Y         TCGA-G3-A25Z         TCGA-G3-A3CG 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-G3-A3CH         TCGA-G3-A3CI         TCGA-G3-A3CJ 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-G3-A3CK         TCGA-G3-A5SI         TCGA-G3-A5SJ 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-G3-A5SL         TCGA-G3-A5SM         TCGA-G3-A6UC 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" 
        TCGA-GJ-A6C0         TCGA-K7-A6G5         TCGA-LG-A6GG 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-MI-A75C         TCGA-MI-A75E         TCGA-MI-A75G 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" 
        TCGA-MI-A75I         TCGA-NI-A4U2         TCGA-O8-A75V 
"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-BC-A69H         TCGA-BC-A69I         TCGA-CC-5258 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-CC-5260         TCGA-CC-5261         TCGA-CC-5262 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-CC-5263         TCGA-CC-A1HT         TCGA-CC-A3M9 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" 
        TCGA-CC-A3MA         TCGA-CC-A3MB         TCGA-CC-A3MC 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-DD-A113         TCGA-DD-A114         TCGA-DD-A115 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-DD-A116         TCGA-DD-A118         TCGA-DD-A119 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-DD-A11A         TCGA-DD-A11B         TCGA-DD-A11C 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-DD-A11D         TCGA-DD-A1E9         TCGA-DD-A1EA 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-DD-A1EB         TCGA-DD-A1EC         TCGA-DD-A1ED 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-DD-A1EE         TCGA-DD-A1EF         TCGA-DD-A1EG 
"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-A1EK         TCGA-DD-A1EL         TCGA-DD-A39V 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-DD-A39X         TCGA-DD-A39Y         TCGA-DD-A39Z 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-DD-A3A0         TCGA-DD-A3A1         TCGA-DD-A3A2 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-DD-A3A3         TCGA-DD-A3A4         TCGA-DD-A3A5 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-DD-A3A6         TCGA-DD-A3A7         TCGA-DD-A3A8 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-DD-A3A9         TCGA-DD-A4NA         TCGA-DD-A4NB 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-DD-A4ND         TCGA-DD-A4NF         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-DD-A4NR 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-DD-A4NS         TCGA-DD-A4NV         TCGA-DD-A73A 
"15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" "15Q GAIN WILD-TYPE" 
        TCGA-DD-A73B         TCGA-DD-A73C         TCGA-DD-A73D 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-DD-A73E         TCGA-DD-A73F         TCGA-DD-A73G 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" 
        TCGA-ED-A459         TCGA-ED-A4XI         TCGA-ED-A5KG 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-ED-A627         TCGA-ED-A66X         TCGA-ED-A66Y 
"15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" "15Q GAIN WILD-TYPE" 
        TCGA-ED-A7PX         TCGA-ED-A7PY         TCGA-ED-A7PZ 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-ED-A7XP         TCGA-ED-A82E         TCGA-EP-A12J 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EP-A26S         TCGA-EP-A2KA         TCGA-EP-A2KB 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EP-A2KC         TCGA-EP-A3JL         TCGA-EP-A3RK 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-ES-A2HS         TCGA-ES-A2HT         TCGA-FV-A23B 
  "15Q GAIN MUTATED" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-FV-A2QR         TCGA-FV-A3I0         TCGA-FV-A3I1 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-FV-A3R2         TCGA-FV-A3R3         TCGA-FV-A495 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-FV-A496         TCGA-FV-A4ZP         TCGA-FV-A4ZQ 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" 
        TCGA-G3-A25S         TCGA-G3-A25T         TCGA-G3-A25U 
"15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" "15Q GAIN WILD-TYPE" 
        TCGA-G3-A25V         TCGA-G3-A25W         TCGA-G3-A25X 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" 
        TCGA-G3-A25Y         TCGA-G3-A25Z         TCGA-G3-A3CG 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-G3-A3CH         TCGA-G3-A3CI         TCGA-G3-A3CJ 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-G3-A3CK         TCGA-G3-A5SI         TCGA-G3-A5SJ 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-G3-A5SL         TCGA-G3-A5SM         TCGA-G3-A6UC 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" 
        TCGA-GJ-A6C0         TCGA-K7-A6G5         TCGA-LG-A6GG 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-MI-A75C         TCGA-MI-A75E         TCGA-MI-A75G 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" 
        TCGA-MI-A75I         TCGA-NI-A4U2         TCGA-O8-A75V 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
[1] "hr=" "2.6"
D27V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  15Q GAIN MUTATED         3        4         0          4          1
  15Q GAIN WILD-TYPE      55       32         2         26          3
                    vv
clus                 STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  15Q GAIN MUTATED            0        0         0         0
  15Q GAIN WILD-TYPE          5        1         1         2
D27V3, multiclass
                    vv
clus                 T1 T2 T3 T4
  15Q GAIN MUTATED    3  5  5  1
  15Q GAIN WILD-TYPE 58 35 35  7
D27V4, multiclass
    clus
vv   15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  T1                3                 58
  T2                5                 35
  T3                5                 35
  T4                1                  7
D27V5, binary
                    cls
clus                  0  1
  15Q GAIN MUTATED    9  0
  15Q GAIN WILD-TYPE 88  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED      9    0
  15Q GAIN WILD-TYPE   88    3
   clus
vv  15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  0                9                 88
  1                0                  3
                    vv
clus                  M0  M1  MX
  15Q GAIN MUTATED    11   0   3
  15Q GAIN WILD-TYPE 104   3  28
D27V6, multiclass
    clus
vv   15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  M0               11                104
  M1                0                  3
  MX                3                 28
D27V7, binary
                    cls
clus                  0  1
  15Q GAIN MUTATED    4 10
  15Q GAIN WILD-TYPE 54 81
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED      4   10
  15Q GAIN WILD-TYPE   54   81
        clus
vv       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  FEMALE                4                 54
  MALE                 10                 81
                    vv
clus                  R0  R1  R2  RX
  15Q GAIN MUTATED    13   1   0   0
  15Q GAIN WILD-TYPE 109  10   1  10
D27V8, multiclass
    clus
vv   15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  R0               13                109
  R1                1                 10
  R2                0                  1
  RX                0                 10

Clustering(28) Variable = 16P GAIN MUTATION ANALYSIS
D28V1, survival
                    sevent
clus2                 0  1
  16P GAIN MUTATED    7  5
  16P GAIN WILD-TYPE 77 58
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                12                135 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                 5                 58 
$`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-ED-A7PZ TCGA-ED-A82E TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A5SM 
       13.41         0.20         0.20         1.22        51.06         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-BC-A69H TCGA-BC-A69I 
       13.84         0.26        22.36         9.50         3.95         0.53 
TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A1HT 
        0.07         2.86         0.39         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        37.78        83.57 
TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D 
       53.33       113.00         7.33         0.46        21.76        51.29 
TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE 
       90.71        79.40        66.31        19.79        75.65         6.71 
TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK 
       12.95        45.11        49.15         6.02        29.16        18.35 
TCGA-DD-A39V TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 
       21.14        55.69         5.62        19.76        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-A4NB TCGA-DD-A4ND TCGA-DD-A4NF TCGA-DD-A4NH 
       30.61        33.14        12.85        73.38        14.07        14.24 
TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO 
       18.44        15.06        39.78        56.25        29.56        61.45 
TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A 
       93.67        12.26         0.30        80.75        66.35        10.98 
TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G 
        9.30         7.56        10.98         1.45        27.72       100.96 
TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PX 
       12.69        15.85        13.91        13.35         0.23         0.20 
TCGA-ED-A7PY TCGA-ED-A7XP TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB 
        0.20         0.20        18.74        19.99        11.74        10.98 
TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A23B 
        0.62         9.96        11.93        22.85        14.40        32.45 
TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 
       19.10         0.20         8.12         6.38         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        30.74 
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         5.92 
TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SL TCGA-G3-A6UC 
       19.53        19.23        14.70        11.97         7.99         7.76 
TCGA-GJ-A6C0 TCGA-K7-A6G5 TCGA-LG-A6GG TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G 
        1.02         4.01         0.49         9.57         5.10        14.24 
TCGA-MI-A75I TCGA-NI-A4U2 TCGA-O8-A75V 
        8.71        58.88         4.44 

  16P GAIN MUTATED 16P GAIN WILD-TYPE 
              0.20               0.03 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
            102.74             113.00 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
              7.58              14.40 
[1] "0.2 - 102.7 (7.6)"  "0.0 - 113.0 (14.4)"
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
  "16P GAIN MUTATED" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
  "16P GAIN MUTATED" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-BC-A5W4 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BC-A69H         TCGA-BC-A69I         TCGA-CC-5258 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-CC-5260         TCGA-CC-5261         TCGA-CC-5262 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-CC-5263         TCGA-CC-A1HT         TCGA-CC-A3M9 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-CC-A3MA         TCGA-CC-A3MB         TCGA-CC-A3MC 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DD-A113         TCGA-DD-A114         TCGA-DD-A115 
  "16P GAIN MUTATED" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DD-A116         TCGA-DD-A118         TCGA-DD-A119 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DD-A11A         TCGA-DD-A11B         TCGA-DD-A11C 
  "16P GAIN MUTATED" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DD-A11D         TCGA-DD-A1E9         TCGA-DD-A1EA 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DD-A1EB         TCGA-DD-A1EC         TCGA-DD-A1ED 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DD-A1EE         TCGA-DD-A1EF         TCGA-DD-A1EG 
"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-A1EK         TCGA-DD-A1EL         TCGA-DD-A39V 
"16P GAIN WILD-TYPE"   "16P GAIN MUTATED" "16P GAIN WILD-TYPE" 
        TCGA-DD-A39X         TCGA-DD-A39Y         TCGA-DD-A39Z 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DD-A3A0         TCGA-DD-A3A1         TCGA-DD-A3A2 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DD-A3A3         TCGA-DD-A3A4         TCGA-DD-A3A5 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE"   "16P GAIN MUTATED" 
        TCGA-DD-A3A6         TCGA-DD-A3A7         TCGA-DD-A3A8 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DD-A3A9         TCGA-DD-A4NA         TCGA-DD-A4NB 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DD-A4ND         TCGA-DD-A4NF         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-DD-A4NR 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DD-A4NS         TCGA-DD-A4NV         TCGA-DD-A73A 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DD-A73B         TCGA-DD-A73C         TCGA-DD-A73D 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DD-A73E         TCGA-DD-A73F         TCGA-DD-A73G 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-ED-A459         TCGA-ED-A4XI         TCGA-ED-A5KG 
  "16P GAIN MUTATED" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-ED-A627         TCGA-ED-A66X         TCGA-ED-A66Y 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-ED-A7PX         TCGA-ED-A7PY         TCGA-ED-A7PZ 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE"   "16P GAIN MUTATED" 
        TCGA-ED-A7XP         TCGA-ED-A82E         TCGA-EP-A12J 
"16P GAIN WILD-TYPE"   "16P GAIN MUTATED" "16P GAIN WILD-TYPE" 
        TCGA-EP-A26S         TCGA-EP-A2KA         TCGA-EP-A2KB 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-EP-A2KC         TCGA-EP-A3JL         TCGA-EP-A3RK 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-ES-A2HS         TCGA-ES-A2HT         TCGA-FV-A23B 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-FV-A2QR         TCGA-FV-A3I0         TCGA-FV-A3I1 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-FV-A3R2         TCGA-FV-A3R3         TCGA-FV-A495 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-FV-A496         TCGA-FV-A4ZP         TCGA-FV-A4ZQ 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-G3-A25S         TCGA-G3-A25T         TCGA-G3-A25U 
  "16P GAIN MUTATED"   "16P GAIN MUTATED" "16P GAIN WILD-TYPE" 
        TCGA-G3-A25V         TCGA-G3-A25W         TCGA-G3-A25X 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-G3-A25Y         TCGA-G3-A25Z         TCGA-G3-A3CG 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-G3-A3CH         TCGA-G3-A3CI         TCGA-G3-A3CJ 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-G3-A3CK         TCGA-G3-A5SI         TCGA-G3-A5SJ 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-G3-A5SL         TCGA-G3-A5SM         TCGA-G3-A6UC 
"16P GAIN WILD-TYPE"   "16P GAIN MUTATED" "16P GAIN WILD-TYPE" 
        TCGA-GJ-A6C0         TCGA-K7-A6G5         TCGA-LG-A6GG 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-MI-A75C         TCGA-MI-A75E         TCGA-MI-A75G 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-MI-A75I         TCGA-NI-A4U2         TCGA-O8-A75V 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
  "16P GAIN MUTATED" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
  "16P GAIN MUTATED" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-BC-A5W4 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BC-A69H         TCGA-BC-A69I         TCGA-CC-5258 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-CC-5260         TCGA-CC-5261         TCGA-CC-5262 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-CC-5263         TCGA-CC-A1HT         TCGA-CC-A3M9 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-CC-A3MA         TCGA-CC-A3MB         TCGA-CC-A3MC 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DD-A113         TCGA-DD-A114         TCGA-DD-A115 
  "16P GAIN MUTATED" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DD-A116         TCGA-DD-A118         TCGA-DD-A119 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DD-A11A         TCGA-DD-A11B         TCGA-DD-A11C 
  "16P GAIN MUTATED" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DD-A11D         TCGA-DD-A1E9         TCGA-DD-A1EA 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DD-A1EB         TCGA-DD-A1EC         TCGA-DD-A1ED 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DD-A1EE         TCGA-DD-A1EF         TCGA-DD-A1EG 
"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-A1EK         TCGA-DD-A1EL         TCGA-DD-A39V 
"16P GAIN WILD-TYPE"   "16P GAIN MUTATED" "16P GAIN WILD-TYPE" 
        TCGA-DD-A39X         TCGA-DD-A39Y         TCGA-DD-A39Z 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DD-A3A0         TCGA-DD-A3A1         TCGA-DD-A3A2 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DD-A3A3         TCGA-DD-A3A4         TCGA-DD-A3A5 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE"   "16P GAIN MUTATED" 
        TCGA-DD-A3A6         TCGA-DD-A3A7         TCGA-DD-A3A8 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DD-A3A9         TCGA-DD-A4NA         TCGA-DD-A4NB 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DD-A4ND         TCGA-DD-A4NF         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-DD-A4NR 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DD-A4NS         TCGA-DD-A4NV         TCGA-DD-A73A 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DD-A73B         TCGA-DD-A73C         TCGA-DD-A73D 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DD-A73E         TCGA-DD-A73F         TCGA-DD-A73G 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-ED-A459         TCGA-ED-A4XI         TCGA-ED-A5KG 
  "16P GAIN MUTATED" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-ED-A627         TCGA-ED-A66X         TCGA-ED-A66Y 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-ED-A7PX         TCGA-ED-A7PY         TCGA-ED-A7PZ 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE"   "16P GAIN MUTATED" 
        TCGA-ED-A7XP         TCGA-ED-A82E         TCGA-EP-A12J 
"16P GAIN WILD-TYPE"   "16P GAIN MUTATED" "16P GAIN WILD-TYPE" 
        TCGA-EP-A26S         TCGA-EP-A2KA         TCGA-EP-A2KB 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-EP-A2KC         TCGA-EP-A3JL         TCGA-EP-A3RK 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-ES-A2HS         TCGA-ES-A2HT         TCGA-FV-A23B 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-FV-A2QR         TCGA-FV-A3I0         TCGA-FV-A3I1 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-FV-A3R2         TCGA-FV-A3R3         TCGA-FV-A495 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-FV-A496         TCGA-FV-A4ZP         TCGA-FV-A4ZQ 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-G3-A25S         TCGA-G3-A25T         TCGA-G3-A25U 
  "16P GAIN MUTATED"   "16P GAIN MUTATED" "16P GAIN WILD-TYPE" 
        TCGA-G3-A25V         TCGA-G3-A25W         TCGA-G3-A25X 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-G3-A25Y         TCGA-G3-A25Z         TCGA-G3-A3CG 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-G3-A3CH         TCGA-G3-A3CI         TCGA-G3-A3CJ 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-G3-A3CK         TCGA-G3-A5SI         TCGA-G3-A5SJ 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-G3-A5SL         TCGA-G3-A5SM         TCGA-G3-A6UC 
"16P GAIN WILD-TYPE"   "16P GAIN MUTATED" "16P GAIN WILD-TYPE" 
        TCGA-GJ-A6C0         TCGA-K7-A6G5         TCGA-LG-A6GG 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-MI-A75C         TCGA-MI-A75E         TCGA-MI-A75G 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-MI-A75I         TCGA-NI-A4U2         TCGA-O8-A75V 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
  "16P GAIN MUTATED" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
  "16P GAIN MUTATED" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-BC-A5W4 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BC-A69H         TCGA-BC-A69I         TCGA-CC-5258 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-CC-5260         TCGA-CC-5261         TCGA-CC-5262 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-CC-5263         TCGA-CC-A1HT         TCGA-CC-A3M9 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-CC-A3MA         TCGA-CC-A3MB         TCGA-CC-A3MC 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DD-A113         TCGA-DD-A114         TCGA-DD-A115 
  "16P GAIN MUTATED" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DD-A116         TCGA-DD-A118         TCGA-DD-A119 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DD-A11A         TCGA-DD-A11B         TCGA-DD-A11C 
  "16P GAIN MUTATED" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DD-A11D         TCGA-DD-A1E9         TCGA-DD-A1EA 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DD-A1EB         TCGA-DD-A1EC         TCGA-DD-A1ED 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DD-A1EE         TCGA-DD-A1EF         TCGA-DD-A1EG 
"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-A1EK         TCGA-DD-A1EL         TCGA-DD-A39V 
"16P GAIN WILD-TYPE"   "16P GAIN MUTATED" "16P GAIN WILD-TYPE" 
        TCGA-DD-A39X         TCGA-DD-A39Y         TCGA-DD-A39Z 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DD-A3A0         TCGA-DD-A3A1         TCGA-DD-A3A2 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DD-A3A3         TCGA-DD-A3A4         TCGA-DD-A3A5 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE"   "16P GAIN MUTATED" 
        TCGA-DD-A3A6         TCGA-DD-A3A7         TCGA-DD-A3A8 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DD-A3A9         TCGA-DD-A4NA         TCGA-DD-A4NB 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DD-A4ND         TCGA-DD-A4NF         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-DD-A4NR 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DD-A4NS         TCGA-DD-A4NV         TCGA-DD-A73A 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DD-A73B         TCGA-DD-A73C         TCGA-DD-A73D 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DD-A73E         TCGA-DD-A73F         TCGA-DD-A73G 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-ED-A459         TCGA-ED-A4XI         TCGA-ED-A5KG 
  "16P GAIN MUTATED" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-ED-A627         TCGA-ED-A66X         TCGA-ED-A66Y 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-ED-A7PX         TCGA-ED-A7PY         TCGA-ED-A7PZ 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE"   "16P GAIN MUTATED" 
        TCGA-ED-A7XP         TCGA-ED-A82E         TCGA-EP-A12J 
"16P GAIN WILD-TYPE"   "16P GAIN MUTATED" "16P GAIN WILD-TYPE" 
        TCGA-EP-A26S         TCGA-EP-A2KA         TCGA-EP-A2KB 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-EP-A2KC         TCGA-EP-A3JL         TCGA-EP-A3RK 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-ES-A2HS         TCGA-ES-A2HT         TCGA-FV-A23B 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-FV-A2QR         TCGA-FV-A3I0         TCGA-FV-A3I1 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-FV-A3R2         TCGA-FV-A3R3         TCGA-FV-A495 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-FV-A496         TCGA-FV-A4ZP         TCGA-FV-A4ZQ 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-G3-A25S         TCGA-G3-A25T         TCGA-G3-A25U 
  "16P GAIN MUTATED"   "16P GAIN MUTATED" "16P GAIN WILD-TYPE" 
        TCGA-G3-A25V         TCGA-G3-A25W         TCGA-G3-A25X 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-G3-A25Y         TCGA-G3-A25Z         TCGA-G3-A3CG 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-G3-A3CH         TCGA-G3-A3CI         TCGA-G3-A3CJ 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-G3-A3CK         TCGA-G3-A5SI         TCGA-G3-A5SJ 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-G3-A5SL         TCGA-G3-A5SM         TCGA-G3-A6UC 
"16P GAIN WILD-TYPE"   "16P GAIN MUTATED" "16P GAIN WILD-TYPE" 
        TCGA-GJ-A6C0         TCGA-K7-A6G5         TCGA-LG-A6GG 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-MI-A75C         TCGA-MI-A75E         TCGA-MI-A75G 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-MI-A75I         TCGA-NI-A4U2         TCGA-O8-A75V 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
[1] "hr=" "1"  
D28V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  16P GAIN MUTATED         2        5         1          2          0
  16P GAIN WILD-TYPE      56       31         1         28          4
                    vv
clus                 STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  16P GAIN MUTATED            0        0         0         0
  16P GAIN WILD-TYPE          5        1         1         2
D28V3, multiclass
                    vv
clus                 T1 T2 T3 T4
  16P GAIN MUTATED    2  5  5  0
  16P GAIN WILD-TYPE 59 35 35  8
D28V4, multiclass
    clus
vv   16P GAIN MUTATED 16P GAIN WILD-TYPE
  T1                2                 59
  T2                5                 35
  T3                5                 35
  T4                0                  8
D28V5, binary
                    cls
clus                  0  1
  16P GAIN MUTATED    8  0
  16P GAIN WILD-TYPE 89  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED      8    0
  16P GAIN WILD-TYPE   89    3
   clus
vv  16P GAIN MUTATED 16P GAIN WILD-TYPE
  0                8                 89
  1                0                  3
                    vv
clus                  M0  M1  MX
  16P GAIN MUTATED    10   0   2
  16P GAIN WILD-TYPE 105   3  29
D28V6, multiclass
    clus
vv   16P GAIN MUTATED 16P GAIN WILD-TYPE
  M0               10                105
  M1                0                  3
  MX                2                 29
D28V7, binary
                    cls
clus                  0  1
  16P GAIN MUTATED    5  7
  16P GAIN WILD-TYPE 53 84
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED      5    7
  16P GAIN WILD-TYPE   53   84
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  FEMALE                5                 53
  MALE                  7                 84
                    vv
clus                  R0  R1  R2  RX
  16P GAIN MUTATED    11   1   0   0
  16P GAIN WILD-TYPE 111  10   1  10
D28V8, multiclass
    clus
vv   16P GAIN MUTATED 16P GAIN WILD-TYPE
  R0               11                111
  R1                1                 10
  R2                0                  1
  RX                0                 10

Clustering(29) Variable = 16Q GAIN MUTATION ANALYSIS
D29V1, survival
                    sevent
clus2                 0  1
  16Q GAIN MUTATED    3  2
  16Q GAIN WILD-TYPE 81 61
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                 5                142 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                 2                 61 
$`16Q GAIN MUTATED`
TCGA-BC-A10R TCGA-DD-A1EL TCGA-ED-A82E TCGA-G3-A25T TCGA-G3-A5SM 
       10.13        13.64         0.20        51.06         4.37 

$`16Q 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-BC-A69H 
       44.42        13.84         0.26        22.36         9.50         3.95 
TCGA-BC-A69I TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 
        0.53         0.07         2.86         0.39         3.39         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-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A 
       37.78        83.57        53.33       113.00         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        51.29        90.71        79.40        66.31 
TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH 
       19.79        75.65         6.71        12.95        45.11        49.15 
TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A39V TCGA-DD-A39X TCGA-DD-A39Y 
        6.02        29.16        18.35        21.14        55.69         5.62 
TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 
       19.76        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        30.61        33.14 
TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ 
       12.85        73.38        14.07        14.24        18.44        15.06 
TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ 
       39.78        56.25        29.56        61.45        93.67        12.26 
TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C 
        0.30        80.75        66.35        10.98         9.30         7.56 
TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G TCGA-ED-A459 TCGA-ED-A4XI 
       10.98         1.45        27.72       100.96        13.41        12.69 
TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY 
       15.85        13.91        13.35         0.23         0.20         0.20 
TCGA-ED-A7PZ TCGA-ED-A7XP TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB 
        0.20         0.20        18.74        19.99        11.74        10.98 
TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A23B 
        0.62         9.96        11.93        22.85        14.40        32.45 
TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 
       19.10         0.20         8.12         6.38         0.13         0.03 
TCGA-FV-A496 TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25U TCGA-G3-A25V 
        0.33        60.36         0.39         1.22        53.79        28.27 
TCGA-G3-A25W TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CH 
       30.74        58.49        14.86        21.53        22.13        25.64 
TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SL 
        5.92        19.53        19.23        14.70        11.97         7.99 
TCGA-G3-A6UC TCGA-GJ-A6C0 TCGA-K7-A6G5 TCGA-LG-A6GG TCGA-MI-A75C TCGA-MI-A75E 
        7.76         1.02         4.01         0.49         9.57         5.10 
TCGA-MI-A75G TCGA-MI-A75I TCGA-NI-A4U2 TCGA-O8-A75V 
       14.24         8.71        58.88         4.44 

  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
              0.20               0.03 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
             51.06             113.00 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
             10.13              14.24 
[1] "0.2 - 51.1 (10.1)"  "0.0 - 113.0 (14.2)"
        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 MUTATED" "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-BC-A69H         TCGA-BC-A69I         TCGA-CC-5258 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-CC-5260         TCGA-CC-5261         TCGA-CC-5262 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-CC-5263         TCGA-CC-A1HT         TCGA-CC-A3M9 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-CC-A3MA         TCGA-CC-A3MB         TCGA-CC-A3MC 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-DD-A113         TCGA-DD-A114         TCGA-DD-A115 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-DD-A116         TCGA-DD-A118         TCGA-DD-A119 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-DD-A11A         TCGA-DD-A11B         TCGA-DD-A11C 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-DD-A11D         TCGA-DD-A1E9         TCGA-DD-A1EA 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-DD-A1EB         TCGA-DD-A1EC         TCGA-DD-A1ED 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-DD-A1EE         TCGA-DD-A1EF         TCGA-DD-A1EG 
"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-A1EK         TCGA-DD-A1EL         TCGA-DD-A39V 
"16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" 
        TCGA-DD-A39X         TCGA-DD-A39Y         TCGA-DD-A39Z 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-DD-A3A0         TCGA-DD-A3A1         TCGA-DD-A3A2 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-DD-A3A3         TCGA-DD-A3A4         TCGA-DD-A3A5 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-DD-A3A6         TCGA-DD-A3A7         TCGA-DD-A3A8 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-DD-A3A9         TCGA-DD-A4NA         TCGA-DD-A4NB 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-DD-A4ND         TCGA-DD-A4NF         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-DD-A4NR 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-DD-A4NS         TCGA-DD-A4NV         TCGA-DD-A73A 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-DD-A73B         TCGA-DD-A73C         TCGA-DD-A73D 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-DD-A73E         TCGA-DD-A73F         TCGA-DD-A73G 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-ED-A459         TCGA-ED-A4XI         TCGA-ED-A5KG 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-ED-A627         TCGA-ED-A66X         TCGA-ED-A66Y 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-ED-A7PX         TCGA-ED-A7PY         TCGA-ED-A7PZ 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-ED-A7XP         TCGA-ED-A82E         TCGA-EP-A12J 
"16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" 
        TCGA-EP-A26S         TCGA-EP-A2KA         TCGA-EP-A2KB 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EP-A2KC         TCGA-EP-A3JL         TCGA-EP-A3RK 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-ES-A2HS         TCGA-ES-A2HT         TCGA-FV-A23B 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-FV-A2QR         TCGA-FV-A3I0         TCGA-FV-A3I1 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-FV-A3R2         TCGA-FV-A3R3         TCGA-FV-A495 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-FV-A496         TCGA-FV-A4ZP         TCGA-FV-A4ZQ 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-G3-A25S         TCGA-G3-A25T         TCGA-G3-A25U 
"16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" 
        TCGA-G3-A25V         TCGA-G3-A25W         TCGA-G3-A25X 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-G3-A25Y         TCGA-G3-A25Z         TCGA-G3-A3CG 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-G3-A3CH         TCGA-G3-A3CI         TCGA-G3-A3CJ 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-G3-A3CK         TCGA-G3-A5SI         TCGA-G3-A5SJ 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-G3-A5SL         TCGA-G3-A5SM         TCGA-G3-A6UC 
"16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" 
        TCGA-GJ-A6C0         TCGA-K7-A6G5         TCGA-LG-A6GG 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-MI-A75C         TCGA-MI-A75E         TCGA-MI-A75G 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-MI-A75I         TCGA-NI-A4U2         TCGA-O8-A75V 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        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 MUTATED" "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-BC-A69H         TCGA-BC-A69I         TCGA-CC-5258 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-CC-5260         TCGA-CC-5261         TCGA-CC-5262 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-CC-5263         TCGA-CC-A1HT         TCGA-CC-A3M9 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-CC-A3MA         TCGA-CC-A3MB         TCGA-CC-A3MC 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-DD-A113         TCGA-DD-A114         TCGA-DD-A115 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-DD-A116         TCGA-DD-A118         TCGA-DD-A119 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-DD-A11A         TCGA-DD-A11B         TCGA-DD-A11C 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-DD-A11D         TCGA-DD-A1E9         TCGA-DD-A1EA 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-DD-A1EB         TCGA-DD-A1EC         TCGA-DD-A1ED 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-DD-A1EE         TCGA-DD-A1EF         TCGA-DD-A1EG 
"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-A1EK         TCGA-DD-A1EL         TCGA-DD-A39V 
"16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" 
        TCGA-DD-A39X         TCGA-DD-A39Y         TCGA-DD-A39Z 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-DD-A3A0         TCGA-DD-A3A1         TCGA-DD-A3A2 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-DD-A3A3         TCGA-DD-A3A4         TCGA-DD-A3A5 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-DD-A3A6         TCGA-DD-A3A7         TCGA-DD-A3A8 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-DD-A3A9         TCGA-DD-A4NA         TCGA-DD-A4NB 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-DD-A4ND         TCGA-DD-A4NF         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-DD-A4NR 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-DD-A4NS         TCGA-DD-A4NV         TCGA-DD-A73A 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-DD-A73B         TCGA-DD-A73C         TCGA-DD-A73D 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-DD-A73E         TCGA-DD-A73F         TCGA-DD-A73G 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-ED-A459         TCGA-ED-A4XI         TCGA-ED-A5KG 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-ED-A627         TCGA-ED-A66X         TCGA-ED-A66Y 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-ED-A7PX         TCGA-ED-A7PY         TCGA-ED-A7PZ 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-ED-A7XP         TCGA-ED-A82E         TCGA-EP-A12J 
"16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" 
        TCGA-EP-A26S         TCGA-EP-A2KA         TCGA-EP-A2KB 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EP-A2KC         TCGA-EP-A3JL         TCGA-EP-A3RK 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-ES-A2HS         TCGA-ES-A2HT         TCGA-FV-A23B 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-FV-A2QR         TCGA-FV-A3I0         TCGA-FV-A3I1 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-FV-A3R2         TCGA-FV-A3R3         TCGA-FV-A495 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-FV-A496         TCGA-FV-A4ZP         TCGA-FV-A4ZQ 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-G3-A25S         TCGA-G3-A25T         TCGA-G3-A25U 
"16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" 
        TCGA-G3-A25V         TCGA-G3-A25W         TCGA-G3-A25X 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-G3-A25Y         TCGA-G3-A25Z         TCGA-G3-A3CG 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-G3-A3CH         TCGA-G3-A3CI         TCGA-G3-A3CJ 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-G3-A3CK         TCGA-G3-A5SI         TCGA-G3-A5SJ 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-G3-A5SL         TCGA-G3-A5SM         TCGA-G3-A6UC 
"16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" 
        TCGA-GJ-A6C0         TCGA-K7-A6G5         TCGA-LG-A6GG 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-MI-A75C         TCGA-MI-A75E         TCGA-MI-A75G 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-MI-A75I         TCGA-NI-A4U2         TCGA-O8-A75V 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        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 MUTATED" "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-BC-A69H         TCGA-BC-A69I         TCGA-CC-5258 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-CC-5260         TCGA-CC-5261         TCGA-CC-5262 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-CC-5263         TCGA-CC-A1HT         TCGA-CC-A3M9 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-CC-A3MA         TCGA-CC-A3MB         TCGA-CC-A3MC 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-DD-A113         TCGA-DD-A114         TCGA-DD-A115 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-DD-A116         TCGA-DD-A118         TCGA-DD-A119 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-DD-A11A         TCGA-DD-A11B         TCGA-DD-A11C 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-DD-A11D         TCGA-DD-A1E9         TCGA-DD-A1EA 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-DD-A1EB         TCGA-DD-A1EC         TCGA-DD-A1ED 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-DD-A1EE         TCGA-DD-A1EF         TCGA-DD-A1EG 
"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-A1EK         TCGA-DD-A1EL         TCGA-DD-A39V 
"16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" 
        TCGA-DD-A39X         TCGA-DD-A39Y         TCGA-DD-A39Z 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-DD-A3A0         TCGA-DD-A3A1         TCGA-DD-A3A2 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-DD-A3A3         TCGA-DD-A3A4         TCGA-DD-A3A5 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-DD-A3A6         TCGA-DD-A3A7         TCGA-DD-A3A8 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-DD-A3A9         TCGA-DD-A4NA         TCGA-DD-A4NB 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-DD-A4ND         TCGA-DD-A4NF         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-DD-A4NR 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-DD-A4NS         TCGA-DD-A4NV         TCGA-DD-A73A 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-DD-A73B         TCGA-DD-A73C         TCGA-DD-A73D 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-DD-A73E         TCGA-DD-A73F         TCGA-DD-A73G 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-ED-A459         TCGA-ED-A4XI         TCGA-ED-A5KG 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-ED-A627         TCGA-ED-A66X         TCGA-ED-A66Y 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-ED-A7PX         TCGA-ED-A7PY         TCGA-ED-A7PZ 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-ED-A7XP         TCGA-ED-A82E         TCGA-EP-A12J 
"16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" 
        TCGA-EP-A26S         TCGA-EP-A2KA         TCGA-EP-A2KB 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EP-A2KC         TCGA-EP-A3JL         TCGA-EP-A3RK 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-ES-A2HS         TCGA-ES-A2HT         TCGA-FV-A23B 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-FV-A2QR         TCGA-FV-A3I0         TCGA-FV-A3I1 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-FV-A3R2         TCGA-FV-A3R3         TCGA-FV-A495 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-FV-A496         TCGA-FV-A4ZP         TCGA-FV-A4ZQ 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-G3-A25S         TCGA-G3-A25T         TCGA-G3-A25U 
"16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" 
        TCGA-G3-A25V         TCGA-G3-A25W         TCGA-G3-A25X 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-G3-A25Y         TCGA-G3-A25Z         TCGA-G3-A3CG 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-G3-A3CH         TCGA-G3-A3CI         TCGA-G3-A3CJ 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-G3-A3CK         TCGA-G3-A5SI         TCGA-G3-A5SJ 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-G3-A5SL         TCGA-G3-A5SM         TCGA-G3-A6UC 
"16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" 
        TCGA-GJ-A6C0         TCGA-K7-A6G5         TCGA-LG-A6GG 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-MI-A75C         TCGA-MI-A75E         TCGA-MI-A75G 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-MI-A75I         TCGA-NI-A4U2         TCGA-O8-A75V 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
[1] "hr=" "1.5"
D29V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  16Q GAIN MUTATED         0        2         0          2          0
  16Q GAIN WILD-TYPE      58       34         2         28          4
                    vv
clus                 STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  16Q GAIN MUTATED            0        0         0         0
  16Q GAIN WILD-TYPE          5        1         1         2
D29V3, multiclass
                    vv
clus                 T1 T2 T3 T4
  16Q GAIN MUTATED    0  2  3  0
  16Q GAIN WILD-TYPE 61 38 37  8
D29V4, multiclass
    clus
vv   16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  T1                0                 61
  T2                2                 38
  T3                3                 37
  T4                0                  8
D29V5, binary
                    cls
clus                  0  1
  16Q GAIN MUTATED    3  0
  16Q GAIN WILD-TYPE 94  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED      3    0
  16Q GAIN WILD-TYPE   94    3
   clus
vv  16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  0                3                 94
  1                0                  3
                    vv
clus                  M0  M1  MX
  16Q GAIN MUTATED     4   0   1
  16Q GAIN WILD-TYPE 111   3  30
D29V6, multiclass
    clus
vv   16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  M0                4                111
  M1                0                  3
  MX                1                 30
D29V7, binary
                    cls
clus                  0  1
  16Q GAIN MUTATED    3  2
  16Q GAIN WILD-TYPE 55 89
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED      3    2
  16Q GAIN WILD-TYPE   55   89
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  FEMALE                3                 55
  MALE                  2                 89
                    vv
clus                  R0  R1  R2  RX
  16Q GAIN MUTATED     5   0   0   0
  16Q GAIN WILD-TYPE 117  11   1  10
D29V8, multiclass
    clus
vv   16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  R0                5                117
  R1                0                 11
  R2                0                  1
  RX                0                 10

Clustering(30) Variable = 17P GAIN MUTATION ANALYSIS
D30V1, survival
                    sevent
clus2                 0  1
  17P GAIN MUTATED    8  5
  17P GAIN WILD-TYPE 76 58
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                13                134 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                 5                 58 
$`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        37.78        13.78        61.45        93.67 
TCGA-DD-A73D TCGA-ED-A66X TCGA-ED-A66Y TCGA-EP-A2KB TCGA-ES-A2HS TCGA-FV-A4ZP 
       10.98        13.35         0.23        10.98        22.85        60.36 
TCGA-G3-A25W 
       30.74 

$`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-BC-A69H 
       44.42        13.84         0.26        22.36         9.50         3.95 
TCGA-BC-A69I TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 
        0.53         0.07         2.86         0.39         3.39         4.24 
TCGA-CC-A1HT TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A113 TCGA-DD-A115 
        3.32         0.07         0.10         0.13        79.73        83.57 
TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C 
       53.33       113.00         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 
       51.29        90.71        79.40        66.31        19.79        75.65 
TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ 
        6.71        12.95        45.11        49.15         6.02        29.16 
TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A39Z 
       18.35        13.64        21.14        55.69         5.62        19.76 
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-A3A8 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4ND 
      107.11         0.36        30.61        33.14        12.85        73.38 
TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL 
       14.07        14.24        18.44        15.06        39.78        56.25 
TCGA-DD-A4NN TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A 
       29.56        12.26         0.30        80.75        66.35        10.98 
TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G TCGA-ED-A459 
        9.30         7.56         1.45        27.72       100.96        13.41 
TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ 
       12.69        15.85        13.91         0.20         0.20         0.20 
TCGA-ED-A7XP TCGA-ED-A82E TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KC 
        0.20         0.20        18.74        19.99        11.74         0.62 
TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-A3I0 
        9.96        11.93        14.40        32.45        19.10         0.20 
TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZQ 
        8.12         6.38         0.13         0.03         0.33         0.39 
TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25X TCGA-G3-A25Y 
        1.22        51.06        53.79        28.27        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         5.92        19.53        19.23 
TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A6UC TCGA-GJ-A6C0 
       14.70        11.97         7.99         4.37         7.76         1.02 
TCGA-K7-A6G5 TCGA-LG-A6GG TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75I 
        4.01         0.49         9.57         5.10        14.24         8.71 
TCGA-NI-A4U2 TCGA-O8-A75V 
       58.88         4.44 

  17P GAIN MUTATED 17P GAIN WILD-TYPE 
              0.10               0.03 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
             93.67             113.00 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
             22.85              13.99 
[1] "0.1 - 93.7 (22.9)"  "0.0 - 113.0 (14.0)"
        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-BC-A69H         TCGA-BC-A69I         TCGA-CC-5258 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-CC-5260         TCGA-CC-5261         TCGA-CC-5262 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-CC-5263         TCGA-CC-A1HT         TCGA-CC-A3M9 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE"   "17P GAIN MUTATED" 
        TCGA-CC-A3MA         TCGA-CC-A3MB         TCGA-CC-A3MC 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DD-A113         TCGA-DD-A114         TCGA-DD-A115 
"17P GAIN WILD-TYPE"   "17P GAIN MUTATED" "17P GAIN WILD-TYPE" 
        TCGA-DD-A116         TCGA-DD-A118         TCGA-DD-A119 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DD-A11A         TCGA-DD-A11B         TCGA-DD-A11C 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DD-A11D         TCGA-DD-A1E9         TCGA-DD-A1EA 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DD-A1EB         TCGA-DD-A1EC         TCGA-DD-A1ED 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DD-A1EE         TCGA-DD-A1EF         TCGA-DD-A1EG 
"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-A1EK         TCGA-DD-A1EL         TCGA-DD-A39V 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DD-A39X         TCGA-DD-A39Y         TCGA-DD-A39Z 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DD-A3A0         TCGA-DD-A3A1         TCGA-DD-A3A2 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DD-A3A3         TCGA-DD-A3A4         TCGA-DD-A3A5 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DD-A3A6         TCGA-DD-A3A7         TCGA-DD-A3A8 
"17P GAIN WILD-TYPE"   "17P GAIN MUTATED" "17P GAIN WILD-TYPE" 
        TCGA-DD-A3A9         TCGA-DD-A4NA         TCGA-DD-A4NB 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DD-A4ND         TCGA-DD-A4NF         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-DD-A4NR 
  "17P GAIN MUTATED" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DD-A4NS         TCGA-DD-A4NV         TCGA-DD-A73A 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DD-A73B         TCGA-DD-A73C         TCGA-DD-A73D 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE"   "17P GAIN MUTATED" 
        TCGA-DD-A73E         TCGA-DD-A73F         TCGA-DD-A73G 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-ED-A459         TCGA-ED-A4XI         TCGA-ED-A5KG 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-ED-A627         TCGA-ED-A66X         TCGA-ED-A66Y 
"17P GAIN WILD-TYPE"   "17P GAIN MUTATED"   "17P GAIN MUTATED" 
        TCGA-ED-A7PX         TCGA-ED-A7PY         TCGA-ED-A7PZ 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-ED-A7XP         TCGA-ED-A82E         TCGA-EP-A12J 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EP-A26S         TCGA-EP-A2KA         TCGA-EP-A2KB 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE"   "17P GAIN MUTATED" 
        TCGA-EP-A2KC         TCGA-EP-A3JL         TCGA-EP-A3RK 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-ES-A2HS         TCGA-ES-A2HT         TCGA-FV-A23B 
  "17P GAIN MUTATED" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-FV-A2QR         TCGA-FV-A3I0         TCGA-FV-A3I1 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-FV-A3R2         TCGA-FV-A3R3         TCGA-FV-A495 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-FV-A496         TCGA-FV-A4ZP         TCGA-FV-A4ZQ 
"17P GAIN WILD-TYPE"   "17P GAIN MUTATED" "17P GAIN WILD-TYPE" 
        TCGA-G3-A25S         TCGA-G3-A25T         TCGA-G3-A25U 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-G3-A25V         TCGA-G3-A25W         TCGA-G3-A25X 
"17P GAIN WILD-TYPE"   "17P GAIN MUTATED" "17P GAIN WILD-TYPE" 
        TCGA-G3-A25Y         TCGA-G3-A25Z         TCGA-G3-A3CG 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-G3-A3CH         TCGA-G3-A3CI         TCGA-G3-A3CJ 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-G3-A3CK         TCGA-G3-A5SI         TCGA-G3-A5SJ 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-G3-A5SL         TCGA-G3-A5SM         TCGA-G3-A6UC 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-GJ-A6C0         TCGA-K7-A6G5         TCGA-LG-A6GG 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-MI-A75C         TCGA-MI-A75E         TCGA-MI-A75G 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-MI-A75I         TCGA-NI-A4U2         TCGA-O8-A75V 
"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-BC-A69H         TCGA-BC-A69I         TCGA-CC-5258 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-CC-5260         TCGA-CC-5261         TCGA-CC-5262 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-CC-5263         TCGA-CC-A1HT         TCGA-CC-A3M9 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE"   "17P GAIN MUTATED" 
        TCGA-CC-A3MA         TCGA-CC-A3MB         TCGA-CC-A3MC 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DD-A113         TCGA-DD-A114         TCGA-DD-A115 
"17P GAIN WILD-TYPE"   "17P GAIN MUTATED" "17P GAIN WILD-TYPE" 
        TCGA-DD-A116         TCGA-DD-A118         TCGA-DD-A119 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DD-A11A         TCGA-DD-A11B         TCGA-DD-A11C 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DD-A11D         TCGA-DD-A1E9         TCGA-DD-A1EA 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DD-A1EB         TCGA-DD-A1EC         TCGA-DD-A1ED 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DD-A1EE         TCGA-DD-A1EF         TCGA-DD-A1EG 
"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-A1EK         TCGA-DD-A1EL         TCGA-DD-A39V 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DD-A39X         TCGA-DD-A39Y         TCGA-DD-A39Z 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DD-A3A0         TCGA-DD-A3A1         TCGA-DD-A3A2 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DD-A3A3         TCGA-DD-A3A4         TCGA-DD-A3A5 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DD-A3A6         TCGA-DD-A3A7         TCGA-DD-A3A8 
"17P GAIN WILD-TYPE"   "17P GAIN MUTATED" "17P GAIN WILD-TYPE" 
        TCGA-DD-A3A9         TCGA-DD-A4NA         TCGA-DD-A4NB 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DD-A4ND         TCGA-DD-A4NF         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-DD-A4NR 
  "17P GAIN MUTATED" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DD-A4NS         TCGA-DD-A4NV         TCGA-DD-A73A 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DD-A73B         TCGA-DD-A73C         TCGA-DD-A73D 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE"   "17P GAIN MUTATED" 
        TCGA-DD-A73E         TCGA-DD-A73F         TCGA-DD-A73G 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-ED-A459         TCGA-ED-A4XI         TCGA-ED-A5KG 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-ED-A627         TCGA-ED-A66X         TCGA-ED-A66Y 
"17P GAIN WILD-TYPE"   "17P GAIN MUTATED"   "17P GAIN MUTATED" 
        TCGA-ED-A7PX         TCGA-ED-A7PY         TCGA-ED-A7PZ 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-ED-A7XP         TCGA-ED-A82E         TCGA-EP-A12J 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EP-A26S         TCGA-EP-A2KA         TCGA-EP-A2KB 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE"   "17P GAIN MUTATED" 
        TCGA-EP-A2KC         TCGA-EP-A3JL         TCGA-EP-A3RK 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-ES-A2HS         TCGA-ES-A2HT         TCGA-FV-A23B 
  "17P GAIN MUTATED" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-FV-A2QR         TCGA-FV-A3I0         TCGA-FV-A3I1 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-FV-A3R2         TCGA-FV-A3R3         TCGA-FV-A495 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-FV-A496         TCGA-FV-A4ZP         TCGA-FV-A4ZQ 
"17P GAIN WILD-TYPE"   "17P GAIN MUTATED" "17P GAIN WILD-TYPE" 
        TCGA-G3-A25S         TCGA-G3-A25T         TCGA-G3-A25U 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-G3-A25V         TCGA-G3-A25W         TCGA-G3-A25X 
"17P GAIN WILD-TYPE"   "17P GAIN MUTATED" "17P GAIN WILD-TYPE" 
        TCGA-G3-A25Y         TCGA-G3-A25Z         TCGA-G3-A3CG 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-G3-A3CH         TCGA-G3-A3CI         TCGA-G3-A3CJ 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-G3-A3CK         TCGA-G3-A5SI         TCGA-G3-A5SJ 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-G3-A5SL         TCGA-G3-A5SM         TCGA-G3-A6UC 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-GJ-A6C0         TCGA-K7-A6G5         TCGA-LG-A6GG 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-MI-A75C         TCGA-MI-A75E         TCGA-MI-A75G 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-MI-A75I         TCGA-NI-A4U2         TCGA-O8-A75V 
"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-BC-A69H         TCGA-BC-A69I         TCGA-CC-5258 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-CC-5260         TCGA-CC-5261         TCGA-CC-5262 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-CC-5263         TCGA-CC-A1HT         TCGA-CC-A3M9 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE"   "17P GAIN MUTATED" 
        TCGA-CC-A3MA         TCGA-CC-A3MB         TCGA-CC-A3MC 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DD-A113         TCGA-DD-A114         TCGA-DD-A115 
"17P GAIN WILD-TYPE"   "17P GAIN MUTATED" "17P GAIN WILD-TYPE" 
        TCGA-DD-A116         TCGA-DD-A118         TCGA-DD-A119 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DD-A11A         TCGA-DD-A11B         TCGA-DD-A11C 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DD-A11D         TCGA-DD-A1E9         TCGA-DD-A1EA 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DD-A1EB         TCGA-DD-A1EC         TCGA-DD-A1ED 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DD-A1EE         TCGA-DD-A1EF         TCGA-DD-A1EG 
"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-A1EK         TCGA-DD-A1EL         TCGA-DD-A39V 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DD-A39X         TCGA-DD-A39Y         TCGA-DD-A39Z 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DD-A3A0         TCGA-DD-A3A1         TCGA-DD-A3A2 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DD-A3A3         TCGA-DD-A3A4         TCGA-DD-A3A5 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DD-A3A6         TCGA-DD-A3A7         TCGA-DD-A3A8 
"17P GAIN WILD-TYPE"   "17P GAIN MUTATED" "17P GAIN WILD-TYPE" 
        TCGA-DD-A3A9         TCGA-DD-A4NA         TCGA-DD-A4NB 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DD-A4ND         TCGA-DD-A4NF         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-DD-A4NR 
  "17P GAIN MUTATED" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DD-A4NS         TCGA-DD-A4NV         TCGA-DD-A73A 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DD-A73B         TCGA-DD-A73C         TCGA-DD-A73D 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE"   "17P GAIN MUTATED" 
        TCGA-DD-A73E         TCGA-DD-A73F         TCGA-DD-A73G 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-ED-A459         TCGA-ED-A4XI         TCGA-ED-A5KG 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-ED-A627         TCGA-ED-A66X         TCGA-ED-A66Y 
"17P GAIN WILD-TYPE"   "17P GAIN MUTATED"   "17P GAIN MUTATED" 
        TCGA-ED-A7PX         TCGA-ED-A7PY         TCGA-ED-A7PZ 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-ED-A7XP         TCGA-ED-A82E         TCGA-EP-A12J 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EP-A26S         TCGA-EP-A2KA         TCGA-EP-A2KB 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE"   "17P GAIN MUTATED" 
        TCGA-EP-A2KC         TCGA-EP-A3JL         TCGA-EP-A3RK 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-ES-A2HS         TCGA-ES-A2HT         TCGA-FV-A23B 
  "17P GAIN MUTATED" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-FV-A2QR         TCGA-FV-A3I0         TCGA-FV-A3I1 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-FV-A3R2         TCGA-FV-A3R3         TCGA-FV-A495 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-FV-A496         TCGA-FV-A4ZP         TCGA-FV-A4ZQ 
"17P GAIN WILD-TYPE"   "17P GAIN MUTATED" "17P GAIN WILD-TYPE" 
        TCGA-G3-A25S         TCGA-G3-A25T         TCGA-G3-A25U 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-G3-A25V         TCGA-G3-A25W         TCGA-G3-A25X 
"17P GAIN WILD-TYPE"   "17P GAIN MUTATED" "17P GAIN WILD-TYPE" 
        TCGA-G3-A25Y         TCGA-G3-A25Z         TCGA-G3-A3CG 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-G3-A3CH         TCGA-G3-A3CI         TCGA-G3-A3CJ 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-G3-A3CK         TCGA-G3-A5SI         TCGA-G3-A5SJ 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-G3-A5SL         TCGA-G3-A5SM         TCGA-G3-A6UC 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-GJ-A6C0         TCGA-K7-A6G5         TCGA-LG-A6GG 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-MI-A75C         TCGA-MI-A75E         TCGA-MI-A75G 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-MI-A75I         TCGA-NI-A4U2         TCGA-O8-A75V 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
[1] "hr=" "1.4"
D30V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  17P GAIN MUTATED         4        2         0          4          2
  17P GAIN WILD-TYPE      54       34         2         26          2
                    vv
clus                 STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  17P GAIN MUTATED            0        0         0         0
  17P GAIN WILD-TYPE          5        1         1         2
D30V3, multiclass
                    vv
clus                 T1 T2 T3 T4
  17P GAIN MUTATED    4  3  6  0
  17P GAIN WILD-TYPE 57 37 34  8
D30V4, multiclass
    clus
vv   17P GAIN MUTATED 17P GAIN WILD-TYPE
  T1                4                 57
  T2                3                 37
  T3                6                 34
  T4                0                  8
D30V5, binary
                    cls
clus                  0  1
  17P GAIN MUTATED    7  0
  17P GAIN WILD-TYPE 90  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED      7    0
  17P GAIN WILD-TYPE   90    3
   clus
vv  17P GAIN MUTATED 17P GAIN WILD-TYPE
  0                7                 90
  1                0                  3
                    vv
clus                  M0  M1  MX
  17P GAIN MUTATED     9   0   4
  17P GAIN WILD-TYPE 106   3  27
D30V6, multiclass
    clus
vv   17P GAIN MUTATED 17P GAIN WILD-TYPE
  M0                9                106
  M1                0                  3
  MX                4                 27
D30V7, binary
                    cls
clus                  0  1
  17P GAIN MUTATED    5  8
  17P GAIN WILD-TYPE 53 83
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED      5    8
  17P GAIN WILD-TYPE   53   83
        clus
vv       17P GAIN MUTATED 17P GAIN WILD-TYPE
  FEMALE                5                 53
  MALE                  8                 83
                    vv
clus                  R0  R1  R2  RX
  17P GAIN MUTATED    11   2   0   0
  17P GAIN WILD-TYPE 111   9   1  10
D30V8, multiclass
    clus
vv   17P GAIN MUTATED 17P GAIN WILD-TYPE
  R0               11                111
  R1                2                  9
  R2                0                  1
  RX                0                 10

Clustering(31) Variable = 17Q GAIN MUTATION ANALYSIS
D31V1, survival
                    sevent
clus2                 0  1
  17Q GAIN MUTATED   21 17
  17Q GAIN WILD-TYPE 63 46
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                38                109 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                17                 46 
$`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-BC-A69H TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5263 TCGA-CC-A3MC 
       13.84         3.95         2.86         0.39         4.24         0.13 
TCGA-DD-A114 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A1EA TCGA-DD-A1EI TCGA-DD-A39Y 
       37.78         7.33         2.60        79.40         6.02         5.62 
TCGA-DD-A3A7 TCGA-DD-A3A9 TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A73D TCGA-DD-A73E 
       13.78        30.61        61.45        93.67        10.98         1.45 
TCGA-ED-A66X TCGA-ED-A66Y TCGA-EP-A2KB TCGA-EP-A2KC TCGA-ES-A2HS TCGA-FV-A495 
       13.35         0.23        10.98         0.62        22.85         0.03 
TCGA-FV-A4ZP TCGA-G3-A25U TCGA-G3-A25W TCGA-G3-A25Z TCGA-G3-A3CK TCGA-G3-A5SJ 
       60.36        53.79        30.74        21.53        19.23        11.97 
TCGA-MI-A75I TCGA-O8-A75V 
        8.71         4.44 

$`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-BC-A69I 
       69.57        44.42         0.26        22.36         9.50         0.53 
TCGA-CC-5258 TCGA-CC-5262 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB 
        0.07         3.39         3.32         0.10         0.07         0.10 
TCGA-DD-A113 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A11B TCGA-DD-A11C 
       79.73        83.57        53.33       113.00         0.46        21.76 
TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE 
       51.29        90.71        66.31        19.79        75.65         6.71 
TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A1EL 
       12.95        45.11        49.15        29.16        18.35        13.64 
TCGA-DD-A39V TCGA-DD-A39X TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 
       21.14        55.69        19.76        25.81         7.66        70.06 
TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A8 TCGA-DD-A4NA 
       17.59        20.12       102.74       107.11         0.36        33.14 
TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ 
       12.85        73.38        14.07        14.24        18.44        15.06 
TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS 
       39.78        56.25        29.56        12.26         0.30        80.75 
TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73F TCGA-DD-A73G 
       66.35        10.98         9.30         7.56        27.72       100.96 
TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A7PX TCGA-ED-A7PY 
       13.41        12.69        15.85        13.91         0.20         0.20 
TCGA-ED-A7PZ TCGA-ED-A7XP TCGA-ED-A82E TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA 
        0.20         0.20         0.20        18.74        19.99        11.74 
TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-A3I0 
        9.96        11.93        14.40        32.45        19.10         0.20 
TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A496 TCGA-FV-A4ZQ TCGA-G3-A25S 
        8.12         6.38         0.13         0.33         0.39         1.22 
TCGA-G3-A25T TCGA-G3-A25V TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A3CG TCGA-G3-A3CH 
       51.06        28.27        58.49        14.86        22.13        25.64 
TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A5SI TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A6UC 
        5.92        19.53        14.70         7.99         4.37         7.76 
TCGA-GJ-A6C0 TCGA-K7-A6G5 TCGA-LG-A6GG TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G 
        1.02         4.01         0.49         9.57         5.10        14.24 
TCGA-NI-A4U2 
       58.88 

  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
              0.03               0.07 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
             93.67             113.00 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
             10.98              14.86 
[1] "0.0 - 93.7 (11.0)"  "0.1 - 113.0 (14.9)"
        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-BC-A69H         TCGA-BC-A69I         TCGA-CC-5258 
  "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-CC-5260         TCGA-CC-5261         TCGA-CC-5262 
  "17Q GAIN MUTATED"   "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" 
        TCGA-CC-5263         TCGA-CC-A1HT         TCGA-CC-A3M9 
  "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-CC-A3MA         TCGA-CC-A3MB         TCGA-CC-A3MC 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
        TCGA-DD-A113         TCGA-DD-A114         TCGA-DD-A115 
"17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" 
        TCGA-DD-A116         TCGA-DD-A118         TCGA-DD-A119 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
        TCGA-DD-A11A         TCGA-DD-A11B         TCGA-DD-A11C 
  "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-DD-A11D         TCGA-DD-A1E9         TCGA-DD-A1EA 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
        TCGA-DD-A1EB         TCGA-DD-A1EC         TCGA-DD-A1ED 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-DD-A1EE         TCGA-DD-A1EF         TCGA-DD-A1EG 
"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 WILD-TYPE" 
        TCGA-DD-A1EK         TCGA-DD-A1EL         TCGA-DD-A39V 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-DD-A39X         TCGA-DD-A39Y         TCGA-DD-A39Z 
"17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" 
        TCGA-DD-A3A0         TCGA-DD-A3A1         TCGA-DD-A3A2 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-DD-A3A3         TCGA-DD-A3A4         TCGA-DD-A3A5 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-DD-A3A6         TCGA-DD-A3A7         TCGA-DD-A3A8 
"17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" 
        TCGA-DD-A3A9         TCGA-DD-A4NA         TCGA-DD-A4NB 
  "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-DD-A4ND         TCGA-DD-A4NF         TCGA-DD-A4NH 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        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-DD-A4NR 
  "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-DD-A4NS         TCGA-DD-A4NV         TCGA-DD-A73A 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-DD-A73B         TCGA-DD-A73C         TCGA-DD-A73D 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
        TCGA-DD-A73E         TCGA-DD-A73F         TCGA-DD-A73G 
  "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-ED-A459         TCGA-ED-A4XI         TCGA-ED-A5KG 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-ED-A627         TCGA-ED-A66X         TCGA-ED-A66Y 
"17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED"   "17Q GAIN MUTATED" 
        TCGA-ED-A7PX         TCGA-ED-A7PY         TCGA-ED-A7PZ 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-ED-A7XP         TCGA-ED-A82E         TCGA-EP-A12J 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-EP-A26S         TCGA-EP-A2KA         TCGA-EP-A2KB 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
        TCGA-EP-A2KC         TCGA-EP-A3JL         TCGA-EP-A3RK 
  "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-ES-A2HS         TCGA-ES-A2HT         TCGA-FV-A23B 
  "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-FV-A2QR         TCGA-FV-A3I0         TCGA-FV-A3I1 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-FV-A3R2         TCGA-FV-A3R3         TCGA-FV-A495 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
        TCGA-FV-A496         TCGA-FV-A4ZP         TCGA-FV-A4ZQ 
"17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" 
        TCGA-G3-A25S         TCGA-G3-A25T         TCGA-G3-A25U 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
        TCGA-G3-A25V         TCGA-G3-A25W         TCGA-G3-A25X 
"17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" 
        TCGA-G3-A25Y         TCGA-G3-A25Z         TCGA-G3-A3CG 
"17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" 
        TCGA-G3-A3CH         TCGA-G3-A3CI         TCGA-G3-A3CJ 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-G3-A3CK         TCGA-G3-A5SI         TCGA-G3-A5SJ 
  "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
        TCGA-G3-A5SL         TCGA-G3-A5SM         TCGA-G3-A6UC 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-GJ-A6C0         TCGA-K7-A6G5         TCGA-LG-A6GG 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-MI-A75C         TCGA-MI-A75E         TCGA-MI-A75G 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-MI-A75I         TCGA-NI-A4U2         TCGA-O8-A75V 
  "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
  "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
  "17Q GAIN MUTATED"   "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
  "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-BC-A5W4 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-BC-A69H         TCGA-BC-A69I         TCGA-CC-5258 
  "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-CC-5260         TCGA-CC-5261         TCGA-CC-5262 
  "17Q GAIN MUTATED"   "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" 
        TCGA-CC-5263         TCGA-CC-A1HT         TCGA-CC-A3M9 
  "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-CC-A3MA         TCGA-CC-A3MB         TCGA-CC-A3MC 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
        TCGA-DD-A113         TCGA-DD-A114         TCGA-DD-A115 
"17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" 
        TCGA-DD-A116         TCGA-DD-A118         TCGA-DD-A119 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
        TCGA-DD-A11A         TCGA-DD-A11B         TCGA-DD-A11C 
  "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-DD-A11D         TCGA-DD-A1E9         TCGA-DD-A1EA 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
        TCGA-DD-A1EB         TCGA-DD-A1EC         TCGA-DD-A1ED 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-DD-A1EE         TCGA-DD-A1EF         TCGA-DD-A1EG 
"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 WILD-TYPE" 
        TCGA-DD-A1EK         TCGA-DD-A1EL         TCGA-DD-A39V 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-DD-A39X         TCGA-DD-A39Y         TCGA-DD-A39Z 
"17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" 
        TCGA-DD-A3A0         TCGA-DD-A3A1         TCGA-DD-A3A2 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-DD-A3A3         TCGA-DD-A3A4         TCGA-DD-A3A5 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-DD-A3A6         TCGA-DD-A3A7         TCGA-DD-A3A8 
"17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" 
        TCGA-DD-A3A9         TCGA-DD-A4NA         TCGA-DD-A4NB 
  "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-DD-A4ND         TCGA-DD-A4NF         TCGA-DD-A4NH 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        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-DD-A4NR 
  "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-DD-A4NS         TCGA-DD-A4NV         TCGA-DD-A73A 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-DD-A73B         TCGA-DD-A73C         TCGA-DD-A73D 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
        TCGA-DD-A73E         TCGA-DD-A73F         TCGA-DD-A73G 
  "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-ED-A459         TCGA-ED-A4XI         TCGA-ED-A5KG 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-ED-A627         TCGA-ED-A66X         TCGA-ED-A66Y 
"17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED"   "17Q GAIN MUTATED" 
        TCGA-ED-A7PX         TCGA-ED-A7PY         TCGA-ED-A7PZ 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-ED-A7XP         TCGA-ED-A82E         TCGA-EP-A12J 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-EP-A26S         TCGA-EP-A2KA         TCGA-EP-A2KB 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
        TCGA-EP-A2KC         TCGA-EP-A3JL         TCGA-EP-A3RK 
  "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-ES-A2HS         TCGA-ES-A2HT         TCGA-FV-A23B 
  "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-FV-A2QR         TCGA-FV-A3I0         TCGA-FV-A3I1 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-FV-A3R2         TCGA-FV-A3R3         TCGA-FV-A495 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
        TCGA-FV-A496         TCGA-FV-A4ZP         TCGA-FV-A4ZQ 
"17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" 
        TCGA-G3-A25S         TCGA-G3-A25T         TCGA-G3-A25U 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
        TCGA-G3-A25V         TCGA-G3-A25W         TCGA-G3-A25X 
"17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" 
        TCGA-G3-A25Y         TCGA-G3-A25Z         TCGA-G3-A3CG 
"17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" 
        TCGA-G3-A3CH         TCGA-G3-A3CI         TCGA-G3-A3CJ 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-G3-A3CK         TCGA-G3-A5SI         TCGA-G3-A5SJ 
  "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
        TCGA-G3-A5SL         TCGA-G3-A5SM         TCGA-G3-A6UC 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-GJ-A6C0         TCGA-K7-A6G5         TCGA-LG-A6GG 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-MI-A75C         TCGA-MI-A75E         TCGA-MI-A75G 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-MI-A75I         TCGA-NI-A4U2         TCGA-O8-A75V 
  "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
  "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
  "17Q GAIN MUTATED"   "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
  "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-BC-A5W4 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-BC-A69H         TCGA-BC-A69I         TCGA-CC-5258 
  "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-CC-5260         TCGA-CC-5261         TCGA-CC-5262 
  "17Q GAIN MUTATED"   "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" 
        TCGA-CC-5263         TCGA-CC-A1HT         TCGA-CC-A3M9 
  "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-CC-A3MA         TCGA-CC-A3MB         TCGA-CC-A3MC 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
        TCGA-DD-A113         TCGA-DD-A114         TCGA-DD-A115 
"17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" 
        TCGA-DD-A116         TCGA-DD-A118         TCGA-DD-A119 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
        TCGA-DD-A11A         TCGA-DD-A11B         TCGA-DD-A11C 
  "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-DD-A11D         TCGA-DD-A1E9         TCGA-DD-A1EA 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
        TCGA-DD-A1EB         TCGA-DD-A1EC         TCGA-DD-A1ED 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-DD-A1EE         TCGA-DD-A1EF         TCGA-DD-A1EG 
"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 WILD-TYPE" 
        TCGA-DD-A1EK         TCGA-DD-A1EL         TCGA-DD-A39V 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-DD-A39X         TCGA-DD-A39Y         TCGA-DD-A39Z 
"17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" 
        TCGA-DD-A3A0         TCGA-DD-A3A1         TCGA-DD-A3A2 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-DD-A3A3         TCGA-DD-A3A4         TCGA-DD-A3A5 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-DD-A3A6         TCGA-DD-A3A7         TCGA-DD-A3A8 
"17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" 
        TCGA-DD-A3A9         TCGA-DD-A4NA         TCGA-DD-A4NB 
  "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-DD-A4ND         TCGA-DD-A4NF         TCGA-DD-A4NH 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        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-DD-A4NR 
  "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-DD-A4NS         TCGA-DD-A4NV         TCGA-DD-A73A 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-DD-A73B         TCGA-DD-A73C         TCGA-DD-A73D 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
        TCGA-DD-A73E         TCGA-DD-A73F         TCGA-DD-A73G 
  "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-ED-A459         TCGA-ED-A4XI         TCGA-ED-A5KG 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-ED-A627         TCGA-ED-A66X         TCGA-ED-A66Y 
"17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED"   "17Q GAIN MUTATED" 
        TCGA-ED-A7PX         TCGA-ED-A7PY         TCGA-ED-A7PZ 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-ED-A7XP         TCGA-ED-A82E         TCGA-EP-A12J 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-EP-A26S         TCGA-EP-A2KA         TCGA-EP-A2KB 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
        TCGA-EP-A2KC         TCGA-EP-A3JL         TCGA-EP-A3RK 
  "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-ES-A2HS         TCGA-ES-A2HT         TCGA-FV-A23B 
  "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-FV-A2QR         TCGA-FV-A3I0         TCGA-FV-A3I1 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-FV-A3R2         TCGA-FV-A3R3         TCGA-FV-A495 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
        TCGA-FV-A496         TCGA-FV-A4ZP         TCGA-FV-A4ZQ 
"17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" 
        TCGA-G3-A25S         TCGA-G3-A25T         TCGA-G3-A25U 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
        TCGA-G3-A25V         TCGA-G3-A25W         TCGA-G3-A25X 
"17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" 
        TCGA-G3-A25Y         TCGA-G3-A25Z         TCGA-G3-A3CG 
"17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" 
        TCGA-G3-A3CH         TCGA-G3-A3CI         TCGA-G3-A3CJ 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-G3-A3CK         TCGA-G3-A5SI         TCGA-G3-A5SJ 
  "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
        TCGA-G3-A5SL         TCGA-G3-A5SM         TCGA-G3-A6UC 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-GJ-A6C0         TCGA-K7-A6G5         TCGA-LG-A6GG 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-MI-A75C         TCGA-MI-A75E         TCGA-MI-A75G 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-MI-A75I         TCGA-NI-A4U2         TCGA-O8-A75V 
  "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
[1] "hr=" "1.4"
D31V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  17Q GAIN MUTATED        15        7         0          7          2
  17Q GAIN WILD-TYPE      43       29         2         23          2
                    vv
clus                 STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  17Q GAIN MUTATED            1        1         0         1
  17Q GAIN WILD-TYPE          4        0         1         1
D31V3, multiclass
                    vv
clus                 T1 T2 T3 T4
  17Q GAIN MUTATED   15  9 11  4
  17Q GAIN WILD-TYPE 46 31 29  4
D31V4, multiclass
    clus
vv   17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  T1               15                 46
  T2                9                 31
  T3               11                 29
  T4                4                  4
D31V5, binary
                    cls
clus                  0  1
  17Q GAIN MUTATED   22  0
  17Q GAIN WILD-TYPE 75  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED     22    0
  17Q GAIN WILD-TYPE   75    3
   clus
vv  17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  0               22                 75
  1                0                  3
                    vv
clus                 M0 M1 MX
  17Q GAIN MUTATED   26  2 11
  17Q GAIN WILD-TYPE 89  1 20
D31V6, multiclass
    clus
vv   17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  M0               26                 89
  M1                2                  1
  MX               11                 20
D31V7, binary
                    cls
clus                  0  1
  17Q GAIN MUTATED   12 27
  17Q GAIN WILD-TYPE 46 64
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED     12   27
  17Q GAIN WILD-TYPE   46   64
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  FEMALE               12                 46
  MALE                 27                 64
                    vv
clus                 R0 R1 R2 RX
  17Q GAIN MUTATED   29  5  1  4
  17Q GAIN WILD-TYPE 93  6  0  6
D31V8, multiclass
    clus
vv   17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  R0               29                 93
  R1                5                  6
  R2                1                  0
  RX                4                  6

Clustering(32) Variable = 18P GAIN MUTATION ANALYSIS
D32V1, survival
                    sevent
clus2                 0  1
  18P GAIN MUTATED    7  3
  18P GAIN WILD-TYPE 77 60
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                10                137 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                 3                 60 
$`18P GAIN MUTATED`
TCGA-CC-5263 TCGA-CC-A3MC TCGA-DD-A113 TCGA-DD-A119 TCGA-DD-A4NN TCGA-ED-A66X 
        4.24         0.13        79.73         7.33        29.56        13.35 
TCGA-EP-A3JL TCGA-FV-A4ZP TCGA-G3-A25T TCGA-G3-A25X 
        9.96        60.36        51.06        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        13.84         0.26        22.36         9.50 
TCGA-BC-A69H TCGA-BC-A69I TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 
        3.95         0.53         0.07         2.86         0.39         3.39 
TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-DD-A114 TCGA-DD-A115 
        3.32         0.10         0.07         0.10        37.78        83.57 
TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D 
       53.33       113.00         2.60         0.46        21.76        51.29 
TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE 
       90.71        79.40        66.31        19.79        75.65         6.71 
TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK 
       12.95        45.11        49.15         6.02        29.16        18.35 
TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A0 
       13.64        21.14        55.69         5.62        19.76        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-A4NB TCGA-DD-A4ND 
       13.78         0.36        30.61        33.14        12.85        73.38 
TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL 
       14.07        14.24        18.44        15.06        39.78        56.25 
TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV 
       61.45        93.67        12.26         0.30        80.75        66.35 
TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F 
       10.98         9.30         7.56        10.98         1.45        27.72 
TCGA-DD-A73G TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66Y 
      100.96        13.41        12.69        15.85        13.91         0.23 
TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XP TCGA-ED-A82E TCGA-EP-A12J 
        0.20         0.20         0.20         0.20         0.20        18.74 
TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3RK TCGA-ES-A2HS 
       19.99        11.74        10.98         0.62        11.93        22.85 
TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R2 
       14.40        32.45        19.10         0.20         8.12         6.38 
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-A25W TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CH 
       28.27        30.74        14.86        21.53        22.13        25.64 
TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SL 
        5.92        19.53        19.23        14.70        11.97         7.99 
TCGA-G3-A5SM TCGA-G3-A6UC TCGA-GJ-A6C0 TCGA-K7-A6G5 TCGA-LG-A6GG TCGA-MI-A75C 
        4.37         7.76         1.02         4.01         0.49         9.57 
TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75I TCGA-NI-A4U2 TCGA-O8-A75V 
        5.10        14.24         8.71        58.88         4.44 

  18P GAIN MUTATED 18P GAIN WILD-TYPE 
              0.13               0.03 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
             79.73             113.00 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
            21.455             14.070 
[1] "0.1 - 79.7 (21.5)"  "0.0 - 113.0 (14.1)"
        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-BC-A69H         TCGA-BC-A69I         TCGA-CC-5258 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-CC-5260         TCGA-CC-5261         TCGA-CC-5262 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-CC-5263         TCGA-CC-A1HT         TCGA-CC-A3M9 
  "18P GAIN MUTATED" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-CC-A3MA         TCGA-CC-A3MB         TCGA-CC-A3MC 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE"   "18P GAIN MUTATED" 
        TCGA-DD-A113         TCGA-DD-A114         TCGA-DD-A115 
  "18P GAIN MUTATED" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DD-A116         TCGA-DD-A118         TCGA-DD-A119 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE"   "18P GAIN MUTATED" 
        TCGA-DD-A11A         TCGA-DD-A11B         TCGA-DD-A11C 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DD-A11D         TCGA-DD-A1E9         TCGA-DD-A1EA 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DD-A1EB         TCGA-DD-A1EC         TCGA-DD-A1ED 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DD-A1EE         TCGA-DD-A1EF         TCGA-DD-A1EG 
"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-A1EK         TCGA-DD-A1EL         TCGA-DD-A39V 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DD-A39X         TCGA-DD-A39Y         TCGA-DD-A39Z 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DD-A3A0         TCGA-DD-A3A1         TCGA-DD-A3A2 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DD-A3A3         TCGA-DD-A3A4         TCGA-DD-A3A5 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DD-A3A6         TCGA-DD-A3A7         TCGA-DD-A3A8 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DD-A3A9         TCGA-DD-A4NA         TCGA-DD-A4NB 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DD-A4ND         TCGA-DD-A4NF         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-DD-A4NR 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DD-A4NS         TCGA-DD-A4NV         TCGA-DD-A73A 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DD-A73B         TCGA-DD-A73C         TCGA-DD-A73D 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DD-A73E         TCGA-DD-A73F         TCGA-DD-A73G 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-ED-A459         TCGA-ED-A4XI         TCGA-ED-A5KG 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-ED-A627         TCGA-ED-A66X         TCGA-ED-A66Y 
"18P GAIN WILD-TYPE"   "18P GAIN MUTATED" "18P GAIN WILD-TYPE" 
        TCGA-ED-A7PX         TCGA-ED-A7PY         TCGA-ED-A7PZ 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-ED-A7XP         TCGA-ED-A82E         TCGA-EP-A12J 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EP-A26S         TCGA-EP-A2KA         TCGA-EP-A2KB 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EP-A2KC         TCGA-EP-A3JL         TCGA-EP-A3RK 
"18P GAIN WILD-TYPE"   "18P GAIN MUTATED" "18P GAIN WILD-TYPE" 
        TCGA-ES-A2HS         TCGA-ES-A2HT         TCGA-FV-A23B 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-FV-A2QR         TCGA-FV-A3I0         TCGA-FV-A3I1 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-FV-A3R2         TCGA-FV-A3R3         TCGA-FV-A495 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-FV-A496         TCGA-FV-A4ZP         TCGA-FV-A4ZQ 
"18P GAIN WILD-TYPE"   "18P GAIN MUTATED" "18P GAIN WILD-TYPE" 
        TCGA-G3-A25S         TCGA-G3-A25T         TCGA-G3-A25U 
"18P GAIN WILD-TYPE"   "18P GAIN MUTATED" "18P GAIN WILD-TYPE" 
        TCGA-G3-A25V         TCGA-G3-A25W         TCGA-G3-A25X 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE"   "18P GAIN MUTATED" 
        TCGA-G3-A25Y         TCGA-G3-A25Z         TCGA-G3-A3CG 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-G3-A3CH         TCGA-G3-A3CI         TCGA-G3-A3CJ 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-G3-A3CK         TCGA-G3-A5SI         TCGA-G3-A5SJ 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-G3-A5SL         TCGA-G3-A5SM         TCGA-G3-A6UC 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-GJ-A6C0         TCGA-K7-A6G5         TCGA-LG-A6GG 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-MI-A75C         TCGA-MI-A75E         TCGA-MI-A75G 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-MI-A75I         TCGA-NI-A4U2         TCGA-O8-A75V 
"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-BC-A69H         TCGA-BC-A69I         TCGA-CC-5258 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-CC-5260         TCGA-CC-5261         TCGA-CC-5262 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-CC-5263         TCGA-CC-A1HT         TCGA-CC-A3M9 
  "18P GAIN MUTATED" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-CC-A3MA         TCGA-CC-A3MB         TCGA-CC-A3MC 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE"   "18P GAIN MUTATED" 
        TCGA-DD-A113         TCGA-DD-A114         TCGA-DD-A115 
  "18P GAIN MUTATED" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DD-A116         TCGA-DD-A118         TCGA-DD-A119 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE"   "18P GAIN MUTATED" 
        TCGA-DD-A11A         TCGA-DD-A11B         TCGA-DD-A11C 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DD-A11D         TCGA-DD-A1E9         TCGA-DD-A1EA 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DD-A1EB         TCGA-DD-A1EC         TCGA-DD-A1ED 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DD-A1EE         TCGA-DD-A1EF         TCGA-DD-A1EG 
"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-A1EK         TCGA-DD-A1EL         TCGA-DD-A39V 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DD-A39X         TCGA-DD-A39Y         TCGA-DD-A39Z 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DD-A3A0         TCGA-DD-A3A1         TCGA-DD-A3A2 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DD-A3A3         TCGA-DD-A3A4         TCGA-DD-A3A5 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DD-A3A6         TCGA-DD-A3A7         TCGA-DD-A3A8 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DD-A3A9         TCGA-DD-A4NA         TCGA-DD-A4NB 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DD-A4ND         TCGA-DD-A4NF         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-DD-A4NR 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DD-A4NS         TCGA-DD-A4NV         TCGA-DD-A73A 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DD-A73B         TCGA-DD-A73C         TCGA-DD-A73D 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DD-A73E         TCGA-DD-A73F         TCGA-DD-A73G 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-ED-A459         TCGA-ED-A4XI         TCGA-ED-A5KG 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-ED-A627         TCGA-ED-A66X         TCGA-ED-A66Y 
"18P GAIN WILD-TYPE"   "18P GAIN MUTATED" "18P GAIN WILD-TYPE" 
        TCGA-ED-A7PX         TCGA-ED-A7PY         TCGA-ED-A7PZ 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-ED-A7XP         TCGA-ED-A82E         TCGA-EP-A12J 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EP-A26S         TCGA-EP-A2KA         TCGA-EP-A2KB 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EP-A2KC         TCGA-EP-A3JL         TCGA-EP-A3RK 
"18P GAIN WILD-TYPE"   "18P GAIN MUTATED" "18P GAIN WILD-TYPE" 
        TCGA-ES-A2HS         TCGA-ES-A2HT         TCGA-FV-A23B 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-FV-A2QR         TCGA-FV-A3I0         TCGA-FV-A3I1 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-FV-A3R2         TCGA-FV-A3R3         TCGA-FV-A495 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-FV-A496         TCGA-FV-A4ZP         TCGA-FV-A4ZQ 
"18P GAIN WILD-TYPE"   "18P GAIN MUTATED" "18P GAIN WILD-TYPE" 
        TCGA-G3-A25S         TCGA-G3-A25T         TCGA-G3-A25U 
"18P GAIN WILD-TYPE"   "18P GAIN MUTATED" "18P GAIN WILD-TYPE" 
        TCGA-G3-A25V         TCGA-G3-A25W         TCGA-G3-A25X 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE"   "18P GAIN MUTATED" 
        TCGA-G3-A25Y         TCGA-G3-A25Z         TCGA-G3-A3CG 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-G3-A3CH         TCGA-G3-A3CI         TCGA-G3-A3CJ 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-G3-A3CK         TCGA-G3-A5SI         TCGA-G3-A5SJ 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-G3-A5SL         TCGA-G3-A5SM         TCGA-G3-A6UC 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-GJ-A6C0         TCGA-K7-A6G5         TCGA-LG-A6GG 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-MI-A75C         TCGA-MI-A75E         TCGA-MI-A75G 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-MI-A75I         TCGA-NI-A4U2         TCGA-O8-A75V 
"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-BC-A69H         TCGA-BC-A69I         TCGA-CC-5258 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-CC-5260         TCGA-CC-5261         TCGA-CC-5262 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-CC-5263         TCGA-CC-A1HT         TCGA-CC-A3M9 
  "18P GAIN MUTATED" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-CC-A3MA         TCGA-CC-A3MB         TCGA-CC-A3MC 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE"   "18P GAIN MUTATED" 
        TCGA-DD-A113         TCGA-DD-A114         TCGA-DD-A115 
  "18P GAIN MUTATED" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DD-A116         TCGA-DD-A118         TCGA-DD-A119 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE"   "18P GAIN MUTATED" 
        TCGA-DD-A11A         TCGA-DD-A11B         TCGA-DD-A11C 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DD-A11D         TCGA-DD-A1E9         TCGA-DD-A1EA 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DD-A1EB         TCGA-DD-A1EC         TCGA-DD-A1ED 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DD-A1EE         TCGA-DD-A1EF         TCGA-DD-A1EG 
"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-A1EK         TCGA-DD-A1EL         TCGA-DD-A39V 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DD-A39X         TCGA-DD-A39Y         TCGA-DD-A39Z 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DD-A3A0         TCGA-DD-A3A1         TCGA-DD-A3A2 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DD-A3A3         TCGA-DD-A3A4         TCGA-DD-A3A5 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DD-A3A6         TCGA-DD-A3A7         TCGA-DD-A3A8 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DD-A3A9         TCGA-DD-A4NA         TCGA-DD-A4NB 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DD-A4ND         TCGA-DD-A4NF         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-DD-A4NR 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DD-A4NS         TCGA-DD-A4NV         TCGA-DD-A73A 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DD-A73B         TCGA-DD-A73C         TCGA-DD-A73D 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DD-A73E         TCGA-DD-A73F         TCGA-DD-A73G 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-ED-A459         TCGA-ED-A4XI         TCGA-ED-A5KG 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-ED-A627         TCGA-ED-A66X         TCGA-ED-A66Y 
"18P GAIN WILD-TYPE"   "18P GAIN MUTATED" "18P GAIN WILD-TYPE" 
        TCGA-ED-A7PX         TCGA-ED-A7PY         TCGA-ED-A7PZ 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-ED-A7XP         TCGA-ED-A82E         TCGA-EP-A12J 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EP-A26S         TCGA-EP-A2KA         TCGA-EP-A2KB 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EP-A2KC         TCGA-EP-A3JL         TCGA-EP-A3RK 
"18P GAIN WILD-TYPE"   "18P GAIN MUTATED" "18P GAIN WILD-TYPE" 
        TCGA-ES-A2HS         TCGA-ES-A2HT         TCGA-FV-A23B 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-FV-A2QR         TCGA-FV-A3I0         TCGA-FV-A3I1 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-FV-A3R2         TCGA-FV-A3R3         TCGA-FV-A495 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-FV-A496         TCGA-FV-A4ZP         TCGA-FV-A4ZQ 
"18P GAIN WILD-TYPE"   "18P GAIN MUTATED" "18P GAIN WILD-TYPE" 
        TCGA-G3-A25S         TCGA-G3-A25T         TCGA-G3-A25U 
"18P GAIN WILD-TYPE"   "18P GAIN MUTATED" "18P GAIN WILD-TYPE" 
        TCGA-G3-A25V         TCGA-G3-A25W         TCGA-G3-A25X 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE"   "18P GAIN MUTATED" 
        TCGA-G3-A25Y         TCGA-G3-A25Z         TCGA-G3-A3CG 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-G3-A3CH         TCGA-G3-A3CI         TCGA-G3-A3CJ 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-G3-A3CK         TCGA-G3-A5SI         TCGA-G3-A5SJ 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-G3-A5SL         TCGA-G3-A5SM         TCGA-G3-A6UC 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-GJ-A6C0         TCGA-K7-A6G5         TCGA-LG-A6GG 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-MI-A75C         TCGA-MI-A75E         TCGA-MI-A75G 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-MI-A75I         TCGA-NI-A4U2         TCGA-O8-A75V 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
[1] "hr=" "1.8"
D32V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  18P GAIN MUTATED         2        2         0          5          0
  18P GAIN WILD-TYPE      56       34         2         25          4
                    vv
clus                 STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  18P GAIN MUTATED            0        1         0         0
  18P GAIN WILD-TYPE          5        0         1         2
D32V3, multiclass
                    vv
clus                 T1 T2 T3 T4
  18P GAIN MUTATED    2  2  6  0
  18P GAIN WILD-TYPE 59 38 34  8
D32V4, multiclass
    clus
vv   18P GAIN MUTATED 18P GAIN WILD-TYPE
  T1                2                 59
  T2                2                 38
  T3                6                 34
  T4                0                  8
D32V5, binary
                    cls
clus                  0  1
  18P GAIN MUTATED    8  0
  18P GAIN WILD-TYPE 89  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED      8    0
  18P GAIN WILD-TYPE   89    3
   clus
vv  18P GAIN MUTATED 18P GAIN WILD-TYPE
  0                8                 89
  1                0                  3
                    vv
clus                  M0  M1  MX
  18P GAIN MUTATED     8   1   1
  18P GAIN WILD-TYPE 107   2  30
D32V6, multiclass
    clus
vv   18P GAIN MUTATED 18P GAIN WILD-TYPE
  M0                8                107
  M1                1                  2
  MX                1                 30
D32V7, binary
                    cls
clus                  0  1
  18P GAIN MUTATED    3  7
  18P GAIN WILD-TYPE 55 84
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED      3    7
  18P GAIN WILD-TYPE   55   84
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  FEMALE                3                 55
  MALE                  7                 84
                    vv
clus                  R0  R1  R2  RX
  18P GAIN MUTATED     6   1   1   1
  18P GAIN WILD-TYPE 116  10   0   9
D32V8, multiclass
    clus
vv   18P GAIN MUTATED 18P GAIN WILD-TYPE
  R0                6                116
  R1                1                 10
  R2                1                  0
  RX                1                  9

Clustering(33) Variable = 18Q GAIN MUTATION ANALYSIS
D33V1, survival
                    sevent
clus2                 0  1
  18Q GAIN MUTATED    6  3
  18Q GAIN WILD-TYPE 78 60
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 9                138 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 3                 60 
$`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         9.96 
TCGA-FV-A4ZP TCGA-G3-A25T TCGA-G3-A25X 
       60.36        51.06        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        13.84         0.26        22.36         9.50 
TCGA-BC-A69H TCGA-BC-A69I TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 
        3.95         0.53         0.07         2.86         0.39         3.39 
TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-DD-A114 TCGA-DD-A115 
        3.32         0.10         0.07         0.10        37.78        83.57 
TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D 
       53.33       113.00         2.60         0.46        21.76        51.29 
TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE 
       90.71        79.40        66.31        19.79        75.65         6.71 
TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK 
       12.95        45.11        49.15         6.02        29.16        18.35 
TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A0 
       13.64        21.14        55.69         5.62        19.76        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-A4NB TCGA-DD-A4ND 
       13.78         0.36        30.61        33.14        12.85        73.38 
TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL 
       14.07        14.24        18.44        15.06        39.78        56.25 
TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV 
       61.45        93.67        12.26         0.30        80.75        66.35 
TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F 
       10.98         9.30         7.56        10.98         1.45        27.72 
TCGA-DD-A73G TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X 
      100.96        13.41        12.69        15.85        13.91        13.35 
TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XP TCGA-ED-A82E 
        0.23         0.20         0.20         0.20         0.20         0.20 
TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3RK 
       18.74        19.99        11.74        10.98         0.62        11.93 
TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3I1 
       22.85        14.40        32.45        19.10         0.20         8.12 
TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZQ TCGA-G3-A25S 
        6.38         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        30.74        14.86        21.53        22.13 
TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ 
       25.64         5.92        19.53        19.23        14.70        11.97 
TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A6UC TCGA-GJ-A6C0 TCGA-K7-A6G5 TCGA-LG-A6GG 
        7.99         4.37         7.76         1.02         4.01         0.49 
TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75I TCGA-NI-A4U2 TCGA-O8-A75V 
        9.57         5.10        14.24         8.71        58.88         4.44 

  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
              0.13               0.03 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
             79.73             113.00 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
             29.56              13.99 
[1] "0.1 - 79.7 (29.6)"  "0.0 - 113.0 (14.0)"
        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-BC-A69H         TCGA-BC-A69I         TCGA-CC-5258 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-CC-5260         TCGA-CC-5261         TCGA-CC-5262 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-CC-5263         TCGA-CC-A1HT         TCGA-CC-A3M9 
  "18Q GAIN MUTATED" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-CC-A3MA         TCGA-CC-A3MB         TCGA-CC-A3MC 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE"   "18Q GAIN MUTATED" 
        TCGA-DD-A113         TCGA-DD-A114         TCGA-DD-A115 
  "18Q GAIN MUTATED" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DD-A116         TCGA-DD-A118         TCGA-DD-A119 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE"   "18Q GAIN MUTATED" 
        TCGA-DD-A11A         TCGA-DD-A11B         TCGA-DD-A11C 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DD-A11D         TCGA-DD-A1E9         TCGA-DD-A1EA 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DD-A1EB         TCGA-DD-A1EC         TCGA-DD-A1ED 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DD-A1EE         TCGA-DD-A1EF         TCGA-DD-A1EG 
"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-A1EK         TCGA-DD-A1EL         TCGA-DD-A39V 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DD-A39X         TCGA-DD-A39Y         TCGA-DD-A39Z 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DD-A3A0         TCGA-DD-A3A1         TCGA-DD-A3A2 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DD-A3A3         TCGA-DD-A3A4         TCGA-DD-A3A5 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DD-A3A6         TCGA-DD-A3A7         TCGA-DD-A3A8 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DD-A3A9         TCGA-DD-A4NA         TCGA-DD-A4NB 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DD-A4ND         TCGA-DD-A4NF         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-DD-A4NR 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DD-A4NS         TCGA-DD-A4NV         TCGA-DD-A73A 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DD-A73B         TCGA-DD-A73C         TCGA-DD-A73D 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DD-A73E         TCGA-DD-A73F         TCGA-DD-A73G 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-ED-A459         TCGA-ED-A4XI         TCGA-ED-A5KG 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-ED-A627         TCGA-ED-A66X         TCGA-ED-A66Y 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-ED-A7PX         TCGA-ED-A7PY         TCGA-ED-A7PZ 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-ED-A7XP         TCGA-ED-A82E         TCGA-EP-A12J 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EP-A26S         TCGA-EP-A2KA         TCGA-EP-A2KB 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EP-A2KC         TCGA-EP-A3JL         TCGA-EP-A3RK 
"18Q GAIN WILD-TYPE"   "18Q GAIN MUTATED" "18Q GAIN WILD-TYPE" 
        TCGA-ES-A2HS         TCGA-ES-A2HT         TCGA-FV-A23B 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-FV-A2QR         TCGA-FV-A3I0         TCGA-FV-A3I1 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-FV-A3R2         TCGA-FV-A3R3         TCGA-FV-A495 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-FV-A496         TCGA-FV-A4ZP         TCGA-FV-A4ZQ 
"18Q GAIN WILD-TYPE"   "18Q GAIN MUTATED" "18Q GAIN WILD-TYPE" 
        TCGA-G3-A25S         TCGA-G3-A25T         TCGA-G3-A25U 
"18Q GAIN WILD-TYPE"   "18Q GAIN MUTATED" "18Q GAIN WILD-TYPE" 
        TCGA-G3-A25V         TCGA-G3-A25W         TCGA-G3-A25X 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE"   "18Q GAIN MUTATED" 
        TCGA-G3-A25Y         TCGA-G3-A25Z         TCGA-G3-A3CG 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-G3-A3CH         TCGA-G3-A3CI         TCGA-G3-A3CJ 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-G3-A3CK         TCGA-G3-A5SI         TCGA-G3-A5SJ 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-G3-A5SL         TCGA-G3-A5SM         TCGA-G3-A6UC 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-GJ-A6C0         TCGA-K7-A6G5         TCGA-LG-A6GG 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-MI-A75C         TCGA-MI-A75E         TCGA-MI-A75G 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-MI-A75I         TCGA-NI-A4U2         TCGA-O8-A75V 
"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-BC-A69H         TCGA-BC-A69I         TCGA-CC-5258 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-CC-5260         TCGA-CC-5261         TCGA-CC-5262 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-CC-5263         TCGA-CC-A1HT         TCGA-CC-A3M9 
  "18Q GAIN MUTATED" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-CC-A3MA         TCGA-CC-A3MB         TCGA-CC-A3MC 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE"   "18Q GAIN MUTATED" 
        TCGA-DD-A113         TCGA-DD-A114         TCGA-DD-A115 
  "18Q GAIN MUTATED" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DD-A116         TCGA-DD-A118         TCGA-DD-A119 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE"   "18Q GAIN MUTATED" 
        TCGA-DD-A11A         TCGA-DD-A11B         TCGA-DD-A11C 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DD-A11D         TCGA-DD-A1E9         TCGA-DD-A1EA 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DD-A1EB         TCGA-DD-A1EC         TCGA-DD-A1ED 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DD-A1EE         TCGA-DD-A1EF         TCGA-DD-A1EG 
"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-A1EK         TCGA-DD-A1EL         TCGA-DD-A39V 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DD-A39X         TCGA-DD-A39Y         TCGA-DD-A39Z 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DD-A3A0         TCGA-DD-A3A1         TCGA-DD-A3A2 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DD-A3A3         TCGA-DD-A3A4         TCGA-DD-A3A5 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DD-A3A6         TCGA-DD-A3A7         TCGA-DD-A3A8 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DD-A3A9         TCGA-DD-A4NA         TCGA-DD-A4NB 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DD-A4ND         TCGA-DD-A4NF         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-DD-A4NR 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DD-A4NS         TCGA-DD-A4NV         TCGA-DD-A73A 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DD-A73B         TCGA-DD-A73C         TCGA-DD-A73D 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DD-A73E         TCGA-DD-A73F         TCGA-DD-A73G 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-ED-A459         TCGA-ED-A4XI         TCGA-ED-A5KG 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-ED-A627         TCGA-ED-A66X         TCGA-ED-A66Y 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-ED-A7PX         TCGA-ED-A7PY         TCGA-ED-A7PZ 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-ED-A7XP         TCGA-ED-A82E         TCGA-EP-A12J 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EP-A26S         TCGA-EP-A2KA         TCGA-EP-A2KB 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EP-A2KC         TCGA-EP-A3JL         TCGA-EP-A3RK 
"18Q GAIN WILD-TYPE"   "18Q GAIN MUTATED" "18Q GAIN WILD-TYPE" 
        TCGA-ES-A2HS         TCGA-ES-A2HT         TCGA-FV-A23B 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-FV-A2QR         TCGA-FV-A3I0         TCGA-FV-A3I1 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-FV-A3R2         TCGA-FV-A3R3         TCGA-FV-A495 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-FV-A496         TCGA-FV-A4ZP         TCGA-FV-A4ZQ 
"18Q GAIN WILD-TYPE"   "18Q GAIN MUTATED" "18Q GAIN WILD-TYPE" 
        TCGA-G3-A25S         TCGA-G3-A25T         TCGA-G3-A25U 
"18Q GAIN WILD-TYPE"   "18Q GAIN MUTATED" "18Q GAIN WILD-TYPE" 
        TCGA-G3-A25V         TCGA-G3-A25W         TCGA-G3-A25X 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE"   "18Q GAIN MUTATED" 
        TCGA-G3-A25Y         TCGA-G3-A25Z         TCGA-G3-A3CG 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-G3-A3CH         TCGA-G3-A3CI         TCGA-G3-A3CJ 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-G3-A3CK         TCGA-G3-A5SI         TCGA-G3-A5SJ 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-G3-A5SL         TCGA-G3-A5SM         TCGA-G3-A6UC 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-GJ-A6C0         TCGA-K7-A6G5         TCGA-LG-A6GG 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-MI-A75C         TCGA-MI-A75E         TCGA-MI-A75G 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-MI-A75I         TCGA-NI-A4U2         TCGA-O8-A75V 
"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-BC-A69H         TCGA-BC-A69I         TCGA-CC-5258 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-CC-5260         TCGA-CC-5261         TCGA-CC-5262 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-CC-5263         TCGA-CC-A1HT         TCGA-CC-A3M9 
  "18Q GAIN MUTATED" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-CC-A3MA         TCGA-CC-A3MB         TCGA-CC-A3MC 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE"   "18Q GAIN MUTATED" 
        TCGA-DD-A113         TCGA-DD-A114         TCGA-DD-A115 
  "18Q GAIN MUTATED" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DD-A116         TCGA-DD-A118         TCGA-DD-A119 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE"   "18Q GAIN MUTATED" 
        TCGA-DD-A11A         TCGA-DD-A11B         TCGA-DD-A11C 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DD-A11D         TCGA-DD-A1E9         TCGA-DD-A1EA 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DD-A1EB         TCGA-DD-A1EC         TCGA-DD-A1ED 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DD-A1EE         TCGA-DD-A1EF         TCGA-DD-A1EG 
"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-A1EK         TCGA-DD-A1EL         TCGA-DD-A39V 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DD-A39X         TCGA-DD-A39Y         TCGA-DD-A39Z 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DD-A3A0         TCGA-DD-A3A1         TCGA-DD-A3A2 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DD-A3A3         TCGA-DD-A3A4         TCGA-DD-A3A5 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DD-A3A6         TCGA-DD-A3A7         TCGA-DD-A3A8 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DD-A3A9         TCGA-DD-A4NA         TCGA-DD-A4NB 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DD-A4ND         TCGA-DD-A4NF         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-DD-A4NR 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DD-A4NS         TCGA-DD-A4NV         TCGA-DD-A73A 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DD-A73B         TCGA-DD-A73C         TCGA-DD-A73D 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DD-A73E         TCGA-DD-A73F         TCGA-DD-A73G 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-ED-A459         TCGA-ED-A4XI         TCGA-ED-A5KG 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-ED-A627         TCGA-ED-A66X         TCGA-ED-A66Y 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-ED-A7PX         TCGA-ED-A7PY         TCGA-ED-A7PZ 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-ED-A7XP         TCGA-ED-A82E         TCGA-EP-A12J 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EP-A26S         TCGA-EP-A2KA         TCGA-EP-A2KB 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EP-A2KC         TCGA-EP-A3JL         TCGA-EP-A3RK 
"18Q GAIN WILD-TYPE"   "18Q GAIN MUTATED" "18Q GAIN WILD-TYPE" 
        TCGA-ES-A2HS         TCGA-ES-A2HT         TCGA-FV-A23B 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-FV-A2QR         TCGA-FV-A3I0         TCGA-FV-A3I1 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-FV-A3R2         TCGA-FV-A3R3         TCGA-FV-A495 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-FV-A496         TCGA-FV-A4ZP         TCGA-FV-A4ZQ 
"18Q GAIN WILD-TYPE"   "18Q GAIN MUTATED" "18Q GAIN WILD-TYPE" 
        TCGA-G3-A25S         TCGA-G3-A25T         TCGA-G3-A25U 
"18Q GAIN WILD-TYPE"   "18Q GAIN MUTATED" "18Q GAIN WILD-TYPE" 
        TCGA-G3-A25V         TCGA-G3-A25W         TCGA-G3-A25X 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE"   "18Q GAIN MUTATED" 
        TCGA-G3-A25Y         TCGA-G3-A25Z         TCGA-G3-A3CG 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-G3-A3CH         TCGA-G3-A3CI         TCGA-G3-A3CJ 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-G3-A3CK         TCGA-G3-A5SI         TCGA-G3-A5SJ 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-G3-A5SL         TCGA-G3-A5SM         TCGA-G3-A6UC 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-GJ-A6C0         TCGA-K7-A6G5         TCGA-LG-A6GG 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-MI-A75C         TCGA-MI-A75E         TCGA-MI-A75G 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-MI-A75I         TCGA-NI-A4U2         TCGA-O8-A75V 
"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          4          0
  18Q GAIN WILD-TYPE      56       34         2         26          4
                    vv
clus                 STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  18Q GAIN MUTATED            0        1         0         0
  18Q GAIN WILD-TYPE          5        0         1         2
D33V3, multiclass
                    vv
clus                 T1 T2 T3 T4
  18Q GAIN MUTATED    2  2  5  0
  18Q GAIN WILD-TYPE 59 38 35  8
D33V4, multiclass
    clus
vv   18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  T1                2                 59
  T2                2                 38
  T3                5                 35
  T4                0                  8
D33V5, binary
                    cls
clus                  0  1
  18Q GAIN MUTATED    7  0
  18Q GAIN WILD-TYPE 90  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      7    0
  18Q GAIN WILD-TYPE   90    3
   clus
vv  18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  0                7                 90
  1                0                  3
                    vv
clus                  M0  M1  MX
  18Q GAIN MUTATED     7   1   1
  18Q GAIN WILD-TYPE 108   2  30
D33V6, multiclass
    clus
vv   18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  M0                7                108
  M1                1                  2
  MX                1                 30
D33V7, binary
                    cls
clus                  0  1
  18Q GAIN MUTATED    3  6
  18Q GAIN WILD-TYPE 55 85
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      3    6
  18Q GAIN WILD-TYPE   55   85
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  FEMALE                3                 55
  MALE                  6                 85
                    vv
clus                  R0  R1  R2  RX
  18Q GAIN MUTATED     5   1   1   1
  18Q GAIN WILD-TYPE 117  10   0   9
D33V8, multiclass
    clus
vv   18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  R0                5                117
  R1                1                 10
  R2                1                  0
  RX                1                  9

Clustering(34) Variable = 19P GAIN MUTATION ANALYSIS
D34V1, survival
                    sevent
clus2                 0  1
  19P GAIN MUTATED   14 15
  19P GAIN WILD-TYPE 70 48
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                29                118 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                15                 48 
$`19P GAIN MUTATED`
TCGA-BC-A10Q TCGA-CC-5261 TCGA-DD-A113 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A1E9 
       37.32         0.39        79.73       113.00         7.33        90.71 
TCGA-DD-A1EC TCGA-DD-A1EF TCGA-DD-A39V TCGA-DD-A39X TCGA-DD-A3A7 TCGA-DD-A3A9 
       19.79        12.95        21.14        55.69        13.78        30.61 
TCGA-DD-A4ND TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NQ TCGA-DD-A4NV TCGA-DD-A73G 
       73.38        29.56        61.45        12.26        66.35       100.96 
TCGA-ED-A66Y TCGA-ED-A7PZ TCGA-ED-A82E TCGA-EP-A2KB TCGA-EP-A2KC TCGA-ES-A2HS 
        0.23         0.20         0.20        10.98         0.62        22.85 
TCGA-FV-A23B TCGA-FV-A3I0 TCGA-G3-A25T TCGA-G3-A25X TCGA-G3-A5SM 
       32.45         0.20        51.06        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-BC-A69H 
       44.42        13.84         0.26        22.36         9.50         3.95 
TCGA-BC-A69I TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A1HT 
        0.53         0.07         2.86         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        37.78        83.57 
TCGA-DD-A116 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1EA 
       53.33         2.60         0.46        21.76        51.29        79.40 
TCGA-DD-A1EB TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI 
       66.31        75.65         6.71        45.11        49.15         6.02 
TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A0 
       29.16        18.35        13.64         5.62        19.76        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-A4NB TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NI 
        0.36        33.14        12.85        14.07        14.24        18.44 
TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NP TCGA-DD-A4NR TCGA-DD-A4NS 
       15.06        39.78        56.25        93.67         0.30        80.75 
TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F 
       10.98         9.30         7.56        10.98         1.45        27.72 
TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A7PX 
       13.41        12.69        15.85        13.91        13.35         0.20 
TCGA-ED-A7PY TCGA-ED-A7XP TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A3JL 
        0.20         0.20        18.74        19.99        11.74         9.96 
TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A2QR TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 
       11.93        14.40        19.10         8.12         6.38         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        30.74        14.86        21.53        22.13        25.64 
TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SL 
        5.92        19.53        19.23        14.70        11.97         7.99 
TCGA-G3-A6UC TCGA-GJ-A6C0 TCGA-K7-A6G5 TCGA-LG-A6GG TCGA-MI-A75C TCGA-MI-A75E 
        7.76         1.02         4.01         0.49         9.57         5.10 
TCGA-MI-A75G TCGA-MI-A75I TCGA-NI-A4U2 TCGA-O8-A75V 
       14.24         8.71        58.88         4.44 

  19P GAIN MUTATED 19P GAIN WILD-TYPE 
              0.20               0.03 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
            113.00             107.11 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
             22.85              13.74 
[1] "0.2 - 113.0 (22.9)" "0.0 - 107.1 (13.7)"
        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-BC-A69H         TCGA-BC-A69I         TCGA-CC-5258 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-CC-5260         TCGA-CC-5261         TCGA-CC-5262 
"19P GAIN WILD-TYPE"   "19P GAIN MUTATED" "19P GAIN WILD-TYPE" 
        TCGA-CC-5263         TCGA-CC-A1HT         TCGA-CC-A3M9 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-CC-A3MA         TCGA-CC-A3MB         TCGA-CC-A3MC 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-DD-A113         TCGA-DD-A114         TCGA-DD-A115 
  "19P GAIN MUTATED" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-DD-A116         TCGA-DD-A118         TCGA-DD-A119 
"19P GAIN WILD-TYPE"   "19P GAIN MUTATED"   "19P GAIN MUTATED" 
        TCGA-DD-A11A         TCGA-DD-A11B         TCGA-DD-A11C 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-DD-A11D         TCGA-DD-A1E9         TCGA-DD-A1EA 
"19P GAIN WILD-TYPE"   "19P GAIN MUTATED" "19P GAIN WILD-TYPE" 
        TCGA-DD-A1EB         TCGA-DD-A1EC         TCGA-DD-A1ED 
"19P GAIN WILD-TYPE"   "19P GAIN MUTATED" "19P GAIN WILD-TYPE" 
        TCGA-DD-A1EE         TCGA-DD-A1EF         TCGA-DD-A1EG 
"19P GAIN WILD-TYPE"   "19P GAIN MUTATED" "19P GAIN WILD-TYPE" 
        TCGA-DD-A1EH         TCGA-DD-A1EI         TCGA-DD-A1EJ 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-DD-A1EK         TCGA-DD-A1EL         TCGA-DD-A39V 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE"   "19P GAIN MUTATED" 
        TCGA-DD-A39X         TCGA-DD-A39Y         TCGA-DD-A39Z 
  "19P GAIN MUTATED" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-DD-A3A0         TCGA-DD-A3A1         TCGA-DD-A3A2 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-DD-A3A3         TCGA-DD-A3A4         TCGA-DD-A3A5 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-DD-A3A6         TCGA-DD-A3A7         TCGA-DD-A3A8 
"19P GAIN WILD-TYPE"   "19P GAIN MUTATED" "19P GAIN WILD-TYPE" 
        TCGA-DD-A3A9         TCGA-DD-A4NA         TCGA-DD-A4NB 
  "19P GAIN MUTATED" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-DD-A4ND         TCGA-DD-A4NF         TCGA-DD-A4NH 
  "19P GAIN MUTATED" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-DD-A4NI         TCGA-DD-A4NJ         TCGA-DD-A4NK 
"19P GAIN WILD-TYPE" "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-DD-A4NR 
"19P GAIN WILD-TYPE"   "19P GAIN MUTATED" "19P GAIN WILD-TYPE" 
        TCGA-DD-A4NS         TCGA-DD-A4NV         TCGA-DD-A73A 
"19P GAIN WILD-TYPE"   "19P GAIN MUTATED" "19P GAIN WILD-TYPE" 
        TCGA-DD-A73B         TCGA-DD-A73C         TCGA-DD-A73D 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-DD-A73E         TCGA-DD-A73F         TCGA-DD-A73G 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE"   "19P GAIN MUTATED" 
        TCGA-ED-A459         TCGA-ED-A4XI         TCGA-ED-A5KG 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-ED-A627         TCGA-ED-A66X         TCGA-ED-A66Y 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE"   "19P GAIN MUTATED" 
        TCGA-ED-A7PX         TCGA-ED-A7PY         TCGA-ED-A7PZ 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE"   "19P GAIN MUTATED" 
        TCGA-ED-A7XP         TCGA-ED-A82E         TCGA-EP-A12J 
"19P GAIN WILD-TYPE"   "19P GAIN MUTATED" "19P GAIN WILD-TYPE" 
        TCGA-EP-A26S         TCGA-EP-A2KA         TCGA-EP-A2KB 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE"   "19P GAIN MUTATED" 
        TCGA-EP-A2KC         TCGA-EP-A3JL         TCGA-EP-A3RK 
  "19P GAIN MUTATED" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-ES-A2HS         TCGA-ES-A2HT         TCGA-FV-A23B 
  "19P GAIN MUTATED" "19P GAIN WILD-TYPE"   "19P GAIN MUTATED" 
        TCGA-FV-A2QR         TCGA-FV-A3I0         TCGA-FV-A3I1 
"19P GAIN WILD-TYPE"   "19P GAIN MUTATED" "19P GAIN WILD-TYPE" 
        TCGA-FV-A3R2         TCGA-FV-A3R3         TCGA-FV-A495 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-FV-A496         TCGA-FV-A4ZP         TCGA-FV-A4ZQ 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-G3-A25S         TCGA-G3-A25T         TCGA-G3-A25U 
"19P GAIN WILD-TYPE"   "19P GAIN MUTATED" "19P GAIN WILD-TYPE" 
        TCGA-G3-A25V         TCGA-G3-A25W         TCGA-G3-A25X 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE"   "19P GAIN MUTATED" 
        TCGA-G3-A25Y         TCGA-G3-A25Z         TCGA-G3-A3CG 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-G3-A3CH         TCGA-G3-A3CI         TCGA-G3-A3CJ 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-G3-A3CK         TCGA-G3-A5SI         TCGA-G3-A5SJ 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-G3-A5SL         TCGA-G3-A5SM         TCGA-G3-A6UC 
"19P GAIN WILD-TYPE"   "19P GAIN MUTATED" "19P GAIN WILD-TYPE" 
        TCGA-GJ-A6C0         TCGA-K7-A6G5         TCGA-LG-A6GG 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-MI-A75C         TCGA-MI-A75E         TCGA-MI-A75G 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-MI-A75I         TCGA-NI-A4U2         TCGA-O8-A75V 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE"   "19P GAIN 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-BC-A69H         TCGA-BC-A69I         TCGA-CC-5258 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-CC-5260         TCGA-CC-5261         TCGA-CC-5262 
"19P GAIN WILD-TYPE"   "19P GAIN MUTATED" "19P GAIN WILD-TYPE" 
        TCGA-CC-5263         TCGA-CC-A1HT         TCGA-CC-A3M9 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-CC-A3MA         TCGA-CC-A3MB         TCGA-CC-A3MC 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-DD-A113         TCGA-DD-A114         TCGA-DD-A115 
  "19P GAIN MUTATED" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-DD-A116         TCGA-DD-A118         TCGA-DD-A119 
"19P GAIN WILD-TYPE"   "19P GAIN MUTATED"   "19P GAIN MUTATED" 
        TCGA-DD-A11A         TCGA-DD-A11B         TCGA-DD-A11C 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-DD-A11D         TCGA-DD-A1E9         TCGA-DD-A1EA 
"19P GAIN WILD-TYPE"   "19P GAIN MUTATED" "19P GAIN WILD-TYPE" 
        TCGA-DD-A1EB         TCGA-DD-A1EC         TCGA-DD-A1ED 
"19P GAIN WILD-TYPE"   "19P GAIN MUTATED" "19P GAIN WILD-TYPE" 
        TCGA-DD-A1EE         TCGA-DD-A1EF         TCGA-DD-A1EG 
"19P GAIN WILD-TYPE"   "19P GAIN MUTATED" "19P GAIN WILD-TYPE" 
        TCGA-DD-A1EH         TCGA-DD-A1EI         TCGA-DD-A1EJ 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-DD-A1EK         TCGA-DD-A1EL         TCGA-DD-A39V 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE"   "19P GAIN MUTATED" 
        TCGA-DD-A39X         TCGA-DD-A39Y         TCGA-DD-A39Z 
  "19P GAIN MUTATED" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-DD-A3A0         TCGA-DD-A3A1         TCGA-DD-A3A2 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-DD-A3A3         TCGA-DD-A3A4         TCGA-DD-A3A5 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-DD-A3A6         TCGA-DD-A3A7         TCGA-DD-A3A8 
"19P GAIN WILD-TYPE"   "19P GAIN MUTATED" "19P GAIN WILD-TYPE" 
        TCGA-DD-A3A9         TCGA-DD-A4NA         TCGA-DD-A4NB 
  "19P GAIN MUTATED" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-DD-A4ND         TCGA-DD-A4NF         TCGA-DD-A4NH 
  "19P GAIN MUTATED" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-DD-A4NI         TCGA-DD-A4NJ         TCGA-DD-A4NK 
"19P GAIN WILD-TYPE" "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-DD-A4NR 
"19P GAIN WILD-TYPE"   "19P GAIN MUTATED" "19P GAIN WILD-TYPE" 
        TCGA-DD-A4NS         TCGA-DD-A4NV         TCGA-DD-A73A 
"19P GAIN WILD-TYPE"   "19P GAIN MUTATED" "19P GAIN WILD-TYPE" 
        TCGA-DD-A73B         TCGA-DD-A73C         TCGA-DD-A73D 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-DD-A73E         TCGA-DD-A73F         TCGA-DD-A73G 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE"   "19P GAIN MUTATED" 
        TCGA-ED-A459         TCGA-ED-A4XI         TCGA-ED-A5KG 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-ED-A627         TCGA-ED-A66X         TCGA-ED-A66Y 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE"   "19P GAIN MUTATED" 
        TCGA-ED-A7PX         TCGA-ED-A7PY         TCGA-ED-A7PZ 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE"   "19P GAIN MUTATED" 
        TCGA-ED-A7XP         TCGA-ED-A82E         TCGA-EP-A12J 
"19P GAIN WILD-TYPE"   "19P GAIN MUTATED" "19P GAIN WILD-TYPE" 
        TCGA-EP-A26S         TCGA-EP-A2KA         TCGA-EP-A2KB 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE"   "19P GAIN MUTATED" 
        TCGA-EP-A2KC         TCGA-EP-A3JL         TCGA-EP-A3RK 
  "19P GAIN MUTATED" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-ES-A2HS         TCGA-ES-A2HT         TCGA-FV-A23B 
  "19P GAIN MUTATED" "19P GAIN WILD-TYPE"   "19P GAIN MUTATED" 
        TCGA-FV-A2QR         TCGA-FV-A3I0         TCGA-FV-A3I1 
"19P GAIN WILD-TYPE"   "19P GAIN MUTATED" "19P GAIN WILD-TYPE" 
        TCGA-FV-A3R2         TCGA-FV-A3R3         TCGA-FV-A495 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-FV-A496         TCGA-FV-A4ZP         TCGA-FV-A4ZQ 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-G3-A25S         TCGA-G3-A25T         TCGA-G3-A25U 
"19P GAIN WILD-TYPE"   "19P GAIN MUTATED" "19P GAIN WILD-TYPE" 
        TCGA-G3-A25V         TCGA-G3-A25W         TCGA-G3-A25X 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE"   "19P GAIN MUTATED" 
        TCGA-G3-A25Y         TCGA-G3-A25Z         TCGA-G3-A3CG 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-G3-A3CH         TCGA-G3-A3CI         TCGA-G3-A3CJ 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-G3-A3CK         TCGA-G3-A5SI         TCGA-G3-A5SJ 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-G3-A5SL         TCGA-G3-A5SM         TCGA-G3-A6UC 
"19P GAIN WILD-TYPE"   "19P GAIN MUTATED" "19P GAIN WILD-TYPE" 
        TCGA-GJ-A6C0         TCGA-K7-A6G5         TCGA-LG-A6GG 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-MI-A75C         TCGA-MI-A75E         TCGA-MI-A75G 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-MI-A75I         TCGA-NI-A4U2         TCGA-O8-A75V 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE"   "19P GAIN 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-BC-A69H         TCGA-BC-A69I         TCGA-CC-5258 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-CC-5260         TCGA-CC-5261         TCGA-CC-5262 
"19P GAIN WILD-TYPE"   "19P GAIN MUTATED" "19P GAIN WILD-TYPE" 
        TCGA-CC-5263         TCGA-CC-A1HT         TCGA-CC-A3M9 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-CC-A3MA         TCGA-CC-A3MB         TCGA-CC-A3MC 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-DD-A113         TCGA-DD-A114         TCGA-DD-A115 
  "19P GAIN MUTATED" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-DD-A116         TCGA-DD-A118         TCGA-DD-A119 
"19P GAIN WILD-TYPE"   "19P GAIN MUTATED"   "19P GAIN MUTATED" 
        TCGA-DD-A11A         TCGA-DD-A11B         TCGA-DD-A11C 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-DD-A11D         TCGA-DD-A1E9         TCGA-DD-A1EA 
"19P GAIN WILD-TYPE"   "19P GAIN MUTATED" "19P GAIN WILD-TYPE" 
        TCGA-DD-A1EB         TCGA-DD-A1EC         TCGA-DD-A1ED 
"19P GAIN WILD-TYPE"   "19P GAIN MUTATED" "19P GAIN WILD-TYPE" 
        TCGA-DD-A1EE         TCGA-DD-A1EF         TCGA-DD-A1EG 
"19P GAIN WILD-TYPE"   "19P GAIN MUTATED" "19P GAIN WILD-TYPE" 
        TCGA-DD-A1EH         TCGA-DD-A1EI         TCGA-DD-A1EJ 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-DD-A1EK         TCGA-DD-A1EL         TCGA-DD-A39V 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE"   "19P GAIN MUTATED" 
        TCGA-DD-A39X         TCGA-DD-A39Y         TCGA-DD-A39Z 
  "19P GAIN MUTATED" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-DD-A3A0         TCGA-DD-A3A1         TCGA-DD-A3A2 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-DD-A3A3         TCGA-DD-A3A4         TCGA-DD-A3A5 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-DD-A3A6         TCGA-DD-A3A7         TCGA-DD-A3A8 
"19P GAIN WILD-TYPE"   "19P GAIN MUTATED" "19P GAIN WILD-TYPE" 
        TCGA-DD-A3A9         TCGA-DD-A4NA         TCGA-DD-A4NB 
  "19P GAIN MUTATED" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-DD-A4ND         TCGA-DD-A4NF         TCGA-DD-A4NH 
  "19P GAIN MUTATED" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-DD-A4NI         TCGA-DD-A4NJ         TCGA-DD-A4NK 
"19P GAIN WILD-TYPE" "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-DD-A4NR 
"19P GAIN WILD-TYPE"   "19P GAIN MUTATED" "19P GAIN WILD-TYPE" 
        TCGA-DD-A4NS         TCGA-DD-A4NV         TCGA-DD-A73A 
"19P GAIN WILD-TYPE"   "19P GAIN MUTATED" "19P GAIN WILD-TYPE" 
        TCGA-DD-A73B         TCGA-DD-A73C         TCGA-DD-A73D 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-DD-A73E         TCGA-DD-A73F         TCGA-DD-A73G 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE"   "19P GAIN MUTATED" 
        TCGA-ED-A459         TCGA-ED-A4XI         TCGA-ED-A5KG 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-ED-A627         TCGA-ED-A66X         TCGA-ED-A66Y 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE"   "19P GAIN MUTATED" 
        TCGA-ED-A7PX         TCGA-ED-A7PY         TCGA-ED-A7PZ 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE"   "19P GAIN MUTATED" 
        TCGA-ED-A7XP         TCGA-ED-A82E         TCGA-EP-A12J 
"19P GAIN WILD-TYPE"   "19P GAIN MUTATED" "19P GAIN WILD-TYPE" 
        TCGA-EP-A26S         TCGA-EP-A2KA         TCGA-EP-A2KB 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE"   "19P GAIN MUTATED" 
        TCGA-EP-A2KC         TCGA-EP-A3JL         TCGA-EP-A3RK 
  "19P GAIN MUTATED" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-ES-A2HS         TCGA-ES-A2HT         TCGA-FV-A23B 
  "19P GAIN MUTATED" "19P GAIN WILD-TYPE"   "19P GAIN MUTATED" 
        TCGA-FV-A2QR         TCGA-FV-A3I0         TCGA-FV-A3I1 
"19P GAIN WILD-TYPE"   "19P GAIN MUTATED" "19P GAIN WILD-TYPE" 
        TCGA-FV-A3R2         TCGA-FV-A3R3         TCGA-FV-A495 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-FV-A496         TCGA-FV-A4ZP         TCGA-FV-A4ZQ 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-G3-A25S         TCGA-G3-A25T         TCGA-G3-A25U 
"19P GAIN WILD-TYPE"   "19P GAIN MUTATED" "19P GAIN WILD-TYPE" 
        TCGA-G3-A25V         TCGA-G3-A25W         TCGA-G3-A25X 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE"   "19P GAIN MUTATED" 
        TCGA-G3-A25Y         TCGA-G3-A25Z         TCGA-G3-A3CG 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-G3-A3CH         TCGA-G3-A3CI         TCGA-G3-A3CJ 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-G3-A3CK         TCGA-G3-A5SI         TCGA-G3-A5SJ 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-G3-A5SL         TCGA-G3-A5SM         TCGA-G3-A6UC 
"19P GAIN WILD-TYPE"   "19P GAIN MUTATED" "19P GAIN WILD-TYPE" 
        TCGA-GJ-A6C0         TCGA-K7-A6G5         TCGA-LG-A6GG 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-MI-A75C         TCGA-MI-A75E         TCGA-MI-A75G 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-MI-A75I         TCGA-NI-A4U2         TCGA-O8-A75V 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
[1] "hr=" "1.2"
D34V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  19P GAIN MUTATED        11       10         0          4          1
  19P GAIN WILD-TYPE      47       26         2         26          3
                    vv
clus                 STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  19P GAIN MUTATED            0        1         1         1
  19P GAIN WILD-TYPE          5        0         0         1
D34V3, multiclass
                    vv
clus                 T1 T2 T3 T4
  19P GAIN MUTATED   12 11  6  1
  19P GAIN WILD-TYPE 49 29 34  7
D34V4, multiclass
    clus
vv   19P GAIN MUTATED 19P GAIN WILD-TYPE
  T1               12                 49
  T2               11                 29
  T3                6                 34
  T4                1                  7
D34V5, binary
                    cls
clus                  0  1
  19P GAIN MUTATED   20  1
  19P GAIN WILD-TYPE 77  2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED     20    1
  19P GAIN WILD-TYPE   77    2
   clus
vv  19P GAIN MUTATED 19P GAIN WILD-TYPE
  0               20                 77
  1                1                  2
                    vv
clus                 M0 M1 MX
  19P GAIN MUTATED   23  2  5
  19P GAIN WILD-TYPE 92  1 26
D34V6, multiclass
    clus
vv   19P GAIN MUTATED 19P GAIN WILD-TYPE
  M0               23                 92
  M1                2                  1
  MX                5                 26
D34V7, binary
                    cls
clus                  0  1
  19P GAIN MUTATED   16 14
  19P GAIN WILD-TYPE 42 77
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED     16   14
  19P GAIN WILD-TYPE   42   77
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  FEMALE               16                 42
  MALE                 14                 77
                    vv
clus                 R0 R1 R2 RX
  19P GAIN MUTATED   27  1  1  1
  19P GAIN WILD-TYPE 95 10  0  9
D34V8, multiclass
    clus
vv   19P GAIN MUTATED 19P GAIN WILD-TYPE
  R0               27                 95
  R1                1                 10
  R2                1                  0
  RX                1                  9

Clustering(35) Variable = 19Q GAIN MUTATION ANALYSIS
D35V1, survival
                    sevent
clus2                 0  1
  19Q GAIN MUTATED   17 16
  19Q GAIN WILD-TYPE 67 47
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                33                114 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                16                 47 
$`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         0.39         0.10        79.73       113.00 
TCGA-DD-A119 TCGA-DD-A1E9 TCGA-DD-A1EC TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A39V 
        7.33        90.71        19.79        12.95        45.11        21.14 
TCGA-DD-A39X TCGA-DD-A3A9 TCGA-DD-A4ND TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NQ 
       55.69        30.61        73.38        29.56        61.45        12.26 
TCGA-DD-A4NV TCGA-DD-A73G TCGA-ED-A66Y TCGA-ED-A7PZ TCGA-ED-A82E TCGA-EP-A2KB 
       66.35       100.96         0.23         0.20         0.20        10.98 
TCGA-EP-A2KC TCGA-ES-A2HS TCGA-FV-A23B TCGA-FV-A3I0 TCGA-FV-A4ZQ TCGA-G3-A25T 
        0.62        22.85        32.45         0.20         0.39        51.06 
TCGA-G3-A25X TCGA-G3-A5SM TCGA-MI-A75G 
       58.49         4.37        14.24 

$`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-BC-A69H TCGA-BC-A69I 
       13.84         0.26        22.36         9.50         3.95         0.53 
TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3MA 
        0.07         2.86         3.39         4.24         3.32         0.07 
TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A11A 
        0.10         0.13        37.78        83.57        53.33         2.60 
TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1ED 
        0.46        21.76        51.29        79.40        66.31        75.65 
TCGA-DD-A1EE TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A1EL 
        6.71        49.15         6.02        29.16        18.35        13.64 
TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 
        5.62        19.76        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-A4NB TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK 
       12.85        14.07        14.24        18.44        15.06        39.78 
TCGA-DD-A4NL TCGA-DD-A4NP TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A73A TCGA-DD-A73B 
       56.25        93.67         0.30        80.75        10.98         9.30 
TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-ED-A459 TCGA-ED-A4XI 
        7.56        10.98         1.45        27.72        13.41        12.69 
TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7XP 
       15.85        13.91        13.35         0.20         0.20         0.20 
TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HT 
       18.74        19.99        11.74         9.96        11.93        14.40 
TCGA-FV-A2QR TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 
       19.10         8.12         6.38         0.13         0.03         0.33 
TCGA-FV-A4ZP TCGA-G3-A25S TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25Y 
       60.36         1.22        53.79        28.27        30.74        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         5.92        19.53        19.23 
TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SL TCGA-G3-A6UC TCGA-GJ-A6C0 TCGA-K7-A6G5 
       14.70        11.97         7.99         7.76         1.02         4.01 
TCGA-LG-A6GG TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75I TCGA-NI-A4U2 TCGA-O8-A75V 
        0.49         9.57         5.10         8.71        58.88         4.44 

  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
              0.10               0.03 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
            113.00             107.11 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
             21.14              13.81 
[1] "0.1 - 113.0 (21.1)" "0.0 - 107.1 (13.8)"
        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-BC-A69H         TCGA-BC-A69I         TCGA-CC-5258 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-CC-5260         TCGA-CC-5261         TCGA-CC-5262 
"19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" 
        TCGA-CC-5263         TCGA-CC-A1HT         TCGA-CC-A3M9 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" 
        TCGA-CC-A3MA         TCGA-CC-A3MB         TCGA-CC-A3MC 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-DD-A113         TCGA-DD-A114         TCGA-DD-A115 
  "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-DD-A116         TCGA-DD-A118         TCGA-DD-A119 
"19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED"   "19Q GAIN MUTATED" 
        TCGA-DD-A11A         TCGA-DD-A11B         TCGA-DD-A11C 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-DD-A11D         TCGA-DD-A1E9         TCGA-DD-A1EA 
"19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" 
        TCGA-DD-A1EB         TCGA-DD-A1EC         TCGA-DD-A1ED 
"19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" 
        TCGA-DD-A1EE         TCGA-DD-A1EF         TCGA-DD-A1EG 
"19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED"   "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-A1EK         TCGA-DD-A1EL         TCGA-DD-A39V 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" 
        TCGA-DD-A39X         TCGA-DD-A39Y         TCGA-DD-A39Z 
  "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-DD-A3A0         TCGA-DD-A3A1         TCGA-DD-A3A2 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-DD-A3A3         TCGA-DD-A3A4         TCGA-DD-A3A5 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-DD-A3A6         TCGA-DD-A3A7         TCGA-DD-A3A8 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-DD-A3A9         TCGA-DD-A4NA         TCGA-DD-A4NB 
  "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-DD-A4ND         TCGA-DD-A4NF         TCGA-DD-A4NH 
  "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-DD-A4NI         TCGA-DD-A4NJ         TCGA-DD-A4NK 
"19Q GAIN WILD-TYPE" "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-DD-A4NR 
"19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" 
        TCGA-DD-A4NS         TCGA-DD-A4NV         TCGA-DD-A73A 
"19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" 
        TCGA-DD-A73B         TCGA-DD-A73C         TCGA-DD-A73D 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-DD-A73E         TCGA-DD-A73F         TCGA-DD-A73G 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" 
        TCGA-ED-A459         TCGA-ED-A4XI         TCGA-ED-A5KG 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-ED-A627         TCGA-ED-A66X         TCGA-ED-A66Y 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" 
        TCGA-ED-A7PX         TCGA-ED-A7PY         TCGA-ED-A7PZ 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" 
        TCGA-ED-A7XP         TCGA-ED-A82E         TCGA-EP-A12J 
"19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" 
        TCGA-EP-A26S         TCGA-EP-A2KA         TCGA-EP-A2KB 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" 
        TCGA-EP-A2KC         TCGA-EP-A3JL         TCGA-EP-A3RK 
  "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-ES-A2HS         TCGA-ES-A2HT         TCGA-FV-A23B 
  "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" 
        TCGA-FV-A2QR         TCGA-FV-A3I0         TCGA-FV-A3I1 
"19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" 
        TCGA-FV-A3R2         TCGA-FV-A3R3         TCGA-FV-A495 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-FV-A496         TCGA-FV-A4ZP         TCGA-FV-A4ZQ 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" 
        TCGA-G3-A25S         TCGA-G3-A25T         TCGA-G3-A25U 
"19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" 
        TCGA-G3-A25V         TCGA-G3-A25W         TCGA-G3-A25X 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" 
        TCGA-G3-A25Y         TCGA-G3-A25Z         TCGA-G3-A3CG 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-G3-A3CH         TCGA-G3-A3CI         TCGA-G3-A3CJ 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-G3-A3CK         TCGA-G3-A5SI         TCGA-G3-A5SJ 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-G3-A5SL         TCGA-G3-A5SM         TCGA-G3-A6UC 
"19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" 
        TCGA-GJ-A6C0         TCGA-K7-A6G5         TCGA-LG-A6GG 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-MI-A75C         TCGA-MI-A75E         TCGA-MI-A75G 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" 
        TCGA-MI-A75I         TCGA-NI-A4U2         TCGA-O8-A75V 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE"   "19Q GAIN 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-BC-A69H         TCGA-BC-A69I         TCGA-CC-5258 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-CC-5260         TCGA-CC-5261         TCGA-CC-5262 
"19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" 
        TCGA-CC-5263         TCGA-CC-A1HT         TCGA-CC-A3M9 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" 
        TCGA-CC-A3MA         TCGA-CC-A3MB         TCGA-CC-A3MC 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-DD-A113         TCGA-DD-A114         TCGA-DD-A115 
  "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-DD-A116         TCGA-DD-A118         TCGA-DD-A119 
"19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED"   "19Q GAIN MUTATED" 
        TCGA-DD-A11A         TCGA-DD-A11B         TCGA-DD-A11C 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-DD-A11D         TCGA-DD-A1E9         TCGA-DD-A1EA 
"19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" 
        TCGA-DD-A1EB         TCGA-DD-A1EC         TCGA-DD-A1ED 
"19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" 
        TCGA-DD-A1EE         TCGA-DD-A1EF         TCGA-DD-A1EG 
"19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED"   "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-A1EK         TCGA-DD-A1EL         TCGA-DD-A39V 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" 
        TCGA-DD-A39X         TCGA-DD-A39Y         TCGA-DD-A39Z 
  "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-DD-A3A0         TCGA-DD-A3A1         TCGA-DD-A3A2 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-DD-A3A3         TCGA-DD-A3A4         TCGA-DD-A3A5 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-DD-A3A6         TCGA-DD-A3A7         TCGA-DD-A3A8 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-DD-A3A9         TCGA-DD-A4NA         TCGA-DD-A4NB 
  "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-DD-A4ND         TCGA-DD-A4NF         TCGA-DD-A4NH 
  "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-DD-A4NI         TCGA-DD-A4NJ         TCGA-DD-A4NK 
"19Q GAIN WILD-TYPE" "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-DD-A4NR 
"19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" 
        TCGA-DD-A4NS         TCGA-DD-A4NV         TCGA-DD-A73A 
"19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" 
        TCGA-DD-A73B         TCGA-DD-A73C         TCGA-DD-A73D 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-DD-A73E         TCGA-DD-A73F         TCGA-DD-A73G 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" 
        TCGA-ED-A459         TCGA-ED-A4XI         TCGA-ED-A5KG 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-ED-A627         TCGA-ED-A66X         TCGA-ED-A66Y 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" 
        TCGA-ED-A7PX         TCGA-ED-A7PY         TCGA-ED-A7PZ 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" 
        TCGA-ED-A7XP         TCGA-ED-A82E         TCGA-EP-A12J 
"19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" 
        TCGA-EP-A26S         TCGA-EP-A2KA         TCGA-EP-A2KB 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" 
        TCGA-EP-A2KC         TCGA-EP-A3JL         TCGA-EP-A3RK 
  "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-ES-A2HS         TCGA-ES-A2HT         TCGA-FV-A23B 
  "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" 
        TCGA-FV-A2QR         TCGA-FV-A3I0         TCGA-FV-A3I1 
"19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" 
        TCGA-FV-A3R2         TCGA-FV-A3R3         TCGA-FV-A495 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-FV-A496         TCGA-FV-A4ZP         TCGA-FV-A4ZQ 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" 
        TCGA-G3-A25S         TCGA-G3-A25T         TCGA-G3-A25U 
"19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" 
        TCGA-G3-A25V         TCGA-G3-A25W         TCGA-G3-A25X 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" 
        TCGA-G3-A25Y         TCGA-G3-A25Z         TCGA-G3-A3CG 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-G3-A3CH         TCGA-G3-A3CI         TCGA-G3-A3CJ 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-G3-A3CK         TCGA-G3-A5SI         TCGA-G3-A5SJ 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-G3-A5SL         TCGA-G3-A5SM         TCGA-G3-A6UC 
"19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" 
        TCGA-GJ-A6C0         TCGA-K7-A6G5         TCGA-LG-A6GG 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-MI-A75C         TCGA-MI-A75E         TCGA-MI-A75G 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" 
        TCGA-MI-A75I         TCGA-NI-A4U2         TCGA-O8-A75V 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE"   "19Q GAIN 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-BC-A69H         TCGA-BC-A69I         TCGA-CC-5258 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-CC-5260         TCGA-CC-5261         TCGA-CC-5262 
"19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" 
        TCGA-CC-5263         TCGA-CC-A1HT         TCGA-CC-A3M9 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" 
        TCGA-CC-A3MA         TCGA-CC-A3MB         TCGA-CC-A3MC 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-DD-A113         TCGA-DD-A114         TCGA-DD-A115 
  "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-DD-A116         TCGA-DD-A118         TCGA-DD-A119 
"19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED"   "19Q GAIN MUTATED" 
        TCGA-DD-A11A         TCGA-DD-A11B         TCGA-DD-A11C 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-DD-A11D         TCGA-DD-A1E9         TCGA-DD-A1EA 
"19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" 
        TCGA-DD-A1EB         TCGA-DD-A1EC         TCGA-DD-A1ED 
"19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" 
        TCGA-DD-A1EE         TCGA-DD-A1EF         TCGA-DD-A1EG 
"19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED"   "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-A1EK         TCGA-DD-A1EL         TCGA-DD-A39V 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" 
        TCGA-DD-A39X         TCGA-DD-A39Y         TCGA-DD-A39Z 
  "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-DD-A3A0         TCGA-DD-A3A1         TCGA-DD-A3A2 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-DD-A3A3         TCGA-DD-A3A4         TCGA-DD-A3A5 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-DD-A3A6         TCGA-DD-A3A7         TCGA-DD-A3A8 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-DD-A3A9         TCGA-DD-A4NA         TCGA-DD-A4NB 
  "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-DD-A4ND         TCGA-DD-A4NF         TCGA-DD-A4NH 
  "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-DD-A4NI         TCGA-DD-A4NJ         TCGA-DD-A4NK 
"19Q GAIN WILD-TYPE" "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-DD-A4NR 
"19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" 
        TCGA-DD-A4NS         TCGA-DD-A4NV         TCGA-DD-A73A 
"19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" 
        TCGA-DD-A73B         TCGA-DD-A73C         TCGA-DD-A73D 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-DD-A73E         TCGA-DD-A73F         TCGA-DD-A73G 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" 
        TCGA-ED-A459         TCGA-ED-A4XI         TCGA-ED-A5KG 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-ED-A627         TCGA-ED-A66X         TCGA-ED-A66Y 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" 
        TCGA-ED-A7PX         TCGA-ED-A7PY         TCGA-ED-A7PZ 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" 
        TCGA-ED-A7XP         TCGA-ED-A82E         TCGA-EP-A12J 
"19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" 
        TCGA-EP-A26S         TCGA-EP-A2KA         TCGA-EP-A2KB 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" 
        TCGA-EP-A2KC         TCGA-EP-A3JL         TCGA-EP-A3RK 
  "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-ES-A2HS         TCGA-ES-A2HT         TCGA-FV-A23B 
  "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" 
        TCGA-FV-A2QR         TCGA-FV-A3I0         TCGA-FV-A3I1 
"19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" 
        TCGA-FV-A3R2         TCGA-FV-A3R3         TCGA-FV-A495 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-FV-A496         TCGA-FV-A4ZP         TCGA-FV-A4ZQ 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" 
        TCGA-G3-A25S         TCGA-G3-A25T         TCGA-G3-A25U 
"19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" 
        TCGA-G3-A25V         TCGA-G3-A25W         TCGA-G3-A25X 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" 
        TCGA-G3-A25Y         TCGA-G3-A25Z         TCGA-G3-A3CG 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-G3-A3CH         TCGA-G3-A3CI         TCGA-G3-A3CJ 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-G3-A3CK         TCGA-G3-A5SI         TCGA-G3-A5SJ 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-G3-A5SL         TCGA-G3-A5SM         TCGA-G3-A6UC 
"19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" 
        TCGA-GJ-A6C0         TCGA-K7-A6G5         TCGA-LG-A6GG 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-MI-A75C         TCGA-MI-A75E         TCGA-MI-A75G 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" 
        TCGA-MI-A75I         TCGA-NI-A4U2         TCGA-O8-A75V 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
[1] "hr=" "1.2"
D35V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  19Q GAIN MUTATED        13       11         0          5          0
  19Q GAIN WILD-TYPE      45       25         2         25          4
                    vv
clus                 STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  19Q GAIN MUTATED            0        1         1         1
  19Q GAIN WILD-TYPE          5        0         0         1
D35V3, multiclass
                    vv
clus                 T1 T2 T3 T4
  19Q GAIN MUTATED   14 12  7  1
  19Q GAIN WILD-TYPE 47 28 33  7
D35V4, multiclass
    clus
vv   19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  T1               14                 47
  T2               12                 28
  T3                7                 33
  T4                1                  7
D35V5, binary
                    cls
clus                  0  1
  19Q GAIN MUTATED   22  1
  19Q GAIN WILD-TYPE 75  2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED     22    1
  19Q GAIN WILD-TYPE   75    2
   clus
vv  19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  0               22                 75
  1                1                  2
                    vv
clus                 M0 M1 MX
  19Q GAIN MUTATED   26  2  6
  19Q GAIN WILD-TYPE 89  1 25
D35V6, multiclass
    clus
vv   19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  M0               26                 89
  M1                2                  1
  MX                6                 25
D35V7, binary
                    cls
clus                  0  1
  19Q GAIN MUTATED   17 17
  19Q GAIN WILD-TYPE 41 74
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED     17   17
  19Q GAIN WILD-TYPE   41   74
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  FEMALE               17                 41
  MALE                 17                 74
                    vv
clus                 R0 R1 R2 RX
  19Q GAIN MUTATED   31  1  1  1
  19Q GAIN WILD-TYPE 91 10  0  9
D35V8, multiclass
    clus
vv   19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  R0               31                 91
  R1                1                 10
  R2                1                  0
  RX                1                  9

Clustering(36) Variable = 20P GAIN MUTATION ANALYSIS
D36V1, survival
                    sevent
clus2                 0  1
  20P GAIN MUTATED   21 21
  20P GAIN WILD-TYPE 63 42
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                42                105 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                21                 42 
$`20P GAIN MUTATED`
TCGA-BC-4072 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A69H 
       48.99        37.32        10.13        13.84         0.26         3.95 
TCGA-CC-5261 TCGA-CC-A3M9 TCGA-CC-A3MB TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A 
        0.39         0.10         0.10       113.00         7.33         2.60 
TCGA-DD-A11B TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EJ TCGA-DD-A39V 
        0.46        12.95        45.11        49.15        29.16        21.14 
TCGA-DD-A3A5 TCGA-DD-A3A7 TCGA-DD-A3A9 TCGA-DD-A4ND TCGA-DD-A4NN TCGA-DD-A4NR 
      102.74        13.78        30.61        73.38        29.56         0.30 
TCGA-DD-A4NV TCGA-DD-A73G TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A82E TCGA-EP-A2KB 
       66.35       100.96        13.35         0.23         0.20        10.98 
TCGA-EP-A3JL TCGA-ES-A2HS TCGA-FV-A23B TCGA-FV-A3R2 TCGA-FV-A4ZQ TCGA-G3-A25S 
        9.96        22.85        32.45         6.38         0.39         1.22 
TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A5SM TCGA-G3-A6UC TCGA-LG-A6GG TCGA-MI-A75G 
       58.49        14.86         4.37         7.76         0.49        14.24 

$`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        22.36 
TCGA-BC-A5W4 TCGA-BC-A69I TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5262 TCGA-CC-5263 
        9.50         0.53         0.07         2.86         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        37.78        83.57 
TCGA-DD-A116 TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB 
       53.33        21.76        51.29        90.71        79.40        66.31 
TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EI TCGA-DD-A1EK TCGA-DD-A1EL 
       19.79        75.65         6.71         6.02        18.35        13.64 
TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 
       55.69         5.62        19.76        25.81         7.66        70.06 
TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A6 TCGA-DD-A3A8 TCGA-DD-A4NA TCGA-DD-A4NB 
       17.59        20.12       107.11         0.36        33.14        12.85 
TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL 
       14.07        14.24        18.44        15.06        39.78        56.25 
TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NS TCGA-DD-A73A TCGA-DD-A73B 
       61.45        93.67        12.26        80.75        10.98         9.30 
TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-ED-A459 TCGA-ED-A4XI 
        7.56        10.98         1.45        27.72        13.41        12.69 
TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XP 
       15.85        13.91         0.20         0.20         0.20         0.20 
TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KC TCGA-EP-A3RK TCGA-ES-A2HT 
       18.74        19.99        11.74         0.62        11.93        14.40 
TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 
       19.10         0.20         8.12         0.13         0.03         0.33 
TCGA-FV-A4ZP TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25Z 
       60.36        51.06        53.79        28.27        30.74        21.53 
TCGA-G3-A3CG TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI 
       22.13        25.64         5.92        19.53        19.23        14.70 
TCGA-G3-A5SJ TCGA-G3-A5SL TCGA-GJ-A6C0 TCGA-K7-A6G5 TCGA-MI-A75C TCGA-MI-A75E 
       11.97         7.99         1.02         4.01         9.57         5.10 
TCGA-MI-A75I TCGA-NI-A4U2 TCGA-O8-A75V 
        8.71        58.88         4.44 

  20P GAIN MUTATED 20P GAIN WILD-TYPE 
              0.10               0.03 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
            113.00             107.11 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
             13.15              14.70 
[1] "0.1 - 113.0 (13.1)" "0.0 - 107.1 (14.7)"
        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-BC-A69H         TCGA-BC-A69I         TCGA-CC-5258 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-CC-5260         TCGA-CC-5261         TCGA-CC-5262 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-CC-5263         TCGA-CC-A1HT         TCGA-CC-A3M9 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-CC-A3MA         TCGA-CC-A3MB         TCGA-CC-A3MC 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-DD-A113         TCGA-DD-A114         TCGA-DD-A115 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-DD-A116         TCGA-DD-A118         TCGA-DD-A119 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED"   "20P GAIN MUTATED" 
        TCGA-DD-A11A         TCGA-DD-A11B         TCGA-DD-A11C 
  "20P GAIN MUTATED"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-DD-A11D         TCGA-DD-A1E9         TCGA-DD-A1EA 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-DD-A1EB         TCGA-DD-A1EC         TCGA-DD-A1ED 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-DD-A1EE         TCGA-DD-A1EF         TCGA-DD-A1EG 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED"   "20P GAIN MUTATED" 
        TCGA-DD-A1EH         TCGA-DD-A1EI         TCGA-DD-A1EJ 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-DD-A1EK         TCGA-DD-A1EL         TCGA-DD-A39V 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-DD-A39X         TCGA-DD-A39Y         TCGA-DD-A39Z 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-DD-A3A0         TCGA-DD-A3A1         TCGA-DD-A3A2 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-DD-A3A3         TCGA-DD-A3A4         TCGA-DD-A3A5 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-DD-A3A6         TCGA-DD-A3A7         TCGA-DD-A3A8 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-DD-A3A9         TCGA-DD-A4NA         TCGA-DD-A4NB 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-DD-A4ND         TCGA-DD-A4NF         TCGA-DD-A4NH 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-DD-A4NI         TCGA-DD-A4NJ         TCGA-DD-A4NK 
"20P GAIN WILD-TYPE" "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-DD-A4NR 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-DD-A4NS         TCGA-DD-A4NV         TCGA-DD-A73A 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-DD-A73B         TCGA-DD-A73C         TCGA-DD-A73D 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-DD-A73E         TCGA-DD-A73F         TCGA-DD-A73G 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-ED-A459         TCGA-ED-A4XI         TCGA-ED-A5KG 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-ED-A627         TCGA-ED-A66X         TCGA-ED-A66Y 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED"   "20P GAIN MUTATED" 
        TCGA-ED-A7PX         TCGA-ED-A7PY         TCGA-ED-A7PZ 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-ED-A7XP         TCGA-ED-A82E         TCGA-EP-A12J 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-EP-A26S         TCGA-EP-A2KA         TCGA-EP-A2KB 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-EP-A2KC         TCGA-EP-A3JL         TCGA-EP-A3RK 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-ES-A2HS         TCGA-ES-A2HT         TCGA-FV-A23B 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-FV-A2QR         TCGA-FV-A3I0         TCGA-FV-A3I1 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-FV-A3R2         TCGA-FV-A3R3         TCGA-FV-A495 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-FV-A496         TCGA-FV-A4ZP         TCGA-FV-A4ZQ 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-G3-A25S         TCGA-G3-A25T         TCGA-G3-A25U 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-G3-A25V         TCGA-G3-A25W         TCGA-G3-A25X 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-G3-A25Y         TCGA-G3-A25Z         TCGA-G3-A3CG 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-G3-A3CH         TCGA-G3-A3CI         TCGA-G3-A3CJ 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-G3-A3CK         TCGA-G3-A5SI         TCGA-G3-A5SJ 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-G3-A5SL         TCGA-G3-A5SM         TCGA-G3-A6UC 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED"   "20P GAIN MUTATED" 
        TCGA-GJ-A6C0         TCGA-K7-A6G5         TCGA-LG-A6GG 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-MI-A75C         TCGA-MI-A75E         TCGA-MI-A75G 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-MI-A75I         TCGA-NI-A4U2         TCGA-O8-A75V 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-BC-A5W4 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-BC-A69H         TCGA-BC-A69I         TCGA-CC-5258 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-CC-5260         TCGA-CC-5261         TCGA-CC-5262 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-CC-5263         TCGA-CC-A1HT         TCGA-CC-A3M9 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-CC-A3MA         TCGA-CC-A3MB         TCGA-CC-A3MC 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-DD-A113         TCGA-DD-A114         TCGA-DD-A115 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-DD-A116         TCGA-DD-A118         TCGA-DD-A119 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED"   "20P GAIN MUTATED" 
        TCGA-DD-A11A         TCGA-DD-A11B         TCGA-DD-A11C 
  "20P GAIN MUTATED"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-DD-A11D         TCGA-DD-A1E9         TCGA-DD-A1EA 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-DD-A1EB         TCGA-DD-A1EC         TCGA-DD-A1ED 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-DD-A1EE         TCGA-DD-A1EF         TCGA-DD-A1EG 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED"   "20P GAIN MUTATED" 
        TCGA-DD-A1EH         TCGA-DD-A1EI         TCGA-DD-A1EJ 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-DD-A1EK         TCGA-DD-A1EL         TCGA-DD-A39V 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-DD-A39X         TCGA-DD-A39Y         TCGA-DD-A39Z 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-DD-A3A0         TCGA-DD-A3A1         TCGA-DD-A3A2 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-DD-A3A3         TCGA-DD-A3A4         TCGA-DD-A3A5 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-DD-A3A6         TCGA-DD-A3A7         TCGA-DD-A3A8 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-DD-A3A9         TCGA-DD-A4NA         TCGA-DD-A4NB 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-DD-A4ND         TCGA-DD-A4NF         TCGA-DD-A4NH 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-DD-A4NI         TCGA-DD-A4NJ         TCGA-DD-A4NK 
"20P GAIN WILD-TYPE" "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-DD-A4NR 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-DD-A4NS         TCGA-DD-A4NV         TCGA-DD-A73A 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-DD-A73B         TCGA-DD-A73C         TCGA-DD-A73D 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-DD-A73E         TCGA-DD-A73F         TCGA-DD-A73G 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-ED-A459         TCGA-ED-A4XI         TCGA-ED-A5KG 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-ED-A627         TCGA-ED-A66X         TCGA-ED-A66Y 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED"   "20P GAIN MUTATED" 
        TCGA-ED-A7PX         TCGA-ED-A7PY         TCGA-ED-A7PZ 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-ED-A7XP         TCGA-ED-A82E         TCGA-EP-A12J 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-EP-A26S         TCGA-EP-A2KA         TCGA-EP-A2KB 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-EP-A2KC         TCGA-EP-A3JL         TCGA-EP-A3RK 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-ES-A2HS         TCGA-ES-A2HT         TCGA-FV-A23B 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-FV-A2QR         TCGA-FV-A3I0         TCGA-FV-A3I1 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-FV-A3R2         TCGA-FV-A3R3         TCGA-FV-A495 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-FV-A496         TCGA-FV-A4ZP         TCGA-FV-A4ZQ 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-G3-A25S         TCGA-G3-A25T         TCGA-G3-A25U 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-G3-A25V         TCGA-G3-A25W         TCGA-G3-A25X 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-G3-A25Y         TCGA-G3-A25Z         TCGA-G3-A3CG 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-G3-A3CH         TCGA-G3-A3CI         TCGA-G3-A3CJ 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-G3-A3CK         TCGA-G3-A5SI         TCGA-G3-A5SJ 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-G3-A5SL         TCGA-G3-A5SM         TCGA-G3-A6UC 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED"   "20P GAIN MUTATED" 
        TCGA-GJ-A6C0         TCGA-K7-A6G5         TCGA-LG-A6GG 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-MI-A75C         TCGA-MI-A75E         TCGA-MI-A75G 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-MI-A75I         TCGA-NI-A4U2         TCGA-O8-A75V 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-BC-A5W4 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-BC-A69H         TCGA-BC-A69I         TCGA-CC-5258 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-CC-5260         TCGA-CC-5261         TCGA-CC-5262 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-CC-5263         TCGA-CC-A1HT         TCGA-CC-A3M9 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-CC-A3MA         TCGA-CC-A3MB         TCGA-CC-A3MC 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-DD-A113         TCGA-DD-A114         TCGA-DD-A115 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-DD-A116         TCGA-DD-A118         TCGA-DD-A119 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED"   "20P GAIN MUTATED" 
        TCGA-DD-A11A         TCGA-DD-A11B         TCGA-DD-A11C 
  "20P GAIN MUTATED"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-DD-A11D         TCGA-DD-A1E9         TCGA-DD-A1EA 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-DD-A1EB         TCGA-DD-A1EC         TCGA-DD-A1ED 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-DD-A1EE         TCGA-DD-A1EF         TCGA-DD-A1EG 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED"   "20P GAIN MUTATED" 
        TCGA-DD-A1EH         TCGA-DD-A1EI         TCGA-DD-A1EJ 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-DD-A1EK         TCGA-DD-A1EL         TCGA-DD-A39V 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-DD-A39X         TCGA-DD-A39Y         TCGA-DD-A39Z 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-DD-A3A0         TCGA-DD-A3A1         TCGA-DD-A3A2 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-DD-A3A3         TCGA-DD-A3A4         TCGA-DD-A3A5 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-DD-A3A6         TCGA-DD-A3A7         TCGA-DD-A3A8 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-DD-A3A9         TCGA-DD-A4NA         TCGA-DD-A4NB 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-DD-A4ND         TCGA-DD-A4NF         TCGA-DD-A4NH 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-DD-A4NI         TCGA-DD-A4NJ         TCGA-DD-A4NK 
"20P GAIN WILD-TYPE" "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-DD-A4NR 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-DD-A4NS         TCGA-DD-A4NV         TCGA-DD-A73A 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-DD-A73B         TCGA-DD-A73C         TCGA-DD-A73D 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-DD-A73E         TCGA-DD-A73F         TCGA-DD-A73G 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-ED-A459         TCGA-ED-A4XI         TCGA-ED-A5KG 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-ED-A627         TCGA-ED-A66X         TCGA-ED-A66Y 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED"   "20P GAIN MUTATED" 
        TCGA-ED-A7PX         TCGA-ED-A7PY         TCGA-ED-A7PZ 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-ED-A7XP         TCGA-ED-A82E         TCGA-EP-A12J 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-EP-A26S         TCGA-EP-A2KA         TCGA-EP-A2KB 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-EP-A2KC         TCGA-EP-A3JL         TCGA-EP-A3RK 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-ES-A2HS         TCGA-ES-A2HT         TCGA-FV-A23B 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-FV-A2QR         TCGA-FV-A3I0         TCGA-FV-A3I1 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-FV-A3R2         TCGA-FV-A3R3         TCGA-FV-A495 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-FV-A496         TCGA-FV-A4ZP         TCGA-FV-A4ZQ 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-G3-A25S         TCGA-G3-A25T         TCGA-G3-A25U 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-G3-A25V         TCGA-G3-A25W         TCGA-G3-A25X 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-G3-A25Y         TCGA-G3-A25Z         TCGA-G3-A3CG 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-G3-A3CH         TCGA-G3-A3CI         TCGA-G3-A3CJ 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-G3-A3CK         TCGA-G3-A5SI         TCGA-G3-A5SJ 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-G3-A5SL         TCGA-G3-A5SM         TCGA-G3-A6UC 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED"   "20P GAIN MUTATED" 
        TCGA-GJ-A6C0         TCGA-K7-A6G5         TCGA-LG-A6GG 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-MI-A75C         TCGA-MI-A75E         TCGA-MI-A75G 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-MI-A75I         TCGA-NI-A4U2         TCGA-O8-A75V 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
[1] "hr=" "1.2"
D36V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  20P GAIN MUTATED        16       10         2          8          2
  20P GAIN WILD-TYPE      42       26         0         22          2
                    vv
clus                 STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  20P GAIN MUTATED            1        1         0         1
  20P GAIN WILD-TYPE          4        0         1         1
D36V3, multiclass
                    vv
clus                 T1 T2 T3 T4
  20P GAIN MUTATED   17 11 14  1
  20P GAIN WILD-TYPE 44 29 26  7
D36V4, multiclass
    clus
vv   20P GAIN MUTATED 20P GAIN WILD-TYPE
  T1               17                 44
  T2               11                 29
  T3               14                 26
  T4                1                  7
D36V5, binary
                    cls
clus                  0  1
  20P GAIN MUTATED   29  1
  20P GAIN WILD-TYPE 68  2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED     29    1
  20P GAIN WILD-TYPE   68    2
   clus
vv  20P GAIN MUTATED 20P GAIN WILD-TYPE
  0               29                 68
  1                1                  2
                    vv
clus                 M0 M1 MX
  20P GAIN MUTATED   35  2  6
  20P GAIN WILD-TYPE 80  1 25
D36V6, multiclass
    clus
vv   20P GAIN MUTATED 20P GAIN WILD-TYPE
  M0               35                 80
  M1                2                  1
  MX                6                 25
D36V7, binary
                    cls
clus                  0  1
  20P GAIN MUTATED   20 23
  20P GAIN WILD-TYPE 38 68
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED     20   23
  20P GAIN WILD-TYPE   38   68
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  FEMALE               20                 38
  MALE                 23                 68
                    vv
clus                 R0 R1 R2 RX
  20P GAIN MUTATED   35  3  1  3
  20P GAIN WILD-TYPE 87  8  0  7
D36V8, multiclass
    clus
vv   20P GAIN MUTATED 20P GAIN WILD-TYPE
  R0               35                 87
  R1                3                  8
  R2                1                  0
  RX                3                  7

Clustering(37) Variable = 20Q GAIN MUTATION ANALYSIS
D37V1, survival
                    sevent
clus2                 0  1
  20Q GAIN MUTATED   23 21
  20Q GAIN WILD-TYPE 61 42
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                44                103 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                21                 42 
$`20Q GAIN MUTATED`
TCGA-BC-4072 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A69H 
       48.99        37.32        10.13        13.84         0.26         3.95 
TCGA-CC-5261 TCGA-CC-A3M9 TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A118 TCGA-DD-A119 
        0.39         0.10         0.10         0.13       113.00         7.33 
TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH 
        2.60         0.46        21.76        12.95        45.11        49.15 
TCGA-DD-A1EJ TCGA-DD-A39V TCGA-DD-A3A5 TCGA-DD-A3A7 TCGA-DD-A3A9 TCGA-DD-A4ND 
       29.16        21.14       102.74        13.78        30.61        73.38 
TCGA-DD-A4NN TCGA-DD-A4NR TCGA-DD-A4NV TCGA-DD-A73G TCGA-ED-A66X TCGA-ED-A66Y 
       29.56         0.30        66.35       100.96        13.35         0.23 
TCGA-ED-A82E TCGA-EP-A2KB TCGA-EP-A3JL TCGA-ES-A2HS TCGA-FV-A23B TCGA-FV-A3R2 
        0.20        10.98         9.96        22.85        32.45         6.38 
TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A5SM TCGA-G3-A6UC 
        0.39         1.22        58.49        14.86         4.37         7.76 
TCGA-LG-A6GG TCGA-MI-A75G 
        0.49        14.24 

$`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        22.36 
TCGA-BC-A5W4 TCGA-BC-A69I TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5262 TCGA-CC-5263 
        9.50         0.53         0.07         2.86         3.39         4.24 
TCGA-CC-A1HT TCGA-CC-A3MA TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 
        3.32         0.07        79.73        37.78        83.57        53.33 
TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED 
       51.29        90.71        79.40        66.31        19.79        75.65 
TCGA-DD-A1EE TCGA-DD-A1EI TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39X TCGA-DD-A39Y 
        6.71         6.02        18.35        13.64        55.69         5.62 
TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 
       19.76        25.81         7.66        70.06        17.59        20.12 
TCGA-DD-A3A6 TCGA-DD-A3A8 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4NF TCGA-DD-A4NH 
      107.11         0.36        33.14        12.85        14.07        14.24 
TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NO TCGA-DD-A4NP 
       18.44        15.06        39.78        56.25        61.45        93.67 
TCGA-DD-A4NQ TCGA-DD-A4NS TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D 
       12.26        80.75        10.98         9.30         7.56        10.98 
TCGA-DD-A73E TCGA-DD-A73F TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 
        1.45        27.72        13.41        12.69        15.85        13.91 
TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XP TCGA-EP-A12J TCGA-EP-A26S 
        0.20         0.20         0.20         0.20        18.74        19.99 
TCGA-EP-A2KA TCGA-EP-A2KC TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A2QR TCGA-FV-A3I0 
       11.74         0.62        11.93        14.40        19.10         0.20 
TCGA-FV-A3I1 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZP TCGA-G3-A25T 
        8.12         0.13         0.03         0.33        60.36        51.06 
TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CH 
       53.79        28.27        30.74        21.53        22.13        25.64 
TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SL 
        5.92        19.53        19.23        14.70        11.97         7.99 
TCGA-GJ-A6C0 TCGA-K7-A6G5 TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75I TCGA-NI-A4U2 
        1.02         4.01         9.57         5.10         8.71        58.88 
TCGA-O8-A75V 
        4.44 

  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
              0.10               0.03 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
            113.00             107.11 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
             13.15              14.70 
[1] "0.1 - 113.0 (13.1)" "0.0 - 107.1 (14.7)"
        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-BC-A69H         TCGA-BC-A69I         TCGA-CC-5258 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-CC-5260         TCGA-CC-5261         TCGA-CC-5262 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-CC-5263         TCGA-CC-A1HT         TCGA-CC-A3M9 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-CC-A3MA         TCGA-CC-A3MB         TCGA-CC-A3MC 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-DD-A113         TCGA-DD-A114         TCGA-DD-A115 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-DD-A116         TCGA-DD-A118         TCGA-DD-A119 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-DD-A11A         TCGA-DD-A11B         TCGA-DD-A11C 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-DD-A11D         TCGA-DD-A1E9         TCGA-DD-A1EA 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-DD-A1EB         TCGA-DD-A1EC         TCGA-DD-A1ED 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-DD-A1EE         TCGA-DD-A1EF         TCGA-DD-A1EG 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-DD-A1EH         TCGA-DD-A1EI         TCGA-DD-A1EJ 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-DD-A1EK         TCGA-DD-A1EL         TCGA-DD-A39V 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-DD-A39X         TCGA-DD-A39Y         TCGA-DD-A39Z 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-DD-A3A0         TCGA-DD-A3A1         TCGA-DD-A3A2 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-DD-A3A3         TCGA-DD-A3A4         TCGA-DD-A3A5 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-DD-A3A6         TCGA-DD-A3A7         TCGA-DD-A3A8 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-DD-A3A9         TCGA-DD-A4NA         TCGA-DD-A4NB 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-DD-A4ND         TCGA-DD-A4NF         TCGA-DD-A4NH 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-DD-A4NI         TCGA-DD-A4NJ         TCGA-DD-A4NK 
"20Q GAIN WILD-TYPE" "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-DD-A4NR 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-DD-A4NS         TCGA-DD-A4NV         TCGA-DD-A73A 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-DD-A73B         TCGA-DD-A73C         TCGA-DD-A73D 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-DD-A73E         TCGA-DD-A73F         TCGA-DD-A73G 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-ED-A459         TCGA-ED-A4XI         TCGA-ED-A5KG 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-ED-A627         TCGA-ED-A66X         TCGA-ED-A66Y 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-ED-A7PX         TCGA-ED-A7PY         TCGA-ED-A7PZ 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-ED-A7XP         TCGA-ED-A82E         TCGA-EP-A12J 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-EP-A26S         TCGA-EP-A2KA         TCGA-EP-A2KB 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-EP-A2KC         TCGA-EP-A3JL         TCGA-EP-A3RK 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-ES-A2HS         TCGA-ES-A2HT         TCGA-FV-A23B 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-FV-A2QR         TCGA-FV-A3I0         TCGA-FV-A3I1 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-FV-A3R2         TCGA-FV-A3R3         TCGA-FV-A495 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-FV-A496         TCGA-FV-A4ZP         TCGA-FV-A4ZQ 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-G3-A25S         TCGA-G3-A25T         TCGA-G3-A25U 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-G3-A25V         TCGA-G3-A25W         TCGA-G3-A25X 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-G3-A25Y         TCGA-G3-A25Z         TCGA-G3-A3CG 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-G3-A3CH         TCGA-G3-A3CI         TCGA-G3-A3CJ 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-G3-A3CK         TCGA-G3-A5SI         TCGA-G3-A5SJ 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-G3-A5SL         TCGA-G3-A5SM         TCGA-G3-A6UC 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-GJ-A6C0         TCGA-K7-A6G5         TCGA-LG-A6GG 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-MI-A75C         TCGA-MI-A75E         TCGA-MI-A75G 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-MI-A75I         TCGA-NI-A4U2         TCGA-O8-A75V 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-BC-A5W4 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-BC-A69H         TCGA-BC-A69I         TCGA-CC-5258 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-CC-5260         TCGA-CC-5261         TCGA-CC-5262 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-CC-5263         TCGA-CC-A1HT         TCGA-CC-A3M9 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-CC-A3MA         TCGA-CC-A3MB         TCGA-CC-A3MC 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-DD-A113         TCGA-DD-A114         TCGA-DD-A115 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-DD-A116         TCGA-DD-A118         TCGA-DD-A119 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-DD-A11A         TCGA-DD-A11B         TCGA-DD-A11C 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-DD-A11D         TCGA-DD-A1E9         TCGA-DD-A1EA 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-DD-A1EB         TCGA-DD-A1EC         TCGA-DD-A1ED 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-DD-A1EE         TCGA-DD-A1EF         TCGA-DD-A1EG 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-DD-A1EH         TCGA-DD-A1EI         TCGA-DD-A1EJ 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-DD-A1EK         TCGA-DD-A1EL         TCGA-DD-A39V 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-DD-A39X         TCGA-DD-A39Y         TCGA-DD-A39Z 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-DD-A3A0         TCGA-DD-A3A1         TCGA-DD-A3A2 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-DD-A3A3         TCGA-DD-A3A4         TCGA-DD-A3A5 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-DD-A3A6         TCGA-DD-A3A7         TCGA-DD-A3A8 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-DD-A3A9         TCGA-DD-A4NA         TCGA-DD-A4NB 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-DD-A4ND         TCGA-DD-A4NF         TCGA-DD-A4NH 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-DD-A4NI         TCGA-DD-A4NJ         TCGA-DD-A4NK 
"20Q GAIN WILD-TYPE" "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-DD-A4NR 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-DD-A4NS         TCGA-DD-A4NV         TCGA-DD-A73A 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-DD-A73B         TCGA-DD-A73C         TCGA-DD-A73D 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-DD-A73E         TCGA-DD-A73F         TCGA-DD-A73G 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-ED-A459         TCGA-ED-A4XI         TCGA-ED-A5KG 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-ED-A627         TCGA-ED-A66X         TCGA-ED-A66Y 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-ED-A7PX         TCGA-ED-A7PY         TCGA-ED-A7PZ 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-ED-A7XP         TCGA-ED-A82E         TCGA-EP-A12J 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-EP-A26S         TCGA-EP-A2KA         TCGA-EP-A2KB 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-EP-A2KC         TCGA-EP-A3JL         TCGA-EP-A3RK 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-ES-A2HS         TCGA-ES-A2HT         TCGA-FV-A23B 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-FV-A2QR         TCGA-FV-A3I0         TCGA-FV-A3I1 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-FV-A3R2         TCGA-FV-A3R3         TCGA-FV-A495 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-FV-A496         TCGA-FV-A4ZP         TCGA-FV-A4ZQ 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-G3-A25S         TCGA-G3-A25T         TCGA-G3-A25U 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-G3-A25V         TCGA-G3-A25W         TCGA-G3-A25X 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-G3-A25Y         TCGA-G3-A25Z         TCGA-G3-A3CG 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-G3-A3CH         TCGA-G3-A3CI         TCGA-G3-A3CJ 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-G3-A3CK         TCGA-G3-A5SI         TCGA-G3-A5SJ 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-G3-A5SL         TCGA-G3-A5SM         TCGA-G3-A6UC 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-GJ-A6C0         TCGA-K7-A6G5         TCGA-LG-A6GG 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-MI-A75C         TCGA-MI-A75E         TCGA-MI-A75G 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-MI-A75I         TCGA-NI-A4U2         TCGA-O8-A75V 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-BC-A5W4 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-BC-A69H         TCGA-BC-A69I         TCGA-CC-5258 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-CC-5260         TCGA-CC-5261         TCGA-CC-5262 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-CC-5263         TCGA-CC-A1HT         TCGA-CC-A3M9 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-CC-A3MA         TCGA-CC-A3MB         TCGA-CC-A3MC 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-DD-A113         TCGA-DD-A114         TCGA-DD-A115 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-DD-A116         TCGA-DD-A118         TCGA-DD-A119 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-DD-A11A         TCGA-DD-A11B         TCGA-DD-A11C 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-DD-A11D         TCGA-DD-A1E9         TCGA-DD-A1EA 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-DD-A1EB         TCGA-DD-A1EC         TCGA-DD-A1ED 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-DD-A1EE         TCGA-DD-A1EF         TCGA-DD-A1EG 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-DD-A1EH         TCGA-DD-A1EI         TCGA-DD-A1EJ 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-DD-A1EK         TCGA-DD-A1EL         TCGA-DD-A39V 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-DD-A39X         TCGA-DD-A39Y         TCGA-DD-A39Z 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-DD-A3A0         TCGA-DD-A3A1         TCGA-DD-A3A2 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-DD-A3A3         TCGA-DD-A3A4         TCGA-DD-A3A5 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-DD-A3A6         TCGA-DD-A3A7         TCGA-DD-A3A8 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-DD-A3A9         TCGA-DD-A4NA         TCGA-DD-A4NB 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-DD-A4ND         TCGA-DD-A4NF         TCGA-DD-A4NH 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-DD-A4NI         TCGA-DD-A4NJ         TCGA-DD-A4NK 
"20Q GAIN WILD-TYPE" "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-DD-A4NR 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-DD-A4NS         TCGA-DD-A4NV         TCGA-DD-A73A 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-DD-A73B         TCGA-DD-A73C         TCGA-DD-A73D 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-DD-A73E         TCGA-DD-A73F         TCGA-DD-A73G 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-ED-A459         TCGA-ED-A4XI         TCGA-ED-A5KG 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-ED-A627         TCGA-ED-A66X         TCGA-ED-A66Y 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-ED-A7PX         TCGA-ED-A7PY         TCGA-ED-A7PZ 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-ED-A7XP         TCGA-ED-A82E         TCGA-EP-A12J 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-EP-A26S         TCGA-EP-A2KA         TCGA-EP-A2KB 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-EP-A2KC         TCGA-EP-A3JL         TCGA-EP-A3RK 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-ES-A2HS         TCGA-ES-A2HT         TCGA-FV-A23B 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-FV-A2QR         TCGA-FV-A3I0         TCGA-FV-A3I1 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-FV-A3R2         TCGA-FV-A3R3         TCGA-FV-A495 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-FV-A496         TCGA-FV-A4ZP         TCGA-FV-A4ZQ 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-G3-A25S         TCGA-G3-A25T         TCGA-G3-A25U 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-G3-A25V         TCGA-G3-A25W         TCGA-G3-A25X 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-G3-A25Y         TCGA-G3-A25Z         TCGA-G3-A3CG 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-G3-A3CH         TCGA-G3-A3CI         TCGA-G3-A3CJ 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-G3-A3CK         TCGA-G3-A5SI         TCGA-G3-A5SJ 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-G3-A5SL         TCGA-G3-A5SM         TCGA-G3-A6UC 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-GJ-A6C0         TCGA-K7-A6G5         TCGA-LG-A6GG 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-MI-A75C         TCGA-MI-A75E         TCGA-MI-A75G 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-MI-A75I         TCGA-NI-A4U2         TCGA-O8-A75V 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
[1] "hr=" "1.2"
D37V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  20Q GAIN MUTATED        17       10         2          9          2
  20Q GAIN WILD-TYPE      41       26         0         21          2
                    vv
clus                 STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  20Q GAIN MUTATED            1        1         0         1
  20Q GAIN WILD-TYPE          4        0         1         1
D37V3, multiclass
                    vv
clus                 T1 T2 T3 T4
  20Q GAIN MUTATED   18 11 15  1
  20Q GAIN WILD-TYPE 43 29 25  7
D37V4, multiclass
    clus
vv   20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  T1               18                 43
  T2               11                 29
  T3               15                 25
  T4                1                  7
D37V5, binary
                    cls
clus                  0  1
  20Q GAIN MUTATED   31  1
  20Q GAIN WILD-TYPE 66  2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED     31    1
  20Q GAIN WILD-TYPE   66    2
   clus
vv  20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  0               31                 66
  1                1                  2
                    vv
clus                 M0 M1 MX
  20Q GAIN MUTATED   37  2  6
  20Q GAIN WILD-TYPE 78  1 25
D37V6, multiclass
    clus
vv   20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  M0               37                 78
  M1                2                  1
  MX                6                 25
D37V7, binary
                    cls
clus                  0  1
  20Q GAIN MUTATED   20 25
  20Q GAIN WILD-TYPE 38 66
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED     20   25
  20Q GAIN WILD-TYPE   38   66
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  FEMALE               20                 38
  MALE                 25                 66
                    vv
clus                 R0 R1 R2 RX
  20Q GAIN MUTATED   36  3  1  4
  20Q GAIN WILD-TYPE 86  8  0  6
D37V8, multiclass
    clus
vv   20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  R0               36                 86
  R1                3                  8
  R2                1                  0
  RX                4                  6

Clustering(38) Variable = 21Q GAIN MUTATION ANALYSIS
D38V1, survival
                    sevent
clus2                 0  1
  21Q GAIN MUTATED    8  5
  21Q GAIN WILD-TYPE 76 58
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                13                134 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                 5                 58 
$`21Q GAIN MUTATED`
TCGA-BC-A217 TCGA-CC-5261 TCGA-CC-5263 TCGA-DD-A113 TCGA-DD-A3A5 TCGA-DD-A4NV 
       13.84         0.39         4.24        79.73       102.74        66.35 
TCGA-ED-A82E TCGA-EP-A2KB TCGA-ES-A2HS TCGA-FV-A3I0 TCGA-G3-A25T TCGA-G3-A3CG 
        0.20        10.98        22.85         0.20        51.06        22.13 
TCGA-MI-A75G 
       14.24 

$`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-BC-A69H 
        5.03        44.42         0.26        22.36         9.50         3.95 
TCGA-BC-A69I TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5262 TCGA-CC-A1HT TCGA-CC-A3M9 
        0.53         0.07         2.86         3.39         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        37.78        83.57        53.33 
TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D 
      113.00         7.33         2.60         0.46        21.76        51.29 
TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE 
       90.71        79.40        66.31        19.79        75.65         6.71 
TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK 
       12.95        45.11        49.15         6.02        29.16        18.35 
TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A0 
       13.64        21.14        55.69         5.62        19.76        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-A4NA TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NF 
        0.36        30.61        33.14        12.85        73.38        14.07 
TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN 
       14.24        18.44        15.06        39.78        56.25        29.56 
TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A73A 
       61.45        93.67        12.26         0.30        80.75        10.98 
TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G 
        9.30         7.56        10.98         1.45        27.72       100.96 
TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y 
       13.41        12.69        15.85        13.91        13.35         0.23 
TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XP TCGA-EP-A12J TCGA-EP-A26S 
        0.20         0.20         0.20         0.20        18.74        19.99 
TCGA-EP-A2KA TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A23B 
       11.74         0.62         9.96        11.93        14.40        32.45 
TCGA-FV-A2QR TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 
       19.10         8.12         6.38         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        30.74 
TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ 
       58.49        14.86        21.53        25.64         5.92        19.53 
TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A6UC 
       19.23        14.70        11.97         7.99         4.37         7.76 
TCGA-GJ-A6C0 TCGA-K7-A6G5 TCGA-LG-A6GG TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75I 
        1.02         4.01         0.49         9.57         5.10         8.71 
TCGA-NI-A4U2 TCGA-O8-A75V 
       58.88         4.44 

  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
              0.20               0.03 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
            102.74             113.00 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
             14.24              13.99 
[1] "0.2 - 102.7 (14.2)" "0.0 - 113.0 (14.0)"
        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-BC-A69H         TCGA-BC-A69I         TCGA-CC-5258 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-CC-5260         TCGA-CC-5261         TCGA-CC-5262 
"21Q GAIN WILD-TYPE"   "21Q GAIN MUTATED" "21Q GAIN WILD-TYPE" 
        TCGA-CC-5263         TCGA-CC-A1HT         TCGA-CC-A3M9 
  "21Q GAIN MUTATED" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-CC-A3MA         TCGA-CC-A3MB         TCGA-CC-A3MC 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DD-A113         TCGA-DD-A114         TCGA-DD-A115 
  "21Q GAIN MUTATED" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DD-A116         TCGA-DD-A118         TCGA-DD-A119 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DD-A11A         TCGA-DD-A11B         TCGA-DD-A11C 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DD-A11D         TCGA-DD-A1E9         TCGA-DD-A1EA 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DD-A1EB         TCGA-DD-A1EC         TCGA-DD-A1ED 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DD-A1EE         TCGA-DD-A1EF         TCGA-DD-A1EG 
"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-A1EK         TCGA-DD-A1EL         TCGA-DD-A39V 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DD-A39X         TCGA-DD-A39Y         TCGA-DD-A39Z 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DD-A3A0         TCGA-DD-A3A1         TCGA-DD-A3A2 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DD-A3A3         TCGA-DD-A3A4         TCGA-DD-A3A5 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE"   "21Q GAIN MUTATED" 
        TCGA-DD-A3A6         TCGA-DD-A3A7         TCGA-DD-A3A8 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DD-A3A9         TCGA-DD-A4NA         TCGA-DD-A4NB 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DD-A4ND         TCGA-DD-A4NF         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-DD-A4NR 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DD-A4NS         TCGA-DD-A4NV         TCGA-DD-A73A 
"21Q GAIN WILD-TYPE"   "21Q GAIN MUTATED" "21Q GAIN WILD-TYPE" 
        TCGA-DD-A73B         TCGA-DD-A73C         TCGA-DD-A73D 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DD-A73E         TCGA-DD-A73F         TCGA-DD-A73G 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-ED-A459         TCGA-ED-A4XI         TCGA-ED-A5KG 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-ED-A627         TCGA-ED-A66X         TCGA-ED-A66Y 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-ED-A7PX         TCGA-ED-A7PY         TCGA-ED-A7PZ 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-ED-A7XP         TCGA-ED-A82E         TCGA-EP-A12J 
"21Q GAIN WILD-TYPE"   "21Q GAIN MUTATED" "21Q GAIN WILD-TYPE" 
        TCGA-EP-A26S         TCGA-EP-A2KA         TCGA-EP-A2KB 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE"   "21Q GAIN MUTATED" 
        TCGA-EP-A2KC         TCGA-EP-A3JL         TCGA-EP-A3RK 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-ES-A2HS         TCGA-ES-A2HT         TCGA-FV-A23B 
  "21Q GAIN MUTATED" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-FV-A2QR         TCGA-FV-A3I0         TCGA-FV-A3I1 
"21Q GAIN WILD-TYPE"   "21Q GAIN MUTATED" "21Q GAIN WILD-TYPE" 
        TCGA-FV-A3R2         TCGA-FV-A3R3         TCGA-FV-A495 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-FV-A496         TCGA-FV-A4ZP         TCGA-FV-A4ZQ 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-G3-A25S         TCGA-G3-A25T         TCGA-G3-A25U 
"21Q GAIN WILD-TYPE"   "21Q GAIN MUTATED" "21Q GAIN WILD-TYPE" 
        TCGA-G3-A25V         TCGA-G3-A25W         TCGA-G3-A25X 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-G3-A25Y         TCGA-G3-A25Z         TCGA-G3-A3CG 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE"   "21Q GAIN MUTATED" 
        TCGA-G3-A3CH         TCGA-G3-A3CI         TCGA-G3-A3CJ 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-G3-A3CK         TCGA-G3-A5SI         TCGA-G3-A5SJ 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-G3-A5SL         TCGA-G3-A5SM         TCGA-G3-A6UC 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-GJ-A6C0         TCGA-K7-A6G5         TCGA-LG-A6GG 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-MI-A75C         TCGA-MI-A75E         TCGA-MI-A75G 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE"   "21Q GAIN MUTATED" 
        TCGA-MI-A75I         TCGA-NI-A4U2         TCGA-O8-A75V 
"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-BC-A69H         TCGA-BC-A69I         TCGA-CC-5258 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-CC-5260         TCGA-CC-5261         TCGA-CC-5262 
"21Q GAIN WILD-TYPE"   "21Q GAIN MUTATED" "21Q GAIN WILD-TYPE" 
        TCGA-CC-5263         TCGA-CC-A1HT         TCGA-CC-A3M9 
  "21Q GAIN MUTATED" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-CC-A3MA         TCGA-CC-A3MB         TCGA-CC-A3MC 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DD-A113         TCGA-DD-A114         TCGA-DD-A115 
  "21Q GAIN MUTATED" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DD-A116         TCGA-DD-A118         TCGA-DD-A119 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DD-A11A         TCGA-DD-A11B         TCGA-DD-A11C 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DD-A11D         TCGA-DD-A1E9         TCGA-DD-A1EA 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DD-A1EB         TCGA-DD-A1EC         TCGA-DD-A1ED 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DD-A1EE         TCGA-DD-A1EF         TCGA-DD-A1EG 
"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-A1EK         TCGA-DD-A1EL         TCGA-DD-A39V 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DD-A39X         TCGA-DD-A39Y         TCGA-DD-A39Z 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DD-A3A0         TCGA-DD-A3A1         TCGA-DD-A3A2 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DD-A3A3         TCGA-DD-A3A4         TCGA-DD-A3A5 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE"   "21Q GAIN MUTATED" 
        TCGA-DD-A3A6         TCGA-DD-A3A7         TCGA-DD-A3A8 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DD-A3A9         TCGA-DD-A4NA         TCGA-DD-A4NB 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DD-A4ND         TCGA-DD-A4NF         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-DD-A4NR 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DD-A4NS         TCGA-DD-A4NV         TCGA-DD-A73A 
"21Q GAIN WILD-TYPE"   "21Q GAIN MUTATED" "21Q GAIN WILD-TYPE" 
        TCGA-DD-A73B         TCGA-DD-A73C         TCGA-DD-A73D 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DD-A73E         TCGA-DD-A73F         TCGA-DD-A73G 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-ED-A459         TCGA-ED-A4XI         TCGA-ED-A5KG 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-ED-A627         TCGA-ED-A66X         TCGA-ED-A66Y 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-ED-A7PX         TCGA-ED-A7PY         TCGA-ED-A7PZ 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-ED-A7XP         TCGA-ED-A82E         TCGA-EP-A12J 
"21Q GAIN WILD-TYPE"   "21Q GAIN MUTATED" "21Q GAIN WILD-TYPE" 
        TCGA-EP-A26S         TCGA-EP-A2KA         TCGA-EP-A2KB 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE"   "21Q GAIN MUTATED" 
        TCGA-EP-A2KC         TCGA-EP-A3JL         TCGA-EP-A3RK 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-ES-A2HS         TCGA-ES-A2HT         TCGA-FV-A23B 
  "21Q GAIN MUTATED" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-FV-A2QR         TCGA-FV-A3I0         TCGA-FV-A3I1 
"21Q GAIN WILD-TYPE"   "21Q GAIN MUTATED" "21Q GAIN WILD-TYPE" 
        TCGA-FV-A3R2         TCGA-FV-A3R3         TCGA-FV-A495 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-FV-A496         TCGA-FV-A4ZP         TCGA-FV-A4ZQ 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-G3-A25S         TCGA-G3-A25T         TCGA-G3-A25U 
"21Q GAIN WILD-TYPE"   "21Q GAIN MUTATED" "21Q GAIN WILD-TYPE" 
        TCGA-G3-A25V         TCGA-G3-A25W         TCGA-G3-A25X 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-G3-A25Y         TCGA-G3-A25Z         TCGA-G3-A3CG 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE"   "21Q GAIN MUTATED" 
        TCGA-G3-A3CH         TCGA-G3-A3CI         TCGA-G3-A3CJ 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-G3-A3CK         TCGA-G3-A5SI         TCGA-G3-A5SJ 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-G3-A5SL         TCGA-G3-A5SM         TCGA-G3-A6UC 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-GJ-A6C0         TCGA-K7-A6G5         TCGA-LG-A6GG 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-MI-A75C         TCGA-MI-A75E         TCGA-MI-A75G 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE"   "21Q GAIN MUTATED" 
        TCGA-MI-A75I         TCGA-NI-A4U2         TCGA-O8-A75V 
"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-BC-A69H         TCGA-BC-A69I         TCGA-CC-5258 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-CC-5260         TCGA-CC-5261         TCGA-CC-5262 
"21Q GAIN WILD-TYPE"   "21Q GAIN MUTATED" "21Q GAIN WILD-TYPE" 
        TCGA-CC-5263         TCGA-CC-A1HT         TCGA-CC-A3M9 
  "21Q GAIN MUTATED" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-CC-A3MA         TCGA-CC-A3MB         TCGA-CC-A3MC 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DD-A113         TCGA-DD-A114         TCGA-DD-A115 
  "21Q GAIN MUTATED" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DD-A116         TCGA-DD-A118         TCGA-DD-A119 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DD-A11A         TCGA-DD-A11B         TCGA-DD-A11C 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DD-A11D         TCGA-DD-A1E9         TCGA-DD-A1EA 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DD-A1EB         TCGA-DD-A1EC         TCGA-DD-A1ED 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DD-A1EE         TCGA-DD-A1EF         TCGA-DD-A1EG 
"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-A1EK         TCGA-DD-A1EL         TCGA-DD-A39V 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DD-A39X         TCGA-DD-A39Y         TCGA-DD-A39Z 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DD-A3A0         TCGA-DD-A3A1         TCGA-DD-A3A2 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DD-A3A3         TCGA-DD-A3A4         TCGA-DD-A3A5 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE"   "21Q GAIN MUTATED" 
        TCGA-DD-A3A6         TCGA-DD-A3A7         TCGA-DD-A3A8 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DD-A3A9         TCGA-DD-A4NA         TCGA-DD-A4NB 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DD-A4ND         TCGA-DD-A4NF         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-DD-A4NR 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DD-A4NS         TCGA-DD-A4NV         TCGA-DD-A73A 
"21Q GAIN WILD-TYPE"   "21Q GAIN MUTATED" "21Q GAIN WILD-TYPE" 
        TCGA-DD-A73B         TCGA-DD-A73C         TCGA-DD-A73D 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DD-A73E         TCGA-DD-A73F         TCGA-DD-A73G 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-ED-A459         TCGA-ED-A4XI         TCGA-ED-A5KG 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-ED-A627         TCGA-ED-A66X         TCGA-ED-A66Y 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-ED-A7PX         TCGA-ED-A7PY         TCGA-ED-A7PZ 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-ED-A7XP         TCGA-ED-A82E         TCGA-EP-A12J 
"21Q GAIN WILD-TYPE"   "21Q GAIN MUTATED" "21Q GAIN WILD-TYPE" 
        TCGA-EP-A26S         TCGA-EP-A2KA         TCGA-EP-A2KB 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE"   "21Q GAIN MUTATED" 
        TCGA-EP-A2KC         TCGA-EP-A3JL         TCGA-EP-A3RK 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-ES-A2HS         TCGA-ES-A2HT         TCGA-FV-A23B 
  "21Q GAIN MUTATED" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-FV-A2QR         TCGA-FV-A3I0         TCGA-FV-A3I1 
"21Q GAIN WILD-TYPE"   "21Q GAIN MUTATED" "21Q GAIN WILD-TYPE" 
        TCGA-FV-A3R2         TCGA-FV-A3R3         TCGA-FV-A495 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-FV-A496         TCGA-FV-A4ZP         TCGA-FV-A4ZQ 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-G3-A25S         TCGA-G3-A25T         TCGA-G3-A25U 
"21Q GAIN WILD-TYPE"   "21Q GAIN MUTATED" "21Q GAIN WILD-TYPE" 
        TCGA-G3-A25V         TCGA-G3-A25W         TCGA-G3-A25X 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-G3-A25Y         TCGA-G3-A25Z         TCGA-G3-A3CG 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE"   "21Q GAIN MUTATED" 
        TCGA-G3-A3CH         TCGA-G3-A3CI         TCGA-G3-A3CJ 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-G3-A3CK         TCGA-G3-A5SI         TCGA-G3-A5SJ 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-G3-A5SL         TCGA-G3-A5SM         TCGA-G3-A6UC 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-GJ-A6C0         TCGA-K7-A6G5         TCGA-LG-A6GG 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-MI-A75C         TCGA-MI-A75E         TCGA-MI-A75G 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE"   "21Q GAIN MUTATED" 
        TCGA-MI-A75I         TCGA-NI-A4U2         TCGA-O8-A75V 
"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        5         1          4          0
  21Q GAIN WILD-TYPE      55       31         1         26          4
                    vv
clus                 STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  21Q GAIN MUTATED            0        0         0         0
  21Q GAIN WILD-TYPE          5        1         1         2
D38V3, multiclass
                    vv
clus                 T1 T2 T3 T4
  21Q GAIN MUTATED    3  5  5  0
  21Q GAIN WILD-TYPE 58 35 35  8
D38V4, multiclass
    clus
vv   21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  T1                3                 58
  T2                5                 35
  T3                5                 35
  T4                0                  8
D38V5, binary
                    cls
clus                  0  1
  21Q GAIN MUTATED    9  0
  21Q GAIN WILD-TYPE 88  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED      9    0
  21Q GAIN WILD-TYPE   88    3
   clus
vv  21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  0                9                 88
  1                0                  3
                    vv
clus                  M0  M1  MX
  21Q GAIN MUTATED    11   0   2
  21Q GAIN WILD-TYPE 104   3  29
D38V6, multiclass
    clus
vv   21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  M0               11                104
  M1                0                  3
  MX                2                 29
D38V7, binary
                    cls
clus                  0  1
  21Q GAIN MUTATED    7  6
  21Q GAIN WILD-TYPE 51 85
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED      7    6
  21Q GAIN WILD-TYPE   51   85
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  FEMALE                7                 51
  MALE                  6                 85
                    vv
clus                  R0  R1  R2  RX
  21Q GAIN MUTATED    10   1   0   2
  21Q GAIN WILD-TYPE 112  10   1   8
D38V8, multiclass
    clus
vv   21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  R0               10                112
  R1                1                 10
  R2                0                  1
  RX                2                  8

Clustering(39) Variable = 22Q GAIN MUTATION ANALYSIS
D39V1, survival
                    sevent
clus2                 0  1
  22Q GAIN MUTATED   12  7
  22Q GAIN WILD-TYPE 72 56
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                19                128 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                 7                 56 
$`22Q GAIN MUTATED`
TCGA-BC-A10R TCGA-BC-A112 TCGA-BC-A69H TCGA-CC-5258 TCGA-CC-5261 TCGA-CC-A3MB 
       10.13         5.03         3.95         0.07         0.39         0.10 
TCGA-DD-A118 TCGA-DD-A11D TCGA-DD-A1EJ TCGA-DD-A4ND TCGA-DD-A73G TCGA-ED-A66X 
      113.00        51.29        29.16        73.38       100.96        13.35 
TCGA-ED-A7PZ TCGA-ED-A82E TCGA-ES-A2HS TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-G3-A25X 
        0.20         0.20        22.85        19.10         0.20        58.49 
TCGA-G3-A3CG 
       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-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-BC-A69I TCGA-CC-5260 
       13.84         0.26        22.36         9.50         0.53         2.86 
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-A11A 
       79.73        37.78        83.57        53.33         7.33         2.60 
TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC 
        0.46        21.76        90.71        79.40        66.31        19.79 
TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI 
       75.65         6.71        12.95        45.11        49.15         6.02 
TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A39Z 
       18.35        13.64        21.14        55.69         5.62        19.76 
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-A4NB 
      107.11        13.78         0.36        30.61        33.14        12.85 
TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL 
       14.07        14.24        18.44        15.06        39.78        56.25 
TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS 
       29.56        61.45        93.67        12.26         0.30        80.75 
TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E 
       66.35        10.98         9.30         7.56        10.98         1.45 
TCGA-DD-A73F TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66Y 
       27.72        13.41        12.69        15.85        13.91         0.23 
TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7XP TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA 
        0.20         0.20         0.20        18.74        19.99        11.74 
TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A23B 
       10.98         0.62         9.96        11.93        14.40        32.45 
TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZP 
        8.12         6.38         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        51.06        53.79        28.27        30.74 
TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK 
       14.86        21.53        25.64         5.92        19.53        19.23 
TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A6UC TCGA-GJ-A6C0 
       14.70        11.97         7.99         4.37         7.76         1.02 
TCGA-K7-A6G5 TCGA-LG-A6GG TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75I 
        4.01         0.49         9.57         5.10        14.24         8.71 
TCGA-NI-A4U2 TCGA-O8-A75V 
       58.88         4.44 

  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
              0.07               0.03 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
            113.00             107.11 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
            13.350             14.155 
[1] "0.1 - 113.0 (13.3)" "0.0 - 107.1 (14.2)"
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
  "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
  "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-BC-A5W4 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BC-A69H         TCGA-BC-A69I         TCGA-CC-5258 
  "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" 
        TCGA-CC-5260         TCGA-CC-5261         TCGA-CC-5262 
"22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" 
        TCGA-CC-5263         TCGA-CC-A1HT         TCGA-CC-A3M9 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-CC-A3MA         TCGA-CC-A3MB         TCGA-CC-A3MC 
"22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" 
        TCGA-DD-A113         TCGA-DD-A114         TCGA-DD-A115 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-DD-A116         TCGA-DD-A118         TCGA-DD-A119 
"22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" 
        TCGA-DD-A11A         TCGA-DD-A11B         TCGA-DD-A11C 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-DD-A11D         TCGA-DD-A1E9         TCGA-DD-A1EA 
  "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-DD-A1EB         TCGA-DD-A1EC         TCGA-DD-A1ED 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-DD-A1EE         TCGA-DD-A1EF         TCGA-DD-A1EG 
"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-A1EK         TCGA-DD-A1EL         TCGA-DD-A39V 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-DD-A39X         TCGA-DD-A39Y         TCGA-DD-A39Z 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-DD-A3A0         TCGA-DD-A3A1         TCGA-DD-A3A2 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-DD-A3A3         TCGA-DD-A3A4         TCGA-DD-A3A5 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-DD-A3A6         TCGA-DD-A3A7         TCGA-DD-A3A8 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-DD-A3A9         TCGA-DD-A4NA         TCGA-DD-A4NB 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-DD-A4ND         TCGA-DD-A4NF         TCGA-DD-A4NH 
  "22Q GAIN MUTATED" "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-DD-A4NR 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-DD-A4NS         TCGA-DD-A4NV         TCGA-DD-A73A 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-DD-A73B         TCGA-DD-A73C         TCGA-DD-A73D 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-DD-A73E         TCGA-DD-A73F         TCGA-DD-A73G 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" 
        TCGA-ED-A459         TCGA-ED-A4XI         TCGA-ED-A5KG 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-ED-A627         TCGA-ED-A66X         TCGA-ED-A66Y 
"22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" 
        TCGA-ED-A7PX         TCGA-ED-A7PY         TCGA-ED-A7PZ 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" 
        TCGA-ED-A7XP         TCGA-ED-A82E         TCGA-EP-A12J 
"22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" 
        TCGA-EP-A26S         TCGA-EP-A2KA         TCGA-EP-A2KB 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EP-A2KC         TCGA-EP-A3JL         TCGA-EP-A3RK 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-ES-A2HS         TCGA-ES-A2HT         TCGA-FV-A23B 
  "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-FV-A2QR         TCGA-FV-A3I0         TCGA-FV-A3I1 
  "22Q GAIN MUTATED"   "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" 
        TCGA-FV-A3R2         TCGA-FV-A3R3         TCGA-FV-A495 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-FV-A496         TCGA-FV-A4ZP         TCGA-FV-A4ZQ 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-G3-A25S         TCGA-G3-A25T         TCGA-G3-A25U 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-G3-A25V         TCGA-G3-A25W         TCGA-G3-A25X 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" 
        TCGA-G3-A25Y         TCGA-G3-A25Z         TCGA-G3-A3CG 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" 
        TCGA-G3-A3CH         TCGA-G3-A3CI         TCGA-G3-A3CJ 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-G3-A3CK         TCGA-G3-A5SI         TCGA-G3-A5SJ 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-G3-A5SL         TCGA-G3-A5SM         TCGA-G3-A6UC 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-GJ-A6C0         TCGA-K7-A6G5         TCGA-LG-A6GG 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-MI-A75C         TCGA-MI-A75E         TCGA-MI-A75G 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-MI-A75I         TCGA-NI-A4U2         TCGA-O8-A75V 
"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 WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
  "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-BC-A5W4 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BC-A69H         TCGA-BC-A69I         TCGA-CC-5258 
  "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" 
        TCGA-CC-5260         TCGA-CC-5261         TCGA-CC-5262 
"22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" 
        TCGA-CC-5263         TCGA-CC-A1HT         TCGA-CC-A3M9 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-CC-A3MA         TCGA-CC-A3MB         TCGA-CC-A3MC 
"22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" 
        TCGA-DD-A113         TCGA-DD-A114         TCGA-DD-A115 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-DD-A116         TCGA-DD-A118         TCGA-DD-A119 
"22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" 
        TCGA-DD-A11A         TCGA-DD-A11B         TCGA-DD-A11C 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-DD-A11D         TCGA-DD-A1E9         TCGA-DD-A1EA 
  "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-DD-A1EB         TCGA-DD-A1EC         TCGA-DD-A1ED 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-DD-A1EE         TCGA-DD-A1EF         TCGA-DD-A1EG 
"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-A1EK         TCGA-DD-A1EL         TCGA-DD-A39V 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-DD-A39X         TCGA-DD-A39Y         TCGA-DD-A39Z 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-DD-A3A0         TCGA-DD-A3A1         TCGA-DD-A3A2 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-DD-A3A3         TCGA-DD-A3A4         TCGA-DD-A3A5 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-DD-A3A6         TCGA-DD-A3A7         TCGA-DD-A3A8 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-DD-A3A9         TCGA-DD-A4NA         TCGA-DD-A4NB 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-DD-A4ND         TCGA-DD-A4NF         TCGA-DD-A4NH 
  "22Q GAIN MUTATED" "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-DD-A4NR 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-DD-A4NS         TCGA-DD-A4NV         TCGA-DD-A73A 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-DD-A73B         TCGA-DD-A73C         TCGA-DD-A73D 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-DD-A73E         TCGA-DD-A73F         TCGA-DD-A73G 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" 
        TCGA-ED-A459         TCGA-ED-A4XI         TCGA-ED-A5KG 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-ED-A627         TCGA-ED-A66X         TCGA-ED-A66Y 
"22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" 
        TCGA-ED-A7PX         TCGA-ED-A7PY         TCGA-ED-A7PZ 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" 
        TCGA-ED-A7XP         TCGA-ED-A82E         TCGA-EP-A12J 
"22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" 
        TCGA-EP-A26S         TCGA-EP-A2KA         TCGA-EP-A2KB 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EP-A2KC         TCGA-EP-A3JL         TCGA-EP-A3RK 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-ES-A2HS         TCGA-ES-A2HT         TCGA-FV-A23B 
  "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-FV-A2QR         TCGA-FV-A3I0         TCGA-FV-A3I1 
  "22Q GAIN MUTATED"   "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" 
        TCGA-FV-A3R2         TCGA-FV-A3R3         TCGA-FV-A495 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-FV-A496         TCGA-FV-A4ZP         TCGA-FV-A4ZQ 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-G3-A25S         TCGA-G3-A25T         TCGA-G3-A25U 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-G3-A25V         TCGA-G3-A25W         TCGA-G3-A25X 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" 
        TCGA-G3-A25Y         TCGA-G3-A25Z         TCGA-G3-A3CG 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" 
        TCGA-G3-A3CH         TCGA-G3-A3CI         TCGA-G3-A3CJ 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-G3-A3CK         TCGA-G3-A5SI         TCGA-G3-A5SJ 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-G3-A5SL         TCGA-G3-A5SM         TCGA-G3-A6UC 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-GJ-A6C0         TCGA-K7-A6G5         TCGA-LG-A6GG 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-MI-A75C         TCGA-MI-A75E         TCGA-MI-A75G 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-MI-A75I         TCGA-NI-A4U2         TCGA-O8-A75V 
"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 WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
  "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-BC-A5W4 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BC-A69H         TCGA-BC-A69I         TCGA-CC-5258 
  "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" 
        TCGA-CC-5260         TCGA-CC-5261         TCGA-CC-5262 
"22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" 
        TCGA-CC-5263         TCGA-CC-A1HT         TCGA-CC-A3M9 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-CC-A3MA         TCGA-CC-A3MB         TCGA-CC-A3MC 
"22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" 
        TCGA-DD-A113         TCGA-DD-A114         TCGA-DD-A115 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-DD-A116         TCGA-DD-A118         TCGA-DD-A119 
"22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" 
        TCGA-DD-A11A         TCGA-DD-A11B         TCGA-DD-A11C 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-DD-A11D         TCGA-DD-A1E9         TCGA-DD-A1EA 
  "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-DD-A1EB         TCGA-DD-A1EC         TCGA-DD-A1ED 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-DD-A1EE         TCGA-DD-A1EF         TCGA-DD-A1EG 
"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-A1EK         TCGA-DD-A1EL         TCGA-DD-A39V 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-DD-A39X         TCGA-DD-A39Y         TCGA-DD-A39Z 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-DD-A3A0         TCGA-DD-A3A1         TCGA-DD-A3A2 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-DD-A3A3         TCGA-DD-A3A4         TCGA-DD-A3A5 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-DD-A3A6         TCGA-DD-A3A7         TCGA-DD-A3A8 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-DD-A3A9         TCGA-DD-A4NA         TCGA-DD-A4NB 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-DD-A4ND         TCGA-DD-A4NF         TCGA-DD-A4NH 
  "22Q GAIN MUTATED" "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-DD-A4NR 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-DD-A4NS         TCGA-DD-A4NV         TCGA-DD-A73A 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-DD-A73B         TCGA-DD-A73C         TCGA-DD-A73D 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-DD-A73E         TCGA-DD-A73F         TCGA-DD-A73G 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" 
        TCGA-ED-A459         TCGA-ED-A4XI         TCGA-ED-A5KG 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-ED-A627         TCGA-ED-A66X         TCGA-ED-A66Y 
"22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" 
        TCGA-ED-A7PX         TCGA-ED-A7PY         TCGA-ED-A7PZ 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" 
        TCGA-ED-A7XP         TCGA-ED-A82E         TCGA-EP-A12J 
"22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" 
        TCGA-EP-A26S         TCGA-EP-A2KA         TCGA-EP-A2KB 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EP-A2KC         TCGA-EP-A3JL         TCGA-EP-A3RK 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-ES-A2HS         TCGA-ES-A2HT         TCGA-FV-A23B 
  "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-FV-A2QR         TCGA-FV-A3I0         TCGA-FV-A3I1 
  "22Q GAIN MUTATED"   "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" 
        TCGA-FV-A3R2         TCGA-FV-A3R3         TCGA-FV-A495 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-FV-A496         TCGA-FV-A4ZP         TCGA-FV-A4ZQ 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-G3-A25S         TCGA-G3-A25T         TCGA-G3-A25U 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-G3-A25V         TCGA-G3-A25W         TCGA-G3-A25X 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" 
        TCGA-G3-A25Y         TCGA-G3-A25Z         TCGA-G3-A3CG 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" 
        TCGA-G3-A3CH         TCGA-G3-A3CI         TCGA-G3-A3CJ 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-G3-A3CK         TCGA-G3-A5SI         TCGA-G3-A5SJ 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-G3-A5SL         TCGA-G3-A5SM         TCGA-G3-A6UC 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-GJ-A6C0         TCGA-K7-A6G5         TCGA-LG-A6GG 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-MI-A75C         TCGA-MI-A75E         TCGA-MI-A75G 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-MI-A75I         TCGA-NI-A4U2         TCGA-O8-A75V 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
[1] "hr=" "1.4"
D39V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  22Q GAIN MUTATED         6        7         0          3          0
  22Q GAIN WILD-TYPE      52       29         2         27          4
                    vv
clus                 STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  22Q GAIN MUTATED            1        0         0         0
  22Q GAIN WILD-TYPE          4        1         1         2
D39V3, multiclass
                    vv
clus                 T1 T2 T3 T4
  22Q GAIN MUTATED    7  7  5  0
  22Q GAIN WILD-TYPE 54 33 35  8
D39V4, multiclass
    clus
vv   22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  T1                7                 54
  T2                7                 33
  T3                5                 35
  T4                0                  8
D39V5, binary
                    cls
clus                  0  1
  22Q GAIN MUTATED   12  1
  22Q GAIN WILD-TYPE 85  2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED     12    1
  22Q GAIN WILD-TYPE   85    2
   clus
vv  22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  0               12                 85
  1                1                  2
                    vv
clus                 M0 M1 MX
  22Q GAIN MUTATED   16  0  3
  22Q GAIN WILD-TYPE 99  3 28
D39V6, multiclass
    clus
vv   22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  M0               16                 99
  M1                0                  3
  MX                3                 28
D39V7, binary
                    cls
clus                  0  1
  22Q GAIN MUTATED    8 11
  22Q GAIN WILD-TYPE 50 80
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED      8   11
  22Q GAIN WILD-TYPE   50   80
        clus
vv       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  FEMALE                8                 50
  MALE                 11                 80
                    vv
clus                  R0  R1  R2  RX
  22Q GAIN MUTATED    15   1   0   3
  22Q GAIN WILD-TYPE 107  10   1   7
D39V8, multiclass
    clus
vv   22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  R0               15                107
  R1                1                 10
  R2                0                  1
  RX                3                  7

Clustering(40) Variable = XQ GAIN MUTATION ANALYSIS
D40V1, survival
                   sevent
clus2                0  1
  XQ GAIN MUTATED   18  9
  XQ GAIN WILD-TYPE 66 54
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               27               120 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
                9                54 
$`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-A3A3 TCGA-DD-A3A7 TCGA-DD-A4NF TCGA-DD-A4NK TCGA-DD-A4NV TCGA-DD-A73D 
       17.59        13.78        14.07        39.78        66.35        10.98 
TCGA-DD-A73G TCGA-EP-A12J TCGA-EP-A2KA TCGA-EP-A3JL TCGA-ES-A2HS TCGA-FV-A4ZQ 
      100.96        18.74        11.74         9.96        22.85         0.39 
TCGA-G3-A25U TCGA-G3-A3CG TCGA-G3-A3CJ TCGA-G3-A5SI TCGA-G3-A5SL TCGA-K7-A6G5 
       53.79        22.13        19.53        14.70         7.99         4.01 
TCGA-LG-A6GG TCGA-MI-A75G TCGA-O8-A75V 
        0.49        14.24         4.44 

$`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-BC-A69H TCGA-BC-A69I TCGA-CC-5258 
       13.84        22.36         9.50         3.95         0.53         0.07 
TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA 
        0.39         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        37.78        83.57        53.33 
TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 
      113.00         7.33         0.46        21.76        51.29        90.71 
TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EF 
       79.40        66.31        19.79        75.65         6.71        12.95 
TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A1EL 
       45.11        49.15         6.02        29.16        18.35        13.64 
TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 
       55.69         5.62        19.76        25.81         7.66        70.06 
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        30.61        33.14 
TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NL 
       12.85        73.38        14.24        18.44        15.06        56.25 
TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS 
       29.56        61.45        93.67        12.26         0.30        80.75 
TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73E TCGA-DD-A73F TCGA-ED-A459 
       10.98         9.30         7.56         1.45        27.72        13.41 
TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PX 
       12.69        15.85        13.91        13.35         0.23         0.20 
TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XP TCGA-ED-A82E TCGA-EP-A26S TCGA-EP-A2KB 
        0.20         0.20         0.20         0.20        19.99        10.98 
TCGA-EP-A2KC TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-A3I0 
        0.62        11.93        14.40        32.45        19.10         0.20 
TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZP 
        8.12         6.38         0.13         0.03         0.33        60.36 
TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25X TCGA-G3-A25Y 
        1.22        51.06        28.27        30.74        58.49        14.86 
TCGA-G3-A25Z TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CK TCGA-G3-A5SJ TCGA-G3-A5SM 
       21.53        25.64         5.92        19.23        11.97         4.37 
TCGA-G3-A6UC TCGA-GJ-A6C0 TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75I TCGA-NI-A4U2 
        7.76         1.02         9.57         5.10         8.71        58.88 

  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
             0.26              0.03 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
           100.96            113.00 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
           14.070            14.075 
[1] "0.3 - 101.0 (14.1)" "0.0 - 113.0 (14.1)"
       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-BC-A69H        TCGA-BC-A69I 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-CC-5258        TCGA-CC-5260        TCGA-CC-5261        TCGA-CC-5262 
"XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-CC-5263        TCGA-CC-A1HT        TCGA-CC-A3M9        TCGA-CC-A3MA 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-CC-A3MB        TCGA-CC-A3MC        TCGA-DD-A113        TCGA-DD-A114 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118        TCGA-DD-A119 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C        TCGA-DD-A11D 
  "XQ GAIN MUTATED" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB        TCGA-DD-A1EC 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EF        TCGA-DD-A1EG 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-DD-A1EH        TCGA-DD-A1EI        TCGA-DD-A1EJ        TCGA-DD-A1EK 
"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 WILD-TYPE" 
       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-A4NB        TCGA-DD-A4ND        TCGA-DD-A4NF        TCGA-DD-A4NH 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED" "XQ GAIN WILD-TYPE" 
       TCGA-DD-A4NI        TCGA-DD-A4NJ        TCGA-DD-A4NK        TCGA-DD-A4NL 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED" "XQ GAIN WILD-TYPE" 
       TCGA-DD-A4NN        TCGA-DD-A4NO        TCGA-DD-A4NP        TCGA-DD-A4NQ 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-DD-A4NR        TCGA-DD-A4NS        TCGA-DD-A4NV        TCGA-DD-A73A 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED" "XQ GAIN WILD-TYPE" 
       TCGA-DD-A73B        TCGA-DD-A73C        TCGA-DD-A73D        TCGA-DD-A73E 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED" "XQ GAIN WILD-TYPE" 
       TCGA-DD-A73F        TCGA-DD-A73G        TCGA-ED-A459        TCGA-ED-A4XI 
"XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-ED-A5KG        TCGA-ED-A627        TCGA-ED-A66X        TCGA-ED-A66Y 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-ED-A7PX        TCGA-ED-A7PY        TCGA-ED-A7PZ        TCGA-ED-A7XP 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-ED-A82E        TCGA-EP-A12J        TCGA-EP-A26S        TCGA-EP-A2KA 
"XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED" "XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED" 
       TCGA-EP-A2KB        TCGA-EP-A2KC        TCGA-EP-A3JL        TCGA-EP-A3RK 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED" "XQ GAIN WILD-TYPE" 
       TCGA-ES-A2HS        TCGA-ES-A2HT        TCGA-FV-A23B        TCGA-FV-A2QR 
  "XQ GAIN MUTATED" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-FV-A3I0        TCGA-FV-A3I1        TCGA-FV-A3R2        TCGA-FV-A3R3 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-FV-A495        TCGA-FV-A496        TCGA-FV-A4ZP        TCGA-FV-A4ZQ 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED" 
       TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U        TCGA-G3-A25V 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED" "XQ GAIN WILD-TYPE" 
       TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y        TCGA-G3-A25Z 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI        TCGA-G3-A3CJ 
  "XQ GAIN MUTATED" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED" 
       TCGA-G3-A3CK        TCGA-G3-A5SI        TCGA-G3-A5SJ        TCGA-G3-A5SL 
"XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED" "XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED" 
       TCGA-G3-A5SM        TCGA-G3-A6UC        TCGA-GJ-A6C0        TCGA-K7-A6G5 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED" 
       TCGA-LG-A6GG        TCGA-MI-A75C        TCGA-MI-A75E        TCGA-MI-A75G 
  "XQ GAIN MUTATED" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED" 
       TCGA-MI-A75I        TCGA-NI-A4U2        TCGA-O8-A75V 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED" 
       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-BC-A69H        TCGA-BC-A69I 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-CC-5258        TCGA-CC-5260        TCGA-CC-5261        TCGA-CC-5262 
"XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-CC-5263        TCGA-CC-A1HT        TCGA-CC-A3M9        TCGA-CC-A3MA 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-CC-A3MB        TCGA-CC-A3MC        TCGA-DD-A113        TCGA-DD-A114 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118        TCGA-DD-A119 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C        TCGA-DD-A11D 
  "XQ GAIN MUTATED" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB        TCGA-DD-A1EC 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EF        TCGA-DD-A1EG 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-DD-A1EH        TCGA-DD-A1EI        TCGA-DD-A1EJ        TCGA-DD-A1EK 
"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 WILD-TYPE" 
       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-A4NB        TCGA-DD-A4ND        TCGA-DD-A4NF        TCGA-DD-A4NH 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED" "XQ GAIN WILD-TYPE" 
       TCGA-DD-A4NI        TCGA-DD-A4NJ        TCGA-DD-A4NK        TCGA-DD-A4NL 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED" "XQ GAIN WILD-TYPE" 
       TCGA-DD-A4NN        TCGA-DD-A4NO        TCGA-DD-A4NP        TCGA-DD-A4NQ 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-DD-A4NR        TCGA-DD-A4NS        TCGA-DD-A4NV        TCGA-DD-A73A 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED" "XQ GAIN WILD-TYPE" 
       TCGA-DD-A73B        TCGA-DD-A73C        TCGA-DD-A73D        TCGA-DD-A73E 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED" "XQ GAIN WILD-TYPE" 
       TCGA-DD-A73F        TCGA-DD-A73G        TCGA-ED-A459        TCGA-ED-A4XI 
"XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-ED-A5KG        TCGA-ED-A627        TCGA-ED-A66X        TCGA-ED-A66Y 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-ED-A7PX        TCGA-ED-A7PY        TCGA-ED-A7PZ        TCGA-ED-A7XP 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-ED-A82E        TCGA-EP-A12J        TCGA-EP-A26S        TCGA-EP-A2KA 
"XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED" "XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED" 
       TCGA-EP-A2KB        TCGA-EP-A2KC        TCGA-EP-A3JL        TCGA-EP-A3RK 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED" "XQ GAIN WILD-TYPE" 
       TCGA-ES-A2HS        TCGA-ES-A2HT        TCGA-FV-A23B        TCGA-FV-A2QR 
  "XQ GAIN MUTATED" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-FV-A3I0        TCGA-FV-A3I1        TCGA-FV-A3R2        TCGA-FV-A3R3 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-FV-A495        TCGA-FV-A496        TCGA-FV-A4ZP        TCGA-FV-A4ZQ 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED" 
       TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U        TCGA-G3-A25V 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED" "XQ GAIN WILD-TYPE" 
       TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y        TCGA-G3-A25Z 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI        TCGA-G3-A3CJ 
  "XQ GAIN MUTATED" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED" 
       TCGA-G3-A3CK        TCGA-G3-A5SI        TCGA-G3-A5SJ        TCGA-G3-A5SL 
"XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED" "XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED" 
       TCGA-G3-A5SM        TCGA-G3-A6UC        TCGA-GJ-A6C0        TCGA-K7-A6G5 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED" 
       TCGA-LG-A6GG        TCGA-MI-A75C        TCGA-MI-A75E        TCGA-MI-A75G 
  "XQ GAIN MUTATED" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED" 
       TCGA-MI-A75I        TCGA-NI-A4U2        TCGA-O8-A75V 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED" 
       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-BC-A69H        TCGA-BC-A69I 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-CC-5258        TCGA-CC-5260        TCGA-CC-5261        TCGA-CC-5262 
"XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-CC-5263        TCGA-CC-A1HT        TCGA-CC-A3M9        TCGA-CC-A3MA 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-CC-A3MB        TCGA-CC-A3MC        TCGA-DD-A113        TCGA-DD-A114 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118        TCGA-DD-A119 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C        TCGA-DD-A11D 
  "XQ GAIN MUTATED" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB        TCGA-DD-A1EC 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EF        TCGA-DD-A1EG 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-DD-A1EH        TCGA-DD-A1EI        TCGA-DD-A1EJ        TCGA-DD-A1EK 
"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 WILD-TYPE" 
       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-A4NB        TCGA-DD-A4ND        TCGA-DD-A4NF        TCGA-DD-A4NH 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED" "XQ GAIN WILD-TYPE" 
       TCGA-DD-A4NI        TCGA-DD-A4NJ        TCGA-DD-A4NK        TCGA-DD-A4NL 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED" "XQ GAIN WILD-TYPE" 
       TCGA-DD-A4NN        TCGA-DD-A4NO        TCGA-DD-A4NP        TCGA-DD-A4NQ 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-DD-A4NR        TCGA-DD-A4NS        TCGA-DD-A4NV        TCGA-DD-A73A 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED" "XQ GAIN WILD-TYPE" 
       TCGA-DD-A73B        TCGA-DD-A73C        TCGA-DD-A73D        TCGA-DD-A73E 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED" "XQ GAIN WILD-TYPE" 
       TCGA-DD-A73F        TCGA-DD-A73G        TCGA-ED-A459        TCGA-ED-A4XI 
"XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-ED-A5KG        TCGA-ED-A627        TCGA-ED-A66X        TCGA-ED-A66Y 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-ED-A7PX        TCGA-ED-A7PY        TCGA-ED-A7PZ        TCGA-ED-A7XP 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-ED-A82E        TCGA-EP-A12J        TCGA-EP-A26S        TCGA-EP-A2KA 
"XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED" "XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED" 
       TCGA-EP-A2KB        TCGA-EP-A2KC        TCGA-EP-A3JL        TCGA-EP-A3RK 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED" "XQ GAIN WILD-TYPE" 
       TCGA-ES-A2HS        TCGA-ES-A2HT        TCGA-FV-A23B        TCGA-FV-A2QR 
  "XQ GAIN MUTATED" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-FV-A3I0        TCGA-FV-A3I1        TCGA-FV-A3R2        TCGA-FV-A3R3 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-FV-A495        TCGA-FV-A496        TCGA-FV-A4ZP        TCGA-FV-A4ZQ 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED" 
       TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U        TCGA-G3-A25V 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED" "XQ GAIN WILD-TYPE" 
       TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y        TCGA-G3-A25Z 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI        TCGA-G3-A3CJ 
  "XQ GAIN MUTATED" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED" 
       TCGA-G3-A3CK        TCGA-G3-A5SI        TCGA-G3-A5SJ        TCGA-G3-A5SL 
"XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED" "XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED" 
       TCGA-G3-A5SM        TCGA-G3-A6UC        TCGA-GJ-A6C0        TCGA-K7-A6G5 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED" 
       TCGA-LG-A6GG        TCGA-MI-A75C        TCGA-MI-A75E        TCGA-MI-A75G 
  "XQ GAIN MUTATED" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED" 
       TCGA-MI-A75I        TCGA-NI-A4U2        TCGA-O8-A75V 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED" 
[1] "hr=" "1"  
D40V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  XQ GAIN MUTATED        14        6         0          5          1          1
  XQ GAIN WILD-TYPE      44       30         2         25          3          4
                   vv
clus                STAGE IV STAGE IVA STAGE IVB
  XQ GAIN MUTATED          0         0         0
  XQ GAIN WILD-TYPE        1         1         2
D40V3, multiclass
                   vv
clus                T1 T2 T3 T4
  XQ GAIN MUTATED   14  7  6  1
  XQ GAIN WILD-TYPE 47 33 34  7
D40V4, multiclass
    clus
vv   XQ GAIN MUTATED XQ GAIN WILD-TYPE
  T1              14                47
  T2               7                33
  T3               6                34
  T4               1                 7
D40V5, binary
                   cls
clus                 0  1
  XQ GAIN MUTATED   16  0
  XQ GAIN WILD-TYPE 81  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED     16    0
  XQ GAIN WILD-TYPE   81    3
   clus
vv  XQ GAIN MUTATED XQ GAIN WILD-TYPE
  0              16                81
  1               0                 3
                   vv
clus                M0 M1 MX
  XQ GAIN MUTATED   19  0  9
  XQ GAIN WILD-TYPE 96  3 22
D40V6, multiclass
    clus
vv   XQ GAIN MUTATED XQ GAIN WILD-TYPE
  M0              19                96
  M1               0                 3
  MX               9                22
D40V7, binary
                   cls
clus                 0  1
  XQ GAIN MUTATED    9 19
  XQ GAIN WILD-TYPE 49 72
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED      9   19
  XQ GAIN WILD-TYPE   49   72
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  FEMALE               9                49
  MALE                19                72
                   vv
clus                 R0  R1  R2  RX
  XQ GAIN MUTATED    21   3   0   3
  XQ GAIN WILD-TYPE 101   8   1   7
D40V8, multiclass
    clus
vv   XQ GAIN MUTATED XQ GAIN WILD-TYPE
  R0              21               101
  R1               3                 8
  R2               0                 1
  RX               3                 7

Clustering(41) Variable = 1P LOSS MUTATION ANALYSIS
D41V1, survival
                   sevent
clus2                0  1
  1P LOSS MUTATED   22 15
  1P LOSS WILD-TYPE 62 48
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               37               110 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               15                48 
$`1P LOSS MUTATED`
TCGA-BC-A10S TCGA-BC-A217 TCGA-BC-A69H TCGA-CC-5258 TCGA-CC-5261 TCGA-CC-A3MB 
       46.78        13.84         3.95         0.07         0.39         0.10 
TCGA-CC-A3MC TCGA-DD-A113 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11B TCGA-DD-A1E9 
        0.13        79.73       113.00         7.33         0.46        90.71 
TCGA-DD-A1EH TCGA-DD-A1EJ TCGA-DD-A3A1 TCGA-DD-A3A9 TCGA-DD-A4NH TCGA-DD-A4NN 
       49.15        29.16         7.66        30.61        14.24        29.56 
TCGA-DD-A73B TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PY TCGA-ED-A82E TCGA-EP-A2KB 
        9.30        13.35         0.23         0.20         0.20        10.98 
TCGA-EP-A2KC TCGA-ES-A2HS TCGA-FV-A3I0 TCGA-FV-A496 TCGA-FV-A4ZP TCGA-G3-A25S 
        0.62        22.85         0.20         0.33        60.36         1.22 
TCGA-G3-A25U TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A5SI TCGA-G3-A5SL TCGA-G3-A5SM 
       53.79        58.49        14.86        14.70         7.99         4.37 
TCGA-MI-A75G 
       14.24 

$`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-BC-A69I TCGA-CC-5260 
       44.42         0.26        22.36         9.50         0.53         2.86 
TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-DD-A114 
        3.39         4.24         3.32         0.10         0.07        37.78 
TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A11A TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1EA 
       83.57        53.33         2.60        21.76        51.29        79.40 
TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EG 
       66.31        19.79        75.65         6.71        12.95        45.11 
TCGA-DD-A1EI TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39X TCGA-DD-A39Y 
        6.02        18.35        13.64        21.14        55.69         5.62 
TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 
       19.76        25.81        70.06        17.59        20.12       102.74 
TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4ND 
      107.11        13.78         0.36        33.14        12.85        73.38 
TCGA-DD-A4NF TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NO 
       14.07        18.44        15.06        39.78        56.25        61.45 
TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A 
       93.67        12.26         0.30        80.75        66.35        10.98 
TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G TCGA-ED-A459 
        7.56        10.98         1.45        27.72       100.96        13.41 
TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A7PX TCGA-ED-A7PZ TCGA-ED-A7XP 
       12.69        15.85        13.91         0.20         0.20         0.20 
TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HT 
       18.74        19.99        11.74         9.96        11.93        14.40 
TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 
       32.45        19.10         8.12         6.38         0.13         0.03 
TCGA-FV-A4ZQ TCGA-G3-A25T TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25Z TCGA-G3-A3CG 
        0.39        51.06        28.27        30.74        21.53        22.13 
TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SJ TCGA-G3-A6UC 
       25.64         5.92        19.53        19.23        11.97         7.76 
TCGA-GJ-A6C0 TCGA-K7-A6G5 TCGA-LG-A6GG TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75I 
        1.02         4.01         0.49         9.57         5.10         8.71 
TCGA-NI-A4U2 TCGA-O8-A75V 
       58.88         4.44 

  1P LOSS MUTATED 1P LOSS WILD-TYPE 
             0.07              0.03 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
           113.00            107.11 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
           10.980            15.455 
[1] "0.1 - 113.0 (11.0)" "0.0 - 107.1 (15.5)"
       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-BC-A69H        TCGA-BC-A69I 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE" 
       TCGA-CC-5258        TCGA-CC-5260        TCGA-CC-5261        TCGA-CC-5262 
  "1P LOSS MUTATED" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE" 
       TCGA-CC-5263        TCGA-CC-A1HT        TCGA-CC-A3M9        TCGA-CC-A3MA 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-CC-A3MB        TCGA-CC-A3MC        TCGA-DD-A113        TCGA-DD-A114 
  "1P LOSS MUTATED"   "1P LOSS MUTATED"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE" 
       TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118        TCGA-DD-A119 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED"   "1P LOSS MUTATED" 
       TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C        TCGA-DD-A11D 
"1P LOSS WILD-TYPE"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB        TCGA-DD-A1EC 
  "1P LOSS MUTATED" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EF        TCGA-DD-A1EG 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DD-A1EH        TCGA-DD-A1EI        TCGA-DD-A1EJ        TCGA-DD-A1EK 
  "1P LOSS MUTATED" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE" 
       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-A4NB        TCGA-DD-A4ND        TCGA-DD-A4NF        TCGA-DD-A4NH 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" 
       TCGA-DD-A4NI        TCGA-DD-A4NJ        TCGA-DD-A4NK        TCGA-DD-A4NL 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DD-A4NN        TCGA-DD-A4NO        TCGA-DD-A4NP        TCGA-DD-A4NQ 
  "1P LOSS MUTATED" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DD-A4NR        TCGA-DD-A4NS        TCGA-DD-A4NV        TCGA-DD-A73A 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DD-A73B        TCGA-DD-A73C        TCGA-DD-A73D        TCGA-DD-A73E 
  "1P LOSS MUTATED" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DD-A73F        TCGA-DD-A73G        TCGA-ED-A459        TCGA-ED-A4XI 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-ED-A5KG        TCGA-ED-A627        TCGA-ED-A66X        TCGA-ED-A66Y 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED"   "1P LOSS MUTATED" 
       TCGA-ED-A7PX        TCGA-ED-A7PY        TCGA-ED-A7PZ        TCGA-ED-A7XP 
"1P LOSS WILD-TYPE"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-ED-A82E        TCGA-EP-A12J        TCGA-EP-A26S        TCGA-EP-A2KA 
  "1P LOSS MUTATED" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EP-A2KB        TCGA-EP-A2KC        TCGA-EP-A3JL        TCGA-EP-A3RK 
  "1P LOSS MUTATED"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-ES-A2HS        TCGA-ES-A2HT        TCGA-FV-A23B        TCGA-FV-A2QR 
  "1P LOSS MUTATED" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-FV-A3I0        TCGA-FV-A3I1        TCGA-FV-A3R2        TCGA-FV-A3R3 
  "1P LOSS MUTATED" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-FV-A495        TCGA-FV-A496        TCGA-FV-A4ZP        TCGA-FV-A4ZQ 
"1P LOSS WILD-TYPE"   "1P LOSS MUTATED"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE" 
       TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U        TCGA-G3-A25V 
  "1P LOSS MUTATED" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE" 
       TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y        TCGA-G3-A25Z 
"1P LOSS WILD-TYPE"   "1P LOSS MUTATED"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE" 
       TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI        TCGA-G3-A3CJ 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-G3-A3CK        TCGA-G3-A5SI        TCGA-G3-A5SJ        TCGA-G3-A5SL 
"1P LOSS WILD-TYPE"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" 
       TCGA-G3-A5SM        TCGA-G3-A6UC        TCGA-GJ-A6C0        TCGA-K7-A6G5 
  "1P LOSS MUTATED" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-LG-A6GG        TCGA-MI-A75C        TCGA-MI-A75E        TCGA-MI-A75G 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" 
       TCGA-MI-A75I        TCGA-NI-A4U2        TCGA-O8-A75V 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
  "1P LOSS MUTATED" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-BC-A5W4        TCGA-BC-A69H        TCGA-BC-A69I 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE" 
       TCGA-CC-5258        TCGA-CC-5260        TCGA-CC-5261        TCGA-CC-5262 
  "1P LOSS MUTATED" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE" 
       TCGA-CC-5263        TCGA-CC-A1HT        TCGA-CC-A3M9        TCGA-CC-A3MA 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-CC-A3MB        TCGA-CC-A3MC        TCGA-DD-A113        TCGA-DD-A114 
  "1P LOSS MUTATED"   "1P LOSS MUTATED"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE" 
       TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118        TCGA-DD-A119 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED"   "1P LOSS MUTATED" 
       TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C        TCGA-DD-A11D 
"1P LOSS WILD-TYPE"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB        TCGA-DD-A1EC 
  "1P LOSS MUTATED" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EF        TCGA-DD-A1EG 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DD-A1EH        TCGA-DD-A1EI        TCGA-DD-A1EJ        TCGA-DD-A1EK 
  "1P LOSS MUTATED" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE" 
       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-A4NB        TCGA-DD-A4ND        TCGA-DD-A4NF        TCGA-DD-A4NH 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" 
       TCGA-DD-A4NI        TCGA-DD-A4NJ        TCGA-DD-A4NK        TCGA-DD-A4NL 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DD-A4NN        TCGA-DD-A4NO        TCGA-DD-A4NP        TCGA-DD-A4NQ 
  "1P LOSS MUTATED" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DD-A4NR        TCGA-DD-A4NS        TCGA-DD-A4NV        TCGA-DD-A73A 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DD-A73B        TCGA-DD-A73C        TCGA-DD-A73D        TCGA-DD-A73E 
  "1P LOSS MUTATED" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DD-A73F        TCGA-DD-A73G        TCGA-ED-A459        TCGA-ED-A4XI 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-ED-A5KG        TCGA-ED-A627        TCGA-ED-A66X        TCGA-ED-A66Y 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED"   "1P LOSS MUTATED" 
       TCGA-ED-A7PX        TCGA-ED-A7PY        TCGA-ED-A7PZ        TCGA-ED-A7XP 
"1P LOSS WILD-TYPE"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-ED-A82E        TCGA-EP-A12J        TCGA-EP-A26S        TCGA-EP-A2KA 
  "1P LOSS MUTATED" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EP-A2KB        TCGA-EP-A2KC        TCGA-EP-A3JL        TCGA-EP-A3RK 
  "1P LOSS MUTATED"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-ES-A2HS        TCGA-ES-A2HT        TCGA-FV-A23B        TCGA-FV-A2QR 
  "1P LOSS MUTATED" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-FV-A3I0        TCGA-FV-A3I1        TCGA-FV-A3R2        TCGA-FV-A3R3 
  "1P LOSS MUTATED" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-FV-A495        TCGA-FV-A496        TCGA-FV-A4ZP        TCGA-FV-A4ZQ 
"1P LOSS WILD-TYPE"   "1P LOSS MUTATED"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE" 
       TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U        TCGA-G3-A25V 
  "1P LOSS MUTATED" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE" 
       TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y        TCGA-G3-A25Z 
"1P LOSS WILD-TYPE"   "1P LOSS MUTATED"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE" 
       TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI        TCGA-G3-A3CJ 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-G3-A3CK        TCGA-G3-A5SI        TCGA-G3-A5SJ        TCGA-G3-A5SL 
"1P LOSS WILD-TYPE"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" 
       TCGA-G3-A5SM        TCGA-G3-A6UC        TCGA-GJ-A6C0        TCGA-K7-A6G5 
  "1P LOSS MUTATED" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-LG-A6GG        TCGA-MI-A75C        TCGA-MI-A75E        TCGA-MI-A75G 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" 
       TCGA-MI-A75I        TCGA-NI-A4U2        TCGA-O8-A75V 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
  "1P LOSS MUTATED" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-BC-A5W4        TCGA-BC-A69H        TCGA-BC-A69I 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE" 
       TCGA-CC-5258        TCGA-CC-5260        TCGA-CC-5261        TCGA-CC-5262 
  "1P LOSS MUTATED" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE" 
       TCGA-CC-5263        TCGA-CC-A1HT        TCGA-CC-A3M9        TCGA-CC-A3MA 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-CC-A3MB        TCGA-CC-A3MC        TCGA-DD-A113        TCGA-DD-A114 
  "1P LOSS MUTATED"   "1P LOSS MUTATED"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE" 
       TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118        TCGA-DD-A119 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED"   "1P LOSS MUTATED" 
       TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C        TCGA-DD-A11D 
"1P LOSS WILD-TYPE"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB        TCGA-DD-A1EC 
  "1P LOSS MUTATED" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EF        TCGA-DD-A1EG 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DD-A1EH        TCGA-DD-A1EI        TCGA-DD-A1EJ        TCGA-DD-A1EK 
  "1P LOSS MUTATED" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE" 
       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-A4NB        TCGA-DD-A4ND        TCGA-DD-A4NF        TCGA-DD-A4NH 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" 
       TCGA-DD-A4NI        TCGA-DD-A4NJ        TCGA-DD-A4NK        TCGA-DD-A4NL 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DD-A4NN        TCGA-DD-A4NO        TCGA-DD-A4NP        TCGA-DD-A4NQ 
  "1P LOSS MUTATED" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DD-A4NR        TCGA-DD-A4NS        TCGA-DD-A4NV        TCGA-DD-A73A 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DD-A73B        TCGA-DD-A73C        TCGA-DD-A73D        TCGA-DD-A73E 
  "1P LOSS MUTATED" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DD-A73F        TCGA-DD-A73G        TCGA-ED-A459        TCGA-ED-A4XI 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-ED-A5KG        TCGA-ED-A627        TCGA-ED-A66X        TCGA-ED-A66Y 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED"   "1P LOSS MUTATED" 
       TCGA-ED-A7PX        TCGA-ED-A7PY        TCGA-ED-A7PZ        TCGA-ED-A7XP 
"1P LOSS WILD-TYPE"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-ED-A82E        TCGA-EP-A12J        TCGA-EP-A26S        TCGA-EP-A2KA 
  "1P LOSS MUTATED" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EP-A2KB        TCGA-EP-A2KC        TCGA-EP-A3JL        TCGA-EP-A3RK 
  "1P LOSS MUTATED"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-ES-A2HS        TCGA-ES-A2HT        TCGA-FV-A23B        TCGA-FV-A2QR 
  "1P LOSS MUTATED" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-FV-A3I0        TCGA-FV-A3I1        TCGA-FV-A3R2        TCGA-FV-A3R3 
  "1P LOSS MUTATED" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-FV-A495        TCGA-FV-A496        TCGA-FV-A4ZP        TCGA-FV-A4ZQ 
"1P LOSS WILD-TYPE"   "1P LOSS MUTATED"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE" 
       TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U        TCGA-G3-A25V 
  "1P LOSS MUTATED" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE" 
       TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y        TCGA-G3-A25Z 
"1P LOSS WILD-TYPE"   "1P LOSS MUTATED"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE" 
       TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI        TCGA-G3-A3CJ 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-G3-A3CK        TCGA-G3-A5SI        TCGA-G3-A5SJ        TCGA-G3-A5SL 
"1P LOSS WILD-TYPE"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" 
       TCGA-G3-A5SM        TCGA-G3-A6UC        TCGA-GJ-A6C0        TCGA-K7-A6G5 
  "1P LOSS MUTATED" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-LG-A6GG        TCGA-MI-A75C        TCGA-MI-A75E        TCGA-MI-A75G 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" 
       TCGA-MI-A75I        TCGA-NI-A4U2        TCGA-O8-A75V 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
[1] "hr=" "1"  
D41V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  1P LOSS MUTATED        11       12         1          8          1          1
  1P LOSS WILD-TYPE      47       24         1         22          3          4
                   vv
clus                STAGE IV STAGE IVA STAGE IVB
  1P LOSS MUTATED          1         0         1
  1P LOSS WILD-TYPE        0         1         1
D41V3, multiclass
                   vv
clus                T1 T2 T3 T4
  1P LOSS MUTATED   12 12 12  1
  1P LOSS WILD-TYPE 49 28 28  7
D41V4, multiclass
    clus
vv   1P LOSS MUTATED 1P LOSS WILD-TYPE
  T1              12                49
  T2              12                28
  T3              12                28
  T4               1                 7
D41V5, binary
                   cls
clus                 0  1
  1P LOSS MUTATED   24  1
  1P LOSS WILD-TYPE 73  2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED     24    1
  1P LOSS WILD-TYPE   73    2
   clus
vv  1P LOSS MUTATED 1P LOSS WILD-TYPE
  0              24                73
  1               1                 2
                   vv
clus                M0 M1 MX
  1P LOSS MUTATED   31  2  4
  1P LOSS WILD-TYPE 84  1 27
D41V6, multiclass
    clus
vv   1P LOSS MUTATED 1P LOSS WILD-TYPE
  M0              31                84
  M1               2                 1
  MX               4                27
D41V7, binary
                   cls
clus                 0  1
  1P LOSS MUTATED   16 21
  1P LOSS WILD-TYPE 42 70
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED     16   21
  1P LOSS WILD-TYPE   42   70
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  FEMALE              16                42
  MALE                21                70
                   vv
clus                R0 R1 R2 RX
  1P LOSS MUTATED   31  2  1  3
  1P LOSS WILD-TYPE 91  9  0  7
D41V8, multiclass
    clus
vv   1P LOSS MUTATED 1P LOSS WILD-TYPE
  R0              31                91
  R1               2                 9
  R2               1                 0
  RX               3                 7

Clustering(42) Variable = 1Q LOSS MUTATION ANALYSIS
D42V1, survival
                   sevent
clus2                0  1
  1Q LOSS MUTATED    6  5
  1Q LOSS WILD-TYPE 78 58
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               11               136 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
                5                58 
$`1Q LOSS MUTATED`
TCGA-BC-A10S TCGA-BC-A217 TCGA-CC-5258 TCGA-CC-A3MB TCGA-DD-A11B TCGA-DD-A1EJ 
       46.78        13.84         0.07         0.10         0.46        29.16 
TCGA-DD-A3A1 TCGA-ED-A82E TCGA-ES-A2HS TCGA-FV-A4ZP TCGA-G3-A25U 
        7.66         0.20        22.85        60.36        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-BC-A69H TCGA-BC-A69I 
       44.42         0.26        22.36         9.50         3.95         0.53 
TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3M9 
        2.86         0.39         3.39         4.24         3.32         0.10 
TCGA-CC-A3MA TCGA-CC-A3MC TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 
        0.07         0.13        79.73        37.78        83.57        53.33 
TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 
      113.00         7.33         2.60        21.76        51.29        90.71 
TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EF 
       79.40        66.31        19.79        75.65         6.71        12.95 
TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V 
       45.11        49.15         6.02        18.35        13.64        21.14 
TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A2 TCGA-DD-A3A3 
       55.69         5.62        19.76        25.81        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        30.61 
TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NI 
       33.14        12.85        73.38        14.07        14.24        18.44 
TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP 
       15.06        39.78        56.25        29.56        61.45        93.67 
TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B 
       12.26         0.30        80.75        66.35        10.98         9.30 
TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G TCGA-ED-A459 
        7.56        10.98         1.45        27.72       100.96        13.41 
TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PX 
       12.69        15.85        13.91        13.35         0.23         0.20 
TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XP TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA 
        0.20         0.20         0.20        18.74        19.99        11.74 
TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A23B 
       10.98         0.62         9.96        11.93        14.40        32.45 
TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 
       19.10         0.20         8.12         6.38         0.13         0.03 
TCGA-FV-A496 TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25V TCGA-G3-A25W 
        0.33         0.39         1.22        51.06        28.27        30.74 
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         5.92 
TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SL TCGA-G3-A5SM 
       19.53        19.23        14.70        11.97         7.99         4.37 
TCGA-G3-A6UC TCGA-GJ-A6C0 TCGA-K7-A6G5 TCGA-LG-A6GG TCGA-MI-A75C TCGA-MI-A75E 
        7.76         1.02         4.01         0.49         9.57         5.10 
TCGA-MI-A75G TCGA-MI-A75I TCGA-NI-A4U2 TCGA-O8-A75V 
       14.24         8.71        58.88         4.44 

  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
             0.07              0.03 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
            60.36            113.00 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
           13.840            14.155 
[1] "0.1 - 60.4 (13.8)"  "0.0 - 113.0 (14.2)"
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
  "1Q LOSS MUTATED" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE"   "1Q LOSS MUTATED" "1Q LOSS WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-BC-A5W4        TCGA-BC-A69H        TCGA-BC-A69I 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-CC-5258        TCGA-CC-5260        TCGA-CC-5261        TCGA-CC-5262 
  "1Q LOSS MUTATED" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-CC-5263        TCGA-CC-A1HT        TCGA-CC-A3M9        TCGA-CC-A3MA 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-CC-A3MB        TCGA-CC-A3MC        TCGA-DD-A113        TCGA-DD-A114 
  "1Q LOSS MUTATED" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118        TCGA-DD-A119 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C        TCGA-DD-A11D 
"1Q LOSS WILD-TYPE"   "1Q LOSS MUTATED" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB        TCGA-DD-A1EC 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EF        TCGA-DD-A1EG 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DD-A1EH        TCGA-DD-A1EI        TCGA-DD-A1EJ        TCGA-DD-A1EK 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE"   "1Q LOSS MUTATED" "1Q LOSS WILD-TYPE" 
       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-A4NB        TCGA-DD-A4ND        TCGA-DD-A4NF        TCGA-DD-A4NH 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DD-A4NI        TCGA-DD-A4NJ        TCGA-DD-A4NK        TCGA-DD-A4NL 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DD-A4NN        TCGA-DD-A4NO        TCGA-DD-A4NP        TCGA-DD-A4NQ 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DD-A4NR        TCGA-DD-A4NS        TCGA-DD-A4NV        TCGA-DD-A73A 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DD-A73B        TCGA-DD-A73C        TCGA-DD-A73D        TCGA-DD-A73E 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DD-A73F        TCGA-DD-A73G        TCGA-ED-A459        TCGA-ED-A4XI 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-ED-A5KG        TCGA-ED-A627        TCGA-ED-A66X        TCGA-ED-A66Y 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-ED-A7PX        TCGA-ED-A7PY        TCGA-ED-A7PZ        TCGA-ED-A7XP 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-ED-A82E        TCGA-EP-A12J        TCGA-EP-A26S        TCGA-EP-A2KA 
  "1Q LOSS MUTATED" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EP-A2KB        TCGA-EP-A2KC        TCGA-EP-A3JL        TCGA-EP-A3RK 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-ES-A2HS        TCGA-ES-A2HT        TCGA-FV-A23B        TCGA-FV-A2QR 
  "1Q LOSS MUTATED" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-FV-A3I0        TCGA-FV-A3I1        TCGA-FV-A3R2        TCGA-FV-A3R3 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-FV-A495        TCGA-FV-A496        TCGA-FV-A4ZP        TCGA-FV-A4ZQ 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE"   "1Q LOSS MUTATED" "1Q LOSS WILD-TYPE" 
       TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U        TCGA-G3-A25V 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE"   "1Q LOSS MUTATED" "1Q LOSS WILD-TYPE" 
       TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y        TCGA-G3-A25Z 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI        TCGA-G3-A3CJ 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-G3-A3CK        TCGA-G3-A5SI        TCGA-G3-A5SJ        TCGA-G3-A5SL 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-G3-A5SM        TCGA-G3-A6UC        TCGA-GJ-A6C0        TCGA-K7-A6G5 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-LG-A6GG        TCGA-MI-A75C        TCGA-MI-A75E        TCGA-MI-A75G 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-MI-A75I        TCGA-NI-A4U2        TCGA-O8-A75V 
"1Q LOSS WILD-TYPE" "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-BC-A69H        TCGA-BC-A69I 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-CC-5258        TCGA-CC-5260        TCGA-CC-5261        TCGA-CC-5262 
  "1Q LOSS MUTATED" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-CC-5263        TCGA-CC-A1HT        TCGA-CC-A3M9        TCGA-CC-A3MA 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-CC-A3MB        TCGA-CC-A3MC        TCGA-DD-A113        TCGA-DD-A114 
  "1Q LOSS MUTATED" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118        TCGA-DD-A119 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C        TCGA-DD-A11D 
"1Q LOSS WILD-TYPE"   "1Q LOSS MUTATED" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB        TCGA-DD-A1EC 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EF        TCGA-DD-A1EG 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DD-A1EH        TCGA-DD-A1EI        TCGA-DD-A1EJ        TCGA-DD-A1EK 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE"   "1Q LOSS MUTATED" "1Q LOSS WILD-TYPE" 
       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-A4NB        TCGA-DD-A4ND        TCGA-DD-A4NF        TCGA-DD-A4NH 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DD-A4NI        TCGA-DD-A4NJ        TCGA-DD-A4NK        TCGA-DD-A4NL 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DD-A4NN        TCGA-DD-A4NO        TCGA-DD-A4NP        TCGA-DD-A4NQ 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DD-A4NR        TCGA-DD-A4NS        TCGA-DD-A4NV        TCGA-DD-A73A 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DD-A73B        TCGA-DD-A73C        TCGA-DD-A73D        TCGA-DD-A73E 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DD-A73F        TCGA-DD-A73G        TCGA-ED-A459        TCGA-ED-A4XI 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-ED-A5KG        TCGA-ED-A627        TCGA-ED-A66X        TCGA-ED-A66Y 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-ED-A7PX        TCGA-ED-A7PY        TCGA-ED-A7PZ        TCGA-ED-A7XP 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-ED-A82E        TCGA-EP-A12J        TCGA-EP-A26S        TCGA-EP-A2KA 
  "1Q LOSS MUTATED" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EP-A2KB        TCGA-EP-A2KC        TCGA-EP-A3JL        TCGA-EP-A3RK 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-ES-A2HS        TCGA-ES-A2HT        TCGA-FV-A23B        TCGA-FV-A2QR 
  "1Q LOSS MUTATED" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-FV-A3I0        TCGA-FV-A3I1        TCGA-FV-A3R2        TCGA-FV-A3R3 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-FV-A495        TCGA-FV-A496        TCGA-FV-A4ZP        TCGA-FV-A4ZQ 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE"   "1Q LOSS MUTATED" "1Q LOSS WILD-TYPE" 
       TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U        TCGA-G3-A25V 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE"   "1Q LOSS MUTATED" "1Q LOSS WILD-TYPE" 
       TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y        TCGA-G3-A25Z 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI        TCGA-G3-A3CJ 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-G3-A3CK        TCGA-G3-A5SI        TCGA-G3-A5SJ        TCGA-G3-A5SL 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-G3-A5SM        TCGA-G3-A6UC        TCGA-GJ-A6C0        TCGA-K7-A6G5 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-LG-A6GG        TCGA-MI-A75C        TCGA-MI-A75E        TCGA-MI-A75G 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-MI-A75I        TCGA-NI-A4U2        TCGA-O8-A75V 
"1Q LOSS WILD-TYPE" "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-BC-A69H        TCGA-BC-A69I 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-CC-5258        TCGA-CC-5260        TCGA-CC-5261        TCGA-CC-5262 
  "1Q LOSS MUTATED" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-CC-5263        TCGA-CC-A1HT        TCGA-CC-A3M9        TCGA-CC-A3MA 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-CC-A3MB        TCGA-CC-A3MC        TCGA-DD-A113        TCGA-DD-A114 
  "1Q LOSS MUTATED" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118        TCGA-DD-A119 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C        TCGA-DD-A11D 
"1Q LOSS WILD-TYPE"   "1Q LOSS MUTATED" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB        TCGA-DD-A1EC 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EF        TCGA-DD-A1EG 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DD-A1EH        TCGA-DD-A1EI        TCGA-DD-A1EJ        TCGA-DD-A1EK 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE"   "1Q LOSS MUTATED" "1Q LOSS WILD-TYPE" 
       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-A4NB        TCGA-DD-A4ND        TCGA-DD-A4NF        TCGA-DD-A4NH 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DD-A4NI        TCGA-DD-A4NJ        TCGA-DD-A4NK        TCGA-DD-A4NL 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DD-A4NN        TCGA-DD-A4NO        TCGA-DD-A4NP        TCGA-DD-A4NQ 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DD-A4NR        TCGA-DD-A4NS        TCGA-DD-A4NV        TCGA-DD-A73A 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DD-A73B        TCGA-DD-A73C        TCGA-DD-A73D        TCGA-DD-A73E 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DD-A73F        TCGA-DD-A73G        TCGA-ED-A459        TCGA-ED-A4XI 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-ED-A5KG        TCGA-ED-A627        TCGA-ED-A66X        TCGA-ED-A66Y 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-ED-A7PX        TCGA-ED-A7PY        TCGA-ED-A7PZ        TCGA-ED-A7XP 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-ED-A82E        TCGA-EP-A12J        TCGA-EP-A26S        TCGA-EP-A2KA 
  "1Q LOSS MUTATED" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EP-A2KB        TCGA-EP-A2KC        TCGA-EP-A3JL        TCGA-EP-A3RK 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-ES-A2HS        TCGA-ES-A2HT        TCGA-FV-A23B        TCGA-FV-A2QR 
  "1Q LOSS MUTATED" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-FV-A3I0        TCGA-FV-A3I1        TCGA-FV-A3R2        TCGA-FV-A3R3 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-FV-A495        TCGA-FV-A496        TCGA-FV-A4ZP        TCGA-FV-A4ZQ 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE"   "1Q LOSS MUTATED" "1Q LOSS WILD-TYPE" 
       TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U        TCGA-G3-A25V 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE"   "1Q LOSS MUTATED" "1Q LOSS WILD-TYPE" 
       TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y        TCGA-G3-A25Z 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI        TCGA-G3-A3CJ 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-G3-A3CK        TCGA-G3-A5SI        TCGA-G3-A5SJ        TCGA-G3-A5SL 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-G3-A5SM        TCGA-G3-A6UC        TCGA-GJ-A6C0        TCGA-K7-A6G5 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-LG-A6GG        TCGA-MI-A75C        TCGA-MI-A75E        TCGA-MI-A75G 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-MI-A75I        TCGA-NI-A4U2        TCGA-O8-A75V 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
[1] "hr=" "1.2"
D42V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  1Q LOSS MUTATED         3        2         0          4          0          1
  1Q LOSS WILD-TYPE      55       34         2         26          4          4
                   vv
clus                STAGE IV STAGE IVA STAGE IVB
  1Q LOSS MUTATED          0         0         0
  1Q LOSS WILD-TYPE        1         1         2
D42V3, multiclass
                   vv
clus                T1 T2 T3 T4
  1Q LOSS MUTATED    4  2  5  0
  1Q LOSS WILD-TYPE 57 38 35  8
D42V4, multiclass
    clus
vv   1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  T1               4                57
  T2               2                38
  T3               5                35
  T4               0                 8
D42V5, binary
                   cls
clus                 0  1
  1Q LOSS MUTATED    6  1
  1Q LOSS WILD-TYPE 91  2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED      6    1
  1Q LOSS WILD-TYPE   91    2
   clus
vv  1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  0               6                91
  1               1                 2
                   vv
clus                 M0  M1  MX
  1Q LOSS MUTATED     9   0   2
  1Q LOSS WILD-TYPE 106   3  29
D42V6, multiclass
    clus
vv   1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  M0               9               106
  M1               0                 3
  MX               2                29
D42V7, binary
                   cls
clus                 0  1
  1Q LOSS MUTATED    4  7
  1Q LOSS WILD-TYPE 54 84
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED      4    7
  1Q LOSS WILD-TYPE   54   84
        clus
vv       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  FEMALE               4                54
  MALE                 7                84
                   vv
clus                 R0  R1  R2  RX
  1Q LOSS MUTATED     8   1   0   2
  1Q LOSS WILD-TYPE 114  10   1   8
D42V8, multiclass
    clus
vv   1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  R0               8               114
  R1               1                10
  R2               0                 1
  RX               2                 8

Clustering(43) Variable = 2P LOSS MUTATION ANALYSIS
D43V1, survival
                   sevent
clus2                0  1
  2P LOSS MUTATED    7  4
  2P LOSS WILD-TYPE 77 59
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               11               136 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
                4                59 
$`2P LOSS MUTATED`
TCGA-BC-A10Y TCGA-BC-A3KF TCGA-BC-A69H TCGA-DD-A11C TCGA-DD-A39Y TCGA-ED-A459 
       23.34         0.26         3.95        21.76         5.62        13.41 
TCGA-ED-A66Y TCGA-ED-A7PZ TCGA-FV-A3I1 TCGA-G3-A25S TCGA-G3-A5SM 
        0.23         0.20         8.12         1.22         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-BC-A69I TCGA-CC-5258 
       44.42        13.84        22.36         9.50         0.53         0.07 
TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3M9 
        2.86         0.39         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        37.78        83.57 
TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11D 
       53.33       113.00         7.33         2.60         0.46        51.29 
TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE 
       90.71        79.40        66.31        19.79        75.65         6.71 
TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK 
       12.95        45.11        49.15         6.02        29.16        18.35 
TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39X TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 
       13.64        21.14        55.69        19.76        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-A4NB TCGA-DD-A4ND TCGA-DD-A4NF 
        0.36        30.61        33.14        12.85        73.38        14.07 
TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN 
       14.24        18.44        15.06        39.78        56.25        29.56 
TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV 
       61.45        93.67        12.26         0.30        80.75        66.35 
TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F 
       10.98         9.30         7.56        10.98         1.45        27.72 
TCGA-DD-A73G TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A7PX 
      100.96        12.69        15.85        13.91        13.35         0.20 
TCGA-ED-A7PY TCGA-ED-A7XP TCGA-ED-A82E TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA 
        0.20         0.20         0.20        18.74        19.99        11.74 
TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT 
       10.98         0.62         9.96        11.93        22.85        14.40 
TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 
       32.45        19.10         0.20         6.38         0.13         0.03 
TCGA-FV-A496 TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V 
        0.33        60.36         0.39        51.06        53.79        28.27 
TCGA-G3-A25W TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CH 
       30.74        58.49        14.86        21.53        22.13        25.64 
TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SL 
        5.92        19.53        19.23        14.70        11.97         7.99 
TCGA-G3-A6UC TCGA-GJ-A6C0 TCGA-K7-A6G5 TCGA-LG-A6GG TCGA-MI-A75C TCGA-MI-A75E 
        7.76         1.02         4.01         0.49         9.57         5.10 
TCGA-MI-A75G TCGA-MI-A75I TCGA-NI-A4U2 TCGA-O8-A75V 
       14.24         8.71        58.88         4.44 

  2P LOSS MUTATED 2P LOSS WILD-TYPE 
             0.20              0.03 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
            23.34            113.00 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
             4.37             14.55 
[1] "0.2 - 23.3 (4.4)"   "0.0 - 113.0 (14.6)"
       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-BC-A69H        TCGA-BC-A69I 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE"   "2P LOSS MUTATED" "2P LOSS WILD-TYPE" 
       TCGA-CC-5258        TCGA-CC-5260        TCGA-CC-5261        TCGA-CC-5262 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CC-5263        TCGA-CC-A1HT        TCGA-CC-A3M9        TCGA-CC-A3MA 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CC-A3MB        TCGA-CC-A3MC        TCGA-DD-A113        TCGA-DD-A114 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118        TCGA-DD-A119 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C        TCGA-DD-A11D 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE"   "2P LOSS MUTATED" "2P LOSS WILD-TYPE" 
       TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB        TCGA-DD-A1EC 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EF        TCGA-DD-A1EG 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-DD-A1EH        TCGA-DD-A1EI        TCGA-DD-A1EJ        TCGA-DD-A1EK 
"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 MUTATED" 
       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-A4NB        TCGA-DD-A4ND        TCGA-DD-A4NF        TCGA-DD-A4NH 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-DD-A4NI        TCGA-DD-A4NJ        TCGA-DD-A4NK        TCGA-DD-A4NL 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-DD-A4NN        TCGA-DD-A4NO        TCGA-DD-A4NP        TCGA-DD-A4NQ 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-DD-A4NR        TCGA-DD-A4NS        TCGA-DD-A4NV        TCGA-DD-A73A 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-DD-A73B        TCGA-DD-A73C        TCGA-DD-A73D        TCGA-DD-A73E 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-DD-A73F        TCGA-DD-A73G        TCGA-ED-A459        TCGA-ED-A4XI 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE"   "2P LOSS MUTATED" "2P LOSS WILD-TYPE" 
       TCGA-ED-A5KG        TCGA-ED-A627        TCGA-ED-A66X        TCGA-ED-A66Y 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE"   "2P LOSS MUTATED" 
       TCGA-ED-A7PX        TCGA-ED-A7PY        TCGA-ED-A7PZ        TCGA-ED-A7XP 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE"   "2P LOSS MUTATED" "2P LOSS WILD-TYPE" 
       TCGA-ED-A82E        TCGA-EP-A12J        TCGA-EP-A26S        TCGA-EP-A2KA 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-EP-A2KB        TCGA-EP-A2KC        TCGA-EP-A3JL        TCGA-EP-A3RK 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-ES-A2HS        TCGA-ES-A2HT        TCGA-FV-A23B        TCGA-FV-A2QR 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-FV-A3I0        TCGA-FV-A3I1        TCGA-FV-A3R2        TCGA-FV-A3R3 
"2P LOSS WILD-TYPE"   "2P LOSS MUTATED" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-FV-A495        TCGA-FV-A496        TCGA-FV-A4ZP        TCGA-FV-A4ZQ 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U        TCGA-G3-A25V 
  "2P LOSS MUTATED" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y        TCGA-G3-A25Z 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI        TCGA-G3-A3CJ 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-G3-A3CK        TCGA-G3-A5SI        TCGA-G3-A5SJ        TCGA-G3-A5SL 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-G3-A5SM        TCGA-G3-A6UC        TCGA-GJ-A6C0        TCGA-K7-A6G5 
  "2P LOSS MUTATED" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-LG-A6GG        TCGA-MI-A75C        TCGA-MI-A75E        TCGA-MI-A75G 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-MI-A75I        TCGA-NI-A4U2        TCGA-O8-A75V 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"2P LOSS WILD-TYPE"   "2P LOSS 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-BC-A69H        TCGA-BC-A69I 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE"   "2P LOSS MUTATED" "2P LOSS WILD-TYPE" 
       TCGA-CC-5258        TCGA-CC-5260        TCGA-CC-5261        TCGA-CC-5262 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CC-5263        TCGA-CC-A1HT        TCGA-CC-A3M9        TCGA-CC-A3MA 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CC-A3MB        TCGA-CC-A3MC        TCGA-DD-A113        TCGA-DD-A114 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118        TCGA-DD-A119 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C        TCGA-DD-A11D 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE"   "2P LOSS MUTATED" "2P LOSS WILD-TYPE" 
       TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB        TCGA-DD-A1EC 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EF        TCGA-DD-A1EG 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-DD-A1EH        TCGA-DD-A1EI        TCGA-DD-A1EJ        TCGA-DD-A1EK 
"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 MUTATED" 
       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-A4NB        TCGA-DD-A4ND        TCGA-DD-A4NF        TCGA-DD-A4NH 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-DD-A4NI        TCGA-DD-A4NJ        TCGA-DD-A4NK        TCGA-DD-A4NL 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-DD-A4NN        TCGA-DD-A4NO        TCGA-DD-A4NP        TCGA-DD-A4NQ 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-DD-A4NR        TCGA-DD-A4NS        TCGA-DD-A4NV        TCGA-DD-A73A 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-DD-A73B        TCGA-DD-A73C        TCGA-DD-A73D        TCGA-DD-A73E 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-DD-A73F        TCGA-DD-A73G        TCGA-ED-A459        TCGA-ED-A4XI 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE"   "2P LOSS MUTATED" "2P LOSS WILD-TYPE" 
       TCGA-ED-A5KG        TCGA-ED-A627        TCGA-ED-A66X        TCGA-ED-A66Y 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE"   "2P LOSS MUTATED" 
       TCGA-ED-A7PX        TCGA-ED-A7PY        TCGA-ED-A7PZ        TCGA-ED-A7XP 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE"   "2P LOSS MUTATED" "2P LOSS WILD-TYPE" 
       TCGA-ED-A82E        TCGA-EP-A12J        TCGA-EP-A26S        TCGA-EP-A2KA 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-EP-A2KB        TCGA-EP-A2KC        TCGA-EP-A3JL        TCGA-EP-A3RK 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-ES-A2HS        TCGA-ES-A2HT        TCGA-FV-A23B        TCGA-FV-A2QR 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-FV-A3I0        TCGA-FV-A3I1        TCGA-FV-A3R2        TCGA-FV-A3R3 
"2P LOSS WILD-TYPE"   "2P LOSS MUTATED" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-FV-A495        TCGA-FV-A496        TCGA-FV-A4ZP        TCGA-FV-A4ZQ 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U        TCGA-G3-A25V 
  "2P LOSS MUTATED" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y        TCGA-G3-A25Z 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI        TCGA-G3-A3CJ 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-G3-A3CK        TCGA-G3-A5SI        TCGA-G3-A5SJ        TCGA-G3-A5SL 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-G3-A5SM        TCGA-G3-A6UC        TCGA-GJ-A6C0        TCGA-K7-A6G5 
  "2P LOSS MUTATED" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-LG-A6GG        TCGA-MI-A75C        TCGA-MI-A75E        TCGA-MI-A75G 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-MI-A75I        TCGA-NI-A4U2        TCGA-O8-A75V 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"2P LOSS WILD-TYPE"   "2P LOSS 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-BC-A69H        TCGA-BC-A69I 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE"   "2P LOSS MUTATED" "2P LOSS WILD-TYPE" 
       TCGA-CC-5258        TCGA-CC-5260        TCGA-CC-5261        TCGA-CC-5262 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CC-5263        TCGA-CC-A1HT        TCGA-CC-A3M9        TCGA-CC-A3MA 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CC-A3MB        TCGA-CC-A3MC        TCGA-DD-A113        TCGA-DD-A114 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118        TCGA-DD-A119 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C        TCGA-DD-A11D 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE"   "2P LOSS MUTATED" "2P LOSS WILD-TYPE" 
       TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB        TCGA-DD-A1EC 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EF        TCGA-DD-A1EG 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-DD-A1EH        TCGA-DD-A1EI        TCGA-DD-A1EJ        TCGA-DD-A1EK 
"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 MUTATED" 
       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-A4NB        TCGA-DD-A4ND        TCGA-DD-A4NF        TCGA-DD-A4NH 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-DD-A4NI        TCGA-DD-A4NJ        TCGA-DD-A4NK        TCGA-DD-A4NL 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-DD-A4NN        TCGA-DD-A4NO        TCGA-DD-A4NP        TCGA-DD-A4NQ 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-DD-A4NR        TCGA-DD-A4NS        TCGA-DD-A4NV        TCGA-DD-A73A 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-DD-A73B        TCGA-DD-A73C        TCGA-DD-A73D        TCGA-DD-A73E 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-DD-A73F        TCGA-DD-A73G        TCGA-ED-A459        TCGA-ED-A4XI 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE"   "2P LOSS MUTATED" "2P LOSS WILD-TYPE" 
       TCGA-ED-A5KG        TCGA-ED-A627        TCGA-ED-A66X        TCGA-ED-A66Y 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE"   "2P LOSS MUTATED" 
       TCGA-ED-A7PX        TCGA-ED-A7PY        TCGA-ED-A7PZ        TCGA-ED-A7XP 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE"   "2P LOSS MUTATED" "2P LOSS WILD-TYPE" 
       TCGA-ED-A82E        TCGA-EP-A12J        TCGA-EP-A26S        TCGA-EP-A2KA 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-EP-A2KB        TCGA-EP-A2KC        TCGA-EP-A3JL        TCGA-EP-A3RK 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-ES-A2HS        TCGA-ES-A2HT        TCGA-FV-A23B        TCGA-FV-A2QR 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-FV-A3I0        TCGA-FV-A3I1        TCGA-FV-A3R2        TCGA-FV-A3R3 
"2P LOSS WILD-TYPE"   "2P LOSS MUTATED" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-FV-A495        TCGA-FV-A496        TCGA-FV-A4ZP        TCGA-FV-A4ZQ 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U        TCGA-G3-A25V 
  "2P LOSS MUTATED" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y        TCGA-G3-A25Z 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI        TCGA-G3-A3CJ 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-G3-A3CK        TCGA-G3-A5SI        TCGA-G3-A5SJ        TCGA-G3-A5SL 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-G3-A5SM        TCGA-G3-A6UC        TCGA-GJ-A6C0        TCGA-K7-A6G5 
  "2P LOSS MUTATED" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-LG-A6GG        TCGA-MI-A75C        TCGA-MI-A75E        TCGA-MI-A75G 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-MI-A75I        TCGA-NI-A4U2        TCGA-O8-A75V 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
[1] "hr=" "2.6"
D43V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  2P LOSS MUTATED         4        5         0          1          0          0
  2P LOSS WILD-TYPE      54       31         2         29          4          5
                   vv
clus                STAGE IV STAGE IVA STAGE IVB
  2P LOSS MUTATED          0         0         0
  2P LOSS WILD-TYPE        1         1         2
D43V3, multiclass
                   vv
clus                T1 T2 T3 T4
  2P LOSS MUTATED    4  5  1  1
  2P LOSS WILD-TYPE 57 35 39  7
D43V4, multiclass
    clus
vv   2P LOSS MUTATED 2P LOSS WILD-TYPE
  T1               4                57
  T2               5                35
  T3               1                39
  T4               1                 7
D43V5, binary
                   cls
clus                 0  1
  2P LOSS MUTATED    5  0
  2P LOSS WILD-TYPE 92  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED      5    0
  2P LOSS WILD-TYPE   92    3
   clus
vv  2P LOSS MUTATED 2P LOSS WILD-TYPE
  0               5                92
  1               0                 3
                   vv
clus                 M0  M1  MX
  2P LOSS MUTATED     9   0   2
  2P LOSS WILD-TYPE 106   3  29
D43V6, multiclass
    clus
vv   2P LOSS MUTATED 2P LOSS WILD-TYPE
  M0               9               106
  M1               0                 3
  MX               2                29
D43V7, binary
                   cls
clus                 0  1
  2P LOSS MUTATED    3  8
  2P LOSS WILD-TYPE 55 83
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED      3    8
  2P LOSS WILD-TYPE   55   83
        clus
vv       2P LOSS MUTATED 2P LOSS WILD-TYPE
  FEMALE               3                55
  MALE                 8                83
                   vv
clus                 R0  R1  R2  RX
  2P LOSS MUTATED     9   1   0   1
  2P LOSS WILD-TYPE 113  10   1   9
D43V8, multiclass
    clus
vv   2P LOSS MUTATED 2P LOSS WILD-TYPE
  R0               9               113
  R1               1                10
  R2               0                 1
  RX               1                 9

Clustering(44) Variable = 2Q LOSS MUTATION ANALYSIS
D44V1, survival
                   sevent
clus2                0  1
  2Q LOSS MUTATED    7  5
  2Q LOSS WILD-TYPE 77 58
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               12               135 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
                5                58 
$`2Q LOSS MUTATED`
TCGA-BC-A10Y TCGA-BC-A3KF TCGA-DD-A115 TCGA-DD-A11C TCGA-DD-A39Y TCGA-DD-A4NJ 
       23.34         0.26        83.57        21.76         5.62        15.06 
TCGA-DD-A73B TCGA-ED-A459 TCGA-ED-A66Y TCGA-ED-A7PZ TCGA-FV-A3I1 TCGA-G3-A5SM 
        9.30        13.41         0.23         0.20         8.12         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-BC-A69H TCGA-BC-A69I 
       44.42        13.84        22.36         9.50         3.95         0.53 
TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A1HT 
        0.07         2.86         0.39         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        37.78 
TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11D 
       53.33       113.00         7.33         2.60         0.46        51.29 
TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE 
       90.71        79.40        66.31        19.79        75.65         6.71 
TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK 
       12.95        45.11        49.15         6.02        29.16        18.35 
TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39X TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 
       13.64        21.14        55.69        19.76        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-A4NB TCGA-DD-A4ND TCGA-DD-A4NF 
        0.36        30.61        33.14        12.85        73.38        14.07 
TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO 
       14.24        18.44        39.78        56.25        29.56        61.45 
TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A 
       93.67        12.26         0.30        80.75        66.35        10.98 
TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G TCGA-ED-A4XI 
        7.56        10.98         1.45        27.72       100.96        12.69 
TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7XP 
       15.85        13.91        13.35         0.20         0.20         0.20 
TCGA-ED-A82E TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC 
        0.20        18.74        19.99        11.74        10.98         0.62 
TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QR 
        9.96        11.93        22.85        14.40        32.45        19.10 
TCGA-FV-A3I0 TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZP 
        0.20         6.38         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        51.06        53.79        28.27        30.74 
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         5.92 
TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SL TCGA-G3-A6UC 
       19.53        19.23        14.70        11.97         7.99         7.76 
TCGA-GJ-A6C0 TCGA-K7-A6G5 TCGA-LG-A6GG TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G 
        1.02         4.01         0.49         9.57         5.10        14.24 
TCGA-MI-A75I TCGA-NI-A4U2 TCGA-O8-A75V 
        8.71        58.88         4.44 

  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
             0.20              0.03 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
            83.57            113.00 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
             8.71             14.24 
[1] "0.2 - 83.6 (8.7)"   "0.0 - 113.0 (14.2)"
       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-BC-A69H        TCGA-BC-A69I 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-CC-5258        TCGA-CC-5260        TCGA-CC-5261        TCGA-CC-5262 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-CC-5263        TCGA-CC-A1HT        TCGA-CC-A3M9        TCGA-CC-A3MA 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-CC-A3MB        TCGA-CC-A3MC        TCGA-DD-A113        TCGA-DD-A114 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118        TCGA-DD-A119 
  "2Q LOSS MUTATED" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C        TCGA-DD-A11D 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE"   "2Q LOSS MUTATED" "2Q LOSS WILD-TYPE" 
       TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB        TCGA-DD-A1EC 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EF        TCGA-DD-A1EG 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-DD-A1EH        TCGA-DD-A1EI        TCGA-DD-A1EJ        TCGA-DD-A1EK 
"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 MUTATED" 
       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-A4NB        TCGA-DD-A4ND        TCGA-DD-A4NF        TCGA-DD-A4NH 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-DD-A4NI        TCGA-DD-A4NJ        TCGA-DD-A4NK        TCGA-DD-A4NL 
"2Q LOSS WILD-TYPE"   "2Q LOSS MUTATED" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-DD-A4NN        TCGA-DD-A4NO        TCGA-DD-A4NP        TCGA-DD-A4NQ 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-DD-A4NR        TCGA-DD-A4NS        TCGA-DD-A4NV        TCGA-DD-A73A 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-DD-A73B        TCGA-DD-A73C        TCGA-DD-A73D        TCGA-DD-A73E 
  "2Q LOSS MUTATED" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-DD-A73F        TCGA-DD-A73G        TCGA-ED-A459        TCGA-ED-A4XI 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE"   "2Q LOSS MUTATED" "2Q LOSS WILD-TYPE" 
       TCGA-ED-A5KG        TCGA-ED-A627        TCGA-ED-A66X        TCGA-ED-A66Y 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE"   "2Q LOSS MUTATED" 
       TCGA-ED-A7PX        TCGA-ED-A7PY        TCGA-ED-A7PZ        TCGA-ED-A7XP 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE"   "2Q LOSS MUTATED" "2Q LOSS WILD-TYPE" 
       TCGA-ED-A82E        TCGA-EP-A12J        TCGA-EP-A26S        TCGA-EP-A2KA 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-EP-A2KB        TCGA-EP-A2KC        TCGA-EP-A3JL        TCGA-EP-A3RK 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-ES-A2HS        TCGA-ES-A2HT        TCGA-FV-A23B        TCGA-FV-A2QR 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-FV-A3I0        TCGA-FV-A3I1        TCGA-FV-A3R2        TCGA-FV-A3R3 
"2Q LOSS WILD-TYPE"   "2Q LOSS MUTATED" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-FV-A495        TCGA-FV-A496        TCGA-FV-A4ZP        TCGA-FV-A4ZQ 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U        TCGA-G3-A25V 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y        TCGA-G3-A25Z 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI        TCGA-G3-A3CJ 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-G3-A3CK        TCGA-G3-A5SI        TCGA-G3-A5SJ        TCGA-G3-A5SL 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-G3-A5SM        TCGA-G3-A6UC        TCGA-GJ-A6C0        TCGA-K7-A6G5 
  "2Q LOSS MUTATED" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-LG-A6GG        TCGA-MI-A75C        TCGA-MI-A75E        TCGA-MI-A75G 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-MI-A75I        TCGA-NI-A4U2        TCGA-O8-A75V 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"2Q LOSS WILD-TYPE"   "2Q LOSS 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-BC-A69H        TCGA-BC-A69I 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-CC-5258        TCGA-CC-5260        TCGA-CC-5261        TCGA-CC-5262 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-CC-5263        TCGA-CC-A1HT        TCGA-CC-A3M9        TCGA-CC-A3MA 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-CC-A3MB        TCGA-CC-A3MC        TCGA-DD-A113        TCGA-DD-A114 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118        TCGA-DD-A119 
  "2Q LOSS MUTATED" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C        TCGA-DD-A11D 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE"   "2Q LOSS MUTATED" "2Q LOSS WILD-TYPE" 
       TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB        TCGA-DD-A1EC 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EF        TCGA-DD-A1EG 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-DD-A1EH        TCGA-DD-A1EI        TCGA-DD-A1EJ        TCGA-DD-A1EK 
"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 MUTATED" 
       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-A4NB        TCGA-DD-A4ND        TCGA-DD-A4NF        TCGA-DD-A4NH 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-DD-A4NI        TCGA-DD-A4NJ        TCGA-DD-A4NK        TCGA-DD-A4NL 
"2Q LOSS WILD-TYPE"   "2Q LOSS MUTATED" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-DD-A4NN        TCGA-DD-A4NO        TCGA-DD-A4NP        TCGA-DD-A4NQ 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-DD-A4NR        TCGA-DD-A4NS        TCGA-DD-A4NV        TCGA-DD-A73A 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-DD-A73B        TCGA-DD-A73C        TCGA-DD-A73D        TCGA-DD-A73E 
  "2Q LOSS MUTATED" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-DD-A73F        TCGA-DD-A73G        TCGA-ED-A459        TCGA-ED-A4XI 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE"   "2Q LOSS MUTATED" "2Q LOSS WILD-TYPE" 
       TCGA-ED-A5KG        TCGA-ED-A627        TCGA-ED-A66X        TCGA-ED-A66Y 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE"   "2Q LOSS MUTATED" 
       TCGA-ED-A7PX        TCGA-ED-A7PY        TCGA-ED-A7PZ        TCGA-ED-A7XP 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE"   "2Q LOSS MUTATED" "2Q LOSS WILD-TYPE" 
       TCGA-ED-A82E        TCGA-EP-A12J        TCGA-EP-A26S        TCGA-EP-A2KA 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-EP-A2KB        TCGA-EP-A2KC        TCGA-EP-A3JL        TCGA-EP-A3RK 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-ES-A2HS        TCGA-ES-A2HT        TCGA-FV-A23B        TCGA-FV-A2QR 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-FV-A3I0        TCGA-FV-A3I1        TCGA-FV-A3R2        TCGA-FV-A3R3 
"2Q LOSS WILD-TYPE"   "2Q LOSS MUTATED" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-FV-A495        TCGA-FV-A496        TCGA-FV-A4ZP        TCGA-FV-A4ZQ 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U        TCGA-G3-A25V 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y        TCGA-G3-A25Z 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI        TCGA-G3-A3CJ 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-G3-A3CK        TCGA-G3-A5SI        TCGA-G3-A5SJ        TCGA-G3-A5SL 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-G3-A5SM        TCGA-G3-A6UC        TCGA-GJ-A6C0        TCGA-K7-A6G5 
  "2Q LOSS MUTATED" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-LG-A6GG        TCGA-MI-A75C        TCGA-MI-A75E        TCGA-MI-A75G 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-MI-A75I        TCGA-NI-A4U2        TCGA-O8-A75V 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"2Q LOSS WILD-TYPE"   "2Q LOSS 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-BC-A69H        TCGA-BC-A69I 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-CC-5258        TCGA-CC-5260        TCGA-CC-5261        TCGA-CC-5262 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-CC-5263        TCGA-CC-A1HT        TCGA-CC-A3M9        TCGA-CC-A3MA 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-CC-A3MB        TCGA-CC-A3MC        TCGA-DD-A113        TCGA-DD-A114 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118        TCGA-DD-A119 
  "2Q LOSS MUTATED" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C        TCGA-DD-A11D 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE"   "2Q LOSS MUTATED" "2Q LOSS WILD-TYPE" 
       TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB        TCGA-DD-A1EC 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EF        TCGA-DD-A1EG 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-DD-A1EH        TCGA-DD-A1EI        TCGA-DD-A1EJ        TCGA-DD-A1EK 
"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 MUTATED" 
       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-A4NB        TCGA-DD-A4ND        TCGA-DD-A4NF        TCGA-DD-A4NH 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-DD-A4NI        TCGA-DD-A4NJ        TCGA-DD-A4NK        TCGA-DD-A4NL 
"2Q LOSS WILD-TYPE"   "2Q LOSS MUTATED" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-DD-A4NN        TCGA-DD-A4NO        TCGA-DD-A4NP        TCGA-DD-A4NQ 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-DD-A4NR        TCGA-DD-A4NS        TCGA-DD-A4NV        TCGA-DD-A73A 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-DD-A73B        TCGA-DD-A73C        TCGA-DD-A73D        TCGA-DD-A73E 
  "2Q LOSS MUTATED" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-DD-A73F        TCGA-DD-A73G        TCGA-ED-A459        TCGA-ED-A4XI 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE"   "2Q LOSS MUTATED" "2Q LOSS WILD-TYPE" 
       TCGA-ED-A5KG        TCGA-ED-A627        TCGA-ED-A66X        TCGA-ED-A66Y 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE"   "2Q LOSS MUTATED" 
       TCGA-ED-A7PX        TCGA-ED-A7PY        TCGA-ED-A7PZ        TCGA-ED-A7XP 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE"   "2Q LOSS MUTATED" "2Q LOSS WILD-TYPE" 
       TCGA-ED-A82E        TCGA-EP-A12J        TCGA-EP-A26S        TCGA-EP-A2KA 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-EP-A2KB        TCGA-EP-A2KC        TCGA-EP-A3JL        TCGA-EP-A3RK 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-ES-A2HS        TCGA-ES-A2HT        TCGA-FV-A23B        TCGA-FV-A2QR 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-FV-A3I0        TCGA-FV-A3I1        TCGA-FV-A3R2        TCGA-FV-A3R3 
"2Q LOSS WILD-TYPE"   "2Q LOSS MUTATED" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-FV-A495        TCGA-FV-A496        TCGA-FV-A4ZP        TCGA-FV-A4ZQ 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U        TCGA-G3-A25V 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y        TCGA-G3-A25Z 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI        TCGA-G3-A3CJ 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-G3-A3CK        TCGA-G3-A5SI        TCGA-G3-A5SJ        TCGA-G3-A5SL 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-G3-A5SM        TCGA-G3-A6UC        TCGA-GJ-A6C0        TCGA-K7-A6G5 
  "2Q LOSS MUTATED" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-LG-A6GG        TCGA-MI-A75C        TCGA-MI-A75E        TCGA-MI-A75G 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-MI-A75I        TCGA-NI-A4U2        TCGA-O8-A75V 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
[1] "hr=" "1.5"
D44V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  2Q LOSS MUTATED         4        5         0          3          0          0
  2Q LOSS WILD-TYPE      54       31         2         27          4          5
                   vv
clus                STAGE IV STAGE IVA STAGE IVB
  2Q LOSS MUTATED          0         0         0
  2Q LOSS WILD-TYPE        1         1         2
D44V3, multiclass
                   vv
clus                T1 T2 T3 T4
  2Q LOSS MUTATED    4  5  3  1
  2Q LOSS WILD-TYPE 57 35 37  7
D44V4, multiclass
    clus
vv   2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  T1               4                57
  T2               5                35
  T3               3                37
  T4               1                 7
D44V5, binary
                   cls
clus                 0  1
  2Q LOSS MUTATED    8  0
  2Q LOSS WILD-TYPE 89  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED      8    0
  2Q LOSS WILD-TYPE   89    3
   clus
vv  2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  0               8                89
  1               0                 3
                   vv
clus                 M0  M1  MX
  2Q LOSS MUTATED    11   0   2
  2Q LOSS WILD-TYPE 104   3  29
D44V6, multiclass
    clus
vv   2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  M0              11               104
  M1               0                 3
  MX               2                29
D44V7, binary
                   cls
clus                 0  1
  2Q LOSS MUTATED    5  8
  2Q LOSS WILD-TYPE 53 83
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED      5    8
  2Q LOSS WILD-TYPE   53   83
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  FEMALE               5                53
  MALE                 8                83
                   vv
clus                 R0  R1  R2  RX
  2Q LOSS MUTATED    11   0   0   2
  2Q LOSS WILD-TYPE 111  11   1   8
D44V8, multiclass
    clus
vv   2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  R0              11               111
  R1               0                11
  R2               0                 1
  RX               2                 8

Clustering(45) Variable = 3P LOSS MUTATION ANALYSIS
D45V1, survival
                   sevent
clus2                0  1
  3P LOSS MUTATED   14  5
  3P LOSS WILD-TYPE 70 58
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               19               128 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
                5                58 
$`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-A4NI TCGA-DD-A4NO 
      113.00        90.71        30.61        33.14        18.44        61.45 
TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PZ TCGA-ED-A82E TCGA-FV-A3I0 TCGA-G3-A25T 
        0.23         0.20         0.20         0.20         0.20        51.06 
TCGA-G3-A25X 
       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-BC-A69H TCGA-BC-A69I 
       13.84         0.26        22.36         9.50         3.95         0.53 
TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-A1HT TCGA-CC-A3M9 
        0.07         2.86         0.39         3.39         3.32         0.10 
TCGA-CC-A3MC TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A119 TCGA-DD-A11A 
        0.13        37.78        83.57        53.33         7.33         2.60 
TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC 
        0.46        21.76        51.29        79.40        66.31        19.79 
TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI 
       75.65         6.71        12.95        45.11        49.15         6.02 
TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39X TCGA-DD-A39Y 
       29.16        18.35        13.64        21.14        55.69         5.62 
TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 
       19.76        25.81         7.66        70.06        17.59        20.12 
TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A4NB TCGA-DD-A4ND 
      102.74       107.11        13.78         0.36        12.85        73.38 
TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN 
       14.07        14.24        15.06        39.78        56.25        29.56 
TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A 
       93.67        12.26         0.30        80.75        66.35        10.98 
TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G 
        9.30         7.56        10.98         1.45        27.72       100.96 
TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A7PY 
       13.41        12.69        15.85        13.91        13.35         0.20 
TCGA-ED-A7XP TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC 
        0.20        18.74        19.99        11.74        10.98         0.62 
TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QR 
        9.96        11.93        22.85        14.40        32.45        19.10 
TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZP 
        8.12         6.38         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        30.74        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         5.92        19.53        19.23 
TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A6UC TCGA-GJ-A6C0 
       14.70        11.97         7.99         4.37         7.76         1.02 
TCGA-K7-A6G5 TCGA-LG-A6GG TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75I 
        4.01         0.49         9.57         5.10        14.24         8.71 
TCGA-NI-A4U2 TCGA-O8-A75V 
       58.88         4.44 

  3P LOSS MUTATED 3P LOSS WILD-TYPE 
             0.07              0.03 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
           113.00            107.11 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
           10.130            14.155 
[1] "0.1 - 113.0 (10.1)" "0.0 - 107.1 (14.2)"
       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-BC-A69H        TCGA-BC-A69I 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-CC-5258        TCGA-CC-5260        TCGA-CC-5261        TCGA-CC-5262 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-CC-5263        TCGA-CC-A1HT        TCGA-CC-A3M9        TCGA-CC-A3MA 
  "3P LOSS MUTATED" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE"   "3P LOSS MUTATED" 
       TCGA-CC-A3MB        TCGA-CC-A3MC        TCGA-DD-A113        TCGA-DD-A114 
  "3P LOSS MUTATED" "3P LOSS WILD-TYPE"   "3P LOSS MUTATED" "3P LOSS WILD-TYPE" 
       TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118        TCGA-DD-A119 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE"   "3P LOSS MUTATED" "3P LOSS WILD-TYPE" 
       TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C        TCGA-DD-A11D 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB        TCGA-DD-A1EC 
  "3P LOSS MUTATED" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EF        TCGA-DD-A1EG 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DD-A1EH        TCGA-DD-A1EI        TCGA-DD-A1EJ        TCGA-DD-A1EK 
"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-A4NB        TCGA-DD-A4ND        TCGA-DD-A4NF        TCGA-DD-A4NH 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DD-A4NI        TCGA-DD-A4NJ        TCGA-DD-A4NK        TCGA-DD-A4NL 
  "3P LOSS MUTATED" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DD-A4NN        TCGA-DD-A4NO        TCGA-DD-A4NP        TCGA-DD-A4NQ 
"3P LOSS WILD-TYPE"   "3P LOSS MUTATED" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DD-A4NR        TCGA-DD-A4NS        TCGA-DD-A4NV        TCGA-DD-A73A 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DD-A73B        TCGA-DD-A73C        TCGA-DD-A73D        TCGA-DD-A73E 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DD-A73F        TCGA-DD-A73G        TCGA-ED-A459        TCGA-ED-A4XI 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-ED-A5KG        TCGA-ED-A627        TCGA-ED-A66X        TCGA-ED-A66Y 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE"   "3P LOSS MUTATED" 
       TCGA-ED-A7PX        TCGA-ED-A7PY        TCGA-ED-A7PZ        TCGA-ED-A7XP 
  "3P LOSS MUTATED" "3P LOSS WILD-TYPE"   "3P LOSS MUTATED" "3P LOSS WILD-TYPE" 
       TCGA-ED-A82E        TCGA-EP-A12J        TCGA-EP-A26S        TCGA-EP-A2KA 
  "3P LOSS MUTATED" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EP-A2KB        TCGA-EP-A2KC        TCGA-EP-A3JL        TCGA-EP-A3RK 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-ES-A2HS        TCGA-ES-A2HT        TCGA-FV-A23B        TCGA-FV-A2QR 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-FV-A3I0        TCGA-FV-A3I1        TCGA-FV-A3R2        TCGA-FV-A3R3 
  "3P LOSS MUTATED" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-FV-A495        TCGA-FV-A496        TCGA-FV-A4ZP        TCGA-FV-A4ZQ 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U        TCGA-G3-A25V 
"3P LOSS WILD-TYPE"   "3P LOSS MUTATED" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y        TCGA-G3-A25Z 
"3P LOSS WILD-TYPE"   "3P LOSS MUTATED" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI        TCGA-G3-A3CJ 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-G3-A3CK        TCGA-G3-A5SI        TCGA-G3-A5SJ        TCGA-G3-A5SL 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-G3-A5SM        TCGA-G3-A6UC        TCGA-GJ-A6C0        TCGA-K7-A6G5 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-LG-A6GG        TCGA-MI-A75C        TCGA-MI-A75E        TCGA-MI-A75G 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-MI-A75I        TCGA-NI-A4U2        TCGA-O8-A75V 
"3P LOSS WILD-TYPE" "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-BC-A69H        TCGA-BC-A69I 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-CC-5258        TCGA-CC-5260        TCGA-CC-5261        TCGA-CC-5262 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-CC-5263        TCGA-CC-A1HT        TCGA-CC-A3M9        TCGA-CC-A3MA 
  "3P LOSS MUTATED" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE"   "3P LOSS MUTATED" 
       TCGA-CC-A3MB        TCGA-CC-A3MC        TCGA-DD-A113        TCGA-DD-A114 
  "3P LOSS MUTATED" "3P LOSS WILD-TYPE"   "3P LOSS MUTATED" "3P LOSS WILD-TYPE" 
       TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118        TCGA-DD-A119 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE"   "3P LOSS MUTATED" "3P LOSS WILD-TYPE" 
       TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C        TCGA-DD-A11D 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB        TCGA-DD-A1EC 
  "3P LOSS MUTATED" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EF        TCGA-DD-A1EG 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DD-A1EH        TCGA-DD-A1EI        TCGA-DD-A1EJ        TCGA-DD-A1EK 
"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-A4NB        TCGA-DD-A4ND        TCGA-DD-A4NF        TCGA-DD-A4NH 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DD-A4NI        TCGA-DD-A4NJ        TCGA-DD-A4NK        TCGA-DD-A4NL 
  "3P LOSS MUTATED" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DD-A4NN        TCGA-DD-A4NO        TCGA-DD-A4NP        TCGA-DD-A4NQ 
"3P LOSS WILD-TYPE"   "3P LOSS MUTATED" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DD-A4NR        TCGA-DD-A4NS        TCGA-DD-A4NV        TCGA-DD-A73A 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DD-A73B        TCGA-DD-A73C        TCGA-DD-A73D        TCGA-DD-A73E 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DD-A73F        TCGA-DD-A73G        TCGA-ED-A459        TCGA-ED-A4XI 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-ED-A5KG        TCGA-ED-A627        TCGA-ED-A66X        TCGA-ED-A66Y 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE"   "3P LOSS MUTATED" 
       TCGA-ED-A7PX        TCGA-ED-A7PY        TCGA-ED-A7PZ        TCGA-ED-A7XP 
  "3P LOSS MUTATED" "3P LOSS WILD-TYPE"   "3P LOSS MUTATED" "3P LOSS WILD-TYPE" 
       TCGA-ED-A82E        TCGA-EP-A12J        TCGA-EP-A26S        TCGA-EP-A2KA 
  "3P LOSS MUTATED" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EP-A2KB        TCGA-EP-A2KC        TCGA-EP-A3JL        TCGA-EP-A3RK 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-ES-A2HS        TCGA-ES-A2HT        TCGA-FV-A23B        TCGA-FV-A2QR 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-FV-A3I0        TCGA-FV-A3I1        TCGA-FV-A3R2        TCGA-FV-A3R3 
  "3P LOSS MUTATED" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-FV-A495        TCGA-FV-A496        TCGA-FV-A4ZP        TCGA-FV-A4ZQ 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U        TCGA-G3-A25V 
"3P LOSS WILD-TYPE"   "3P LOSS MUTATED" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y        TCGA-G3-A25Z 
"3P LOSS WILD-TYPE"   "3P LOSS MUTATED" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI        TCGA-G3-A3CJ 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-G3-A3CK        TCGA-G3-A5SI        TCGA-G3-A5SJ        TCGA-G3-A5SL 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-G3-A5SM        TCGA-G3-A6UC        TCGA-GJ-A6C0        TCGA-K7-A6G5 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-LG-A6GG        TCGA-MI-A75C        TCGA-MI-A75E        TCGA-MI-A75G 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-MI-A75I        TCGA-NI-A4U2        TCGA-O8-A75V 
"3P LOSS WILD-TYPE" "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-BC-A69H        TCGA-BC-A69I 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-CC-5258        TCGA-CC-5260        TCGA-CC-5261        TCGA-CC-5262 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-CC-5263        TCGA-CC-A1HT        TCGA-CC-A3M9        TCGA-CC-A3MA 
  "3P LOSS MUTATED" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE"   "3P LOSS MUTATED" 
       TCGA-CC-A3MB        TCGA-CC-A3MC        TCGA-DD-A113        TCGA-DD-A114 
  "3P LOSS MUTATED" "3P LOSS WILD-TYPE"   "3P LOSS MUTATED" "3P LOSS WILD-TYPE" 
       TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118        TCGA-DD-A119 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE"   "3P LOSS MUTATED" "3P LOSS WILD-TYPE" 
       TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C        TCGA-DD-A11D 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB        TCGA-DD-A1EC 
  "3P LOSS MUTATED" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EF        TCGA-DD-A1EG 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DD-A1EH        TCGA-DD-A1EI        TCGA-DD-A1EJ        TCGA-DD-A1EK 
"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-A4NB        TCGA-DD-A4ND        TCGA-DD-A4NF        TCGA-DD-A4NH 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DD-A4NI        TCGA-DD-A4NJ        TCGA-DD-A4NK        TCGA-DD-A4NL 
  "3P LOSS MUTATED" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DD-A4NN        TCGA-DD-A4NO        TCGA-DD-A4NP        TCGA-DD-A4NQ 
"3P LOSS WILD-TYPE"   "3P LOSS MUTATED" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DD-A4NR        TCGA-DD-A4NS        TCGA-DD-A4NV        TCGA-DD-A73A 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DD-A73B        TCGA-DD-A73C        TCGA-DD-A73D        TCGA-DD-A73E 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DD-A73F        TCGA-DD-A73G        TCGA-ED-A459        TCGA-ED-A4XI 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-ED-A5KG        TCGA-ED-A627        TCGA-ED-A66X        TCGA-ED-A66Y 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE"   "3P LOSS MUTATED" 
       TCGA-ED-A7PX        TCGA-ED-A7PY        TCGA-ED-A7PZ        TCGA-ED-A7XP 
  "3P LOSS MUTATED" "3P LOSS WILD-TYPE"   "3P LOSS MUTATED" "3P LOSS WILD-TYPE" 
       TCGA-ED-A82E        TCGA-EP-A12J        TCGA-EP-A26S        TCGA-EP-A2KA 
  "3P LOSS MUTATED" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EP-A2KB        TCGA-EP-A2KC        TCGA-EP-A3JL        TCGA-EP-A3RK 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-ES-A2HS        TCGA-ES-A2HT        TCGA-FV-A23B        TCGA-FV-A2QR 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-FV-A3I0        TCGA-FV-A3I1        TCGA-FV-A3R2        TCGA-FV-A3R3 
  "3P LOSS MUTATED" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-FV-A495        TCGA-FV-A496        TCGA-FV-A4ZP        TCGA-FV-A4ZQ 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U        TCGA-G3-A25V 
"3P LOSS WILD-TYPE"   "3P LOSS MUTATED" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y        TCGA-G3-A25Z 
"3P LOSS WILD-TYPE"   "3P LOSS MUTATED" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI        TCGA-G3-A3CJ 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-G3-A3CK        TCGA-G3-A5SI        TCGA-G3-A5SJ        TCGA-G3-A5SL 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-G3-A5SM        TCGA-G3-A6UC        TCGA-GJ-A6C0        TCGA-K7-A6G5 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-LG-A6GG        TCGA-MI-A75C        TCGA-MI-A75E        TCGA-MI-A75G 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-MI-A75I        TCGA-NI-A4U2        TCGA-O8-A75V 
"3P LOSS WILD-TYPE" "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        7         0          6          0          1
  3P LOSS WILD-TYPE      56       29         2         24          4          4
                   vv
clus                STAGE IV STAGE IVA STAGE IVB
  3P LOSS MUTATED          0         0         1
  3P LOSS WILD-TYPE        1         1         1
D45V3, multiclass
                   vv
clus                T1 T2 T3 T4
  3P LOSS MUTATED    2  8  8  1
  3P LOSS WILD-TYPE 59 32 32  7
D45V4, multiclass
    clus
vv   3P LOSS MUTATED 3P LOSS WILD-TYPE
  T1               2                59
  T2               8                32
  T3               8                32
  T4               1                 7
D45V5, binary
                   cls
clus                 0  1
  3P LOSS MUTATED   12  1
  3P LOSS WILD-TYPE 85  2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED     12    1
  3P LOSS WILD-TYPE   85    2
   clus
vv  3P LOSS MUTATED 3P LOSS WILD-TYPE
  0              12                85
  1               1                 2
                   vv
clus                M0 M1 MX
  3P LOSS MUTATED   16  1  2
  3P LOSS WILD-TYPE 99  2 29
D45V6, multiclass
    clus
vv   3P LOSS MUTATED 3P LOSS WILD-TYPE
  M0              16                99
  M1               1                 2
  MX               2                29
D45V7, binary
                   cls
clus                 0  1
  3P LOSS MUTATED   10  9
  3P LOSS WILD-TYPE 48 82
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED     10    9
  3P LOSS WILD-TYPE   48   82
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  FEMALE              10                48
  MALE                 9                82
                   vv
clus                 R0  R1  R2  RX
  3P LOSS MUTATED    18   0   0   1
  3P LOSS WILD-TYPE 104  11   1   9
D45V8, multiclass
    clus
vv   3P LOSS MUTATED 3P LOSS WILD-TYPE
  R0              18               104
  R1               0                11
  R2               0                 1
  RX               1                 9

Clustering(46) Variable = 3Q LOSS MUTATION ANALYSIS
D46V1, survival
                   sevent
clus2                0  1
  3Q LOSS MUTATED    8  2
  3Q LOSS WILD-TYPE 76 61
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               10               137 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
                2                61 
$`3Q LOSS MUTATED`
TCGA-BC-A112 TCGA-DD-A113 TCGA-DD-A118 TCGA-DD-A1E9 TCGA-DD-A4NA TCGA-DD-A4NI 
        5.03        79.73       113.00        90.71        33.14        18.44 
TCGA-DD-A4NO TCGA-ED-A66Y TCGA-ED-A7PZ TCGA-ED-A82E 
       61.45         0.23         0.20         0.20 

$`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-BC-A69H 
       44.42        13.84         0.26        22.36         9.50         3.95 
TCGA-BC-A69I TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 
        0.53         0.07         2.86         0.39         3.39         4.24 
TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A114 
        3.32         0.10         0.07         0.10         0.13        37.78 
TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C 
       83.57        53.33         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 
       51.29        79.40        66.31        19.79        75.65         6.71 
TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK 
       12.95        45.11        49.15         6.02        29.16        18.35 
TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A0 
       13.64        21.14        55.69         5.62        19.76        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-A4NB TCGA-DD-A4ND TCGA-DD-A4NF 
       13.78         0.36        30.61        12.85        73.38        14.07 
TCGA-DD-A4NH TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NP 
       14.24        15.06        39.78        56.25        29.56        93.67 
TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B 
       12.26         0.30        80.75        66.35        10.98         9.30 
TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G TCGA-ED-A459 
        7.56        10.98         1.45        27.72       100.96        13.41 
TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A7PX TCGA-ED-A7PY 
       12.69        15.85        13.91        13.35         0.20         0.20 
TCGA-ED-A7XP TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC 
        0.20        18.74        19.99        11.74        10.98         0.62 
TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QR 
        9.96        11.93        22.85        14.40        32.45        19.10 
TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 
        0.20         8.12         6.38         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        51.06        53.79        28.27 
TCGA-G3-A25W TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CH 
       30.74        58.49        14.86        21.53        22.13        25.64 
TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SL 
        5.92        19.53        19.23        14.70        11.97         7.99 
TCGA-G3-A5SM TCGA-G3-A6UC TCGA-GJ-A6C0 TCGA-K7-A6G5 TCGA-LG-A6GG TCGA-MI-A75C 
        4.37         7.76         1.02         4.01         0.49         9.57 
TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75I TCGA-NI-A4U2 TCGA-O8-A75V 
        5.10        14.24         8.71        58.88         4.44 

  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
             0.20              0.03 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
           113.00            107.11 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
            25.79             13.91 
[1] "0.2 - 113.0 (25.8)" "0.0 - 107.1 (13.9)"
       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-BC-A69H        TCGA-BC-A69I 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-CC-5258        TCGA-CC-5260        TCGA-CC-5261        TCGA-CC-5262 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-CC-5263        TCGA-CC-A1HT        TCGA-CC-A3M9        TCGA-CC-A3MA 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-CC-A3MB        TCGA-CC-A3MC        TCGA-DD-A113        TCGA-DD-A114 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE"   "3Q LOSS MUTATED" "3Q LOSS WILD-TYPE" 
       TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118        TCGA-DD-A119 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE"   "3Q LOSS MUTATED" "3Q LOSS WILD-TYPE" 
       TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C        TCGA-DD-A11D 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB        TCGA-DD-A1EC 
  "3Q LOSS MUTATED" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EF        TCGA-DD-A1EG 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-DD-A1EH        TCGA-DD-A1EI        TCGA-DD-A1EJ        TCGA-DD-A1EK 
"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-A4NB        TCGA-DD-A4ND        TCGA-DD-A4NF        TCGA-DD-A4NH 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-DD-A4NI        TCGA-DD-A4NJ        TCGA-DD-A4NK        TCGA-DD-A4NL 
  "3Q LOSS MUTATED" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-DD-A4NN        TCGA-DD-A4NO        TCGA-DD-A4NP        TCGA-DD-A4NQ 
"3Q LOSS WILD-TYPE"   "3Q LOSS MUTATED" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-DD-A4NR        TCGA-DD-A4NS        TCGA-DD-A4NV        TCGA-DD-A73A 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-DD-A73B        TCGA-DD-A73C        TCGA-DD-A73D        TCGA-DD-A73E 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-DD-A73F        TCGA-DD-A73G        TCGA-ED-A459        TCGA-ED-A4XI 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-ED-A5KG        TCGA-ED-A627        TCGA-ED-A66X        TCGA-ED-A66Y 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE"   "3Q LOSS MUTATED" 
       TCGA-ED-A7PX        TCGA-ED-A7PY        TCGA-ED-A7PZ        TCGA-ED-A7XP 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE"   "3Q LOSS MUTATED" "3Q LOSS WILD-TYPE" 
       TCGA-ED-A82E        TCGA-EP-A12J        TCGA-EP-A26S        TCGA-EP-A2KA 
  "3Q LOSS MUTATED" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-EP-A2KB        TCGA-EP-A2KC        TCGA-EP-A3JL        TCGA-EP-A3RK 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-ES-A2HS        TCGA-ES-A2HT        TCGA-FV-A23B        TCGA-FV-A2QR 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-FV-A3I0        TCGA-FV-A3I1        TCGA-FV-A3R2        TCGA-FV-A3R3 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-FV-A495        TCGA-FV-A496        TCGA-FV-A4ZP        TCGA-FV-A4ZQ 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U        TCGA-G3-A25V 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y        TCGA-G3-A25Z 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI        TCGA-G3-A3CJ 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-G3-A3CK        TCGA-G3-A5SI        TCGA-G3-A5SJ        TCGA-G3-A5SL 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-G3-A5SM        TCGA-G3-A6UC        TCGA-GJ-A6C0        TCGA-K7-A6G5 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-LG-A6GG        TCGA-MI-A75C        TCGA-MI-A75E        TCGA-MI-A75G 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-MI-A75I        TCGA-NI-A4U2        TCGA-O8-A75V 
"3Q LOSS WILD-TYPE" "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-BC-A69H        TCGA-BC-A69I 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-CC-5258        TCGA-CC-5260        TCGA-CC-5261        TCGA-CC-5262 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-CC-5263        TCGA-CC-A1HT        TCGA-CC-A3M9        TCGA-CC-A3MA 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-CC-A3MB        TCGA-CC-A3MC        TCGA-DD-A113        TCGA-DD-A114 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE"   "3Q LOSS MUTATED" "3Q LOSS WILD-TYPE" 
       TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118        TCGA-DD-A119 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE"   "3Q LOSS MUTATED" "3Q LOSS WILD-TYPE" 
       TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C        TCGA-DD-A11D 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB        TCGA-DD-A1EC 
  "3Q LOSS MUTATED" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EF        TCGA-DD-A1EG 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-DD-A1EH        TCGA-DD-A1EI        TCGA-DD-A1EJ        TCGA-DD-A1EK 
"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-A4NB        TCGA-DD-A4ND        TCGA-DD-A4NF        TCGA-DD-A4NH 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-DD-A4NI        TCGA-DD-A4NJ        TCGA-DD-A4NK        TCGA-DD-A4NL 
  "3Q LOSS MUTATED" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-DD-A4NN        TCGA-DD-A4NO        TCGA-DD-A4NP        TCGA-DD-A4NQ 
"3Q LOSS WILD-TYPE"   "3Q LOSS MUTATED" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-DD-A4NR        TCGA-DD-A4NS        TCGA-DD-A4NV        TCGA-DD-A73A 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-DD-A73B        TCGA-DD-A73C        TCGA-DD-A73D        TCGA-DD-A73E 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-DD-A73F        TCGA-DD-A73G        TCGA-ED-A459        TCGA-ED-A4XI 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-ED-A5KG        TCGA-ED-A627        TCGA-ED-A66X        TCGA-ED-A66Y 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE"   "3Q LOSS MUTATED" 
       TCGA-ED-A7PX        TCGA-ED-A7PY        TCGA-ED-A7PZ        TCGA-ED-A7XP 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE"   "3Q LOSS MUTATED" "3Q LOSS WILD-TYPE" 
       TCGA-ED-A82E        TCGA-EP-A12J        TCGA-EP-A26S        TCGA-EP-A2KA 
  "3Q LOSS MUTATED" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-EP-A2KB        TCGA-EP-A2KC        TCGA-EP-A3JL        TCGA-EP-A3RK 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-ES-A2HS        TCGA-ES-A2HT        TCGA-FV-A23B        TCGA-FV-A2QR 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-FV-A3I0        TCGA-FV-A3I1        TCGA-FV-A3R2        TCGA-FV-A3R3 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-FV-A495        TCGA-FV-A496        TCGA-FV-A4ZP        TCGA-FV-A4ZQ 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U        TCGA-G3-A25V 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y        TCGA-G3-A25Z 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI        TCGA-G3-A3CJ 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-G3-A3CK        TCGA-G3-A5SI        TCGA-G3-A5SJ        TCGA-G3-A5SL 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-G3-A5SM        TCGA-G3-A6UC        TCGA-GJ-A6C0        TCGA-K7-A6G5 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-LG-A6GG        TCGA-MI-A75C        TCGA-MI-A75E        TCGA-MI-A75G 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-MI-A75I        TCGA-NI-A4U2        TCGA-O8-A75V 
"3Q LOSS WILD-TYPE" "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-BC-A69H        TCGA-BC-A69I 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-CC-5258        TCGA-CC-5260        TCGA-CC-5261        TCGA-CC-5262 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-CC-5263        TCGA-CC-A1HT        TCGA-CC-A3M9        TCGA-CC-A3MA 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-CC-A3MB        TCGA-CC-A3MC        TCGA-DD-A113        TCGA-DD-A114 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE"   "3Q LOSS MUTATED" "3Q LOSS WILD-TYPE" 
       TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118        TCGA-DD-A119 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE"   "3Q LOSS MUTATED" "3Q LOSS WILD-TYPE" 
       TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C        TCGA-DD-A11D 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB        TCGA-DD-A1EC 
  "3Q LOSS MUTATED" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EF        TCGA-DD-A1EG 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-DD-A1EH        TCGA-DD-A1EI        TCGA-DD-A1EJ        TCGA-DD-A1EK 
"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-A4NB        TCGA-DD-A4ND        TCGA-DD-A4NF        TCGA-DD-A4NH 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-DD-A4NI        TCGA-DD-A4NJ        TCGA-DD-A4NK        TCGA-DD-A4NL 
  "3Q LOSS MUTATED" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-DD-A4NN        TCGA-DD-A4NO        TCGA-DD-A4NP        TCGA-DD-A4NQ 
"3Q LOSS WILD-TYPE"   "3Q LOSS MUTATED" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-DD-A4NR        TCGA-DD-A4NS        TCGA-DD-A4NV        TCGA-DD-A73A 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-DD-A73B        TCGA-DD-A73C        TCGA-DD-A73D        TCGA-DD-A73E 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-DD-A73F        TCGA-DD-A73G        TCGA-ED-A459        TCGA-ED-A4XI 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-ED-A5KG        TCGA-ED-A627        TCGA-ED-A66X        TCGA-ED-A66Y 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE"   "3Q LOSS MUTATED" 
       TCGA-ED-A7PX        TCGA-ED-A7PY        TCGA-ED-A7PZ        TCGA-ED-A7XP 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE"   "3Q LOSS MUTATED" "3Q LOSS WILD-TYPE" 
       TCGA-ED-A82E        TCGA-EP-A12J        TCGA-EP-A26S        TCGA-EP-A2KA 
  "3Q LOSS MUTATED" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-EP-A2KB        TCGA-EP-A2KC        TCGA-EP-A3JL        TCGA-EP-A3RK 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-ES-A2HS        TCGA-ES-A2HT        TCGA-FV-A23B        TCGA-FV-A2QR 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-FV-A3I0        TCGA-FV-A3I1        TCGA-FV-A3R2        TCGA-FV-A3R3 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-FV-A495        TCGA-FV-A496        TCGA-FV-A4ZP        TCGA-FV-A4ZQ 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U        TCGA-G3-A25V 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y        TCGA-G3-A25Z 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI        TCGA-G3-A3CJ 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-G3-A3CK        TCGA-G3-A5SI        TCGA-G3-A5SJ        TCGA-G3-A5SL 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-G3-A5SM        TCGA-G3-A6UC        TCGA-GJ-A6C0        TCGA-K7-A6G5 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-LG-A6GG        TCGA-MI-A75C        TCGA-MI-A75E        TCGA-MI-A75G 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-MI-A75I        TCGA-NI-A4U2        TCGA-O8-A75V 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
[1] "hr=" "4.2"
D46V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  3Q LOSS MUTATED         2        4         0          2          0          1
  3Q LOSS WILD-TYPE      56       32         2         28          4          4
                   vv
clus                STAGE IV STAGE IVA STAGE IVB
  3Q LOSS MUTATED          0         0         0
  3Q LOSS WILD-TYPE        1         1         2
D46V3, multiclass
                   vv
clus                T1 T2 T3 T4
  3Q LOSS MUTATED    2  5  3  0
  3Q LOSS WILD-TYPE 59 35 37  8
D46V4, multiclass
    clus
vv   3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  T1               2                59
  T2               5                35
  T3               3                37
  T4               0                 8
D46V5, binary
                   cls
clus                 0  1
  3Q LOSS MUTATED    6  1
  3Q LOSS WILD-TYPE 91  2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED      6    1
  3Q LOSS WILD-TYPE   91    2
   clus
vv  3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  0               6                91
  1               1                 2
                   vv
clus                 M0  M1  MX
  3Q LOSS MUTATED     9   0   1
  3Q LOSS WILD-TYPE 106   3  30
D46V6, multiclass
    clus
vv   3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  M0               9               106
  M1               0                 3
  MX               1                30
D46V7, binary
                   cls
clus                 0  1
  3Q LOSS MUTATED    5  5
  3Q LOSS WILD-TYPE 53 86
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED      5    5
  3Q LOSS WILD-TYPE   53   86
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  FEMALE               5                53
  MALE                 5                86
                   vv
clus                 R0  R1  R2  RX
  3Q LOSS MUTATED    10   0   0   0
  3Q LOSS WILD-TYPE 112  11   1  10
D46V8, multiclass
    clus
vv   3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  R0              10               112
  R1               0                11
  R2               0                 1
  RX               0                10

Clustering(47) Variable = 4P LOSS MUTATION ANALYSIS
D47V1, survival
                   sevent
clus2                0  1
  4P LOSS MUTATED   16 13
  4P LOSS WILD-TYPE 68 50
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               29               118 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               13                50 
$`4P LOSS MUTATED`
TCGA-BC-A10Y TCGA-BC-A112 TCGA-BC-A217 TCGA-BC-A5W4 TCGA-BC-A69H TCGA-CC-A3MC 
       23.34         5.03        13.84         9.50         3.95         0.13 
TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A119 TCGA-DD-A1EJ TCGA-DD-A1EL TCGA-DD-A39X 
       79.73        37.78         7.33        29.16        13.64        55.69 
TCGA-DD-A39Y TCGA-DD-A3A9 TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NN TCGA-ED-A459 
        5.62        30.61        18.44        15.06        29.56        13.41 
TCGA-ED-A66X TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-EP-A2KB TCGA-EP-A2KC TCGA-FV-A496 
       13.35         0.20         0.20        10.98         0.62         0.33 
TCGA-FV-A4ZP TCGA-G3-A25S TCGA-G3-A25U TCGA-G3-A25X TCGA-MI-A75G 
       60.36         1.22        53.79        58.49        14.24 

$`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-BC-A3KG TCGA-BC-A69I TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5261 
        0.26        22.36         0.53         0.07         2.86         0.39 
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-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C 
       83.57        53.33       113.00         2.60         0.46        21.76 
TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED 
       51.29        90.71        79.40        66.31        19.79        75.65 
TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EK 
        6.71        12.95        45.11        49.15         6.02        18.35 
TCGA-DD-A39V TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 
       21.14        19.76        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-A4NB TCGA-DD-A4ND TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NK TCGA-DD-A4NL 
       12.85        73.38        14.07        14.24        39.78        56.25 
TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV 
       61.45        93.67        12.26         0.30        80.75        66.35 
TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F 
       10.98         9.30         7.56        10.98         1.45        27.72 
TCGA-DD-A73G TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66Y TCGA-ED-A7PX 
      100.96        12.69        15.85        13.91         0.23         0.20 
TCGA-ED-A7XP TCGA-ED-A82E TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A3JL 
        0.20         0.20        18.74        19.99        11.74         9.96 
TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-A3I0 
       11.93        22.85        14.40        32.45        19.10         0.20 
TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A4ZQ TCGA-G3-A25T 
        8.12         6.38         0.13         0.03         0.39        51.06 
TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CH 
       28.27        30.74        14.86        21.53        22.13        25.64 
TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SL 
        5.92        19.53        19.23        14.70        11.97         7.99 
TCGA-G3-A5SM TCGA-G3-A6UC TCGA-GJ-A6C0 TCGA-K7-A6G5 TCGA-LG-A6GG TCGA-MI-A75C 
        4.37         7.76         1.02         4.01         0.49         9.57 
TCGA-MI-A75E TCGA-MI-A75I TCGA-NI-A4U2 TCGA-O8-A75V 
        5.10         8.71        58.88         4.44 

  4P LOSS MUTATED 4P LOSS WILD-TYPE 
             0.13              0.03 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
            79.73            113.00 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
            13.64             14.32 
[1] "0.1 - 79.7 (13.6)"  "0.0 - 113.0 (14.3)"
       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-BC-A69H        TCGA-BC-A69I 
"4P LOSS WILD-TYPE"   "4P LOSS MUTATED"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" 
       TCGA-CC-5258        TCGA-CC-5260        TCGA-CC-5261        TCGA-CC-5262 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-CC-5263        TCGA-CC-A1HT        TCGA-CC-A3M9        TCGA-CC-A3MA 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-CC-A3MB        TCGA-CC-A3MC        TCGA-DD-A113        TCGA-DD-A114 
"4P LOSS WILD-TYPE"   "4P LOSS MUTATED"   "4P LOSS MUTATED"   "4P LOSS MUTATED" 
       TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118        TCGA-DD-A119 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" 
       TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C        TCGA-DD-A11D 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB        TCGA-DD-A1EC 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EF        TCGA-DD-A1EG 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-DD-A1EH        TCGA-DD-A1EI        TCGA-DD-A1EJ        TCGA-DD-A1EK 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" 
       TCGA-DD-A1EL        TCGA-DD-A39V        TCGA-DD-A39X        TCGA-DD-A39Y 
  "4P LOSS MUTATED" "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-A4NB        TCGA-DD-A4ND        TCGA-DD-A4NF        TCGA-DD-A4NH 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-DD-A4NI        TCGA-DD-A4NJ        TCGA-DD-A4NK        TCGA-DD-A4NL 
  "4P LOSS MUTATED"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-DD-A4NN        TCGA-DD-A4NO        TCGA-DD-A4NP        TCGA-DD-A4NQ 
  "4P LOSS MUTATED" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-DD-A4NR        TCGA-DD-A4NS        TCGA-DD-A4NV        TCGA-DD-A73A 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-DD-A73B        TCGA-DD-A73C        TCGA-DD-A73D        TCGA-DD-A73E 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-DD-A73F        TCGA-DD-A73G        TCGA-ED-A459        TCGA-ED-A4XI 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" 
       TCGA-ED-A5KG        TCGA-ED-A627        TCGA-ED-A66X        TCGA-ED-A66Y 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" 
       TCGA-ED-A7PX        TCGA-ED-A7PY        TCGA-ED-A7PZ        TCGA-ED-A7XP 
"4P LOSS WILD-TYPE"   "4P LOSS MUTATED"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" 
       TCGA-ED-A82E        TCGA-EP-A12J        TCGA-EP-A26S        TCGA-EP-A2KA 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-EP-A2KB        TCGA-EP-A2KC        TCGA-EP-A3JL        TCGA-EP-A3RK 
  "4P LOSS MUTATED"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-ES-A2HS        TCGA-ES-A2HT        TCGA-FV-A23B        TCGA-FV-A2QR 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-FV-A3I0        TCGA-FV-A3I1        TCGA-FV-A3R2        TCGA-FV-A3R3 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-FV-A495        TCGA-FV-A496        TCGA-FV-A4ZP        TCGA-FV-A4ZQ 
"4P LOSS WILD-TYPE"   "4P LOSS MUTATED"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" 
       TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U        TCGA-G3-A25V 
  "4P LOSS MUTATED" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" 
       TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y        TCGA-G3-A25Z 
"4P LOSS WILD-TYPE"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI        TCGA-G3-A3CJ 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-G3-A3CK        TCGA-G3-A5SI        TCGA-G3-A5SJ        TCGA-G3-A5SL 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-G3-A5SM        TCGA-G3-A6UC        TCGA-GJ-A6C0        TCGA-K7-A6G5 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-LG-A6GG        TCGA-MI-A75C        TCGA-MI-A75E        TCGA-MI-A75G 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" 
       TCGA-MI-A75I        TCGA-NI-A4U2        TCGA-O8-A75V 
"4P LOSS WILD-TYPE" "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-BC-A69H        TCGA-BC-A69I 
"4P LOSS WILD-TYPE"   "4P LOSS MUTATED"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" 
       TCGA-CC-5258        TCGA-CC-5260        TCGA-CC-5261        TCGA-CC-5262 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-CC-5263        TCGA-CC-A1HT        TCGA-CC-A3M9        TCGA-CC-A3MA 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-CC-A3MB        TCGA-CC-A3MC        TCGA-DD-A113        TCGA-DD-A114 
"4P LOSS WILD-TYPE"   "4P LOSS MUTATED"   "4P LOSS MUTATED"   "4P LOSS MUTATED" 
       TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118        TCGA-DD-A119 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" 
       TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C        TCGA-DD-A11D 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB        TCGA-DD-A1EC 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EF        TCGA-DD-A1EG 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-DD-A1EH        TCGA-DD-A1EI        TCGA-DD-A1EJ        TCGA-DD-A1EK 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" 
       TCGA-DD-A1EL        TCGA-DD-A39V        TCGA-DD-A39X        TCGA-DD-A39Y 
  "4P LOSS MUTATED" "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-A4NB        TCGA-DD-A4ND        TCGA-DD-A4NF        TCGA-DD-A4NH 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-DD-A4NI        TCGA-DD-A4NJ        TCGA-DD-A4NK        TCGA-DD-A4NL 
  "4P LOSS MUTATED"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-DD-A4NN        TCGA-DD-A4NO        TCGA-DD-A4NP        TCGA-DD-A4NQ 
  "4P LOSS MUTATED" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-DD-A4NR        TCGA-DD-A4NS        TCGA-DD-A4NV        TCGA-DD-A73A 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-DD-A73B        TCGA-DD-A73C        TCGA-DD-A73D        TCGA-DD-A73E 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-DD-A73F        TCGA-DD-A73G        TCGA-ED-A459        TCGA-ED-A4XI 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" 
       TCGA-ED-A5KG        TCGA-ED-A627        TCGA-ED-A66X        TCGA-ED-A66Y 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" 
       TCGA-ED-A7PX        TCGA-ED-A7PY        TCGA-ED-A7PZ        TCGA-ED-A7XP 
"4P LOSS WILD-TYPE"   "4P LOSS MUTATED"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" 
       TCGA-ED-A82E        TCGA-EP-A12J        TCGA-EP-A26S        TCGA-EP-A2KA 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-EP-A2KB        TCGA-EP-A2KC        TCGA-EP-A3JL        TCGA-EP-A3RK 
  "4P LOSS MUTATED"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-ES-A2HS        TCGA-ES-A2HT        TCGA-FV-A23B        TCGA-FV-A2QR 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-FV-A3I0        TCGA-FV-A3I1        TCGA-FV-A3R2        TCGA-FV-A3R3 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-FV-A495        TCGA-FV-A496        TCGA-FV-A4ZP        TCGA-FV-A4ZQ 
"4P LOSS WILD-TYPE"   "4P LOSS MUTATED"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" 
       TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U        TCGA-G3-A25V 
  "4P LOSS MUTATED" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" 
       TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y        TCGA-G3-A25Z 
"4P LOSS WILD-TYPE"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI        TCGA-G3-A3CJ 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-G3-A3CK        TCGA-G3-A5SI        TCGA-G3-A5SJ        TCGA-G3-A5SL 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-G3-A5SM        TCGA-G3-A6UC        TCGA-GJ-A6C0        TCGA-K7-A6G5 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-LG-A6GG        TCGA-MI-A75C        TCGA-MI-A75E        TCGA-MI-A75G 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" 
       TCGA-MI-A75I        TCGA-NI-A4U2        TCGA-O8-A75V 
"4P LOSS WILD-TYPE" "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-BC-A69H        TCGA-BC-A69I 
"4P LOSS WILD-TYPE"   "4P LOSS MUTATED"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" 
       TCGA-CC-5258        TCGA-CC-5260        TCGA-CC-5261        TCGA-CC-5262 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-CC-5263        TCGA-CC-A1HT        TCGA-CC-A3M9        TCGA-CC-A3MA 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-CC-A3MB        TCGA-CC-A3MC        TCGA-DD-A113        TCGA-DD-A114 
"4P LOSS WILD-TYPE"   "4P LOSS MUTATED"   "4P LOSS MUTATED"   "4P LOSS MUTATED" 
       TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118        TCGA-DD-A119 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" 
       TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C        TCGA-DD-A11D 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB        TCGA-DD-A1EC 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EF        TCGA-DD-A1EG 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-DD-A1EH        TCGA-DD-A1EI        TCGA-DD-A1EJ        TCGA-DD-A1EK 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" 
       TCGA-DD-A1EL        TCGA-DD-A39V        TCGA-DD-A39X        TCGA-DD-A39Y 
  "4P LOSS MUTATED" "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-A4NB        TCGA-DD-A4ND        TCGA-DD-A4NF        TCGA-DD-A4NH 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-DD-A4NI        TCGA-DD-A4NJ        TCGA-DD-A4NK        TCGA-DD-A4NL 
  "4P LOSS MUTATED"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-DD-A4NN        TCGA-DD-A4NO        TCGA-DD-A4NP        TCGA-DD-A4NQ 
  "4P LOSS MUTATED" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-DD-A4NR        TCGA-DD-A4NS        TCGA-DD-A4NV        TCGA-DD-A73A 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-DD-A73B        TCGA-DD-A73C        TCGA-DD-A73D        TCGA-DD-A73E 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-DD-A73F        TCGA-DD-A73G        TCGA-ED-A459        TCGA-ED-A4XI 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" 
       TCGA-ED-A5KG        TCGA-ED-A627        TCGA-ED-A66X        TCGA-ED-A66Y 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" 
       TCGA-ED-A7PX        TCGA-ED-A7PY        TCGA-ED-A7PZ        TCGA-ED-A7XP 
"4P LOSS WILD-TYPE"   "4P LOSS MUTATED"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" 
       TCGA-ED-A82E        TCGA-EP-A12J        TCGA-EP-A26S        TCGA-EP-A2KA 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-EP-A2KB        TCGA-EP-A2KC        TCGA-EP-A3JL        TCGA-EP-A3RK 
  "4P LOSS MUTATED"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-ES-A2HS        TCGA-ES-A2HT        TCGA-FV-A23B        TCGA-FV-A2QR 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-FV-A3I0        TCGA-FV-A3I1        TCGA-FV-A3R2        TCGA-FV-A3R3 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-FV-A495        TCGA-FV-A496        TCGA-FV-A4ZP        TCGA-FV-A4ZQ 
"4P LOSS WILD-TYPE"   "4P LOSS MUTATED"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" 
       TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U        TCGA-G3-A25V 
  "4P LOSS MUTATED" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" 
       TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y        TCGA-G3-A25Z 
"4P LOSS WILD-TYPE"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI        TCGA-G3-A3CJ 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-G3-A3CK        TCGA-G3-A5SI        TCGA-G3-A5SJ        TCGA-G3-A5SL 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-G3-A5SM        TCGA-G3-A6UC        TCGA-GJ-A6C0        TCGA-K7-A6G5 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-LG-A6GG        TCGA-MI-A75C        TCGA-MI-A75E        TCGA-MI-A75G 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" 
       TCGA-MI-A75I        TCGA-NI-A4U2        TCGA-O8-A75V 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
[1] "hr=" "1.3"
D47V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  4P LOSS MUTATED         8       12         0          5          0          1
  4P LOSS WILD-TYPE      50       24         2         25          4          4
                   vv
clus                STAGE IV STAGE IVA STAGE IVB
  4P LOSS MUTATED          1         1         1
  4P LOSS WILD-TYPE        0         0         1
D47V3, multiclass
                   vv
clus                T1 T2 T3 T4
  4P LOSS MUTATED   10 12  7  2
  4P LOSS WILD-TYPE 51 28 33  6
D47V4, multiclass
    clus
vv   4P LOSS MUTATED 4P LOSS WILD-TYPE
  T1              10                51
  T2              12                28
  T3               7                33
  T4               2                 6
D47V5, binary
                   cls
clus                 0  1
  4P LOSS MUTATED   14  2
  4P LOSS WILD-TYPE 83  1
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED     14    2
  4P LOSS WILD-TYPE   83    1
   clus
vv  4P LOSS MUTATED 4P LOSS WILD-TYPE
  0              14                83
  1               2                 1
                   vv
clus                M0 M1 MX
  4P LOSS MUTATED   24  2  5
  4P LOSS WILD-TYPE 91  1 26
D47V6, multiclass
    clus
vv   4P LOSS MUTATED 4P LOSS WILD-TYPE
  M0              24                91
  M1               2                 1
  MX               5                26
D47V7, binary
                   cls
clus                 0  1
  4P LOSS MUTATED   11 20
  4P LOSS WILD-TYPE 47 71
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED     11   20
  4P LOSS WILD-TYPE   47   71
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  FEMALE              11                47
  MALE                20                71
                   vv
clus                R0 R1 R2 RX
  4P LOSS MUTATED   26  3  1  1
  4P LOSS WILD-TYPE 96  8  0  9
D47V8, multiclass
    clus
vv   4P LOSS MUTATED 4P LOSS WILD-TYPE
  R0              26                96
  R1               3                 8
  R2               1                 0
  RX               1                 9

Clustering(48) Variable = 4Q LOSS MUTATION ANALYSIS
D48V1, survival
                   sevent
clus2                0  1
  4Q LOSS MUTATED   27 19
  4Q LOSS WILD-TYPE 57 44
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               46               101 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               19                44 
$`4Q LOSS MUTATED`
TCGA-BC-A10T TCGA-BC-A10Y TCGA-BC-A112 TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A5W4 
       27.52        23.34         5.03        13.84         0.26         9.50 
TCGA-BC-A69H TCGA-CC-A3M9 TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A113 TCGA-DD-A114 
        3.95         0.10         0.10         0.13        79.73        37.78 
TCGA-DD-A116 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI 
       53.33         7.33         2.60        45.11        49.15         6.02 
TCGA-DD-A1EJ TCGA-DD-A1EL TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A3A9 TCGA-DD-A4NH 
       29.16        13.64        55.69         5.62        30.61        14.24 
TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A73B TCGA-ED-A459 
       18.44        15.06        29.56        61.45         9.30        13.41 
TCGA-ED-A66X TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XP TCGA-EP-A2KB TCGA-EP-A2KC 
       13.35         0.20         0.20         0.20        10.98         0.62 
TCGA-FV-A3I1 TCGA-FV-A4ZP TCGA-G3-A25S TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A25Z 
        8.12        60.36         1.22        58.49        14.86        21.53 
TCGA-G3-A5SI TCGA-G3-A5SM TCGA-LG-A6GG TCGA-MI-A75G 
       14.70         4.37         0.49        14.24 

$`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-A3KG 
        2.99        25.32         1.12        69.57        44.42        22.36 
TCGA-BC-A69I TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 
        0.53         0.07         2.86         0.39         3.39         4.24 
TCGA-CC-A1HT TCGA-CC-A3MA TCGA-DD-A115 TCGA-DD-A118 TCGA-DD-A11B TCGA-DD-A11C 
        3.32         0.07        83.57       113.00         0.46        21.76 
TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED 
       51.29        90.71        79.40        66.31        19.79        75.65 
TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EK TCGA-DD-A39V TCGA-DD-A39Z TCGA-DD-A3A0 
        6.71        12.95        18.35        21.14        19.76        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-A4NB TCGA-DD-A4ND TCGA-DD-A4NF 
       13.78         0.36        33.14        12.85        73.38        14.07 
TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS 
       39.78        56.25        93.67        12.26         0.30        80.75 
TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F 
       66.35        10.98         7.56        10.98         1.45        27.72 
TCGA-DD-A73G TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66Y TCGA-ED-A7PX 
      100.96        12.69        15.85        13.91         0.23         0.20 
TCGA-ED-A82E TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A3JL TCGA-EP-A3RK 
        0.20        18.74        19.99        11.74         9.96        11.93 
TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3R2 
       22.85        14.40        32.45        19.10         0.20         6.38 
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        51.06        53.79 
TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A3CG TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ 
       28.27        30.74        22.13        25.64         5.92        19.53 
TCGA-G3-A3CK TCGA-G3-A5SJ TCGA-G3-A5SL TCGA-G3-A6UC TCGA-GJ-A6C0 TCGA-K7-A6G5 
       19.23        11.97         7.99         7.76         1.02         4.01 
TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75I TCGA-NI-A4U2 TCGA-O8-A75V 
        9.57         5.10         8.71        58.88         4.44 

  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
             0.10              0.03 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
            79.73            113.00 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
           13.525            15.850 
[1] "0.1 - 79.7 (13.5)"  "0.0 - 113.0 (15.8)"
       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 MUTATED" 
       TCGA-BC-A3KG        TCGA-BC-A5W4        TCGA-BC-A69H        TCGA-BC-A69I 
"4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" 
       TCGA-CC-5258        TCGA-CC-5260        TCGA-CC-5261        TCGA-CC-5262 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-CC-5263        TCGA-CC-A1HT        TCGA-CC-A3M9        TCGA-CC-A3MA 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" 
       TCGA-CC-A3MB        TCGA-CC-A3MC        TCGA-DD-A113        TCGA-DD-A114 
  "4Q LOSS MUTATED"   "4Q LOSS MUTATED"   "4Q LOSS MUTATED"   "4Q LOSS MUTATED" 
       TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118        TCGA-DD-A119 
"4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" 
       TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C        TCGA-DD-A11D 
  "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB        TCGA-DD-A1EC 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EF        TCGA-DD-A1EG 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" 
       TCGA-DD-A1EH        TCGA-DD-A1EI        TCGA-DD-A1EJ        TCGA-DD-A1EK 
  "4Q LOSS MUTATED"   "4Q LOSS MUTATED"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" 
       TCGA-DD-A1EL        TCGA-DD-A39V        TCGA-DD-A39X        TCGA-DD-A39Y 
  "4Q LOSS MUTATED" "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-A4NB        TCGA-DD-A4ND        TCGA-DD-A4NF        TCGA-DD-A4NH 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" 
       TCGA-DD-A4NI        TCGA-DD-A4NJ        TCGA-DD-A4NK        TCGA-DD-A4NL 
  "4Q LOSS MUTATED"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-DD-A4NN        TCGA-DD-A4NO        TCGA-DD-A4NP        TCGA-DD-A4NQ 
  "4Q LOSS MUTATED"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-DD-A4NR        TCGA-DD-A4NS        TCGA-DD-A4NV        TCGA-DD-A73A 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-DD-A73B        TCGA-DD-A73C        TCGA-DD-A73D        TCGA-DD-A73E 
  "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-DD-A73F        TCGA-DD-A73G        TCGA-ED-A459        TCGA-ED-A4XI 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" 
       TCGA-ED-A5KG        TCGA-ED-A627        TCGA-ED-A66X        TCGA-ED-A66Y 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" 
       TCGA-ED-A7PX        TCGA-ED-A7PY        TCGA-ED-A7PZ        TCGA-ED-A7XP 
"4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED"   "4Q LOSS MUTATED"   "4Q LOSS MUTATED" 
       TCGA-ED-A82E        TCGA-EP-A12J        TCGA-EP-A26S        TCGA-EP-A2KA 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-EP-A2KB        TCGA-EP-A2KC        TCGA-EP-A3JL        TCGA-EP-A3RK 
  "4Q LOSS MUTATED"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-ES-A2HS        TCGA-ES-A2HT        TCGA-FV-A23B        TCGA-FV-A2QR 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-FV-A3I0        TCGA-FV-A3I1        TCGA-FV-A3R2        TCGA-FV-A3R3 
"4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-FV-A495        TCGA-FV-A496        TCGA-FV-A4ZP        TCGA-FV-A4ZQ 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" 
       TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U        TCGA-G3-A25V 
  "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y        TCGA-G3-A25Z 
"4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED"   "4Q LOSS MUTATED"   "4Q LOSS MUTATED" 
       TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI        TCGA-G3-A3CJ 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-G3-A3CK        TCGA-G3-A5SI        TCGA-G3-A5SJ        TCGA-G3-A5SL 
"4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-G3-A5SM        TCGA-G3-A6UC        TCGA-GJ-A6C0        TCGA-K7-A6G5 
  "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-LG-A6GG        TCGA-MI-A75C        TCGA-MI-A75E        TCGA-MI-A75G 
  "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" 
       TCGA-MI-A75I        TCGA-NI-A4U2        TCGA-O8-A75V 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
  "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED"   "4Q LOSS MUTATED" 
       TCGA-BC-A3KG        TCGA-BC-A5W4        TCGA-BC-A69H        TCGA-BC-A69I 
"4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" 
       TCGA-CC-5258        TCGA-CC-5260        TCGA-CC-5261        TCGA-CC-5262 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-CC-5263        TCGA-CC-A1HT        TCGA-CC-A3M9        TCGA-CC-A3MA 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" 
       TCGA-CC-A3MB        TCGA-CC-A3MC        TCGA-DD-A113        TCGA-DD-A114 
  "4Q LOSS MUTATED"   "4Q LOSS MUTATED"   "4Q LOSS MUTATED"   "4Q LOSS MUTATED" 
       TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118        TCGA-DD-A119 
"4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" 
       TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C        TCGA-DD-A11D 
  "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB        TCGA-DD-A1EC 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EF        TCGA-DD-A1EG 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" 
       TCGA-DD-A1EH        TCGA-DD-A1EI        TCGA-DD-A1EJ        TCGA-DD-A1EK 
  "4Q LOSS MUTATED"   "4Q LOSS MUTATED"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" 
       TCGA-DD-A1EL        TCGA-DD-A39V        TCGA-DD-A39X        TCGA-DD-A39Y 
  "4Q LOSS MUTATED" "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-A4NB        TCGA-DD-A4ND        TCGA-DD-A4NF        TCGA-DD-A4NH 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" 
       TCGA-DD-A4NI        TCGA-DD-A4NJ        TCGA-DD-A4NK        TCGA-DD-A4NL 
  "4Q LOSS MUTATED"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-DD-A4NN        TCGA-DD-A4NO        TCGA-DD-A4NP        TCGA-DD-A4NQ 
  "4Q LOSS MUTATED"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-DD-A4NR        TCGA-DD-A4NS        TCGA-DD-A4NV        TCGA-DD-A73A 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-DD-A73B        TCGA-DD-A73C        TCGA-DD-A73D        TCGA-DD-A73E 
  "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-DD-A73F        TCGA-DD-A73G        TCGA-ED-A459        TCGA-ED-A4XI 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" 
       TCGA-ED-A5KG        TCGA-ED-A627        TCGA-ED-A66X        TCGA-ED-A66Y 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" 
       TCGA-ED-A7PX        TCGA-ED-A7PY        TCGA-ED-A7PZ        TCGA-ED-A7XP 
"4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED"   "4Q LOSS MUTATED"   "4Q LOSS MUTATED" 
       TCGA-ED-A82E        TCGA-EP-A12J        TCGA-EP-A26S        TCGA-EP-A2KA 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-EP-A2KB        TCGA-EP-A2KC        TCGA-EP-A3JL        TCGA-EP-A3RK 
  "4Q LOSS MUTATED"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-ES-A2HS        TCGA-ES-A2HT        TCGA-FV-A23B        TCGA-FV-A2QR 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-FV-A3I0        TCGA-FV-A3I1        TCGA-FV-A3R2        TCGA-FV-A3R3 
"4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-FV-A495        TCGA-FV-A496        TCGA-FV-A4ZP        TCGA-FV-A4ZQ 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" 
       TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U        TCGA-G3-A25V 
  "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y        TCGA-G3-A25Z 
"4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED"   "4Q LOSS MUTATED"   "4Q LOSS MUTATED" 
       TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI        TCGA-G3-A3CJ 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-G3-A3CK        TCGA-G3-A5SI        TCGA-G3-A5SJ        TCGA-G3-A5SL 
"4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-G3-A5SM        TCGA-G3-A6UC        TCGA-GJ-A6C0        TCGA-K7-A6G5 
  "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-LG-A6GG        TCGA-MI-A75C        TCGA-MI-A75E        TCGA-MI-A75G 
  "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" 
       TCGA-MI-A75I        TCGA-NI-A4U2        TCGA-O8-A75V 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
  "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED"   "4Q LOSS MUTATED" 
       TCGA-BC-A3KG        TCGA-BC-A5W4        TCGA-BC-A69H        TCGA-BC-A69I 
"4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" 
       TCGA-CC-5258        TCGA-CC-5260        TCGA-CC-5261        TCGA-CC-5262 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-CC-5263        TCGA-CC-A1HT        TCGA-CC-A3M9        TCGA-CC-A3MA 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" 
       TCGA-CC-A3MB        TCGA-CC-A3MC        TCGA-DD-A113        TCGA-DD-A114 
  "4Q LOSS MUTATED"   "4Q LOSS MUTATED"   "4Q LOSS MUTATED"   "4Q LOSS MUTATED" 
       TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118        TCGA-DD-A119 
"4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" 
       TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C        TCGA-DD-A11D 
  "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB        TCGA-DD-A1EC 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EF        TCGA-DD-A1EG 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" 
       TCGA-DD-A1EH        TCGA-DD-A1EI        TCGA-DD-A1EJ        TCGA-DD-A1EK 
  "4Q LOSS MUTATED"   "4Q LOSS MUTATED"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" 
       TCGA-DD-A1EL        TCGA-DD-A39V        TCGA-DD-A39X        TCGA-DD-A39Y 
  "4Q LOSS MUTATED" "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-A4NB        TCGA-DD-A4ND        TCGA-DD-A4NF        TCGA-DD-A4NH 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" 
       TCGA-DD-A4NI        TCGA-DD-A4NJ        TCGA-DD-A4NK        TCGA-DD-A4NL 
  "4Q LOSS MUTATED"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-DD-A4NN        TCGA-DD-A4NO        TCGA-DD-A4NP        TCGA-DD-A4NQ 
  "4Q LOSS MUTATED"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-DD-A4NR        TCGA-DD-A4NS        TCGA-DD-A4NV        TCGA-DD-A73A 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-DD-A73B        TCGA-DD-A73C        TCGA-DD-A73D        TCGA-DD-A73E 
  "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-DD-A73F        TCGA-DD-A73G        TCGA-ED-A459        TCGA-ED-A4XI 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" 
       TCGA-ED-A5KG        TCGA-ED-A627        TCGA-ED-A66X        TCGA-ED-A66Y 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" 
       TCGA-ED-A7PX        TCGA-ED-A7PY        TCGA-ED-A7PZ        TCGA-ED-A7XP 
"4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED"   "4Q LOSS MUTATED"   "4Q LOSS MUTATED" 
       TCGA-ED-A82E        TCGA-EP-A12J        TCGA-EP-A26S        TCGA-EP-A2KA 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-EP-A2KB        TCGA-EP-A2KC        TCGA-EP-A3JL        TCGA-EP-A3RK 
  "4Q LOSS MUTATED"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-ES-A2HS        TCGA-ES-A2HT        TCGA-FV-A23B        TCGA-FV-A2QR 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-FV-A3I0        TCGA-FV-A3I1        TCGA-FV-A3R2        TCGA-FV-A3R3 
"4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-FV-A495        TCGA-FV-A496        TCGA-FV-A4ZP        TCGA-FV-A4ZQ 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" 
       TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U        TCGA-G3-A25V 
  "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y        TCGA-G3-A25Z 
"4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED"   "4Q LOSS MUTATED"   "4Q LOSS MUTATED" 
       TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI        TCGA-G3-A3CJ 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-G3-A3CK        TCGA-G3-A5SI        TCGA-G3-A5SJ        TCGA-G3-A5SL 
"4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-G3-A5SM        TCGA-G3-A6UC        TCGA-GJ-A6C0        TCGA-K7-A6G5 
  "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-LG-A6GG        TCGA-MI-A75C        TCGA-MI-A75E        TCGA-MI-A75G 
  "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" 
       TCGA-MI-A75I        TCGA-NI-A4U2        TCGA-O8-A75V 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
[1] "hr=" "1.3"
D48V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  4Q LOSS MUTATED        14       17         1          8          1          1
  4Q LOSS WILD-TYPE      44       19         1         22          3          4
                   vv
clus                STAGE IV STAGE IVA STAGE IVB
  4Q LOSS MUTATED          1         1         1
  4Q LOSS WILD-TYPE        0         0         1
D48V3, multiclass
                   vv
clus                T1 T2 T3 T4
  4Q LOSS MUTATED   16 17 12  3
  4Q LOSS WILD-TYPE 45 23 28  5
D48V4, multiclass
    clus
vv   4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  T1              16                45
  T2              17                23
  T3              12                28
  T4               3                 5
D48V5, binary
                   cls
clus                 0  1
  4Q LOSS MUTATED   28  2
  4Q LOSS WILD-TYPE 69  1
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED     28    2
  4Q LOSS WILD-TYPE   69    1
   clus
vv  4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  0              28                69
  1               2                 1
                   vv
clus                M0 M1 MX
  4Q LOSS MUTATED   39  2  7
  4Q LOSS WILD-TYPE 76  1 24
D48V6, multiclass
    clus
vv   4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  M0              39                76
  M1               2                 1
  MX               7                24
D48V7, binary
                   cls
clus                 0  1
  4Q LOSS MUTATED   16 32
  4Q LOSS WILD-TYPE 42 59
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED     16   32
  4Q LOSS WILD-TYPE   42   59
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  FEMALE              16                42
  MALE                32                59
                   vv
clus                R0 R1 R2 RX
  4Q LOSS MUTATED   42  4  1  1
  4Q LOSS WILD-TYPE 80  7  0  9
D48V8, multiclass
    clus
vv   4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  R0              42                80
  R1               4                 7
  R2               1                 0
  RX               1                 9

Clustering(49) Variable = 5P LOSS MUTATION ANALYSIS
D49V1, survival
                   sevent
clus2                0  1
  5P LOSS MUTATED    6  4
  5P LOSS WILD-TYPE 78 59
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               10               137 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
                4                59 
$`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-DD-A4NB TCGA-ES-A2HS TCGA-FV-A496 TCGA-G3-A25S 
       12.85        22.85         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-BC-A69H 
       44.42        13.84         0.26        22.36         9.50         3.95 
TCGA-BC-A69I TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A1HT 
        0.53         2.86         0.39         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        37.78        83.57 
TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D 
       53.33       113.00         7.33         0.46        21.76        51.29 
TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE 
       90.71        79.40        66.31        19.79        75.65         6.71 
TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EI TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V 
       12.95        45.11         6.02        18.35        13.64        21.14 
TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 
       55.69         5.62        19.76        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-A4NH TCGA-DD-A4NI 
       30.61        33.14        73.38        14.07        14.24        18.44 
TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP 
       15.06        39.78        56.25        29.56        61.45        93.67 
TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B 
       12.26         0.30        80.75        66.35        10.98         9.30 
TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G TCGA-ED-A459 
        7.56        10.98         1.45        27.72       100.96        13.41 
TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PX 
       12.69        15.85        13.91        13.35         0.23         0.20 
TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XP TCGA-ED-A82E TCGA-EP-A12J TCGA-EP-A26S 
        0.20         0.20         0.20         0.20        18.74        19.99 
TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HT 
       11.74        10.98         0.62         9.96        11.93        14.40 
TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 
       32.45        19.10         0.20         8.12         6.38         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        51.06        53.79        28.27 
TCGA-G3-A25W TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CH 
       30.74        58.49        14.86        21.53        22.13        25.64 
TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SL 
        5.92        19.53        19.23        14.70        11.97         7.99 
TCGA-G3-A5SM TCGA-G3-A6UC TCGA-GJ-A6C0 TCGA-K7-A6G5 TCGA-LG-A6GG TCGA-MI-A75C 
        4.37         7.76         1.02         4.01         0.49         9.57 
TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75I TCGA-NI-A4U2 TCGA-O8-A75V 
        5.10        14.24         8.71        58.88         4.44 

  5P LOSS MUTATED 5P LOSS WILD-TYPE 
             0.07              0.03 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
            49.15            113.00 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
            7.725            14.240 
[1] "0.1 - 49.1 (7.7)"   "0.0 - 113.0 (14.2)"
       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-BC-A69H        TCGA-BC-A69I 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-CC-5258        TCGA-CC-5260        TCGA-CC-5261        TCGA-CC-5262 
  "5P LOSS MUTATED" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-CC-5263        TCGA-CC-A1HT        TCGA-CC-A3M9        TCGA-CC-A3MA 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE"   "5P LOSS MUTATED" "5P LOSS WILD-TYPE" 
       TCGA-CC-A3MB        TCGA-CC-A3MC        TCGA-DD-A113        TCGA-DD-A114 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118        TCGA-DD-A119 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C        TCGA-DD-A11D 
  "5P LOSS MUTATED" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB        TCGA-DD-A1EC 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EF        TCGA-DD-A1EG 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-DD-A1EH        TCGA-DD-A1EI        TCGA-DD-A1EJ        TCGA-DD-A1EK 
  "5P LOSS MUTATED" "5P LOSS WILD-TYPE"   "5P LOSS MUTATED" "5P LOSS WILD-TYPE" 
       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-A4NB        TCGA-DD-A4ND        TCGA-DD-A4NF        TCGA-DD-A4NH 
  "5P LOSS MUTATED" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-DD-A4NI        TCGA-DD-A4NJ        TCGA-DD-A4NK        TCGA-DD-A4NL 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-DD-A4NN        TCGA-DD-A4NO        TCGA-DD-A4NP        TCGA-DD-A4NQ 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-DD-A4NR        TCGA-DD-A4NS        TCGA-DD-A4NV        TCGA-DD-A73A 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-DD-A73B        TCGA-DD-A73C        TCGA-DD-A73D        TCGA-DD-A73E 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-DD-A73F        TCGA-DD-A73G        TCGA-ED-A459        TCGA-ED-A4XI 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-ED-A5KG        TCGA-ED-A627        TCGA-ED-A66X        TCGA-ED-A66Y 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-ED-A7PX        TCGA-ED-A7PY        TCGA-ED-A7PZ        TCGA-ED-A7XP 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-ED-A82E        TCGA-EP-A12J        TCGA-EP-A26S        TCGA-EP-A2KA 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-EP-A2KB        TCGA-EP-A2KC        TCGA-EP-A3JL        TCGA-EP-A3RK 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-ES-A2HS        TCGA-ES-A2HT        TCGA-FV-A23B        TCGA-FV-A2QR 
  "5P LOSS MUTATED" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-FV-A3I0        TCGA-FV-A3I1        TCGA-FV-A3R2        TCGA-FV-A3R3 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-FV-A495        TCGA-FV-A496        TCGA-FV-A4ZP        TCGA-FV-A4ZQ 
"5P LOSS WILD-TYPE"   "5P LOSS MUTATED" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U        TCGA-G3-A25V 
  "5P LOSS MUTATED" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y        TCGA-G3-A25Z 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI        TCGA-G3-A3CJ 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-G3-A3CK        TCGA-G3-A5SI        TCGA-G3-A5SJ        TCGA-G3-A5SL 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-G3-A5SM        TCGA-G3-A6UC        TCGA-GJ-A6C0        TCGA-K7-A6G5 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-LG-A6GG        TCGA-MI-A75C        TCGA-MI-A75E        TCGA-MI-A75G 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-MI-A75I        TCGA-NI-A4U2        TCGA-O8-A75V 
"5P LOSS WILD-TYPE" "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-BC-A69H        TCGA-BC-A69I 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-CC-5258        TCGA-CC-5260        TCGA-CC-5261        TCGA-CC-5262 
  "5P LOSS MUTATED" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-CC-5263        TCGA-CC-A1HT        TCGA-CC-A3M9        TCGA-CC-A3MA 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE"   "5P LOSS MUTATED" "5P LOSS WILD-TYPE" 
       TCGA-CC-A3MB        TCGA-CC-A3MC        TCGA-DD-A113        TCGA-DD-A114 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118        TCGA-DD-A119 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C        TCGA-DD-A11D 
  "5P LOSS MUTATED" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB        TCGA-DD-A1EC 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EF        TCGA-DD-A1EG 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-DD-A1EH        TCGA-DD-A1EI        TCGA-DD-A1EJ        TCGA-DD-A1EK 
  "5P LOSS MUTATED" "5P LOSS WILD-TYPE"   "5P LOSS MUTATED" "5P LOSS WILD-TYPE" 
       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-A4NB        TCGA-DD-A4ND        TCGA-DD-A4NF        TCGA-DD-A4NH 
  "5P LOSS MUTATED" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-DD-A4NI        TCGA-DD-A4NJ        TCGA-DD-A4NK        TCGA-DD-A4NL 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-DD-A4NN        TCGA-DD-A4NO        TCGA-DD-A4NP        TCGA-DD-A4NQ 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-DD-A4NR        TCGA-DD-A4NS        TCGA-DD-A4NV        TCGA-DD-A73A 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-DD-A73B        TCGA-DD-A73C        TCGA-DD-A73D        TCGA-DD-A73E 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-DD-A73F        TCGA-DD-A73G        TCGA-ED-A459        TCGA-ED-A4XI 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-ED-A5KG        TCGA-ED-A627        TCGA-ED-A66X        TCGA-ED-A66Y 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-ED-A7PX        TCGA-ED-A7PY        TCGA-ED-A7PZ        TCGA-ED-A7XP 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-ED-A82E        TCGA-EP-A12J        TCGA-EP-A26S        TCGA-EP-A2KA 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-EP-A2KB        TCGA-EP-A2KC        TCGA-EP-A3JL        TCGA-EP-A3RK 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-ES-A2HS        TCGA-ES-A2HT        TCGA-FV-A23B        TCGA-FV-A2QR 
  "5P LOSS MUTATED" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-FV-A3I0        TCGA-FV-A3I1        TCGA-FV-A3R2        TCGA-FV-A3R3 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-FV-A495        TCGA-FV-A496        TCGA-FV-A4ZP        TCGA-FV-A4ZQ 
"5P LOSS WILD-TYPE"   "5P LOSS MUTATED" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U        TCGA-G3-A25V 
  "5P LOSS MUTATED" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y        TCGA-G3-A25Z 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI        TCGA-G3-A3CJ 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-G3-A3CK        TCGA-G3-A5SI        TCGA-G3-A5SJ        TCGA-G3-A5SL 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-G3-A5SM        TCGA-G3-A6UC        TCGA-GJ-A6C0        TCGA-K7-A6G5 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-LG-A6GG        TCGA-MI-A75C        TCGA-MI-A75E        TCGA-MI-A75G 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-MI-A75I        TCGA-NI-A4U2        TCGA-O8-A75V 
"5P LOSS WILD-TYPE" "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-BC-A69H        TCGA-BC-A69I 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-CC-5258        TCGA-CC-5260        TCGA-CC-5261        TCGA-CC-5262 
  "5P LOSS MUTATED" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-CC-5263        TCGA-CC-A1HT        TCGA-CC-A3M9        TCGA-CC-A3MA 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE"   "5P LOSS MUTATED" "5P LOSS WILD-TYPE" 
       TCGA-CC-A3MB        TCGA-CC-A3MC        TCGA-DD-A113        TCGA-DD-A114 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118        TCGA-DD-A119 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C        TCGA-DD-A11D 
  "5P LOSS MUTATED" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB        TCGA-DD-A1EC 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EF        TCGA-DD-A1EG 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-DD-A1EH        TCGA-DD-A1EI        TCGA-DD-A1EJ        TCGA-DD-A1EK 
  "5P LOSS MUTATED" "5P LOSS WILD-TYPE"   "5P LOSS MUTATED" "5P LOSS WILD-TYPE" 
       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-A4NB        TCGA-DD-A4ND        TCGA-DD-A4NF        TCGA-DD-A4NH 
  "5P LOSS MUTATED" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-DD-A4NI        TCGA-DD-A4NJ        TCGA-DD-A4NK        TCGA-DD-A4NL 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-DD-A4NN        TCGA-DD-A4NO        TCGA-DD-A4NP        TCGA-DD-A4NQ 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-DD-A4NR        TCGA-DD-A4NS        TCGA-DD-A4NV        TCGA-DD-A73A 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-DD-A73B        TCGA-DD-A73C        TCGA-DD-A73D        TCGA-DD-A73E 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-DD-A73F        TCGA-DD-A73G        TCGA-ED-A459        TCGA-ED-A4XI 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-ED-A5KG        TCGA-ED-A627        TCGA-ED-A66X        TCGA-ED-A66Y 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-ED-A7PX        TCGA-ED-A7PY        TCGA-ED-A7PZ        TCGA-ED-A7XP 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-ED-A82E        TCGA-EP-A12J        TCGA-EP-A26S        TCGA-EP-A2KA 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-EP-A2KB        TCGA-EP-A2KC        TCGA-EP-A3JL        TCGA-EP-A3RK 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-ES-A2HS        TCGA-ES-A2HT        TCGA-FV-A23B        TCGA-FV-A2QR 
  "5P LOSS MUTATED" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-FV-A3I0        TCGA-FV-A3I1        TCGA-FV-A3R2        TCGA-FV-A3R3 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-FV-A495        TCGA-FV-A496        TCGA-FV-A4ZP        TCGA-FV-A4ZQ 
"5P LOSS WILD-TYPE"   "5P LOSS MUTATED" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U        TCGA-G3-A25V 
  "5P LOSS MUTATED" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y        TCGA-G3-A25Z 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI        TCGA-G3-A3CJ 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-G3-A3CK        TCGA-G3-A5SI        TCGA-G3-A5SJ        TCGA-G3-A5SL 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-G3-A5SM        TCGA-G3-A6UC        TCGA-GJ-A6C0        TCGA-K7-A6G5 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-LG-A6GG        TCGA-MI-A75C        TCGA-MI-A75E        TCGA-MI-A75G 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-MI-A75I        TCGA-NI-A4U2        TCGA-O8-A75V 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
[1] "hr=" "1.4"
D49V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  5P LOSS MUTATED         5        1         1          1          0          1
  5P LOSS WILD-TYPE      53       35         1         29          4          4
                   vv
clus                STAGE IV STAGE IVA STAGE IVB
  5P LOSS MUTATED          0         0         0
  5P LOSS WILD-TYPE        1         1         2
D49V3, multiclass
                   vv
clus                T1 T2 T3 T4
  5P LOSS MUTATED    6  1  3  0
  5P LOSS WILD-TYPE 55 39 37  8
D49V4, multiclass
    clus
vv   5P LOSS MUTATED 5P LOSS WILD-TYPE
  T1               6                55
  T2               1                39
  T3               3                37
  T4               0                 8
D49V5, binary
                   cls
clus                 0  1
  5P LOSS MUTATED    6  1
  5P LOSS WILD-TYPE 91  2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED      6    1
  5P LOSS WILD-TYPE   91    2
   clus
vv  5P LOSS MUTATED 5P LOSS WILD-TYPE
  0               6                91
  1               1                 2
                   vv
clus                 M0  M1  MX
  5P LOSS MUTATED     8   0   2
  5P LOSS WILD-TYPE 107   3  29
D49V6, multiclass
    clus
vv   5P LOSS MUTATED 5P LOSS WILD-TYPE
  M0               8               107
  M1               0                 3
  MX               2                29
D49V7, binary
                   cls
clus                 0  1
  5P LOSS MUTATED    2  8
  5P LOSS WILD-TYPE 56 83
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED      2    8
  5P LOSS WILD-TYPE   56   83
        clus
vv       5P LOSS MUTATED 5P LOSS WILD-TYPE
  FEMALE               2                56
  MALE                 8                83
                   vv
clus                 R0  R1  R2  RX
  5P LOSS MUTATED     8   1   0   1
  5P LOSS WILD-TYPE 114  10   1   9
D49V8, multiclass
    clus
vv   5P LOSS MUTATED 5P LOSS WILD-TYPE
  R0               8               114
  R1               1                10
  R2               0                 1
  RX               1                 9

Clustering(50) Variable = 5Q LOSS MUTATION ANALYSIS
D50V1, survival
                   sevent
clus2                0  1
  5Q LOSS MUTATED    7  7
  5Q LOSS WILD-TYPE 77 56
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               14               133 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
                7                56 
$`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-DD-A4NB TCGA-ES-A2HS TCGA-FV-A3I0 TCGA-FV-A496 
       49.15        29.16        12.85        22.85         0.20         0.33 
TCGA-FV-A4ZP TCGA-G3-A25S 
       60.36         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-BC-A69H TCGA-BC-A69I 
       13.84         0.26        22.36         9.50         3.95         0.53 
TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-A1HT TCGA-CC-A3MA 
        0.07         2.86         0.39         3.39         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        37.78        83.57        53.33 
TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 
      113.00         7.33         0.46        21.76        51.29        90.71 
TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EG 
       79.40        66.31        19.79        75.65         6.71        45.11 
TCGA-DD-A1EI TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39X TCGA-DD-A39Y 
        6.02        18.35        13.64        21.14        55.69         5.62 
TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 
       19.76        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        30.61        33.14 
TCGA-DD-A4ND TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK 
       73.38        14.07        14.24        18.44        15.06        39.78 
TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR 
       56.25        29.56        61.45        93.67        12.26         0.30 
TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D 
       80.75        66.35        10.98         9.30         7.56        10.98 
TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG 
        1.45        27.72       100.96        13.41        12.69        15.85 
TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ 
       13.91        13.35         0.23         0.20         0.20         0.20 
TCGA-ED-A7XP TCGA-ED-A82E TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB 
        0.20         0.20        18.74        19.99        11.74        10.98 
TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QR 
        0.62         9.96        11.93        14.40        32.45        19.10 
TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A4ZQ TCGA-G3-A25T 
        8.12         6.38         0.13         0.03         0.39        51.06 
TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A25Z 
       53.79        28.27        30.74        58.49        14.86        21.53 
TCGA-G3-A3CG TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI 
       22.13        25.64         5.92        19.53        19.23        14.70 
TCGA-G3-A5SJ TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A6UC TCGA-GJ-A6C0 TCGA-K7-A6G5 
       11.97         7.99         4.37         7.76         1.02         4.01 
TCGA-LG-A6GG TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75I TCGA-NI-A4U2 
        0.49         9.57         5.10        14.24         8.71        58.88 
TCGA-O8-A75V 
        4.44 

  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
             0.10              0.03 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
            60.36            113.00 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
            11.49             14.24 
[1] "0.1 - 60.4 (11.5)"  "0.0 - 113.0 (14.2)"
       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-BC-A69H        TCGA-BC-A69I 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-CC-5258        TCGA-CC-5260        TCGA-CC-5261        TCGA-CC-5262 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-CC-5263        TCGA-CC-A1HT        TCGA-CC-A3M9        TCGA-CC-A3MA 
  "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" 
       TCGA-CC-A3MB        TCGA-CC-A3MC        TCGA-DD-A113        TCGA-DD-A114 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118        TCGA-DD-A119 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C        TCGA-DD-A11D 
  "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB        TCGA-DD-A1EC 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EF        TCGA-DD-A1EG 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" 
       TCGA-DD-A1EH        TCGA-DD-A1EI        TCGA-DD-A1EJ        TCGA-DD-A1EK 
  "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" 
       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-A4NB        TCGA-DD-A4ND        TCGA-DD-A4NF        TCGA-DD-A4NH 
  "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-DD-A4NI        TCGA-DD-A4NJ        TCGA-DD-A4NK        TCGA-DD-A4NL 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-DD-A4NN        TCGA-DD-A4NO        TCGA-DD-A4NP        TCGA-DD-A4NQ 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-DD-A4NR        TCGA-DD-A4NS        TCGA-DD-A4NV        TCGA-DD-A73A 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-DD-A73B        TCGA-DD-A73C        TCGA-DD-A73D        TCGA-DD-A73E 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-DD-A73F        TCGA-DD-A73G        TCGA-ED-A459        TCGA-ED-A4XI 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-ED-A5KG        TCGA-ED-A627        TCGA-ED-A66X        TCGA-ED-A66Y 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-ED-A7PX        TCGA-ED-A7PY        TCGA-ED-A7PZ        TCGA-ED-A7XP 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-ED-A82E        TCGA-EP-A12J        TCGA-EP-A26S        TCGA-EP-A2KA 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-EP-A2KB        TCGA-EP-A2KC        TCGA-EP-A3JL        TCGA-EP-A3RK 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-ES-A2HS        TCGA-ES-A2HT        TCGA-FV-A23B        TCGA-FV-A2QR 
  "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-FV-A3I0        TCGA-FV-A3I1        TCGA-FV-A3R2        TCGA-FV-A3R3 
  "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-FV-A495        TCGA-FV-A496        TCGA-FV-A4ZP        TCGA-FV-A4ZQ 
"5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" 
       TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U        TCGA-G3-A25V 
  "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y        TCGA-G3-A25Z 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI        TCGA-G3-A3CJ 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-G3-A3CK        TCGA-G3-A5SI        TCGA-G3-A5SJ        TCGA-G3-A5SL 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-G3-A5SM        TCGA-G3-A6UC        TCGA-GJ-A6C0        TCGA-K7-A6G5 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-LG-A6GG        TCGA-MI-A75C        TCGA-MI-A75E        TCGA-MI-A75G 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-MI-A75I        TCGA-NI-A4U2        TCGA-O8-A75V 
"5Q LOSS WILD-TYPE" "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-BC-A69H        TCGA-BC-A69I 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-CC-5258        TCGA-CC-5260        TCGA-CC-5261        TCGA-CC-5262 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-CC-5263        TCGA-CC-A1HT        TCGA-CC-A3M9        TCGA-CC-A3MA 
  "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" 
       TCGA-CC-A3MB        TCGA-CC-A3MC        TCGA-DD-A113        TCGA-DD-A114 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118        TCGA-DD-A119 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C        TCGA-DD-A11D 
  "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB        TCGA-DD-A1EC 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EF        TCGA-DD-A1EG 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" 
       TCGA-DD-A1EH        TCGA-DD-A1EI        TCGA-DD-A1EJ        TCGA-DD-A1EK 
  "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" 
       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-A4NB        TCGA-DD-A4ND        TCGA-DD-A4NF        TCGA-DD-A4NH 
  "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-DD-A4NI        TCGA-DD-A4NJ        TCGA-DD-A4NK        TCGA-DD-A4NL 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-DD-A4NN        TCGA-DD-A4NO        TCGA-DD-A4NP        TCGA-DD-A4NQ 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-DD-A4NR        TCGA-DD-A4NS        TCGA-DD-A4NV        TCGA-DD-A73A 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-DD-A73B        TCGA-DD-A73C        TCGA-DD-A73D        TCGA-DD-A73E 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-DD-A73F        TCGA-DD-A73G        TCGA-ED-A459        TCGA-ED-A4XI 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-ED-A5KG        TCGA-ED-A627        TCGA-ED-A66X        TCGA-ED-A66Y 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-ED-A7PX        TCGA-ED-A7PY        TCGA-ED-A7PZ        TCGA-ED-A7XP 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-ED-A82E        TCGA-EP-A12J        TCGA-EP-A26S        TCGA-EP-A2KA 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-EP-A2KB        TCGA-EP-A2KC        TCGA-EP-A3JL        TCGA-EP-A3RK 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-ES-A2HS        TCGA-ES-A2HT        TCGA-FV-A23B        TCGA-FV-A2QR 
  "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-FV-A3I0        TCGA-FV-A3I1        TCGA-FV-A3R2        TCGA-FV-A3R3 
  "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-FV-A495        TCGA-FV-A496        TCGA-FV-A4ZP        TCGA-FV-A4ZQ 
"5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" 
       TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U        TCGA-G3-A25V 
  "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y        TCGA-G3-A25Z 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI        TCGA-G3-A3CJ 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-G3-A3CK        TCGA-G3-A5SI        TCGA-G3-A5SJ        TCGA-G3-A5SL 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-G3-A5SM        TCGA-G3-A6UC        TCGA-GJ-A6C0        TCGA-K7-A6G5 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-LG-A6GG        TCGA-MI-A75C        TCGA-MI-A75E        TCGA-MI-A75G 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-MI-A75I        TCGA-NI-A4U2        TCGA-O8-A75V 
"5Q LOSS WILD-TYPE" "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-BC-A69H        TCGA-BC-A69I 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-CC-5258        TCGA-CC-5260        TCGA-CC-5261        TCGA-CC-5262 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-CC-5263        TCGA-CC-A1HT        TCGA-CC-A3M9        TCGA-CC-A3MA 
  "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" 
       TCGA-CC-A3MB        TCGA-CC-A3MC        TCGA-DD-A113        TCGA-DD-A114 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118        TCGA-DD-A119 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C        TCGA-DD-A11D 
  "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB        TCGA-DD-A1EC 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EF        TCGA-DD-A1EG 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" 
       TCGA-DD-A1EH        TCGA-DD-A1EI        TCGA-DD-A1EJ        TCGA-DD-A1EK 
  "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" 
       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-A4NB        TCGA-DD-A4ND        TCGA-DD-A4NF        TCGA-DD-A4NH 
  "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-DD-A4NI        TCGA-DD-A4NJ        TCGA-DD-A4NK        TCGA-DD-A4NL 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-DD-A4NN        TCGA-DD-A4NO        TCGA-DD-A4NP        TCGA-DD-A4NQ 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-DD-A4NR        TCGA-DD-A4NS        TCGA-DD-A4NV        TCGA-DD-A73A 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-DD-A73B        TCGA-DD-A73C        TCGA-DD-A73D        TCGA-DD-A73E 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-DD-A73F        TCGA-DD-A73G        TCGA-ED-A459        TCGA-ED-A4XI 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-ED-A5KG        TCGA-ED-A627        TCGA-ED-A66X        TCGA-ED-A66Y 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-ED-A7PX        TCGA-ED-A7PY        TCGA-ED-A7PZ        TCGA-ED-A7XP 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-ED-A82E        TCGA-EP-A12J        TCGA-EP-A26S        TCGA-EP-A2KA 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-EP-A2KB        TCGA-EP-A2KC        TCGA-EP-A3JL        TCGA-EP-A3RK 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-ES-A2HS        TCGA-ES-A2HT        TCGA-FV-A23B        TCGA-FV-A2QR 
  "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-FV-A3I0        TCGA-FV-A3I1        TCGA-FV-A3R2        TCGA-FV-A3R3 
  "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-FV-A495        TCGA-FV-A496        TCGA-FV-A4ZP        TCGA-FV-A4ZQ 
"5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" 
       TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U        TCGA-G3-A25V 
  "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y        TCGA-G3-A25Z 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI        TCGA-G3-A3CJ 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-G3-A3CK        TCGA-G3-A5SI        TCGA-G3-A5SJ        TCGA-G3-A5SL 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-G3-A5SM        TCGA-G3-A6UC        TCGA-GJ-A6C0        TCGA-K7-A6G5 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-LG-A6GG        TCGA-MI-A75C        TCGA-MI-A75E        TCGA-MI-A75G 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-MI-A75I        TCGA-NI-A4U2        TCGA-O8-A75V 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
[1] "hr=" "1.6"
D50V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  5Q LOSS MUTATED         6        1         1          3          0          1
  5Q LOSS WILD-TYPE      52       35         1         27          4          4
                   vv
clus                STAGE IV STAGE IVA STAGE IVB
  5Q LOSS MUTATED          0         0         0
  5Q LOSS WILD-TYPE        1         1         2
D50V3, multiclass
                   vv
clus                T1 T2 T3 T4
  5Q LOSS MUTATED    7  1  6  0
  5Q LOSS WILD-TYPE 54 39 34  8
D50V4, multiclass
    clus
vv   5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  T1               7                54
  T2               1                39
  T3               6                34
  T4               0                 8
D50V5, binary
                   cls
clus                 0  1
  5Q LOSS MUTATED    7  1
  5Q LOSS WILD-TYPE 90  2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED      7    1
  5Q LOSS WILD-TYPE   90    2
   clus
vv  5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  0               7                90
  1               1                 2
                   vv
clus                 M0  M1  MX
  5Q LOSS MUTATED    11   0   3
  5Q LOSS WILD-TYPE 104   3  28
D50V6, multiclass
    clus
vv   5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  M0              11               104
  M1               0                 3
  MX               3                28
D50V7, binary
                   cls
clus                 0  1
  5Q LOSS MUTATED    5  9
  5Q LOSS WILD-TYPE 53 82
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED      5    9
  5Q LOSS WILD-TYPE   53   82
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  FEMALE               5                53
  MALE                 9                82
                   vv
clus                 R0  R1  R2  RX
  5Q LOSS MUTATED    11   2   0   1
  5Q LOSS WILD-TYPE 111   9   1   9
D50V8, multiclass
    clus
vv   5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  R0              11               111
  R1               2                 9
  R2               0                 1
  RX               1                 9

Clustering(51) Variable = 6P LOSS MUTATION ANALYSIS
D51V1, survival
                   sevent
clus2                0  1
  6P LOSS MUTATED   10  7
  6P LOSS WILD-TYPE 74 56
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               17               130 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
                7                56 
$`6P LOSS MUTATED`
TCGA-BC-A5W4 TCGA-BC-A69I TCGA-CC-A3M9 TCGA-DD-A118 TCGA-DD-A11A TCGA-DD-A11C 
        9.50         0.53         0.10       113.00         2.60        21.76 
TCGA-DD-A1E9 TCGA-DD-A1EC TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EI TCGA-DD-A1EJ 
       90.71        19.79         6.71        12.95         6.02        29.16 
TCGA-DD-A1EK TCGA-DD-A39Z TCGA-DD-A4NH TCGA-DD-A4NK TCGA-ED-A66Y 
       18.35        19.76        14.24        39.78         0.23 

$`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-BC-A69H 
        5.03        44.42        13.84         0.26        22.36         3.95 
TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A1HT 
        0.07         2.86         0.39         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        37.78        83.57 
TCGA-DD-A116 TCGA-DD-A119 TCGA-DD-A11B TCGA-DD-A11D TCGA-DD-A1EA TCGA-DD-A1EB 
       53.33         7.33         0.46        51.29        79.40        66.31 
TCGA-DD-A1ED TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39X 
       75.65        45.11        49.15        13.64        21.14        55.69 
TCGA-DD-A39Y TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 
        5.62        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        30.61        33.14 
TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NF TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NL 
       12.85        73.38        14.07        18.44        15.06        56.25 
TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS 
       29.56        61.45        93.67        12.26         0.30        80.75 
TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E 
       66.35        10.98         9.30         7.56        10.98         1.45 
TCGA-DD-A73F TCGA-DD-A73G TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 
       27.72       100.96        13.41        12.69        15.85        13.91 
TCGA-ED-A66X TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XP TCGA-ED-A82E 
       13.35         0.20         0.20         0.20         0.20         0.20 
TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL 
       18.74        19.99        11.74        10.98         0.62         9.96 
TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-A3I0 
       11.93        22.85        14.40        32.45        19.10         0.20 
TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZP 
        8.12         6.38         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        51.06        53.79        28.27        30.74 
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         5.92 
TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SL TCGA-G3-A5SM 
       19.53        19.23        14.70        11.97         7.99         4.37 
TCGA-G3-A6UC TCGA-GJ-A6C0 TCGA-K7-A6G5 TCGA-LG-A6GG TCGA-MI-A75C TCGA-MI-A75E 
        7.76         1.02         4.01         0.49         9.57         5.10 
TCGA-MI-A75G TCGA-MI-A75I TCGA-NI-A4U2 TCGA-O8-A75V 
       14.24         8.71        58.88         4.44 

  6P LOSS MUTATED 6P LOSS WILD-TYPE 
             0.10              0.03 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
           113.00            107.11 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
            14.24             13.99 
[1] "0.1 - 113.0 (14.2)" "0.0 - 107.1 (14.0)"
       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-BC-A69H        TCGA-BC-A69I 
"6P LOSS WILD-TYPE"   "6P LOSS MUTATED" "6P LOSS WILD-TYPE"   "6P LOSS MUTATED" 
       TCGA-CC-5258        TCGA-CC-5260        TCGA-CC-5261        TCGA-CC-5262 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-CC-5263        TCGA-CC-A1HT        TCGA-CC-A3M9        TCGA-CC-A3MA 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE"   "6P LOSS MUTATED" "6P LOSS WILD-TYPE" 
       TCGA-CC-A3MB        TCGA-CC-A3MC        TCGA-DD-A113        TCGA-DD-A114 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118        TCGA-DD-A119 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE"   "6P LOSS MUTATED" "6P LOSS WILD-TYPE" 
       TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C        TCGA-DD-A11D 
  "6P LOSS MUTATED" "6P LOSS WILD-TYPE"   "6P LOSS MUTATED" "6P LOSS WILD-TYPE" 
       TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB        TCGA-DD-A1EC 
  "6P LOSS MUTATED" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE"   "6P LOSS MUTATED" 
       TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EF        TCGA-DD-A1EG 
"6P LOSS WILD-TYPE"   "6P LOSS MUTATED"   "6P LOSS MUTATED" "6P LOSS WILD-TYPE" 
       TCGA-DD-A1EH        TCGA-DD-A1EI        TCGA-DD-A1EJ        TCGA-DD-A1EK 
"6P LOSS WILD-TYPE"   "6P LOSS MUTATED"   "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 WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-DD-A4NB        TCGA-DD-A4ND        TCGA-DD-A4NF        TCGA-DD-A4NH 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE"   "6P LOSS MUTATED" 
       TCGA-DD-A4NI        TCGA-DD-A4NJ        TCGA-DD-A4NK        TCGA-DD-A4NL 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE"   "6P LOSS MUTATED" "6P LOSS WILD-TYPE" 
       TCGA-DD-A4NN        TCGA-DD-A4NO        TCGA-DD-A4NP        TCGA-DD-A4NQ 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-DD-A4NR        TCGA-DD-A4NS        TCGA-DD-A4NV        TCGA-DD-A73A 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-DD-A73B        TCGA-DD-A73C        TCGA-DD-A73D        TCGA-DD-A73E 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-DD-A73F        TCGA-DD-A73G        TCGA-ED-A459        TCGA-ED-A4XI 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-ED-A5KG        TCGA-ED-A627        TCGA-ED-A66X        TCGA-ED-A66Y 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE"   "6P LOSS MUTATED" 
       TCGA-ED-A7PX        TCGA-ED-A7PY        TCGA-ED-A7PZ        TCGA-ED-A7XP 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-ED-A82E        TCGA-EP-A12J        TCGA-EP-A26S        TCGA-EP-A2KA 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EP-A2KB        TCGA-EP-A2KC        TCGA-EP-A3JL        TCGA-EP-A3RK 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-ES-A2HS        TCGA-ES-A2HT        TCGA-FV-A23B        TCGA-FV-A2QR 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-FV-A3I0        TCGA-FV-A3I1        TCGA-FV-A3R2        TCGA-FV-A3R3 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-FV-A495        TCGA-FV-A496        TCGA-FV-A4ZP        TCGA-FV-A4ZQ 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U        TCGA-G3-A25V 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y        TCGA-G3-A25Z 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI        TCGA-G3-A3CJ 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-G3-A3CK        TCGA-G3-A5SI        TCGA-G3-A5SJ        TCGA-G3-A5SL 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-G3-A5SM        TCGA-G3-A6UC        TCGA-GJ-A6C0        TCGA-K7-A6G5 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-LG-A6GG        TCGA-MI-A75C        TCGA-MI-A75E        TCGA-MI-A75G 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-MI-A75I        TCGA-NI-A4U2        TCGA-O8-A75V 
"6P LOSS WILD-TYPE" "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-BC-A69H        TCGA-BC-A69I 
"6P LOSS WILD-TYPE"   "6P LOSS MUTATED" "6P LOSS WILD-TYPE"   "6P LOSS MUTATED" 
       TCGA-CC-5258        TCGA-CC-5260        TCGA-CC-5261        TCGA-CC-5262 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-CC-5263        TCGA-CC-A1HT        TCGA-CC-A3M9        TCGA-CC-A3MA 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE"   "6P LOSS MUTATED" "6P LOSS WILD-TYPE" 
       TCGA-CC-A3MB        TCGA-CC-A3MC        TCGA-DD-A113        TCGA-DD-A114 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118        TCGA-DD-A119 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE"   "6P LOSS MUTATED" "6P LOSS WILD-TYPE" 
       TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C        TCGA-DD-A11D 
  "6P LOSS MUTATED" "6P LOSS WILD-TYPE"   "6P LOSS MUTATED" "6P LOSS WILD-TYPE" 
       TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB        TCGA-DD-A1EC 
  "6P LOSS MUTATED" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE"   "6P LOSS MUTATED" 
       TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EF        TCGA-DD-A1EG 
"6P LOSS WILD-TYPE"   "6P LOSS MUTATED"   "6P LOSS MUTATED" "6P LOSS WILD-TYPE" 
       TCGA-DD-A1EH        TCGA-DD-A1EI        TCGA-DD-A1EJ        TCGA-DD-A1EK 
"6P LOSS WILD-TYPE"   "6P LOSS MUTATED"   "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 WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-DD-A4NB        TCGA-DD-A4ND        TCGA-DD-A4NF        TCGA-DD-A4NH 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE"   "6P LOSS MUTATED" 
       TCGA-DD-A4NI        TCGA-DD-A4NJ        TCGA-DD-A4NK        TCGA-DD-A4NL 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE"   "6P LOSS MUTATED" "6P LOSS WILD-TYPE" 
       TCGA-DD-A4NN        TCGA-DD-A4NO        TCGA-DD-A4NP        TCGA-DD-A4NQ 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-DD-A4NR        TCGA-DD-A4NS        TCGA-DD-A4NV        TCGA-DD-A73A 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-DD-A73B        TCGA-DD-A73C        TCGA-DD-A73D        TCGA-DD-A73E 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-DD-A73F        TCGA-DD-A73G        TCGA-ED-A459        TCGA-ED-A4XI 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-ED-A5KG        TCGA-ED-A627        TCGA-ED-A66X        TCGA-ED-A66Y 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE"   "6P LOSS MUTATED" 
       TCGA-ED-A7PX        TCGA-ED-A7PY        TCGA-ED-A7PZ        TCGA-ED-A7XP 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-ED-A82E        TCGA-EP-A12J        TCGA-EP-A26S        TCGA-EP-A2KA 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EP-A2KB        TCGA-EP-A2KC        TCGA-EP-A3JL        TCGA-EP-A3RK 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-ES-A2HS        TCGA-ES-A2HT        TCGA-FV-A23B        TCGA-FV-A2QR 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-FV-A3I0        TCGA-FV-A3I1        TCGA-FV-A3R2        TCGA-FV-A3R3 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-FV-A495        TCGA-FV-A496        TCGA-FV-A4ZP        TCGA-FV-A4ZQ 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U        TCGA-G3-A25V 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y        TCGA-G3-A25Z 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI        TCGA-G3-A3CJ 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-G3-A3CK        TCGA-G3-A5SI        TCGA-G3-A5SJ        TCGA-G3-A5SL 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-G3-A5SM        TCGA-G3-A6UC        TCGA-GJ-A6C0        TCGA-K7-A6G5 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-LG-A6GG        TCGA-MI-A75C        TCGA-MI-A75E        TCGA-MI-A75G 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-MI-A75I        TCGA-NI-A4U2        TCGA-O8-A75V 
"6P LOSS WILD-TYPE" "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-BC-A69H        TCGA-BC-A69I 
"6P LOSS WILD-TYPE"   "6P LOSS MUTATED" "6P LOSS WILD-TYPE"   "6P LOSS MUTATED" 
       TCGA-CC-5258        TCGA-CC-5260        TCGA-CC-5261        TCGA-CC-5262 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-CC-5263        TCGA-CC-A1HT        TCGA-CC-A3M9        TCGA-CC-A3MA 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE"   "6P LOSS MUTATED" "6P LOSS WILD-TYPE" 
       TCGA-CC-A3MB        TCGA-CC-A3MC        TCGA-DD-A113        TCGA-DD-A114 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118        TCGA-DD-A119 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE"   "6P LOSS MUTATED" "6P LOSS WILD-TYPE" 
       TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C        TCGA-DD-A11D 
  "6P LOSS MUTATED" "6P LOSS WILD-TYPE"   "6P LOSS MUTATED" "6P LOSS WILD-TYPE" 
       TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB        TCGA-DD-A1EC 
  "6P LOSS MUTATED" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE"   "6P LOSS MUTATED" 
       TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EF        TCGA-DD-A1EG 
"6P LOSS WILD-TYPE"   "6P LOSS MUTATED"   "6P LOSS MUTATED" "6P LOSS WILD-TYPE" 
       TCGA-DD-A1EH        TCGA-DD-A1EI        TCGA-DD-A1EJ        TCGA-DD-A1EK 
"6P LOSS WILD-TYPE"   "6P LOSS MUTATED"   "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 WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-DD-A4NB        TCGA-DD-A4ND        TCGA-DD-A4NF        TCGA-DD-A4NH 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE"   "6P LOSS MUTATED" 
       TCGA-DD-A4NI        TCGA-DD-A4NJ        TCGA-DD-A4NK        TCGA-DD-A4NL 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE"   "6P LOSS MUTATED" "6P LOSS WILD-TYPE" 
       TCGA-DD-A4NN        TCGA-DD-A4NO        TCGA-DD-A4NP        TCGA-DD-A4NQ 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-DD-A4NR        TCGA-DD-A4NS        TCGA-DD-A4NV        TCGA-DD-A73A 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-DD-A73B        TCGA-DD-A73C        TCGA-DD-A73D        TCGA-DD-A73E 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-DD-A73F        TCGA-DD-A73G        TCGA-ED-A459        TCGA-ED-A4XI 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-ED-A5KG        TCGA-ED-A627        TCGA-ED-A66X        TCGA-ED-A66Y 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE"   "6P LOSS MUTATED" 
       TCGA-ED-A7PX        TCGA-ED-A7PY        TCGA-ED-A7PZ        TCGA-ED-A7XP 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-ED-A82E        TCGA-EP-A12J        TCGA-EP-A26S        TCGA-EP-A2KA 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EP-A2KB        TCGA-EP-A2KC        TCGA-EP-A3JL        TCGA-EP-A3RK 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-ES-A2HS        TCGA-ES-A2HT        TCGA-FV-A23B        TCGA-FV-A2QR 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-FV-A3I0        TCGA-FV-A3I1        TCGA-FV-A3R2        TCGA-FV-A3R3 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-FV-A495        TCGA-FV-A496        TCGA-FV-A4ZP        TCGA-FV-A4ZQ 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U        TCGA-G3-A25V 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y        TCGA-G3-A25Z 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI        TCGA-G3-A3CJ 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-G3-A3CK        TCGA-G3-A5SI        TCGA-G3-A5SJ        TCGA-G3-A5SL 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-G3-A5SM        TCGA-G3-A6UC        TCGA-GJ-A6C0        TCGA-K7-A6G5 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-LG-A6GG        TCGA-MI-A75C        TCGA-MI-A75E        TCGA-MI-A75G 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-MI-A75I        TCGA-NI-A4U2        TCGA-O8-A75V 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
[1] "hr=" "1.1"
D51V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  6P LOSS MUTATED         7        2         0          5          1          1
  6P LOSS WILD-TYPE      51       34         2         25          3          4
                   vv
clus                STAGE IV STAGE IVA STAGE IVB
  6P LOSS MUTATED          0         0         1
  6P LOSS WILD-TYPE        1         1         1
D51V3, multiclass
                   vv
clus                T1 T2 T3 T4
  6P LOSS MUTATED    8  2  6  1
  6P LOSS WILD-TYPE 53 38 34  7
D51V4, multiclass
    clus
vv   6P LOSS MUTATED 6P LOSS WILD-TYPE
  T1               8                53
  T2               2                38
  T3               6                34
  T4               1                 7
D51V5, binary
                   cls
clus                 0  1
  6P LOSS MUTATED   14  1
  6P LOSS WILD-TYPE 83  2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED     14    1
  6P LOSS WILD-TYPE   83    2
   clus
vv  6P LOSS MUTATED 6P LOSS WILD-TYPE
  0              14                83
  1               1                 2
                   vv
clus                M0 M1 MX
  6P LOSS MUTATED   16  1  0
  6P LOSS WILD-TYPE 99  2 31
D51V6, multiclass
    clus
vv   6P LOSS MUTATED 6P LOSS WILD-TYPE
  M0              16                99
  M1               1                 2
  MX               0                31
D51V7, binary
                   cls
clus                 0  1
  6P LOSS MUTATED    9  8
  6P LOSS WILD-TYPE 49 83
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED      9    8
  6P LOSS WILD-TYPE   49   83
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  FEMALE               9                49
  MALE                 8                83
                   vv
clus                 R0  R1  R2  RX
  6P LOSS MUTATED    15   1   0   1
  6P LOSS WILD-TYPE 107  10   1   9
D51V8, multiclass
    clus
vv   6P LOSS MUTATED 6P LOSS WILD-TYPE
  R0              15               107
  R1               1                10
  R2               0                 1
  RX               1                 9

Clustering(52) Variable = 6Q LOSS MUTATION ANALYSIS
D52V1, survival
                   sevent
clus2                0  1
  6Q LOSS MUTATED   27 19
  6Q LOSS WILD-TYPE 57 44
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               46               101 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               19                44 
$`6Q LOSS MUTATED`
TCGA-BC-A10Q TCGA-BC-A3KF TCGA-BC-A5W4 TCGA-BC-A69I TCGA-CC-5260 TCGA-CC-A3M9 
       37.32         0.26         9.50         0.53         2.86         0.10 
TCGA-CC-A3MA TCGA-DD-A118 TCGA-DD-A11A TCGA-DD-A11C TCGA-DD-A1E9 TCGA-DD-A1EC 
        0.07       113.00         2.60        21.76        90.71        19.79 
TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK 
        6.71        12.95        45.11         6.02        29.16        18.35 
TCGA-DD-A39X TCGA-DD-A39Z TCGA-DD-A3A1 TCGA-DD-A3A8 TCGA-DD-A4NA TCGA-DD-A4NH 
       55.69        19.76         7.66         0.36        33.14        14.24 
TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NS TCGA-DD-A73E TCGA-ED-A66Y TCGA-ED-A7PZ 
       15.06        39.78        80.75         1.45         0.23         0.20 
TCGA-ED-A82E TCGA-EP-A12J TCGA-EP-A3RK TCGA-ES-A2HS TCGA-FV-A23B TCGA-FV-A2QR 
        0.20        18.74        11.93        22.85        32.45        19.10 
TCGA-FV-A3I0 TCGA-FV-A3R2 TCGA-FV-A4ZP TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25X 
        0.20         6.38        60.36         1.22        51.06        58.49 
TCGA-G3-A5SL TCGA-G3-A6UC TCGA-MI-A75E TCGA-MI-A75I 
        7.99         7.76         5.10         8.71 

$`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-BC-A69H TCGA-CC-5258 TCGA-CC-5261 
       44.42        13.84        22.36         3.95         0.07         0.39 
TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A113 
        3.39         4.24         3.32         0.10         0.13        79.73 
TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A119 TCGA-DD-A11B TCGA-DD-A11D 
       37.78        83.57        53.33         7.33         0.46        51.29 
TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1ED TCGA-DD-A1EH TCGA-DD-A1EL TCGA-DD-A39V 
       79.40        66.31        75.65        49.15        13.64        21.14 
TCGA-DD-A39Y TCGA-DD-A3A0 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 
        5.62        25.81        70.06        17.59        20.12       102.74 
TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A9 TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NF 
      107.11        13.78        30.61        12.85        73.38        14.07 
TCGA-DD-A4NI TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ 
       18.44        56.25        29.56        61.45        93.67        12.26 
TCGA-DD-A4NR TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D 
        0.30        66.35        10.98         9.30         7.56        10.98 
TCGA-DD-A73F TCGA-DD-A73G TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 
       27.72       100.96        13.41        12.69        15.85        13.91 
TCGA-ED-A66X TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7XP TCGA-EP-A26S TCGA-EP-A2KA 
       13.35         0.20         0.20         0.20        19.99        11.74 
TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL TCGA-ES-A2HT TCGA-FV-A3I1 TCGA-FV-A3R3 
       10.98         0.62         9.96        14.40         8.12         0.13 
TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZQ TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W 
        0.03         0.33         0.39        53.79        28.27        30.74 
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         5.92        19.53 
TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SM TCGA-GJ-A6C0 TCGA-K7-A6G5 
       19.23        14.70        11.97         4.37         1.02         4.01 
TCGA-LG-A6GG TCGA-MI-A75C TCGA-MI-A75G TCGA-NI-A4U2 TCGA-O8-A75V 
        0.49         9.57        14.24        58.88         4.44 

  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
             0.07              0.03 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
           113.00            107.11 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
            12.44             14.24 
[1] "0.1 - 113.0 (12.4)" "0.0 - 107.1 (14.2)"
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" 
       TCGA-BC-A3KG        TCGA-BC-A5W4        TCGA-BC-A69H        TCGA-BC-A69I 
"6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" 
       TCGA-CC-5258        TCGA-CC-5260        TCGA-CC-5261        TCGA-CC-5262 
"6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-CC-5263        TCGA-CC-A1HT        TCGA-CC-A3M9        TCGA-CC-A3MA 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED"   "6Q LOSS MUTATED" 
       TCGA-CC-A3MB        TCGA-CC-A3MC        TCGA-DD-A113        TCGA-DD-A114 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118        TCGA-DD-A119 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" 
       TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C        TCGA-DD-A11D 
  "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" 
       TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB        TCGA-DD-A1EC 
  "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" 
       TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EF        TCGA-DD-A1EG 
"6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED"   "6Q LOSS MUTATED"   "6Q LOSS MUTATED" 
       TCGA-DD-A1EH        TCGA-DD-A1EI        TCGA-DD-A1EJ        TCGA-DD-A1EK 
"6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED"   "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-A4NB        TCGA-DD-A4ND        TCGA-DD-A4NF        TCGA-DD-A4NH 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" 
       TCGA-DD-A4NI        TCGA-DD-A4NJ        TCGA-DD-A4NK        TCGA-DD-A4NL 
"6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" 
       TCGA-DD-A4NN        TCGA-DD-A4NO        TCGA-DD-A4NP        TCGA-DD-A4NQ 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-DD-A4NR        TCGA-DD-A4NS        TCGA-DD-A4NV        TCGA-DD-A73A 
"6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-DD-A73B        TCGA-DD-A73C        TCGA-DD-A73D        TCGA-DD-A73E 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" 
       TCGA-DD-A73F        TCGA-DD-A73G        TCGA-ED-A459        TCGA-ED-A4XI 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-ED-A5KG        TCGA-ED-A627        TCGA-ED-A66X        TCGA-ED-A66Y 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" 
       TCGA-ED-A7PX        TCGA-ED-A7PY        TCGA-ED-A7PZ        TCGA-ED-A7XP 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" 
       TCGA-ED-A82E        TCGA-EP-A12J        TCGA-EP-A26S        TCGA-EP-A2KA 
  "6Q LOSS MUTATED"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-EP-A2KB        TCGA-EP-A2KC        TCGA-EP-A3JL        TCGA-EP-A3RK 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" 
       TCGA-ES-A2HS        TCGA-ES-A2HT        TCGA-FV-A23B        TCGA-FV-A2QR 
  "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED"   "6Q LOSS MUTATED" 
       TCGA-FV-A3I0        TCGA-FV-A3I1        TCGA-FV-A3R2        TCGA-FV-A3R3 
  "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" 
       TCGA-FV-A495        TCGA-FV-A496        TCGA-FV-A4ZP        TCGA-FV-A4ZQ 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" 
       TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U        TCGA-G3-A25V 
  "6Q LOSS MUTATED"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y        TCGA-G3-A25Z 
"6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI        TCGA-G3-A3CJ 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-G3-A3CK        TCGA-G3-A5SI        TCGA-G3-A5SJ        TCGA-G3-A5SL 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" 
       TCGA-G3-A5SM        TCGA-G3-A6UC        TCGA-GJ-A6C0        TCGA-K7-A6G5 
"6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-LG-A6GG        TCGA-MI-A75C        TCGA-MI-A75E        TCGA-MI-A75G 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" 
       TCGA-MI-A75I        TCGA-NI-A4U2        TCGA-O8-A75V 
  "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" 
       TCGA-BC-A3KG        TCGA-BC-A5W4        TCGA-BC-A69H        TCGA-BC-A69I 
"6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" 
       TCGA-CC-5258        TCGA-CC-5260        TCGA-CC-5261        TCGA-CC-5262 
"6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-CC-5263        TCGA-CC-A1HT        TCGA-CC-A3M9        TCGA-CC-A3MA 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED"   "6Q LOSS MUTATED" 
       TCGA-CC-A3MB        TCGA-CC-A3MC        TCGA-DD-A113        TCGA-DD-A114 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118        TCGA-DD-A119 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" 
       TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C        TCGA-DD-A11D 
  "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" 
       TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB        TCGA-DD-A1EC 
  "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" 
       TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EF        TCGA-DD-A1EG 
"6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED"   "6Q LOSS MUTATED"   "6Q LOSS MUTATED" 
       TCGA-DD-A1EH        TCGA-DD-A1EI        TCGA-DD-A1EJ        TCGA-DD-A1EK 
"6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED"   "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-A4NB        TCGA-DD-A4ND        TCGA-DD-A4NF        TCGA-DD-A4NH 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" 
       TCGA-DD-A4NI        TCGA-DD-A4NJ        TCGA-DD-A4NK        TCGA-DD-A4NL 
"6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" 
       TCGA-DD-A4NN        TCGA-DD-A4NO        TCGA-DD-A4NP        TCGA-DD-A4NQ 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-DD-A4NR        TCGA-DD-A4NS        TCGA-DD-A4NV        TCGA-DD-A73A 
"6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-DD-A73B        TCGA-DD-A73C        TCGA-DD-A73D        TCGA-DD-A73E 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" 
       TCGA-DD-A73F        TCGA-DD-A73G        TCGA-ED-A459        TCGA-ED-A4XI 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-ED-A5KG        TCGA-ED-A627        TCGA-ED-A66X        TCGA-ED-A66Y 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" 
       TCGA-ED-A7PX        TCGA-ED-A7PY        TCGA-ED-A7PZ        TCGA-ED-A7XP 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" 
       TCGA-ED-A82E        TCGA-EP-A12J        TCGA-EP-A26S        TCGA-EP-A2KA 
  "6Q LOSS MUTATED"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-EP-A2KB        TCGA-EP-A2KC        TCGA-EP-A3JL        TCGA-EP-A3RK 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" 
       TCGA-ES-A2HS        TCGA-ES-A2HT        TCGA-FV-A23B        TCGA-FV-A2QR 
  "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED"   "6Q LOSS MUTATED" 
       TCGA-FV-A3I0        TCGA-FV-A3I1        TCGA-FV-A3R2        TCGA-FV-A3R3 
  "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" 
       TCGA-FV-A495        TCGA-FV-A496        TCGA-FV-A4ZP        TCGA-FV-A4ZQ 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" 
       TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U        TCGA-G3-A25V 
  "6Q LOSS MUTATED"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y        TCGA-G3-A25Z 
"6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI        TCGA-G3-A3CJ 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-G3-A3CK        TCGA-G3-A5SI        TCGA-G3-A5SJ        TCGA-G3-A5SL 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" 
       TCGA-G3-A5SM        TCGA-G3-A6UC        TCGA-GJ-A6C0        TCGA-K7-A6G5 
"6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-LG-A6GG        TCGA-MI-A75C        TCGA-MI-A75E        TCGA-MI-A75G 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" 
       TCGA-MI-A75I        TCGA-NI-A4U2        TCGA-O8-A75V 
  "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" 
       TCGA-BC-A3KG        TCGA-BC-A5W4        TCGA-BC-A69H        TCGA-BC-A69I 
"6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" 
       TCGA-CC-5258        TCGA-CC-5260        TCGA-CC-5261        TCGA-CC-5262 
"6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-CC-5263        TCGA-CC-A1HT        TCGA-CC-A3M9        TCGA-CC-A3MA 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED"   "6Q LOSS MUTATED" 
       TCGA-CC-A3MB        TCGA-CC-A3MC        TCGA-DD-A113        TCGA-DD-A114 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118        TCGA-DD-A119 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" 
       TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C        TCGA-DD-A11D 
  "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" 
       TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB        TCGA-DD-A1EC 
  "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" 
       TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EF        TCGA-DD-A1EG 
"6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED"   "6Q LOSS MUTATED"   "6Q LOSS MUTATED" 
       TCGA-DD-A1EH        TCGA-DD-A1EI        TCGA-DD-A1EJ        TCGA-DD-A1EK 
"6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED"   "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-A4NB        TCGA-DD-A4ND        TCGA-DD-A4NF        TCGA-DD-A4NH 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" 
       TCGA-DD-A4NI        TCGA-DD-A4NJ        TCGA-DD-A4NK        TCGA-DD-A4NL 
"6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" 
       TCGA-DD-A4NN        TCGA-DD-A4NO        TCGA-DD-A4NP        TCGA-DD-A4NQ 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-DD-A4NR        TCGA-DD-A4NS        TCGA-DD-A4NV        TCGA-DD-A73A 
"6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-DD-A73B        TCGA-DD-A73C        TCGA-DD-A73D        TCGA-DD-A73E 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" 
       TCGA-DD-A73F        TCGA-DD-A73G        TCGA-ED-A459        TCGA-ED-A4XI 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-ED-A5KG        TCGA-ED-A627        TCGA-ED-A66X        TCGA-ED-A66Y 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" 
       TCGA-ED-A7PX        TCGA-ED-A7PY        TCGA-ED-A7PZ        TCGA-ED-A7XP 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" 
       TCGA-ED-A82E        TCGA-EP-A12J        TCGA-EP-A26S        TCGA-EP-A2KA 
  "6Q LOSS MUTATED"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-EP-A2KB        TCGA-EP-A2KC        TCGA-EP-A3JL        TCGA-EP-A3RK 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" 
       TCGA-ES-A2HS        TCGA-ES-A2HT        TCGA-FV-A23B        TCGA-FV-A2QR 
  "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED"   "6Q LOSS MUTATED" 
       TCGA-FV-A3I0        TCGA-FV-A3I1        TCGA-FV-A3R2        TCGA-FV-A3R3 
  "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" 
       TCGA-FV-A495        TCGA-FV-A496        TCGA-FV-A4ZP        TCGA-FV-A4ZQ 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" 
       TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U        TCGA-G3-A25V 
  "6Q LOSS MUTATED"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y        TCGA-G3-A25Z 
"6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI        TCGA-G3-A3CJ 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-G3-A3CK        TCGA-G3-A5SI        TCGA-G3-A5SJ        TCGA-G3-A5SL 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" 
       TCGA-G3-A5SM        TCGA-G3-A6UC        TCGA-GJ-A6C0        TCGA-K7-A6G5 
"6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-LG-A6GG        TCGA-MI-A75C        TCGA-MI-A75E        TCGA-MI-A75G 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" 
       TCGA-MI-A75I        TCGA-NI-A4U2        TCGA-O8-A75V 
  "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" "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        17        8         0         12          2          4
  6Q LOSS WILD-TYPE      41       28         2         18          2          1
                   vv
clus                STAGE IV STAGE IVA STAGE IVB
  6Q LOSS MUTATED          0         0         1
  6Q LOSS WILD-TYPE        1         1         1
D52V3, multiclass
                   vv
clus                T1 T2 T3 T4
  6Q LOSS MUTATED   18 11 14  3
  6Q LOSS WILD-TYPE 43 29 26  5
D52V4, multiclass
    clus
vv   6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  T1              18                43
  T2              11                29
  T3              14                26
  T4               3                 5
D52V5, binary
                   cls
clus                 0  1
  6Q LOSS MUTATED   30  2
  6Q LOSS WILD-TYPE 67  1
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED     30    2
  6Q LOSS WILD-TYPE   67    1
   clus
vv  6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  0              30                67
  1               2                 1
                   vv
clus                M0 M1 MX
  6Q LOSS MUTATED   39  1  6
  6Q LOSS WILD-TYPE 76  2 25
D52V6, multiclass
    clus
vv   6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  M0              39                76
  M1               1                 2
  MX               6                25
D52V7, binary
                   cls
clus                 0  1
  6Q LOSS MUTATED   20 26
  6Q LOSS WILD-TYPE 38 65
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED     20   26
  6Q LOSS WILD-TYPE   38   65
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  FEMALE              20                38
  MALE                26                65
                   vv
clus                R0 R1 R2 RX
  6Q LOSS MUTATED   38  4  0  3
  6Q LOSS WILD-TYPE 84  7  1  7
D52V8, multiclass
    clus
vv   6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  R0              38                84
  R1               4                 7
  R2               0                 1
  RX               3                 7

Clustering(53) Variable = 7P LOSS MUTATION ANALYSIS
D53V1, survival
                   sevent
clus2                0  1
  7P LOSS MUTATED    3  5
  7P LOSS WILD-TYPE 81 58
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
                8               139 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
                5                58 
$`7P LOSS MUTATED`
TCGA-BC-A217 TCGA-BC-A3KG TCGA-CC-5261 TCGA-CC-A3M9 TCGA-DD-A1EF TCGA-DD-A39X 
       13.84        22.36         0.39         0.10        12.95        55.69 
TCGA-EP-A2KB TCGA-FV-A3I1 
       10.98         8.12 

$`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-BC-A69H TCGA-BC-A69I 
        5.03        44.42         0.26         9.50         3.95         0.53 
TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3MA 
        0.07         2.86         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        37.78        83.57        53.33 
TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D 
      113.00         7.33         2.60         0.46        21.76        51.29 
TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE 
       90.71        79.40        66.31        19.79        75.65         6.71 
TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A1EL 
       45.11        49.15         6.02        29.16        18.35        13.64 
TCGA-DD-A39V TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 
       21.14         5.62        19.76        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-A4NB TCGA-DD-A4ND TCGA-DD-A4NF TCGA-DD-A4NH 
       30.61        33.14        12.85        73.38        14.07        14.24 
TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO 
       18.44        15.06        39.78        56.25        29.56        61.45 
TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A 
       93.67        12.26         0.30        80.75        66.35        10.98 
TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G 
        9.30         7.56        10.98         1.45        27.72       100.96 
TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y 
       13.41        12.69        15.85        13.91        13.35         0.23 
TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XP TCGA-ED-A82E TCGA-EP-A12J 
        0.20         0.20         0.20         0.20         0.20        18.74 
TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS 
       19.99        11.74         0.62         9.96        11.93        22.85 
TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3R2 TCGA-FV-A3R3 
       14.40        32.45        19.10         0.20         6.38         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        51.06 
TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A25Z 
       53.79        28.27        30.74        58.49        14.86        21.53 
TCGA-G3-A3CG TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI 
       22.13        25.64         5.92        19.53        19.23        14.70 
TCGA-G3-A5SJ TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A6UC TCGA-GJ-A6C0 TCGA-K7-A6G5 
       11.97         7.99         4.37         7.76         1.02         4.01 
TCGA-LG-A6GG TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75I TCGA-NI-A4U2 
        0.49         9.57         5.10        14.24         8.71        58.88 
TCGA-O8-A75V 
        4.44 

  7P LOSS MUTATED 7P LOSS WILD-TYPE 
             0.10              0.03 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
            55.69            113.00 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
           11.965            14.240 
[1] "0.1 - 55.7 (12.0)"  "0.0 - 113.0 (14.2)"
       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-BC-A69H        TCGA-BC-A69I 
  "7P LOSS MUTATED" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-CC-5258        TCGA-CC-5260        TCGA-CC-5261        TCGA-CC-5262 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE"   "7P LOSS MUTATED" "7P LOSS WILD-TYPE" 
       TCGA-CC-5263        TCGA-CC-A1HT        TCGA-CC-A3M9        TCGA-CC-A3MA 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE"   "7P LOSS MUTATED" "7P LOSS WILD-TYPE" 
       TCGA-CC-A3MB        TCGA-CC-A3MC        TCGA-DD-A113        TCGA-DD-A114 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118        TCGA-DD-A119 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C        TCGA-DD-A11D 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB        TCGA-DD-A1EC 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EF        TCGA-DD-A1EG 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE"   "7P LOSS MUTATED" "7P LOSS WILD-TYPE" 
       TCGA-DD-A1EH        TCGA-DD-A1EI        TCGA-DD-A1EJ        TCGA-DD-A1EK 
"7P LOSS WILD-TYPE" "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-A4NB        TCGA-DD-A4ND        TCGA-DD-A4NF        TCGA-DD-A4NH 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DD-A4NI        TCGA-DD-A4NJ        TCGA-DD-A4NK        TCGA-DD-A4NL 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DD-A4NN        TCGA-DD-A4NO        TCGA-DD-A4NP        TCGA-DD-A4NQ 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DD-A4NR        TCGA-DD-A4NS        TCGA-DD-A4NV        TCGA-DD-A73A 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DD-A73B        TCGA-DD-A73C        TCGA-DD-A73D        TCGA-DD-A73E 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DD-A73F        TCGA-DD-A73G        TCGA-ED-A459        TCGA-ED-A4XI 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-ED-A5KG        TCGA-ED-A627        TCGA-ED-A66X        TCGA-ED-A66Y 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-ED-A7PX        TCGA-ED-A7PY        TCGA-ED-A7PZ        TCGA-ED-A7XP 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-ED-A82E        TCGA-EP-A12J        TCGA-EP-A26S        TCGA-EP-A2KA 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-EP-A2KB        TCGA-EP-A2KC        TCGA-EP-A3JL        TCGA-EP-A3RK 
  "7P LOSS MUTATED" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-ES-A2HS        TCGA-ES-A2HT        TCGA-FV-A23B        TCGA-FV-A2QR 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-FV-A3I0        TCGA-FV-A3I1        TCGA-FV-A3R2        TCGA-FV-A3R3 
"7P LOSS WILD-TYPE"   "7P LOSS MUTATED" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-FV-A495        TCGA-FV-A496        TCGA-FV-A4ZP        TCGA-FV-A4ZQ 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U        TCGA-G3-A25V 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y        TCGA-G3-A25Z 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI        TCGA-G3-A3CJ 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-G3-A3CK        TCGA-G3-A5SI        TCGA-G3-A5SJ        TCGA-G3-A5SL 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-G3-A5SM        TCGA-G3-A6UC        TCGA-GJ-A6C0        TCGA-K7-A6G5 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-LG-A6GG        TCGA-MI-A75C        TCGA-MI-A75E        TCGA-MI-A75G 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-MI-A75I        TCGA-NI-A4U2        TCGA-O8-A75V 
"7P LOSS WILD-TYPE" "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-BC-A69H        TCGA-BC-A69I 
  "7P LOSS MUTATED" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-CC-5258        TCGA-CC-5260        TCGA-CC-5261        TCGA-CC-5262 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE"   "7P LOSS MUTATED" "7P LOSS WILD-TYPE" 
       TCGA-CC-5263        TCGA-CC-A1HT        TCGA-CC-A3M9        TCGA-CC-A3MA 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE"   "7P LOSS MUTATED" "7P LOSS WILD-TYPE" 
       TCGA-CC-A3MB        TCGA-CC-A3MC        TCGA-DD-A113        TCGA-DD-A114 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118        TCGA-DD-A119 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C        TCGA-DD-A11D 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB        TCGA-DD-A1EC 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EF        TCGA-DD-A1EG 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE"   "7P LOSS MUTATED" "7P LOSS WILD-TYPE" 
       TCGA-DD-A1EH        TCGA-DD-A1EI        TCGA-DD-A1EJ        TCGA-DD-A1EK 
"7P LOSS WILD-TYPE" "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-A4NB        TCGA-DD-A4ND        TCGA-DD-A4NF        TCGA-DD-A4NH 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DD-A4NI        TCGA-DD-A4NJ        TCGA-DD-A4NK        TCGA-DD-A4NL 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DD-A4NN        TCGA-DD-A4NO        TCGA-DD-A4NP        TCGA-DD-A4NQ 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DD-A4NR        TCGA-DD-A4NS        TCGA-DD-A4NV        TCGA-DD-A73A 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DD-A73B        TCGA-DD-A73C        TCGA-DD-A73D        TCGA-DD-A73E 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DD-A73F        TCGA-DD-A73G        TCGA-ED-A459        TCGA-ED-A4XI 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-ED-A5KG        TCGA-ED-A627        TCGA-ED-A66X        TCGA-ED-A66Y 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-ED-A7PX        TCGA-ED-A7PY        TCGA-ED-A7PZ        TCGA-ED-A7XP 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-ED-A82E        TCGA-EP-A12J        TCGA-EP-A26S        TCGA-EP-A2KA 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-EP-A2KB        TCGA-EP-A2KC        TCGA-EP-A3JL        TCGA-EP-A3RK 
  "7P LOSS MUTATED" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-ES-A2HS        TCGA-ES-A2HT        TCGA-FV-A23B        TCGA-FV-A2QR 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-FV-A3I0        TCGA-FV-A3I1        TCGA-FV-A3R2        TCGA-FV-A3R3 
"7P LOSS WILD-TYPE"   "7P LOSS MUTATED" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-FV-A495        TCGA-FV-A496        TCGA-FV-A4ZP        TCGA-FV-A4ZQ 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U        TCGA-G3-A25V 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y        TCGA-G3-A25Z 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI        TCGA-G3-A3CJ 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-G3-A3CK        TCGA-G3-A5SI        TCGA-G3-A5SJ        TCGA-G3-A5SL 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-G3-A5SM        TCGA-G3-A6UC        TCGA-GJ-A6C0        TCGA-K7-A6G5 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-LG-A6GG        TCGA-MI-A75C        TCGA-MI-A75E        TCGA-MI-A75G 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-MI-A75I        TCGA-NI-A4U2        TCGA-O8-A75V 
"7P LOSS WILD-TYPE" "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-BC-A69H        TCGA-BC-A69I 
  "7P LOSS MUTATED" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-CC-5258        TCGA-CC-5260        TCGA-CC-5261        TCGA-CC-5262 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE"   "7P LOSS MUTATED" "7P LOSS WILD-TYPE" 
       TCGA-CC-5263        TCGA-CC-A1HT        TCGA-CC-A3M9        TCGA-CC-A3MA 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE"   "7P LOSS MUTATED" "7P LOSS WILD-TYPE" 
       TCGA-CC-A3MB        TCGA-CC-A3MC        TCGA-DD-A113        TCGA-DD-A114 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118        TCGA-DD-A119 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C        TCGA-DD-A11D 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB        TCGA-DD-A1EC 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EF        TCGA-DD-A1EG 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE"   "7P LOSS MUTATED" "7P LOSS WILD-TYPE" 
       TCGA-DD-A1EH        TCGA-DD-A1EI        TCGA-DD-A1EJ        TCGA-DD-A1EK 
"7P LOSS WILD-TYPE" "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-A4NB        TCGA-DD-A4ND        TCGA-DD-A4NF        TCGA-DD-A4NH 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DD-A4NI        TCGA-DD-A4NJ        TCGA-DD-A4NK        TCGA-DD-A4NL 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DD-A4NN        TCGA-DD-A4NO        TCGA-DD-A4NP        TCGA-DD-A4NQ 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DD-A4NR        TCGA-DD-A4NS        TCGA-DD-A4NV        TCGA-DD-A73A 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DD-A73B        TCGA-DD-A73C        TCGA-DD-A73D        TCGA-DD-A73E 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DD-A73F        TCGA-DD-A73G        TCGA-ED-A459        TCGA-ED-A4XI 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-ED-A5KG        TCGA-ED-A627        TCGA-ED-A66X        TCGA-ED-A66Y 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-ED-A7PX        TCGA-ED-A7PY        TCGA-ED-A7PZ        TCGA-ED-A7XP 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-ED-A82E        TCGA-EP-A12J        TCGA-EP-A26S        TCGA-EP-A2KA 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-EP-A2KB        TCGA-EP-A2KC        TCGA-EP-A3JL        TCGA-EP-A3RK 
  "7P LOSS MUTATED" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-ES-A2HS        TCGA-ES-A2HT        TCGA-FV-A23B        TCGA-FV-A2QR 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-FV-A3I0        TCGA-FV-A3I1        TCGA-FV-A3R2        TCGA-FV-A3R3 
"7P LOSS WILD-TYPE"   "7P LOSS MUTATED" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-FV-A495        TCGA-FV-A496        TCGA-FV-A4ZP        TCGA-FV-A4ZQ 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U        TCGA-G3-A25V 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y        TCGA-G3-A25Z 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI        TCGA-G3-A3CJ 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-G3-A3CK        TCGA-G3-A5SI        TCGA-G3-A5SJ        TCGA-G3-A5SL 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-G3-A5SM        TCGA-G3-A6UC        TCGA-GJ-A6C0        TCGA-K7-A6G5 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-LG-A6GG        TCGA-MI-A75C        TCGA-MI-A75E        TCGA-MI-A75G 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-MI-A75I        TCGA-NI-A4U2        TCGA-O8-A75V 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
[1] "hr=" "2.3"
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      55       32         2         29          4          5
                   vv
clus                STAGE IV STAGE IVA STAGE IVB
  7P LOSS MUTATED          0         0         0
  7P LOSS WILD-TYPE        1         1         2
D53V3, multiclass
                   vv
clus                T1 T2 T3 T4
  7P LOSS MUTATED    3  4  1  0
  7P LOSS WILD-TYPE 58 36 39  8
D53V4, multiclass
    clus
vv   7P LOSS MUTATED 7P LOSS WILD-TYPE
  T1               3                58
  T2               4                36
  T3               1                39
  T4               0                 8
D53V5, binary
                   cls
clus                 0  1
  7P LOSS MUTATED    5  0
  7P LOSS WILD-TYPE 92  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED      5    0
  7P LOSS WILD-TYPE   92    3
   clus
vv  7P LOSS MUTATED 7P LOSS WILD-TYPE
  0               5                92
  1               0                 3
                   vv
clus                 M0  M1  MX
  7P LOSS MUTATED     6   0   2
  7P LOSS WILD-TYPE 109   3  29
D53V6, multiclass
    clus
vv   7P LOSS MUTATED 7P LOSS WILD-TYPE
  M0               6               109
  M1               0                 3
  MX               2                29
D53V7, binary
                   cls
clus                 0  1
  7P LOSS MUTATED    6  2
  7P LOSS WILD-TYPE 52 89
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED      6    2
  7P LOSS WILD-TYPE   52   89
        clus
vv       7P LOSS MUTATED 7P LOSS WILD-TYPE
  FEMALE               6                52
  MALE                 2                89
                   vv
clus                 R0  R1  R2  RX
  7P LOSS MUTATED     7   0   0   1
  7P LOSS WILD-TYPE 115  11   1   9
D53V8, multiclass
    clus
vv   7P LOSS MUTATED 7P LOSS WILD-TYPE
  R0               7               115
  R1               0                11
  R2               0                 1
  RX               1                 9

Clustering(54) Variable = 7Q LOSS MUTATION ANALYSIS
D54V1, survival
                   sevent
clus2                0  1
  7Q LOSS MUTATED    4  7
  7Q LOSS WILD-TYPE 80 56
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
               11               136 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
                7                56 
$`7Q LOSS MUTATED`
TCGA-BC-4072 TCGA-BC-A217 TCGA-BC-A3KG TCGA-CC-5261 TCGA-DD-A1EF TCGA-DD-A1EL 
       48.99        13.84        22.36         0.39        12.95        13.64 
TCGA-DD-A39X TCGA-DD-A4ND TCGA-ED-A7PX TCGA-EP-A2KB TCGA-G3-A25S 
       55.69        73.38         0.20        10.98         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-BC-A69H TCGA-BC-A69I TCGA-CC-5258 
       44.42         0.26         9.50         3.95         0.53         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-A113 TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 
        0.10         0.13        79.73        37.78        83.57        53.33 
TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D 
      113.00         7.33         2.60         0.46        21.76        51.29 
TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE 
       90.71        79.40        66.31        19.79        75.65         6.71 
TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A39V 
       45.11        49.15         6.02        29.16        18.35        21.14 
TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 
        5.62        19.76        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        30.61 
TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ 
       33.14        12.85        14.07        14.24        18.44        15.06 
TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ 
       39.78        56.25        29.56        61.45        93.67        12.26 
TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C 
        0.30        80.75        66.35        10.98         9.30         7.56 
TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G TCGA-ED-A459 TCGA-ED-A4XI 
       10.98         1.45        27.72       100.96        13.41        12.69 
TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PY TCGA-ED-A7PZ 
       15.85        13.91        13.35         0.23         0.20         0.20 
TCGA-ED-A7XP TCGA-ED-A82E TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KC 
        0.20         0.20        18.74        19.99        11.74         0.62 
TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QR 
        9.96        11.93        22.85        14.40        32.45        19.10 
TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 
        0.20         8.12         6.38         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        51.06        53.79        28.27        30.74 
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         5.92 
TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SL TCGA-G3-A5SM 
       19.53        19.23        14.70        11.97         7.99         4.37 
TCGA-G3-A6UC TCGA-GJ-A6C0 TCGA-K7-A6G5 TCGA-LG-A6GG TCGA-MI-A75C TCGA-MI-A75E 
        7.76         1.02         4.01         0.49         9.57         5.10 
TCGA-MI-A75G TCGA-MI-A75I TCGA-NI-A4U2 TCGA-O8-A75V 
       14.24         8.71        58.88         4.44 

  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
             0.20              0.03 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
            73.38            113.00 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
            13.64             14.24 
[1] "0.2 - 73.4 (13.6)"  "0.0 - 113.0 (14.2)"
       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-BC-A69H        TCGA-BC-A69I 
  "7Q LOSS MUTATED" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-CC-5258        TCGA-CC-5260        TCGA-CC-5261        TCGA-CC-5262 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE"   "7Q LOSS MUTATED" "7Q LOSS WILD-TYPE" 
       TCGA-CC-5263        TCGA-CC-A1HT        TCGA-CC-A3M9        TCGA-CC-A3MA 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-CC-A3MB        TCGA-CC-A3MC        TCGA-DD-A113        TCGA-DD-A114 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118        TCGA-DD-A119 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C        TCGA-DD-A11D 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB        TCGA-DD-A1EC 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EF        TCGA-DD-A1EG 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE"   "7Q LOSS MUTATED" "7Q LOSS WILD-TYPE" 
       TCGA-DD-A1EH        TCGA-DD-A1EI        TCGA-DD-A1EJ        TCGA-DD-A1EK 
"7Q LOSS WILD-TYPE" "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-A4NB        TCGA-DD-A4ND        TCGA-DD-A4NF        TCGA-DD-A4NH 
"7Q LOSS WILD-TYPE"   "7Q LOSS MUTATED" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-DD-A4NI        TCGA-DD-A4NJ        TCGA-DD-A4NK        TCGA-DD-A4NL 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-DD-A4NN        TCGA-DD-A4NO        TCGA-DD-A4NP        TCGA-DD-A4NQ 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-DD-A4NR        TCGA-DD-A4NS        TCGA-DD-A4NV        TCGA-DD-A73A 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-DD-A73B        TCGA-DD-A73C        TCGA-DD-A73D        TCGA-DD-A73E 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-DD-A73F        TCGA-DD-A73G        TCGA-ED-A459        TCGA-ED-A4XI 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-ED-A5KG        TCGA-ED-A627        TCGA-ED-A66X        TCGA-ED-A66Y 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-ED-A7PX        TCGA-ED-A7PY        TCGA-ED-A7PZ        TCGA-ED-A7XP 
  "7Q LOSS MUTATED" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-ED-A82E        TCGA-EP-A12J        TCGA-EP-A26S        TCGA-EP-A2KA 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-EP-A2KB        TCGA-EP-A2KC        TCGA-EP-A3JL        TCGA-EP-A3RK 
  "7Q LOSS MUTATED" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-ES-A2HS        TCGA-ES-A2HT        TCGA-FV-A23B        TCGA-FV-A2QR 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-FV-A3I0        TCGA-FV-A3I1        TCGA-FV-A3R2        TCGA-FV-A3R3 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-FV-A495        TCGA-FV-A496        TCGA-FV-A4ZP        TCGA-FV-A4ZQ 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U        TCGA-G3-A25V 
  "7Q LOSS MUTATED" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y        TCGA-G3-A25Z 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI        TCGA-G3-A3CJ 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-G3-A3CK        TCGA-G3-A5SI        TCGA-G3-A5SJ        TCGA-G3-A5SL 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-G3-A5SM        TCGA-G3-A6UC        TCGA-GJ-A6C0        TCGA-K7-A6G5 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-LG-A6GG        TCGA-MI-A75C        TCGA-MI-A75E        TCGA-MI-A75G 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-MI-A75I        TCGA-NI-A4U2        TCGA-O8-A75V 
"7Q LOSS WILD-TYPE" "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-BC-A69H        TCGA-BC-A69I 
  "7Q LOSS MUTATED" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-CC-5258        TCGA-CC-5260        TCGA-CC-5261        TCGA-CC-5262 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE"   "7Q LOSS MUTATED" "7Q LOSS WILD-TYPE" 
       TCGA-CC-5263        TCGA-CC-A1HT        TCGA-CC-A3M9        TCGA-CC-A3MA 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-CC-A3MB        TCGA-CC-A3MC        TCGA-DD-A113        TCGA-DD-A114 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118        TCGA-DD-A119 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C        TCGA-DD-A11D 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB        TCGA-DD-A1EC 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EF        TCGA-DD-A1EG 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE"   "7Q LOSS MUTATED" "7Q LOSS WILD-TYPE" 
       TCGA-DD-A1EH        TCGA-DD-A1EI        TCGA-DD-A1EJ        TCGA-DD-A1EK 
"7Q LOSS WILD-TYPE" "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-A4NB        TCGA-DD-A4ND        TCGA-DD-A4NF        TCGA-DD-A4NH 
"7Q LOSS WILD-TYPE"   "7Q LOSS MUTATED" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-DD-A4NI        TCGA-DD-A4NJ        TCGA-DD-A4NK        TCGA-DD-A4NL 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-DD-A4NN        TCGA-DD-A4NO        TCGA-DD-A4NP        TCGA-DD-A4NQ 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-DD-A4NR        TCGA-DD-A4NS        TCGA-DD-A4NV        TCGA-DD-A73A 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-DD-A73B        TCGA-DD-A73C        TCGA-DD-A73D        TCGA-DD-A73E 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-DD-A73F        TCGA-DD-A73G        TCGA-ED-A459        TCGA-ED-A4XI 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-ED-A5KG        TCGA-ED-A627        TCGA-ED-A66X        TCGA-ED-A66Y 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-ED-A7PX        TCGA-ED-A7PY        TCGA-ED-A7PZ        TCGA-ED-A7XP 
  "7Q LOSS MUTATED" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-ED-A82E        TCGA-EP-A12J        TCGA-EP-A26S        TCGA-EP-A2KA 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-EP-A2KB        TCGA-EP-A2KC        TCGA-EP-A3JL        TCGA-EP-A3RK 
  "7Q LOSS MUTATED" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-ES-A2HS        TCGA-ES-A2HT        TCGA-FV-A23B        TCGA-FV-A2QR 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-FV-A3I0        TCGA-FV-A3I1        TCGA-FV-A3R2        TCGA-FV-A3R3 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-FV-A495        TCGA-FV-A496        TCGA-FV-A4ZP        TCGA-FV-A4ZQ 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U        TCGA-G3-A25V 
  "7Q LOSS MUTATED" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y        TCGA-G3-A25Z 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI        TCGA-G3-A3CJ 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-G3-A3CK        TCGA-G3-A5SI        TCGA-G3-A5SJ        TCGA-G3-A5SL 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-G3-A5SM        TCGA-G3-A6UC        TCGA-GJ-A6C0        TCGA-K7-A6G5 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-LG-A6GG        TCGA-MI-A75C        TCGA-MI-A75E        TCGA-MI-A75G 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-MI-A75I        TCGA-NI-A4U2        TCGA-O8-A75V 
"7Q LOSS WILD-TYPE" "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-BC-A69H        TCGA-BC-A69I 
  "7Q LOSS MUTATED" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-CC-5258        TCGA-CC-5260        TCGA-CC-5261        TCGA-CC-5262 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE"   "7Q LOSS MUTATED" "7Q LOSS WILD-TYPE" 
       TCGA-CC-5263        TCGA-CC-A1HT        TCGA-CC-A3M9        TCGA-CC-A3MA 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-CC-A3MB        TCGA-CC-A3MC        TCGA-DD-A113        TCGA-DD-A114 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118        TCGA-DD-A119 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C        TCGA-DD-A11D 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB        TCGA-DD-A1EC 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EF        TCGA-DD-A1EG 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE"   "7Q LOSS MUTATED" "7Q LOSS WILD-TYPE" 
       TCGA-DD-A1EH        TCGA-DD-A1EI        TCGA-DD-A1EJ        TCGA-DD-A1EK 
"7Q LOSS WILD-TYPE" "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-A4NB        TCGA-DD-A4ND        TCGA-DD-A4NF        TCGA-DD-A4NH 
"7Q LOSS WILD-TYPE"   "7Q LOSS MUTATED" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-DD-A4NI        TCGA-DD-A4NJ        TCGA-DD-A4NK        TCGA-DD-A4NL 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-DD-A4NN        TCGA-DD-A4NO        TCGA-DD-A4NP        TCGA-DD-A4NQ 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-DD-A4NR        TCGA-DD-A4NS        TCGA-DD-A4NV        TCGA-DD-A73A 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-DD-A73B        TCGA-DD-A73C        TCGA-DD-A73D        TCGA-DD-A73E 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-DD-A73F        TCGA-DD-A73G        TCGA-ED-A459        TCGA-ED-A4XI 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-ED-A5KG        TCGA-ED-A627        TCGA-ED-A66X        TCGA-ED-A66Y 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-ED-A7PX        TCGA-ED-A7PY        TCGA-ED-A7PZ        TCGA-ED-A7XP 
  "7Q LOSS MUTATED" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-ED-A82E        TCGA-EP-A12J        TCGA-EP-A26S        TCGA-EP-A2KA 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-EP-A2KB        TCGA-EP-A2KC        TCGA-EP-A3JL        TCGA-EP-A3RK 
  "7Q LOSS MUTATED" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-ES-A2HS        TCGA-ES-A2HT        TCGA-FV-A23B        TCGA-FV-A2QR 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-FV-A3I0        TCGA-FV-A3I1        TCGA-FV-A3R2        TCGA-FV-A3R3 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-FV-A495        TCGA-FV-A496        TCGA-FV-A4ZP        TCGA-FV-A4ZQ 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U        TCGA-G3-A25V 
  "7Q LOSS MUTATED" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y        TCGA-G3-A25Z 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI        TCGA-G3-A3CJ 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-G3-A3CK        TCGA-G3-A5SI        TCGA-G3-A5SJ        TCGA-G3-A5SL 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-G3-A5SM        TCGA-G3-A6UC        TCGA-GJ-A6C0        TCGA-K7-A6G5 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-LG-A6GG        TCGA-MI-A75C        TCGA-MI-A75E        TCGA-MI-A75G 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-MI-A75I        TCGA-NI-A4U2        TCGA-O8-A75V 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
[1] "hr=" "1.7"
D54V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  7Q LOSS MUTATED         5        5         0          1          0          0
  7Q LOSS WILD-TYPE      53       31         2         29          4          5
                   vv
clus                STAGE IV STAGE IVA STAGE IVB
  7Q LOSS MUTATED          0         0         0
  7Q LOSS WILD-TYPE        1         1         2
D54V3, multiclass
                   vv
clus                T1 T2 T3 T4
  7Q LOSS MUTATED    5  5  1  0
  7Q LOSS WILD-TYPE 56 35 39  8
D54V4, multiclass
    clus
vv   7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  T1               5                56
  T2               5                35
  T3               1                39
  T4               0                 8
D54V5, binary
                   cls
clus                 0  1
  7Q LOSS MUTATED    7  0
  7Q LOSS WILD-TYPE 90  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED      7    0
  7Q LOSS WILD-TYPE   90    3
   clus
vv  7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  0               7                90
  1               0                 3
                   vv
clus                 M0  M1  MX
  7Q LOSS MUTATED    10   0   1
  7Q LOSS WILD-TYPE 105   3  30
D54V6, multiclass
    clus
vv   7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  M0              10               105
  M1               0                 3
  MX               1                30
D54V7, binary
                   cls
clus                 0  1
  7Q LOSS MUTATED    8  3
  7Q LOSS WILD-TYPE 50 88
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED      8    3
  7Q LOSS WILD-TYPE   50   88
        clus
vv       7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  FEMALE               8                50
  MALE                 3                88
                   vv
clus                 R0  R1  R2  RX
  7Q LOSS MUTATED     8   2   0   1
  7Q LOSS WILD-TYPE 114   9   1   9
D54V8, multiclass
    clus
vv   7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  R0               8               114
  R1               2                 9
  R2               0                 1
  RX               1                 9

Clustering(55) Variable = 8P LOSS MUTATION ANALYSIS
D55V1, survival
                   sevent
clus2                0  1
  8P LOSS MUTATED   41 32
  8P LOSS WILD-TYPE 43 31
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               73                74 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               32                31 
$`8P LOSS MUTATED`
TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A112 TCGA-BC-A216 
       37.32        10.13        27.52        27.52         5.03        44.42 
TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A69H TCGA-BC-A69I TCGA-CC-5261 
       13.84         0.26        22.36         3.95         0.53         0.39 
TCGA-CC-5262 TCGA-DD-A113 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A11C 
        3.39        79.73        83.57        53.33       113.00        21.76 
TCGA-DD-A1EE TCGA-DD-A1EG TCGA-DD-A1EJ TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39Y 
        6.71        45.11        29.16        13.64        21.14         5.62 
TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A3 TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A3A9 
       19.76        25.81        17.59        13.78         0.36        30.61 
TCGA-DD-A4NA TCGA-DD-A4ND TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK 
       33.14        73.38        14.24        18.44        15.06        39.78 
TCGA-DD-A4NR TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D 
        0.30        66.35        10.98         9.30         7.56        10.98 
TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-EP-A12J 
        1.45        27.72       100.96         0.20         0.20        18.74 
TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KC TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT 
       19.99        11.74         0.62        11.93        22.85        14.40 
TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A495 TCGA-FV-A4ZP 
       19.10         0.20         8.12         6.38         0.03        60.36 
TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A3CG TCGA-G3-A3CJ 
        0.39         1.22        28.27        30.74        22.13        19.53 
TCGA-G3-A5SJ TCGA-G3-A6UC TCGA-K7-A6G5 TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75I 
       11.97         7.76         4.01         9.57         5.10         8.71 
TCGA-O8-A75V 
        4.44 

$`8P LOSS WILD-TYPE`
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10S TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y 
       48.99        27.91        46.78         2.99        25.32        23.34 
TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A5W4 TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5263 
        1.12        69.57         9.50         0.07         2.86         4.24 
TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A114 
        3.32         0.10         0.07         0.10         0.13        37.78 
TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA 
        7.33         2.60         0.46        51.29        90.71        79.40 
TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EF TCGA-DD-A1EH TCGA-DD-A1EI 
       66.31        19.79        75.65        12.95        49.15         6.02 
TCGA-DD-A1EK TCGA-DD-A39X TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A4 TCGA-DD-A3A5 
       18.35        55.69         7.66        70.06        20.12       102.74 
TCGA-DD-A3A6 TCGA-DD-A4NB TCGA-DD-A4NF TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO 
      107.11        12.85        14.07        56.25        29.56        61.45 
TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NS TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG 
       93.67        12.26        80.75        13.41        12.69        15.85 
TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7XP TCGA-ED-A82E 
       13.91        13.35         0.23         0.20         0.20         0.20 
TCGA-EP-A2KB TCGA-EP-A3JL TCGA-FV-A23B TCGA-FV-A3R3 TCGA-FV-A496 TCGA-G3-A25T 
       10.98         9.96        32.45         0.13         0.33        51.06 
TCGA-G3-A25U TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CH TCGA-G3-A3CI 
       53.79        58.49        14.86        21.53        25.64         5.92 
TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SL TCGA-G3-A5SM TCGA-GJ-A6C0 TCGA-LG-A6GG 
       19.23        14.70         7.99         4.37         1.02         0.49 
TCGA-MI-A75G TCGA-NI-A4U2 
       14.24        58.88 

  8P LOSS MUTATED 8P LOSS WILD-TYPE 
             0.03              0.07 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
           113.00            107.11 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
           13.840            14.155 
[1] "0.0 - 113.0 (13.8)" "0.1 - 107.1 (14.2)"
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
"8P LOSS WILD-TYPE" "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-BC-A69H        TCGA-BC-A69I 
  "8P LOSS MUTATED" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED"   "8P LOSS MUTATED" 
       TCGA-CC-5258        TCGA-CC-5260        TCGA-CC-5261        TCGA-CC-5262 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED"   "8P LOSS MUTATED" 
       TCGA-CC-5263        TCGA-CC-A1HT        TCGA-CC-A3M9        TCGA-CC-A3MA 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-CC-A3MB        TCGA-CC-A3MC        TCGA-DD-A113        TCGA-DD-A114 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" 
       TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118        TCGA-DD-A119 
  "8P LOSS MUTATED"   "8P LOSS MUTATED"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" 
       TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C        TCGA-DD-A11D 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" 
       TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB        TCGA-DD-A1EC 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EF        TCGA-DD-A1EG 
"8P LOSS WILD-TYPE"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" 
       TCGA-DD-A1EH        TCGA-DD-A1EI        TCGA-DD-A1EJ        TCGA-DD-A1EK 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" 
       TCGA-DD-A1EL        TCGA-DD-A39V        TCGA-DD-A39X        TCGA-DD-A39Y 
  "8P LOSS MUTATED"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE"   "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-A4NB        TCGA-DD-A4ND        TCGA-DD-A4NF        TCGA-DD-A4NH 
"8P LOSS WILD-TYPE"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" 
       TCGA-DD-A4NI        TCGA-DD-A4NJ        TCGA-DD-A4NK        TCGA-DD-A4NL 
  "8P LOSS MUTATED"   "8P LOSS MUTATED"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" 
       TCGA-DD-A4NN        TCGA-DD-A4NO        TCGA-DD-A4NP        TCGA-DD-A4NQ 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-DD-A4NR        TCGA-DD-A4NS        TCGA-DD-A4NV        TCGA-DD-A73A 
  "8P LOSS MUTATED" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED"   "8P LOSS MUTATED" 
       TCGA-DD-A73B        TCGA-DD-A73C        TCGA-DD-A73D        TCGA-DD-A73E 
  "8P LOSS MUTATED"   "8P LOSS MUTATED"   "8P LOSS MUTATED"   "8P LOSS MUTATED" 
       TCGA-DD-A73F        TCGA-DD-A73G        TCGA-ED-A459        TCGA-ED-A4XI 
  "8P LOSS MUTATED"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-ED-A5KG        TCGA-ED-A627        TCGA-ED-A66X        TCGA-ED-A66Y 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-ED-A7PX        TCGA-ED-A7PY        TCGA-ED-A7PZ        TCGA-ED-A7XP 
"8P LOSS WILD-TYPE"   "8P LOSS MUTATED"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" 
       TCGA-ED-A82E        TCGA-EP-A12J        TCGA-EP-A26S        TCGA-EP-A2KA 
"8P LOSS WILD-TYPE"   "8P LOSS MUTATED"   "8P LOSS MUTATED"   "8P LOSS MUTATED" 
       TCGA-EP-A2KB        TCGA-EP-A2KC        TCGA-EP-A3JL        TCGA-EP-A3RK 
"8P LOSS WILD-TYPE"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" 
       TCGA-ES-A2HS        TCGA-ES-A2HT        TCGA-FV-A23B        TCGA-FV-A2QR 
  "8P LOSS MUTATED"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" 
       TCGA-FV-A3I0        TCGA-FV-A3I1        TCGA-FV-A3R2        TCGA-FV-A3R3 
  "8P LOSS MUTATED"   "8P LOSS MUTATED"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" 
       TCGA-FV-A495        TCGA-FV-A496        TCGA-FV-A4ZP        TCGA-FV-A4ZQ 
  "8P LOSS MUTATED" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED"   "8P LOSS MUTATED" 
       TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U        TCGA-G3-A25V 
  "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" 
       TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y        TCGA-G3-A25Z 
  "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI        TCGA-G3-A3CJ 
  "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" 
       TCGA-G3-A3CK        TCGA-G3-A5SI        TCGA-G3-A5SJ        TCGA-G3-A5SL 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" 
       TCGA-G3-A5SM        TCGA-G3-A6UC        TCGA-GJ-A6C0        TCGA-K7-A6G5 
"8P LOSS WILD-TYPE"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" 
       TCGA-LG-A6GG        TCGA-MI-A75C        TCGA-MI-A75E        TCGA-MI-A75G 
"8P LOSS WILD-TYPE"   "8P LOSS MUTATED"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" 
       TCGA-MI-A75I        TCGA-NI-A4U2        TCGA-O8-A75V 
  "8P LOSS MUTATED" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" 
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
"8P LOSS WILD-TYPE" "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-BC-A69H        TCGA-BC-A69I 
  "8P LOSS MUTATED" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED"   "8P LOSS MUTATED" 
       TCGA-CC-5258        TCGA-CC-5260        TCGA-CC-5261        TCGA-CC-5262 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED"   "8P LOSS MUTATED" 
       TCGA-CC-5263        TCGA-CC-A1HT        TCGA-CC-A3M9        TCGA-CC-A3MA 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-CC-A3MB        TCGA-CC-A3MC        TCGA-DD-A113        TCGA-DD-A114 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" 
       TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118        TCGA-DD-A119 
  "8P LOSS MUTATED"   "8P LOSS MUTATED"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" 
       TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C        TCGA-DD-A11D 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" 
       TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB        TCGA-DD-A1EC 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EF        TCGA-DD-A1EG 
"8P LOSS WILD-TYPE"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" 
       TCGA-DD-A1EH        TCGA-DD-A1EI        TCGA-DD-A1EJ        TCGA-DD-A1EK 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" 
       TCGA-DD-A1EL        TCGA-DD-A39V        TCGA-DD-A39X        TCGA-DD-A39Y 
  "8P LOSS MUTATED"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE"   "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-A4NB        TCGA-DD-A4ND        TCGA-DD-A4NF        TCGA-DD-A4NH 
"8P LOSS WILD-TYPE"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" 
       TCGA-DD-A4NI        TCGA-DD-A4NJ        TCGA-DD-A4NK        TCGA-DD-A4NL 
  "8P LOSS MUTATED"   "8P LOSS MUTATED"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" 
       TCGA-DD-A4NN        TCGA-DD-A4NO        TCGA-DD-A4NP        TCGA-DD-A4NQ 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-DD-A4NR        TCGA-DD-A4NS        TCGA-DD-A4NV        TCGA-DD-A73A 
  "8P LOSS MUTATED" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED"   "8P LOSS MUTATED" 
       TCGA-DD-A73B        TCGA-DD-A73C        TCGA-DD-A73D        TCGA-DD-A73E 
  "8P LOSS MUTATED"   "8P LOSS MUTATED"   "8P LOSS MUTATED"   "8P LOSS MUTATED" 
       TCGA-DD-A73F        TCGA-DD-A73G        TCGA-ED-A459        TCGA-ED-A4XI 
  "8P LOSS MUTATED"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-ED-A5KG        TCGA-ED-A627        TCGA-ED-A66X        TCGA-ED-A66Y 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-ED-A7PX        TCGA-ED-A7PY        TCGA-ED-A7PZ        TCGA-ED-A7XP 
"8P LOSS WILD-TYPE"   "8P LOSS MUTATED"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" 
       TCGA-ED-A82E        TCGA-EP-A12J        TCGA-EP-A26S        TCGA-EP-A2KA 
"8P LOSS WILD-TYPE"   "8P LOSS MUTATED"   "8P LOSS MUTATED"   "8P LOSS MUTATED" 
       TCGA-EP-A2KB        TCGA-EP-A2KC        TCGA-EP-A3JL        TCGA-EP-A3RK 
"8P LOSS WILD-TYPE"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" 
       TCGA-ES-A2HS        TCGA-ES-A2HT        TCGA-FV-A23B        TCGA-FV-A2QR 
  "8P LOSS MUTATED"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" 
       TCGA-FV-A3I0        TCGA-FV-A3I1        TCGA-FV-A3R2        TCGA-FV-A3R3 
  "8P LOSS MUTATED"   "8P LOSS MUTATED"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" 
       TCGA-FV-A495        TCGA-FV-A496        TCGA-FV-A4ZP        TCGA-FV-A4ZQ 
  "8P LOSS MUTATED" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED"   "8P LOSS MUTATED" 
       TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U        TCGA-G3-A25V 
  "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" 
       TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y        TCGA-G3-A25Z 
  "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI        TCGA-G3-A3CJ 
  "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" 
       TCGA-G3-A3CK        TCGA-G3-A5SI        TCGA-G3-A5SJ        TCGA-G3-A5SL 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" 
       TCGA-G3-A5SM        TCGA-G3-A6UC        TCGA-GJ-A6C0        TCGA-K7-A6G5 
"8P LOSS WILD-TYPE"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" 
       TCGA-LG-A6GG        TCGA-MI-A75C        TCGA-MI-A75E        TCGA-MI-A75G 
"8P LOSS WILD-TYPE"   "8P LOSS MUTATED"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" 
       TCGA-MI-A75I        TCGA-NI-A4U2        TCGA-O8-A75V 
  "8P LOSS MUTATED" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" 
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
"8P LOSS WILD-TYPE" "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-BC-A69H        TCGA-BC-A69I 
  "8P LOSS MUTATED" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED"   "8P LOSS MUTATED" 
       TCGA-CC-5258        TCGA-CC-5260        TCGA-CC-5261        TCGA-CC-5262 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED"   "8P LOSS MUTATED" 
       TCGA-CC-5263        TCGA-CC-A1HT        TCGA-CC-A3M9        TCGA-CC-A3MA 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-CC-A3MB        TCGA-CC-A3MC        TCGA-DD-A113        TCGA-DD-A114 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" 
       TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118        TCGA-DD-A119 
  "8P LOSS MUTATED"   "8P LOSS MUTATED"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" 
       TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C        TCGA-DD-A11D 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" 
       TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB        TCGA-DD-A1EC 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EF        TCGA-DD-A1EG 
"8P LOSS WILD-TYPE"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" 
       TCGA-DD-A1EH        TCGA-DD-A1EI        TCGA-DD-A1EJ        TCGA-DD-A1EK 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" 
       TCGA-DD-A1EL        TCGA-DD-A39V        TCGA-DD-A39X        TCGA-DD-A39Y 
  "8P LOSS MUTATED"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE"   "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-A4NB        TCGA-DD-A4ND        TCGA-DD-A4NF        TCGA-DD-A4NH 
"8P LOSS WILD-TYPE"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" 
       TCGA-DD-A4NI        TCGA-DD-A4NJ        TCGA-DD-A4NK        TCGA-DD-A4NL 
  "8P LOSS MUTATED"   "8P LOSS MUTATED"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" 
       TCGA-DD-A4NN        TCGA-DD-A4NO        TCGA-DD-A4NP        TCGA-DD-A4NQ 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-DD-A4NR        TCGA-DD-A4NS        TCGA-DD-A4NV        TCGA-DD-A73A 
  "8P LOSS MUTATED" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED"   "8P LOSS MUTATED" 
       TCGA-DD-A73B        TCGA-DD-A73C        TCGA-DD-A73D        TCGA-DD-A73E 
  "8P LOSS MUTATED"   "8P LOSS MUTATED"   "8P LOSS MUTATED"   "8P LOSS MUTATED" 
       TCGA-DD-A73F        TCGA-DD-A73G        TCGA-ED-A459        TCGA-ED-A4XI 
  "8P LOSS MUTATED"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-ED-A5KG        TCGA-ED-A627        TCGA-ED-A66X        TCGA-ED-A66Y 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-ED-A7PX        TCGA-ED-A7PY        TCGA-ED-A7PZ        TCGA-ED-A7XP 
"8P LOSS WILD-TYPE"   "8P LOSS MUTATED"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" 
       TCGA-ED-A82E        TCGA-EP-A12J        TCGA-EP-A26S        TCGA-EP-A2KA 
"8P LOSS WILD-TYPE"   "8P LOSS MUTATED"   "8P LOSS MUTATED"   "8P LOSS MUTATED" 
       TCGA-EP-A2KB        TCGA-EP-A2KC        TCGA-EP-A3JL        TCGA-EP-A3RK 
"8P LOSS WILD-TYPE"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" 
       TCGA-ES-A2HS        TCGA-ES-A2HT        TCGA-FV-A23B        TCGA-FV-A2QR 
  "8P LOSS MUTATED"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" 
       TCGA-FV-A3I0        TCGA-FV-A3I1        TCGA-FV-A3R2        TCGA-FV-A3R3 
  "8P LOSS MUTATED"   "8P LOSS MUTATED"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" 
       TCGA-FV-A495        TCGA-FV-A496        TCGA-FV-A4ZP        TCGA-FV-A4ZQ 
  "8P LOSS MUTATED" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED"   "8P LOSS MUTATED" 
       TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U        TCGA-G3-A25V 
  "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" 
       TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y        TCGA-G3-A25Z 
  "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI        TCGA-G3-A3CJ 
  "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" 
       TCGA-G3-A3CK        TCGA-G3-A5SI        TCGA-G3-A5SJ        TCGA-G3-A5SL 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" 
       TCGA-G3-A5SM        TCGA-G3-A6UC        TCGA-GJ-A6C0        TCGA-K7-A6G5 
"8P LOSS WILD-TYPE"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" 
       TCGA-LG-A6GG        TCGA-MI-A75C        TCGA-MI-A75E        TCGA-MI-A75G 
"8P LOSS WILD-TYPE"   "8P LOSS MUTATED"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" 
       TCGA-MI-A75I        TCGA-NI-A4U2        TCGA-O8-A75V 
  "8P LOSS MUTATED" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" 
[1] "hr=" "1.3"
D55V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  8P LOSS MUTATED        29       19         0         10          4          4
  8P LOSS WILD-TYPE      29       17         2         20          0          1
                   vv
clus                STAGE IV STAGE IVA STAGE IVB
  8P LOSS MUTATED          0         1         1
  8P LOSS WILD-TYPE        1         0         1
D55V3, multiclass
                   vv
clus                T1 T2 T3 T4
  8P LOSS MUTATED   31 23 16  4
  8P LOSS WILD-TYPE 30 17 24  4
D55V4, multiclass
    clus
vv   8P LOSS MUTATED 8P LOSS WILD-TYPE
  T1              31                30
  T2              23                17
  T3              16                24
  T4               4                 4
D55V5, binary
                   cls
clus                 0  1
  8P LOSS MUTATED   40  3
  8P LOSS WILD-TYPE 57  0
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED     40    3
  8P LOSS WILD-TYPE   57    0
   clus
vv  8P LOSS MUTATED 8P LOSS WILD-TYPE
  0              40                57
  1               3                 0
                   vv
clus                M0 M1 MX
  8P LOSS MUTATED   54  1 19
  8P LOSS WILD-TYPE 61  2 12
D55V6, multiclass
    clus
vv   8P LOSS MUTATED 8P LOSS WILD-TYPE
  M0              54                61
  M1               1                 2
  MX              19                12
D55V7, binary
                   cls
clus                 0  1
  8P LOSS MUTATED   28 46
  8P LOSS WILD-TYPE 30 45
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED     28   46
  8P LOSS WILD-TYPE   30   45
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  FEMALE              28                30
  MALE                46                45
                   vv
clus                R0 R1 R2 RX
  8P LOSS MUTATED   60  7  0  4
  8P LOSS WILD-TYPE 62  4  1  6
D55V8, multiclass
    clus
vv   8P LOSS MUTATED 8P LOSS WILD-TYPE
  R0              60                62
  R1               7                 4
  R2               0                 1
  RX               4                 6

Clustering(56) Variable = 8Q LOSS MUTATION ANALYSIS
D56V1, survival
                   sevent
clus2                0  1
  8Q LOSS MUTATED    8  7
  8Q LOSS WILD-TYPE 76 56
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               15               132 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                7                56 
$`8Q LOSS MUTATED`
TCGA-BC-A10T TCGA-BC-A217 TCGA-BC-A3KG TCGA-CC-5261 TCGA-DD-A115 TCGA-DD-A3A0 
       27.52        13.84        22.36         0.39        83.57        25.81 
TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NK TCGA-DD-A73C TCGA-ED-A7PY TCGA-EP-A2KA 
       30.61        33.14        39.78         7.56         0.20        11.74 
TCGA-FV-A3I0 TCGA-FV-A495 TCGA-G3-A25V 
        0.20         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-BC-A69H TCGA-BC-A69I TCGA-CC-5258 
       44.42         0.26         9.50         3.95         0.53         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-A113 TCGA-DD-A114 TCGA-DD-A116 TCGA-DD-A118 
        0.10         0.13        79.73        37.78        53.33       113.00 
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        51.29        90.71 
TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EF 
       79.40        66.31        19.79        75.65         6.71        12.95 
TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A1EL 
       45.11        49.15         6.02        29.16        18.35        13.64 
TCGA-DD-A39V TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A1 TCGA-DD-A3A2 
       21.14        55.69         5.62        19.76         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-A4NB TCGA-DD-A4ND TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ 
       12.85        73.38        14.07        14.24        18.44        15.06 
TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR 
       56.25        29.56        61.45        93.67        12.26         0.30 
TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73D TCGA-DD-A73E 
       80.75        66.35        10.98         9.30        10.98         1.45 
TCGA-DD-A73F TCGA-DD-A73G TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 
       27.72       100.96        13.41        12.69        15.85        13.91 
TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PZ TCGA-ED-A7XP TCGA-ED-A82E 
       13.35         0.23         0.20         0.20         0.20         0.20 
TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK 
       18.74        19.99        10.98         0.62         9.96        11.93 
TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-A3I1 TCGA-FV-A3R2 
       22.85        14.40        32.45        19.10         8.12         6.38 
TCGA-FV-A3R3 TCGA-FV-A496 TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T 
        0.13         0.33        60.36         0.39         1.22        51.06 
TCGA-G3-A25U TCGA-G3-A25W TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG 
       53.79        30.74        58.49        14.86        21.53        22.13 
TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ 
       25.64         5.92        19.53        19.23        14.70        11.97 
TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A6UC TCGA-GJ-A6C0 TCGA-K7-A6G5 TCGA-LG-A6GG 
        7.99         4.37         7.76         1.02         4.01         0.49 
TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75I TCGA-NI-A4U2 TCGA-O8-A75V 
        9.57         5.10        14.24         8.71        58.88         4.44 

  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
             0.03              0.07 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
            83.57            113.00 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
            22.36             13.99 
[1] "0.0 - 83.6 (22.4)"  "0.1 - 113.0 (14.0)"
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"8Q LOSS WILD-TYPE"   "8Q LOSS MUTATED" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE"   "8Q LOSS MUTATED" "8Q LOSS WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-BC-A5W4        TCGA-BC-A69H        TCGA-BC-A69I 
  "8Q LOSS MUTATED" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-CC-5258        TCGA-CC-5260        TCGA-CC-5261        TCGA-CC-5262 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE"   "8Q LOSS MUTATED" "8Q LOSS WILD-TYPE" 
       TCGA-CC-5263        TCGA-CC-A1HT        TCGA-CC-A3M9        TCGA-CC-A3MA 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-CC-A3MB        TCGA-CC-A3MC        TCGA-DD-A113        TCGA-DD-A114 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118        TCGA-DD-A119 
  "8Q LOSS MUTATED" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C        TCGA-DD-A11D 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB        TCGA-DD-A1EC 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EF        TCGA-DD-A1EG 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DD-A1EH        TCGA-DD-A1EI        TCGA-DD-A1EJ        TCGA-DD-A1EK 
"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 WILD-TYPE"   "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-A4NB        TCGA-DD-A4ND        TCGA-DD-A4NF        TCGA-DD-A4NH 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DD-A4NI        TCGA-DD-A4NJ        TCGA-DD-A4NK        TCGA-DD-A4NL 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE"   "8Q LOSS MUTATED" "8Q LOSS WILD-TYPE" 
       TCGA-DD-A4NN        TCGA-DD-A4NO        TCGA-DD-A4NP        TCGA-DD-A4NQ 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DD-A4NR        TCGA-DD-A4NS        TCGA-DD-A4NV        TCGA-DD-A73A 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DD-A73B        TCGA-DD-A73C        TCGA-DD-A73D        TCGA-DD-A73E 
"8Q LOSS WILD-TYPE"   "8Q LOSS MUTATED" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DD-A73F        TCGA-DD-A73G        TCGA-ED-A459        TCGA-ED-A4XI 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-ED-A5KG        TCGA-ED-A627        TCGA-ED-A66X        TCGA-ED-A66Y 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-ED-A7PX        TCGA-ED-A7PY        TCGA-ED-A7PZ        TCGA-ED-A7XP 
"8Q LOSS WILD-TYPE"   "8Q LOSS MUTATED" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-ED-A82E        TCGA-EP-A12J        TCGA-EP-A26S        TCGA-EP-A2KA 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE"   "8Q LOSS MUTATED" 
       TCGA-EP-A2KB        TCGA-EP-A2KC        TCGA-EP-A3JL        TCGA-EP-A3RK 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-ES-A2HS        TCGA-ES-A2HT        TCGA-FV-A23B        TCGA-FV-A2QR 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-FV-A3I0        TCGA-FV-A3I1        TCGA-FV-A3R2        TCGA-FV-A3R3 
  "8Q LOSS MUTATED" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-FV-A495        TCGA-FV-A496        TCGA-FV-A4ZP        TCGA-FV-A4ZQ 
  "8Q LOSS MUTATED" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U        TCGA-G3-A25V 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE"   "8Q LOSS MUTATED" 
       TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y        TCGA-G3-A25Z 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI        TCGA-G3-A3CJ 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-G3-A3CK        TCGA-G3-A5SI        TCGA-G3-A5SJ        TCGA-G3-A5SL 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-G3-A5SM        TCGA-G3-A6UC        TCGA-GJ-A6C0        TCGA-K7-A6G5 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-LG-A6GG        TCGA-MI-A75C        TCGA-MI-A75E        TCGA-MI-A75G 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-MI-A75I        TCGA-NI-A4U2        TCGA-O8-A75V 
"8Q LOSS WILD-TYPE" "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-BC-A69H        TCGA-BC-A69I 
  "8Q LOSS MUTATED" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-CC-5258        TCGA-CC-5260        TCGA-CC-5261        TCGA-CC-5262 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE"   "8Q LOSS MUTATED" "8Q LOSS WILD-TYPE" 
       TCGA-CC-5263        TCGA-CC-A1HT        TCGA-CC-A3M9        TCGA-CC-A3MA 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-CC-A3MB        TCGA-CC-A3MC        TCGA-DD-A113        TCGA-DD-A114 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118        TCGA-DD-A119 
  "8Q LOSS MUTATED" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C        TCGA-DD-A11D 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB        TCGA-DD-A1EC 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EF        TCGA-DD-A1EG 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DD-A1EH        TCGA-DD-A1EI        TCGA-DD-A1EJ        TCGA-DD-A1EK 
"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 WILD-TYPE"   "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-A4NB        TCGA-DD-A4ND        TCGA-DD-A4NF        TCGA-DD-A4NH 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DD-A4NI        TCGA-DD-A4NJ        TCGA-DD-A4NK        TCGA-DD-A4NL 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE"   "8Q LOSS MUTATED" "8Q LOSS WILD-TYPE" 
       TCGA-DD-A4NN        TCGA-DD-A4NO        TCGA-DD-A4NP        TCGA-DD-A4NQ 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DD-A4NR        TCGA-DD-A4NS        TCGA-DD-A4NV        TCGA-DD-A73A 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DD-A73B        TCGA-DD-A73C        TCGA-DD-A73D        TCGA-DD-A73E 
"8Q LOSS WILD-TYPE"   "8Q LOSS MUTATED" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DD-A73F        TCGA-DD-A73G        TCGA-ED-A459        TCGA-ED-A4XI 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-ED-A5KG        TCGA-ED-A627        TCGA-ED-A66X        TCGA-ED-A66Y 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-ED-A7PX        TCGA-ED-A7PY        TCGA-ED-A7PZ        TCGA-ED-A7XP 
"8Q LOSS WILD-TYPE"   "8Q LOSS MUTATED" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-ED-A82E        TCGA-EP-A12J        TCGA-EP-A26S        TCGA-EP-A2KA 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE"   "8Q LOSS MUTATED" 
       TCGA-EP-A2KB        TCGA-EP-A2KC        TCGA-EP-A3JL        TCGA-EP-A3RK 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-ES-A2HS        TCGA-ES-A2HT        TCGA-FV-A23B        TCGA-FV-A2QR 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-FV-A3I0        TCGA-FV-A3I1        TCGA-FV-A3R2        TCGA-FV-A3R3 
  "8Q LOSS MUTATED" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-FV-A495        TCGA-FV-A496        TCGA-FV-A4ZP        TCGA-FV-A4ZQ 
  "8Q LOSS MUTATED" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U        TCGA-G3-A25V 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE"   "8Q LOSS MUTATED" 
       TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y        TCGA-G3-A25Z 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI        TCGA-G3-A3CJ 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-G3-A3CK        TCGA-G3-A5SI        TCGA-G3-A5SJ        TCGA-G3-A5SL 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-G3-A5SM        TCGA-G3-A6UC        TCGA-GJ-A6C0        TCGA-K7-A6G5 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-LG-A6GG        TCGA-MI-A75C        TCGA-MI-A75E        TCGA-MI-A75G 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-MI-A75I        TCGA-NI-A4U2        TCGA-O8-A75V 
"8Q LOSS WILD-TYPE" "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-BC-A69H        TCGA-BC-A69I 
  "8Q LOSS MUTATED" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-CC-5258        TCGA-CC-5260        TCGA-CC-5261        TCGA-CC-5262 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE"   "8Q LOSS MUTATED" "8Q LOSS WILD-TYPE" 
       TCGA-CC-5263        TCGA-CC-A1HT        TCGA-CC-A3M9        TCGA-CC-A3MA 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-CC-A3MB        TCGA-CC-A3MC        TCGA-DD-A113        TCGA-DD-A114 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118        TCGA-DD-A119 
  "8Q LOSS MUTATED" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C        TCGA-DD-A11D 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB        TCGA-DD-A1EC 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EF        TCGA-DD-A1EG 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DD-A1EH        TCGA-DD-A1EI        TCGA-DD-A1EJ        TCGA-DD-A1EK 
"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 WILD-TYPE"   "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-A4NB        TCGA-DD-A4ND        TCGA-DD-A4NF        TCGA-DD-A4NH 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DD-A4NI        TCGA-DD-A4NJ        TCGA-DD-A4NK        TCGA-DD-A4NL 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE"   "8Q LOSS MUTATED" "8Q LOSS WILD-TYPE" 
       TCGA-DD-A4NN        TCGA-DD-A4NO        TCGA-DD-A4NP        TCGA-DD-A4NQ 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DD-A4NR        TCGA-DD-A4NS        TCGA-DD-A4NV        TCGA-DD-A73A 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DD-A73B        TCGA-DD-A73C        TCGA-DD-A73D        TCGA-DD-A73E 
"8Q LOSS WILD-TYPE"   "8Q LOSS MUTATED" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DD-A73F        TCGA-DD-A73G        TCGA-ED-A459        TCGA-ED-A4XI 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-ED-A5KG        TCGA-ED-A627        TCGA-ED-A66X        TCGA-ED-A66Y 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-ED-A7PX        TCGA-ED-A7PY        TCGA-ED-A7PZ        TCGA-ED-A7XP 
"8Q LOSS WILD-TYPE"   "8Q LOSS MUTATED" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-ED-A82E        TCGA-EP-A12J        TCGA-EP-A26S        TCGA-EP-A2KA 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE"   "8Q LOSS MUTATED" 
       TCGA-EP-A2KB        TCGA-EP-A2KC        TCGA-EP-A3JL        TCGA-EP-A3RK 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-ES-A2HS        TCGA-ES-A2HT        TCGA-FV-A23B        TCGA-FV-A2QR 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-FV-A3I0        TCGA-FV-A3I1        TCGA-FV-A3R2        TCGA-FV-A3R3 
  "8Q LOSS MUTATED" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-FV-A495        TCGA-FV-A496        TCGA-FV-A4ZP        TCGA-FV-A4ZQ 
  "8Q LOSS MUTATED" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U        TCGA-G3-A25V 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE"   "8Q LOSS MUTATED" 
       TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y        TCGA-G3-A25Z 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI        TCGA-G3-A3CJ 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-G3-A3CK        TCGA-G3-A5SI        TCGA-G3-A5SJ        TCGA-G3-A5SL 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-G3-A5SM        TCGA-G3-A6UC        TCGA-GJ-A6C0        TCGA-K7-A6G5 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-LG-A6GG        TCGA-MI-A75C        TCGA-MI-A75E        TCGA-MI-A75G 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-MI-A75I        TCGA-NI-A4U2        TCGA-O8-A75V 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
[1] "hr=" "1.2"
D56V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  8Q LOSS MUTATED         2        6         0          4          0          1
  8Q LOSS WILD-TYPE      56       30         2         26          4          4
                   vv
clus                STAGE IV STAGE IVA STAGE IVB
  8Q LOSS MUTATED          0         0         1
  8Q LOSS WILD-TYPE        1         1         1
D56V3, multiclass
                   vv
clus                T1 T2 T3 T4
  8Q LOSS MUTATED    2  7  4  2
  8Q LOSS WILD-TYPE 59 33 36  6
D56V4, multiclass
    clus
vv   8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  T1               2                59
  T2               7                33
  T3               4                36
  T4               2                 6
D56V5, binary
                   cls
clus                 0  1
  8Q LOSS MUTATED    7  1
  8Q LOSS WILD-TYPE 90  2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED      7    1
  8Q LOSS WILD-TYPE   90    2
   clus
vv  8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  0               7                90
  1               1                 2
                   vv
clus                 M0  M1  MX
  8Q LOSS MUTATED    12   1   2
  8Q LOSS WILD-TYPE 103   2  29
D56V6, multiclass
    clus
vv   8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  M0              12               103
  M1               1                 2
  MX               2                29
D56V7, binary
                   cls
clus                 0  1
  8Q LOSS MUTATED   10  5
  8Q LOSS WILD-TYPE 48 86
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED     10    5
  8Q LOSS WILD-TYPE   48   86
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  FEMALE              10                48
  MALE                 5                86
                   vv
clus                 R0  R1  R2  RX
  8Q LOSS MUTATED    13   1   0   1
  8Q LOSS WILD-TYPE 109  10   1   9
D56V8, multiclass
    clus
vv   8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  R0              13               109
  R1               1                10
  R2               0                 1
  RX               1                 9

Clustering(57) Variable = 9P LOSS MUTATION ANALYSIS
D57V1, survival
                   sevent
clus2                0  1
  9P LOSS MUTATED   22 23
  9P LOSS WILD-TYPE 62 40
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               45               102 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               23                40 
$`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-BC-A69H TCGA-CC-5258 TCGA-CC-5263 TCGA-CC-A1HT 
       13.84         9.50         3.95         0.07         4.24         3.32 
TCGA-CC-A3M9 TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A113 TCGA-DD-A115 TCGA-DD-A116 
        0.10         0.10         0.13        79.73        83.57        53.33 
TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A1EF TCGA-DD-A1EG 
        7.33         2.60         0.46        21.76        12.95        45.11 
TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A3A0 
        6.02        29.16        18.35        55.69         5.62        25.81 
TCGA-DD-A3A9 TCGA-DD-A4ND TCGA-DD-A4NI TCGA-DD-A4NO TCGA-ED-A459 TCGA-ED-A66X 
       30.61        73.38        18.44        61.45        13.41        13.35 
TCGA-ED-A7PZ TCGA-ED-A7XP TCGA-EP-A2KC TCGA-EP-A3RK TCGA-FV-A3I1 TCGA-G3-A25S 
        0.20         0.20         0.62        11.93         8.12         1.22 
TCGA-G3-A25T TCGA-MI-A75G TCGA-MI-A75I 
       51.06        14.24         8.71 

$`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-BC-A69I TCGA-CC-5260 
       69.57        44.42         0.26        22.36         0.53         2.86 
TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-A3MA TCGA-DD-A114 TCGA-DD-A118 TCGA-DD-A11D 
        0.39         3.39         0.07        37.78       113.00        51.29 
TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE 
       90.71        79.40        66.31        19.79        75.65         6.71 
TCGA-DD-A1EH TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39Z TCGA-DD-A3A1 TCGA-DD-A3A2 
       49.15        13.64        21.14        19.76         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-A4NB TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NJ TCGA-DD-A4NK 
       33.14        12.85        14.07        14.24        15.06        39.78 
TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS 
       56.25        29.56        93.67        12.26         0.30        80.75 
TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E 
       66.35        10.98         9.30         7.56        10.98         1.45 
TCGA-DD-A73F TCGA-DD-A73G TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66Y 
       27.72       100.96        12.69        15.85        13.91         0.23 
TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A82E TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA 
        0.20         0.20         0.20        18.74        19.99        11.74 
TCGA-EP-A2KB TCGA-EP-A3JL TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QR 
       10.98         9.96        22.85        14.40        32.45        19.10 
TCGA-FV-A3I0 TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZP 
        0.20         6.38         0.13         0.03         0.33        60.36 
TCGA-FV-A4ZQ TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25X TCGA-G3-A25Y 
        0.39        53.79        28.27        30.74        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         5.92        19.53        19.23 
TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A6UC TCGA-GJ-A6C0 
       14.70        11.97         7.99         4.37         7.76         1.02 
TCGA-K7-A6G5 TCGA-LG-A6GG TCGA-MI-A75C TCGA-MI-A75E TCGA-NI-A4U2 TCGA-O8-A75V 
        4.01         0.49         9.57         5.10        58.88         4.44 

  9P LOSS MUTATED 9P LOSS WILD-TYPE 
             0.07              0.03 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
            83.57            113.00 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
            12.95             14.78 
[1] "0.1 - 83.6 (12.9)"  "0.0 - 113.0 (14.8)"
       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-BC-A69H        TCGA-BC-A69I 
"9P LOSS WILD-TYPE"   "9P LOSS MUTATED"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" 
       TCGA-CC-5258        TCGA-CC-5260        TCGA-CC-5261        TCGA-CC-5262 
  "9P LOSS MUTATED" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-CC-5263        TCGA-CC-A1HT        TCGA-CC-A3M9        TCGA-CC-A3MA 
  "9P LOSS MUTATED"   "9P LOSS MUTATED"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" 
       TCGA-CC-A3MB        TCGA-CC-A3MC        TCGA-DD-A113        TCGA-DD-A114 
  "9P LOSS MUTATED"   "9P LOSS MUTATED"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" 
       TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118        TCGA-DD-A119 
  "9P LOSS MUTATED"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" 
       TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C        TCGA-DD-A11D 
  "9P LOSS MUTATED"   "9P LOSS MUTATED"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" 
       TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB        TCGA-DD-A1EC 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EF        TCGA-DD-A1EG 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED"   "9P LOSS MUTATED" 
       TCGA-DD-A1EH        TCGA-DD-A1EI        TCGA-DD-A1EJ        TCGA-DD-A1EK 
"9P LOSS WILD-TYPE"   "9P LOSS MUTATED"   "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 MUTATED" 
       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-A4NB        TCGA-DD-A4ND        TCGA-DD-A4NF        TCGA-DD-A4NH 
"9P LOSS WILD-TYPE"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-DD-A4NI        TCGA-DD-A4NJ        TCGA-DD-A4NK        TCGA-DD-A4NL 
  "9P LOSS MUTATED" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-DD-A4NN        TCGA-DD-A4NO        TCGA-DD-A4NP        TCGA-DD-A4NQ 
"9P LOSS WILD-TYPE"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-DD-A4NR        TCGA-DD-A4NS        TCGA-DD-A4NV        TCGA-DD-A73A 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-DD-A73B        TCGA-DD-A73C        TCGA-DD-A73D        TCGA-DD-A73E 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-DD-A73F        TCGA-DD-A73G        TCGA-ED-A459        TCGA-ED-A4XI 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" 
       TCGA-ED-A5KG        TCGA-ED-A627        TCGA-ED-A66X        TCGA-ED-A66Y 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" 
       TCGA-ED-A7PX        TCGA-ED-A7PY        TCGA-ED-A7PZ        TCGA-ED-A7XP 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED"   "9P LOSS MUTATED" 
       TCGA-ED-A82E        TCGA-EP-A12J        TCGA-EP-A26S        TCGA-EP-A2KA 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-EP-A2KB        TCGA-EP-A2KC        TCGA-EP-A3JL        TCGA-EP-A3RK 
"9P LOSS WILD-TYPE"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" 
       TCGA-ES-A2HS        TCGA-ES-A2HT        TCGA-FV-A23B        TCGA-FV-A2QR 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-FV-A3I0        TCGA-FV-A3I1        TCGA-FV-A3R2        TCGA-FV-A3R3 
"9P LOSS WILD-TYPE"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-FV-A495        TCGA-FV-A496        TCGA-FV-A4ZP        TCGA-FV-A4ZQ 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U        TCGA-G3-A25V 
  "9P LOSS MUTATED"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y        TCGA-G3-A25Z 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI        TCGA-G3-A3CJ 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-G3-A3CK        TCGA-G3-A5SI        TCGA-G3-A5SJ        TCGA-G3-A5SL 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-G3-A5SM        TCGA-G3-A6UC        TCGA-GJ-A6C0        TCGA-K7-A6G5 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-LG-A6GG        TCGA-MI-A75C        TCGA-MI-A75E        TCGA-MI-A75G 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" 
       TCGA-MI-A75I        TCGA-NI-A4U2        TCGA-O8-A75V 
  "9P LOSS MUTATED" "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-BC-A69H        TCGA-BC-A69I 
"9P LOSS WILD-TYPE"   "9P LOSS MUTATED"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" 
       TCGA-CC-5258        TCGA-CC-5260        TCGA-CC-5261        TCGA-CC-5262 
  "9P LOSS MUTATED" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-CC-5263        TCGA-CC-A1HT        TCGA-CC-A3M9        TCGA-CC-A3MA 
  "9P LOSS MUTATED"   "9P LOSS MUTATED"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" 
       TCGA-CC-A3MB        TCGA-CC-A3MC        TCGA-DD-A113        TCGA-DD-A114 
  "9P LOSS MUTATED"   "9P LOSS MUTATED"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" 
       TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118        TCGA-DD-A119 
  "9P LOSS MUTATED"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" 
       TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C        TCGA-DD-A11D 
  "9P LOSS MUTATED"   "9P LOSS MUTATED"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" 
       TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB        TCGA-DD-A1EC 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EF        TCGA-DD-A1EG 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED"   "9P LOSS MUTATED" 
       TCGA-DD-A1EH        TCGA-DD-A1EI        TCGA-DD-A1EJ        TCGA-DD-A1EK 
"9P LOSS WILD-TYPE"   "9P LOSS MUTATED"   "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 MUTATED" 
       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-A4NB        TCGA-DD-A4ND        TCGA-DD-A4NF        TCGA-DD-A4NH 
"9P LOSS WILD-TYPE"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-DD-A4NI        TCGA-DD-A4NJ        TCGA-DD-A4NK        TCGA-DD-A4NL 
  "9P LOSS MUTATED" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-DD-A4NN        TCGA-DD-A4NO        TCGA-DD-A4NP        TCGA-DD-A4NQ 
"9P LOSS WILD-TYPE"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-DD-A4NR        TCGA-DD-A4NS        TCGA-DD-A4NV        TCGA-DD-A73A 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-DD-A73B        TCGA-DD-A73C        TCGA-DD-A73D        TCGA-DD-A73E 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-DD-A73F        TCGA-DD-A73G        TCGA-ED-A459        TCGA-ED-A4XI 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" 
       TCGA-ED-A5KG        TCGA-ED-A627        TCGA-ED-A66X        TCGA-ED-A66Y 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" 
       TCGA-ED-A7PX        TCGA-ED-A7PY        TCGA-ED-A7PZ        TCGA-ED-A7XP 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED"   "9P LOSS MUTATED" 
       TCGA-ED-A82E        TCGA-EP-A12J        TCGA-EP-A26S        TCGA-EP-A2KA 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-EP-A2KB        TCGA-EP-A2KC        TCGA-EP-A3JL        TCGA-EP-A3RK 
"9P LOSS WILD-TYPE"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" 
       TCGA-ES-A2HS        TCGA-ES-A2HT        TCGA-FV-A23B        TCGA-FV-A2QR 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-FV-A3I0        TCGA-FV-A3I1        TCGA-FV-A3R2        TCGA-FV-A3R3 
"9P LOSS WILD-TYPE"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-FV-A495        TCGA-FV-A496        TCGA-FV-A4ZP        TCGA-FV-A4ZQ 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U        TCGA-G3-A25V 
  "9P LOSS MUTATED"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y        TCGA-G3-A25Z 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI        TCGA-G3-A3CJ 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-G3-A3CK        TCGA-G3-A5SI        TCGA-G3-A5SJ        TCGA-G3-A5SL 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-G3-A5SM        TCGA-G3-A6UC        TCGA-GJ-A6C0        TCGA-K7-A6G5 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-LG-A6GG        TCGA-MI-A75C        TCGA-MI-A75E        TCGA-MI-A75G 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" 
       TCGA-MI-A75I        TCGA-NI-A4U2        TCGA-O8-A75V 
  "9P LOSS MUTATED" "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-BC-A69H        TCGA-BC-A69I 
"9P LOSS WILD-TYPE"   "9P LOSS MUTATED"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" 
       TCGA-CC-5258        TCGA-CC-5260        TCGA-CC-5261        TCGA-CC-5262 
  "9P LOSS MUTATED" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-CC-5263        TCGA-CC-A1HT        TCGA-CC-A3M9        TCGA-CC-A3MA 
  "9P LOSS MUTATED"   "9P LOSS MUTATED"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" 
       TCGA-CC-A3MB        TCGA-CC-A3MC        TCGA-DD-A113        TCGA-DD-A114 
  "9P LOSS MUTATED"   "9P LOSS MUTATED"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" 
       TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118        TCGA-DD-A119 
  "9P LOSS MUTATED"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" 
       TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C        TCGA-DD-A11D 
  "9P LOSS MUTATED"   "9P LOSS MUTATED"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" 
       TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB        TCGA-DD-A1EC 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EF        TCGA-DD-A1EG 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED"   "9P LOSS MUTATED" 
       TCGA-DD-A1EH        TCGA-DD-A1EI        TCGA-DD-A1EJ        TCGA-DD-A1EK 
"9P LOSS WILD-TYPE"   "9P LOSS MUTATED"   "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 MUTATED" 
       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-A4NB        TCGA-DD-A4ND        TCGA-DD-A4NF        TCGA-DD-A4NH 
"9P LOSS WILD-TYPE"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-DD-A4NI        TCGA-DD-A4NJ        TCGA-DD-A4NK        TCGA-DD-A4NL 
  "9P LOSS MUTATED" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-DD-A4NN        TCGA-DD-A4NO        TCGA-DD-A4NP        TCGA-DD-A4NQ 
"9P LOSS WILD-TYPE"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-DD-A4NR        TCGA-DD-A4NS        TCGA-DD-A4NV        TCGA-DD-A73A 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-DD-A73B        TCGA-DD-A73C        TCGA-DD-A73D        TCGA-DD-A73E 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-DD-A73F        TCGA-DD-A73G        TCGA-ED-A459        TCGA-ED-A4XI 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" 
       TCGA-ED-A5KG        TCGA-ED-A627        TCGA-ED-A66X        TCGA-ED-A66Y 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" 
       TCGA-ED-A7PX        TCGA-ED-A7PY        TCGA-ED-A7PZ        TCGA-ED-A7XP 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED"   "9P LOSS MUTATED" 
       TCGA-ED-A82E        TCGA-EP-A12J        TCGA-EP-A26S        TCGA-EP-A2KA 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-EP-A2KB        TCGA-EP-A2KC        TCGA-EP-A3JL        TCGA-EP-A3RK 
"9P LOSS WILD-TYPE"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" 
       TCGA-ES-A2HS        TCGA-ES-A2HT        TCGA-FV-A23B        TCGA-FV-A2QR 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-FV-A3I0        TCGA-FV-A3I1        TCGA-FV-A3R2        TCGA-FV-A3R3 
"9P LOSS WILD-TYPE"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-FV-A495        TCGA-FV-A496        TCGA-FV-A4ZP        TCGA-FV-A4ZQ 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U        TCGA-G3-A25V 
  "9P LOSS MUTATED"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y        TCGA-G3-A25Z 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI        TCGA-G3-A3CJ 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-G3-A3CK        TCGA-G3-A5SI        TCGA-G3-A5SJ        TCGA-G3-A5SL 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-G3-A5SM        TCGA-G3-A6UC        TCGA-GJ-A6C0        TCGA-K7-A6G5 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-LG-A6GG        TCGA-MI-A75C        TCGA-MI-A75E        TCGA-MI-A75G 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" 
       TCGA-MI-A75I        TCGA-NI-A4U2        TCGA-O8-A75V 
  "9P LOSS MUTATED" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
[1] "hr=" "1.6"
D57V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  9P LOSS MUTATED        13       10         0         12          0          1
  9P LOSS WILD-TYPE      45       26         2         18          4          4
                   vv
clus                STAGE IV STAGE IVA STAGE IVB
  9P LOSS MUTATED          1         1         2
  9P LOSS WILD-TYPE        0         0         0
D57V3, multiclass
                   vv
clus                T1 T2 T3 T4
  9P LOSS MUTATED   15 13 16  2
  9P LOSS WILD-TYPE 46 27 24  6
D57V4, multiclass
    clus
vv   9P LOSS MUTATED 9P LOSS WILD-TYPE
  T1              15                46
  T2              13                27
  T3              16                24
  T4               2                 6
D57V5, binary
                   cls
clus                 0  1
  9P LOSS MUTATED   28  2
  9P LOSS WILD-TYPE 69  1
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED     28    2
  9P LOSS WILD-TYPE   69    1
   clus
vv  9P LOSS MUTATED 9P LOSS WILD-TYPE
  0              28                69
  1               2                 1
                   vv
clus                M0 M1 MX
  9P LOSS MUTATED   33  3 10
  9P LOSS WILD-TYPE 82  0 21
D57V6, multiclass
    clus
vv   9P LOSS MUTATED 9P LOSS WILD-TYPE
  M0              33                82
  M1               3                 0
  MX              10                21
D57V7, binary
                   cls
clus                 0  1
  9P LOSS MUTATED   14 32
  9P LOSS WILD-TYPE 44 59
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED     14   32
  9P LOSS WILD-TYPE   44   59
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  FEMALE              14                44
  MALE                32                59
                   vv
clus                R0 R1 R2 RX
  9P LOSS MUTATED   34  5  1  4
  9P LOSS WILD-TYPE 88  6  0  6
D57V8, multiclass
    clus
vv   9P LOSS MUTATED 9P LOSS WILD-TYPE
  R0              34                88
  R1               5                 6
  R2               1                 0
  RX               4                 6

Clustering(58) Variable = 9Q LOSS MUTATION ANALYSIS
D58V1, survival
                   sevent
clus2                0  1
  9Q LOSS MUTATED   25 22
  9Q LOSS WILD-TYPE 59 41
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               47               100 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               22                41 
$`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        13.84 
TCGA-BC-A5W4 TCGA-BC-A69H TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5263 TCGA-CC-A1HT 
        9.50         3.95         0.07         2.86         4.24         3.32 
TCGA-CC-A3M9 TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A113 TCGA-DD-A116 TCGA-DD-A119 
        0.10         0.10         0.13        79.73        53.33         7.33 
TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EI 
        2.60         0.46        21.76        12.95        45.11         6.02 
TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A3A9 TCGA-DD-A4NA 
       29.16        18.35        55.69         5.62        30.61        33.14 
TCGA-DD-A4NI TCGA-DD-A4NO TCGA-ED-A459 TCGA-ED-A66X TCGA-ED-A7PZ TCGA-ED-A7XP 
       18.44        61.45        13.41        13.35         0.20         0.20 
TCGA-EP-A2KC TCGA-EP-A3RK TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 
        0.62        11.93         0.20         8.12         6.38         0.13 
TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A3CH TCGA-MI-A75G TCGA-MI-A75I 
        1.22        51.06        25.64        14.24         8.71 

$`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-BC-A69I 
        1.12        69.57        44.42         0.26        22.36         0.53 
TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-A3MA TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A118 
        0.39         3.39         0.07        37.78        83.57       113.00 
TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED 
       51.29        90.71        79.40        66.31        19.79        75.65 
TCGA-DD-A1EE TCGA-DD-A1EH TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39Z TCGA-DD-A3A0 
        6.71        49.15        13.64        21.14        19.76        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-A4NB TCGA-DD-A4ND TCGA-DD-A4NF TCGA-DD-A4NH 
       13.78         0.36        12.85        73.38        14.07        14.24 
TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NP TCGA-DD-A4NQ 
       15.06        39.78        56.25        29.56        93.67        12.26 
TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C 
        0.30        80.75        66.35        10.98         9.30         7.56 
TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G TCGA-ED-A4XI TCGA-ED-A5KG 
       10.98         1.45        27.72       100.96        12.69        15.85 
TCGA-ED-A627 TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A82E TCGA-EP-A12J 
       13.91         0.23         0.20         0.20         0.20        18.74 
TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A3JL TCGA-ES-A2HS TCGA-ES-A2HT 
       19.99        11.74        10.98         9.96        22.85        14.40 
TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZP TCGA-FV-A4ZQ 
       32.45        19.10         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        30.74        58.49        14.86        21.53 
TCGA-G3-A3CG TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ 
       22.13         5.92        19.53        19.23        14.70        11.97 
TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A6UC TCGA-GJ-A6C0 TCGA-K7-A6G5 TCGA-LG-A6GG 
        7.99         4.37         7.76         1.02         4.01         0.49 
TCGA-MI-A75C TCGA-MI-A75E TCGA-NI-A4U2 TCGA-O8-A75V 
        9.57         5.10        58.88         4.44 

  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
             0.07              0.03 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
            79.73            113.00 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
             9.50             16.72 
[1] "0.1 - 79.7 (9.5)"   "0.0 - 113.0 (16.7)"
       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-BC-A69H        TCGA-BC-A69I 
"9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" 
       TCGA-CC-5258        TCGA-CC-5260        TCGA-CC-5261        TCGA-CC-5262 
  "9Q LOSS MUTATED"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-CC-5263        TCGA-CC-A1HT        TCGA-CC-A3M9        TCGA-CC-A3MA 
  "9Q LOSS MUTATED"   "9Q LOSS MUTATED"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" 
       TCGA-CC-A3MB        TCGA-CC-A3MC        TCGA-DD-A113        TCGA-DD-A114 
  "9Q LOSS MUTATED"   "9Q LOSS MUTATED"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" 
       TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118        TCGA-DD-A119 
"9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" 
       TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C        TCGA-DD-A11D 
  "9Q LOSS MUTATED"   "9Q LOSS MUTATED"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" 
       TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB        TCGA-DD-A1EC 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EF        TCGA-DD-A1EG 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED"   "9Q LOSS MUTATED" 
       TCGA-DD-A1EH        TCGA-DD-A1EI        TCGA-DD-A1EJ        TCGA-DD-A1EK 
"9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED"   "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 MUTATED" 
       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-A4NB        TCGA-DD-A4ND        TCGA-DD-A4NF        TCGA-DD-A4NH 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-DD-A4NI        TCGA-DD-A4NJ        TCGA-DD-A4NK        TCGA-DD-A4NL 
  "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-DD-A4NN        TCGA-DD-A4NO        TCGA-DD-A4NP        TCGA-DD-A4NQ 
"9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-DD-A4NR        TCGA-DD-A4NS        TCGA-DD-A4NV        TCGA-DD-A73A 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-DD-A73B        TCGA-DD-A73C        TCGA-DD-A73D        TCGA-DD-A73E 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-DD-A73F        TCGA-DD-A73G        TCGA-ED-A459        TCGA-ED-A4XI 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" 
       TCGA-ED-A5KG        TCGA-ED-A627        TCGA-ED-A66X        TCGA-ED-A66Y 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" 
       TCGA-ED-A7PX        TCGA-ED-A7PY        TCGA-ED-A7PZ        TCGA-ED-A7XP 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED"   "9Q LOSS MUTATED" 
       TCGA-ED-A82E        TCGA-EP-A12J        TCGA-EP-A26S        TCGA-EP-A2KA 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-EP-A2KB        TCGA-EP-A2KC        TCGA-EP-A3JL        TCGA-EP-A3RK 
"9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" 
       TCGA-ES-A2HS        TCGA-ES-A2HT        TCGA-FV-A23B        TCGA-FV-A2QR 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-FV-A3I0        TCGA-FV-A3I1        TCGA-FV-A3R2        TCGA-FV-A3R3 
  "9Q LOSS MUTATED"   "9Q LOSS MUTATED"   "9Q LOSS MUTATED"   "9Q LOSS MUTATED" 
       TCGA-FV-A495        TCGA-FV-A496        TCGA-FV-A4ZP        TCGA-FV-A4ZQ 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U        TCGA-G3-A25V 
  "9Q LOSS MUTATED"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y        TCGA-G3-A25Z 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI        TCGA-G3-A3CJ 
"9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-G3-A3CK        TCGA-G3-A5SI        TCGA-G3-A5SJ        TCGA-G3-A5SL 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-G3-A5SM        TCGA-G3-A6UC        TCGA-GJ-A6C0        TCGA-K7-A6G5 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-LG-A6GG        TCGA-MI-A75C        TCGA-MI-A75E        TCGA-MI-A75G 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" 
       TCGA-MI-A75I        TCGA-NI-A4U2        TCGA-O8-A75V 
  "9Q LOSS MUTATED" "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-BC-A69H        TCGA-BC-A69I 
"9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" 
       TCGA-CC-5258        TCGA-CC-5260        TCGA-CC-5261        TCGA-CC-5262 
  "9Q LOSS MUTATED"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-CC-5263        TCGA-CC-A1HT        TCGA-CC-A3M9        TCGA-CC-A3MA 
  "9Q LOSS MUTATED"   "9Q LOSS MUTATED"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" 
       TCGA-CC-A3MB        TCGA-CC-A3MC        TCGA-DD-A113        TCGA-DD-A114 
  "9Q LOSS MUTATED"   "9Q LOSS MUTATED"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" 
       TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118        TCGA-DD-A119 
"9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" 
       TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C        TCGA-DD-A11D 
  "9Q LOSS MUTATED"   "9Q LOSS MUTATED"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" 
       TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB        TCGA-DD-A1EC 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EF        TCGA-DD-A1EG 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED"   "9Q LOSS MUTATED" 
       TCGA-DD-A1EH        TCGA-DD-A1EI        TCGA-DD-A1EJ        TCGA-DD-A1EK 
"9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED"   "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 MUTATED" 
       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-A4NB        TCGA-DD-A4ND        TCGA-DD-A4NF        TCGA-DD-A4NH 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-DD-A4NI        TCGA-DD-A4NJ        TCGA-DD-A4NK        TCGA-DD-A4NL 
  "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-DD-A4NN        TCGA-DD-A4NO        TCGA-DD-A4NP        TCGA-DD-A4NQ 
"9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-DD-A4NR        TCGA-DD-A4NS        TCGA-DD-A4NV        TCGA-DD-A73A 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-DD-A73B        TCGA-DD-A73C        TCGA-DD-A73D        TCGA-DD-A73E 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-DD-A73F        TCGA-DD-A73G        TCGA-ED-A459        TCGA-ED-A4XI 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" 
       TCGA-ED-A5KG        TCGA-ED-A627        TCGA-ED-A66X        TCGA-ED-A66Y 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" 
       TCGA-ED-A7PX        TCGA-ED-A7PY        TCGA-ED-A7PZ        TCGA-ED-A7XP 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED"   "9Q LOSS MUTATED" 
       TCGA-ED-A82E        TCGA-EP-A12J        TCGA-EP-A26S        TCGA-EP-A2KA 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-EP-A2KB        TCGA-EP-A2KC        TCGA-EP-A3JL        TCGA-EP-A3RK 
"9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" 
       TCGA-ES-A2HS        TCGA-ES-A2HT        TCGA-FV-A23B        TCGA-FV-A2QR 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-FV-A3I0        TCGA-FV-A3I1        TCGA-FV-A3R2        TCGA-FV-A3R3 
  "9Q LOSS MUTATED"   "9Q LOSS MUTATED"   "9Q LOSS MUTATED"   "9Q LOSS MUTATED" 
       TCGA-FV-A495        TCGA-FV-A496        TCGA-FV-A4ZP        TCGA-FV-A4ZQ 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U        TCGA-G3-A25V 
  "9Q LOSS MUTATED"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y        TCGA-G3-A25Z 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI        TCGA-G3-A3CJ 
"9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-G3-A3CK        TCGA-G3-A5SI        TCGA-G3-A5SJ        TCGA-G3-A5SL 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-G3-A5SM        TCGA-G3-A6UC        TCGA-GJ-A6C0        TCGA-K7-A6G5 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-LG-A6GG        TCGA-MI-A75C        TCGA-MI-A75E        TCGA-MI-A75G 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" 
       TCGA-MI-A75I        TCGA-NI-A4U2        TCGA-O8-A75V 
  "9Q LOSS MUTATED" "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-BC-A69H        TCGA-BC-A69I 
"9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" 
       TCGA-CC-5258        TCGA-CC-5260        TCGA-CC-5261        TCGA-CC-5262 
  "9Q LOSS MUTATED"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-CC-5263        TCGA-CC-A1HT        TCGA-CC-A3M9        TCGA-CC-A3MA 
  "9Q LOSS MUTATED"   "9Q LOSS MUTATED"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" 
       TCGA-CC-A3MB        TCGA-CC-A3MC        TCGA-DD-A113        TCGA-DD-A114 
  "9Q LOSS MUTATED"   "9Q LOSS MUTATED"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" 
       TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118        TCGA-DD-A119 
"9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" 
       TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C        TCGA-DD-A11D 
  "9Q LOSS MUTATED"   "9Q LOSS MUTATED"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" 
       TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB        TCGA-DD-A1EC 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EF        TCGA-DD-A1EG 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED"   "9Q LOSS MUTATED" 
       TCGA-DD-A1EH        TCGA-DD-A1EI        TCGA-DD-A1EJ        TCGA-DD-A1EK 
"9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED"   "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 MUTATED" 
       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-A4NB        TCGA-DD-A4ND        TCGA-DD-A4NF        TCGA-DD-A4NH 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-DD-A4NI        TCGA-DD-A4NJ        TCGA-DD-A4NK        TCGA-DD-A4NL 
  "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-DD-A4NN        TCGA-DD-A4NO        TCGA-DD-A4NP        TCGA-DD-A4NQ 
"9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-DD-A4NR        TCGA-DD-A4NS        TCGA-DD-A4NV        TCGA-DD-A73A 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-DD-A73B        TCGA-DD-A73C        TCGA-DD-A73D        TCGA-DD-A73E 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-DD-A73F        TCGA-DD-A73G        TCGA-ED-A459        TCGA-ED-A4XI 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" 
       TCGA-ED-A5KG        TCGA-ED-A627        TCGA-ED-A66X        TCGA-ED-A66Y 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" 
       TCGA-ED-A7PX        TCGA-ED-A7PY        TCGA-ED-A7PZ        TCGA-ED-A7XP 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED"   "9Q LOSS MUTATED" 
       TCGA-ED-A82E        TCGA-EP-A12J        TCGA-EP-A26S        TCGA-EP-A2KA 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-EP-A2KB        TCGA-EP-A2KC        TCGA-EP-A3JL        TCGA-EP-A3RK 
"9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" 
       TCGA-ES-A2HS        TCGA-ES-A2HT        TCGA-FV-A23B        TCGA-FV-A2QR 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-FV-A3I0        TCGA-FV-A3I1        TCGA-FV-A3R2        TCGA-FV-A3R3 
  "9Q LOSS MUTATED"   "9Q LOSS MUTATED"   "9Q LOSS MUTATED"   "9Q LOSS MUTATED" 
       TCGA-FV-A495        TCGA-FV-A496        TCGA-FV-A4ZP        TCGA-FV-A4ZQ 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U        TCGA-G3-A25V 
  "9Q LOSS MUTATED"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y        TCGA-G3-A25Z 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI        TCGA-G3-A3CJ 
"9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-G3-A3CK        TCGA-G3-A5SI        TCGA-G3-A5SJ        TCGA-G3-A5SL 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-G3-A5SM        TCGA-G3-A6UC        TCGA-GJ-A6C0        TCGA-K7-A6G5 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-LG-A6GG        TCGA-MI-A75C        TCGA-MI-A75E        TCGA-MI-A75G 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" 
       TCGA-MI-A75I        TCGA-NI-A4U2        TCGA-O8-A75V 
  "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
[1] "hr=" "1.9"
D58V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  9Q LOSS MUTATED        13       11         0         11          0          3
  9Q LOSS WILD-TYPE      45       25         2         19          4          2
                   vv
clus                STAGE IV STAGE IVA STAGE IVB
  9Q LOSS MUTATED          1         1         2
  9Q LOSS WILD-TYPE        0         0         0
D58V3, multiclass
                   vv
clus                T1 T2 T3 T4
  9Q LOSS MUTATED   15 15 15  3
  9Q LOSS WILD-TYPE 46 25 25  5
D58V4, multiclass
    clus
vv   9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  T1              15                46
  T2              15                25
  T3              15                25
  T4               3                 5
D58V5, binary
                   cls
clus                 0  1
  9Q LOSS MUTATED   27  3
  9Q LOSS WILD-TYPE 70  0
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED     27    3
  9Q LOSS WILD-TYPE   70    0
   clus
vv  9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  0              27                70
  1               3                 0
                   vv
clus                M0 M1 MX
  9Q LOSS MUTATED   33  3 12
  9Q LOSS WILD-TYPE 82  0 19
D58V6, multiclass
    clus
vv   9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  M0              33                82
  M1               3                 0
  MX              12                19
D58V7, binary
                   cls
clus                 0  1
  9Q LOSS MUTATED   16 32
  9Q LOSS WILD-TYPE 42 59
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED     16   32
  9Q LOSS WILD-TYPE   42   59
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  FEMALE              16                42
  MALE                32                59
                   vv
clus                R0 R1 R2 RX
  9Q LOSS MUTATED   36  4  1  5
  9Q LOSS WILD-TYPE 86  7  0  5
D58V8, multiclass
    clus
vv   9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  R0              36                86
  R1               4                 7
  R2               1                 0
  RX               5                 5

Clustering(59) Variable = 10P LOSS MUTATION ANALYSIS
D59V1, survival
                    sevent
clus2                 0  1
  10P LOSS MUTATED   12  4
  10P LOSS WILD-TYPE 72 59
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                16                131 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                 4                 59 
$`10P LOSS MUTATED`
TCGA-BC-4073 TCGA-BC-A112 TCGA-BC-A217 TCGA-BC-A5W4 TCGA-CC-A3M9 TCGA-CC-A3MA 
       27.91         5.03        13.84         9.50         0.10         0.07 
TCGA-CC-A3MC TCGA-DD-A11A TCGA-DD-A11C TCGA-DD-A39Y TCGA-DD-A4NI TCGA-DD-A4NQ 
        0.13         2.60        21.76         5.62        18.44        12.26 
TCGA-ED-A7PX TCGA-FV-A3I0 TCGA-G3-A25X TCGA-NI-A4U2 
        0.20         0.20        58.49        58.88 

$`10P LOSS WILD-TYPE`
TCGA-BC-4072 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U 
       48.99        37.32        10.13        46.78        27.52        27.52 
TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A216 
        2.99        25.32        23.34         1.12        69.57        44.42 
TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A69H TCGA-BC-A69I TCGA-CC-5258 TCGA-CC-5260 
        0.26        22.36         3.95         0.53         0.07         2.86 
TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3MB TCGA-DD-A113 
        0.39         3.39         4.24         3.32         0.10        79.73 
TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11B 
       37.78        83.57        53.33       113.00         7.33         0.46 
TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED 
       51.29        90.71        79.40        66.31        19.79        75.65 
TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ 
        6.71        12.95        45.11        49.15         6.02        29.16 
TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39X TCGA-DD-A39Z TCGA-DD-A3A0 
       18.35        13.64        21.14        55.69        19.76        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-A4NB TCGA-DD-A4ND 
       13.78         0.36        30.61        33.14        12.85        73.38 
TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN 
       14.07        14.24        15.06        39.78        56.25        29.56 
TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A 
       61.45        93.67         0.30        80.75        66.35        10.98 
TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G 
        9.30         7.56        10.98         1.45        27.72       100.96 
TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y 
       13.41        12.69        15.85        13.91        13.35         0.23 
TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XP TCGA-ED-A82E TCGA-EP-A12J TCGA-EP-A26S 
        0.20         0.20         0.20         0.20        18.74        19.99 
TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS 
       11.74        10.98         0.62         9.96        11.93        22.85 
TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 
       14.40        32.45        19.10         8.12         6.38         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        51.06 
TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG 
       53.79        28.27        30.74        14.86        21.53        22.13 
TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ 
       25.64         5.92        19.53        19.23        14.70        11.97 
TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A6UC TCGA-GJ-A6C0 TCGA-K7-A6G5 TCGA-LG-A6GG 
        7.99         4.37         7.76         1.02         4.01         0.49 
TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75I TCGA-O8-A75V 
        9.57         5.10        14.24         8.71         4.44 

  10P LOSS MUTATED 10P LOSS WILD-TYPE 
              0.07               0.03 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
             58.88             113.00 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
              7.56              14.40 
[1] "0.1 - 58.9 (7.6)"   "0.0 - 113.0 (14.4)"
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"10P LOSS WILD-TYPE"   "10P LOSS MUTATED" "10P LOSS WILD-TYPE" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
  "10P LOSS MUTATED" "10P LOSS WILD-TYPE"   "10P LOSS MUTATED" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-BC-A5W4 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE"   "10P LOSS MUTATED" 
        TCGA-BC-A69H         TCGA-BC-A69I         TCGA-CC-5258 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-CC-5260         TCGA-CC-5261         TCGA-CC-5262 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-CC-5263         TCGA-CC-A1HT         TCGA-CC-A3M9 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE"   "10P LOSS MUTATED" 
        TCGA-CC-A3MA         TCGA-CC-A3MB         TCGA-CC-A3MC 
  "10P LOSS MUTATED" "10P LOSS WILD-TYPE"   "10P LOSS MUTATED" 
        TCGA-DD-A113         TCGA-DD-A114         TCGA-DD-A115 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-DD-A116         TCGA-DD-A118         TCGA-DD-A119 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-DD-A11A         TCGA-DD-A11B         TCGA-DD-A11C 
  "10P LOSS MUTATED" "10P LOSS WILD-TYPE"   "10P LOSS MUTATED" 
        TCGA-DD-A11D         TCGA-DD-A1E9         TCGA-DD-A1EA 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-DD-A1EB         TCGA-DD-A1EC         TCGA-DD-A1ED 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-DD-A1EE         TCGA-DD-A1EF         TCGA-DD-A1EG 
"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-A1EK         TCGA-DD-A1EL         TCGA-DD-A39V 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-DD-A39X         TCGA-DD-A39Y         TCGA-DD-A39Z 
"10P LOSS WILD-TYPE"   "10P LOSS MUTATED" "10P LOSS WILD-TYPE" 
        TCGA-DD-A3A0         TCGA-DD-A3A1         TCGA-DD-A3A2 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-DD-A3A3         TCGA-DD-A3A4         TCGA-DD-A3A5 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-DD-A3A6         TCGA-DD-A3A7         TCGA-DD-A3A8 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-DD-A3A9         TCGA-DD-A4NA         TCGA-DD-A4NB 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-DD-A4ND         TCGA-DD-A4NF         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 MUTATED" "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-DD-A4NR 
"10P LOSS WILD-TYPE"   "10P LOSS MUTATED" "10P LOSS WILD-TYPE" 
        TCGA-DD-A4NS         TCGA-DD-A4NV         TCGA-DD-A73A 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-DD-A73B         TCGA-DD-A73C         TCGA-DD-A73D 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-DD-A73E         TCGA-DD-A73F         TCGA-DD-A73G 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-ED-A459         TCGA-ED-A4XI         TCGA-ED-A5KG 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-ED-A627         TCGA-ED-A66X         TCGA-ED-A66Y 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-ED-A7PX         TCGA-ED-A7PY         TCGA-ED-A7PZ 
  "10P LOSS MUTATED" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-ED-A7XP         TCGA-ED-A82E         TCGA-EP-A12J 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-EP-A26S         TCGA-EP-A2KA         TCGA-EP-A2KB 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-EP-A2KC         TCGA-EP-A3JL         TCGA-EP-A3RK 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-ES-A2HS         TCGA-ES-A2HT         TCGA-FV-A23B 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-FV-A2QR         TCGA-FV-A3I0         TCGA-FV-A3I1 
"10P LOSS WILD-TYPE"   "10P LOSS MUTATED" "10P LOSS WILD-TYPE" 
        TCGA-FV-A3R2         TCGA-FV-A3R3         TCGA-FV-A495 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-FV-A496         TCGA-FV-A4ZP         TCGA-FV-A4ZQ 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-G3-A25S         TCGA-G3-A25T         TCGA-G3-A25U 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-G3-A25V         TCGA-G3-A25W         TCGA-G3-A25X 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE"   "10P LOSS MUTATED" 
        TCGA-G3-A25Y         TCGA-G3-A25Z         TCGA-G3-A3CG 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-G3-A3CH         TCGA-G3-A3CI         TCGA-G3-A3CJ 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-G3-A3CK         TCGA-G3-A5SI         TCGA-G3-A5SJ 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-G3-A5SL         TCGA-G3-A5SM         TCGA-G3-A6UC 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-GJ-A6C0         TCGA-K7-A6G5         TCGA-LG-A6GG 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-MI-A75C         TCGA-MI-A75E         TCGA-MI-A75G 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-MI-A75I         TCGA-NI-A4U2         TCGA-O8-A75V 
"10P LOSS WILD-TYPE"   "10P LOSS MUTATED" "10P LOSS WILD-TYPE" 
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"10P LOSS WILD-TYPE"   "10P LOSS MUTATED" "10P LOSS WILD-TYPE" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
  "10P LOSS MUTATED" "10P LOSS WILD-TYPE"   "10P LOSS MUTATED" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-BC-A5W4 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE"   "10P LOSS MUTATED" 
        TCGA-BC-A69H         TCGA-BC-A69I         TCGA-CC-5258 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-CC-5260         TCGA-CC-5261         TCGA-CC-5262 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-CC-5263         TCGA-CC-A1HT         TCGA-CC-A3M9 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE"   "10P LOSS MUTATED" 
        TCGA-CC-A3MA         TCGA-CC-A3MB         TCGA-CC-A3MC 
  "10P LOSS MUTATED" "10P LOSS WILD-TYPE"   "10P LOSS MUTATED" 
        TCGA-DD-A113         TCGA-DD-A114         TCGA-DD-A115 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-DD-A116         TCGA-DD-A118         TCGA-DD-A119 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-DD-A11A         TCGA-DD-A11B         TCGA-DD-A11C 
  "10P LOSS MUTATED" "10P LOSS WILD-TYPE"   "10P LOSS MUTATED" 
        TCGA-DD-A11D         TCGA-DD-A1E9         TCGA-DD-A1EA 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-DD-A1EB         TCGA-DD-A1EC         TCGA-DD-A1ED 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-DD-A1EE         TCGA-DD-A1EF         TCGA-DD-A1EG 
"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-A1EK         TCGA-DD-A1EL         TCGA-DD-A39V 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-DD-A39X         TCGA-DD-A39Y         TCGA-DD-A39Z 
"10P LOSS WILD-TYPE"   "10P LOSS MUTATED" "10P LOSS WILD-TYPE" 
        TCGA-DD-A3A0         TCGA-DD-A3A1         TCGA-DD-A3A2 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-DD-A3A3         TCGA-DD-A3A4         TCGA-DD-A3A5 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-DD-A3A6         TCGA-DD-A3A7         TCGA-DD-A3A8 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-DD-A3A9         TCGA-DD-A4NA         TCGA-DD-A4NB 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-DD-A4ND         TCGA-DD-A4NF         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 MUTATED" "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-DD-A4NR 
"10P LOSS WILD-TYPE"   "10P LOSS MUTATED" "10P LOSS WILD-TYPE" 
        TCGA-DD-A4NS         TCGA-DD-A4NV         TCGA-DD-A73A 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-DD-A73B         TCGA-DD-A73C         TCGA-DD-A73D 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-DD-A73E         TCGA-DD-A73F         TCGA-DD-A73G 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-ED-A459         TCGA-ED-A4XI         TCGA-ED-A5KG 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-ED-A627         TCGA-ED-A66X         TCGA-ED-A66Y 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-ED-A7PX         TCGA-ED-A7PY         TCGA-ED-A7PZ 
  "10P LOSS MUTATED" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-ED-A7XP         TCGA-ED-A82E         TCGA-EP-A12J 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-EP-A26S         TCGA-EP-A2KA         TCGA-EP-A2KB 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-EP-A2KC         TCGA-EP-A3JL         TCGA-EP-A3RK 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-ES-A2HS         TCGA-ES-A2HT         TCGA-FV-A23B 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-FV-A2QR         TCGA-FV-A3I0         TCGA-FV-A3I1 
"10P LOSS WILD-TYPE"   "10P LOSS MUTATED" "10P LOSS WILD-TYPE" 
        TCGA-FV-A3R2         TCGA-FV-A3R3         TCGA-FV-A495 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-FV-A496         TCGA-FV-A4ZP         TCGA-FV-A4ZQ 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-G3-A25S         TCGA-G3-A25T         TCGA-G3-A25U 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-G3-A25V         TCGA-G3-A25W         TCGA-G3-A25X 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE"   "10P LOSS MUTATED" 
        TCGA-G3-A25Y         TCGA-G3-A25Z         TCGA-G3-A3CG 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-G3-A3CH         TCGA-G3-A3CI         TCGA-G3-A3CJ 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-G3-A3CK         TCGA-G3-A5SI         TCGA-G3-A5SJ 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-G3-A5SL         TCGA-G3-A5SM         TCGA-G3-A6UC 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-GJ-A6C0         TCGA-K7-A6G5         TCGA-LG-A6GG 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-MI-A75C         TCGA-MI-A75E         TCGA-MI-A75G 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-MI-A75I         TCGA-NI-A4U2         TCGA-O8-A75V 
"10P LOSS WILD-TYPE"   "10P LOSS MUTATED" "10P LOSS WILD-TYPE" 
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"10P LOSS WILD-TYPE"   "10P LOSS MUTATED" "10P LOSS WILD-TYPE" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
  "10P LOSS MUTATED" "10P LOSS WILD-TYPE"   "10P LOSS MUTATED" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-BC-A5W4 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE"   "10P LOSS MUTATED" 
        TCGA-BC-A69H         TCGA-BC-A69I         TCGA-CC-5258 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-CC-5260         TCGA-CC-5261         TCGA-CC-5262 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-CC-5263         TCGA-CC-A1HT         TCGA-CC-A3M9 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE"   "10P LOSS MUTATED" 
        TCGA-CC-A3MA         TCGA-CC-A3MB         TCGA-CC-A3MC 
  "10P LOSS MUTATED" "10P LOSS WILD-TYPE"   "10P LOSS MUTATED" 
        TCGA-DD-A113         TCGA-DD-A114         TCGA-DD-A115 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-DD-A116         TCGA-DD-A118         TCGA-DD-A119 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-DD-A11A         TCGA-DD-A11B         TCGA-DD-A11C 
  "10P LOSS MUTATED" "10P LOSS WILD-TYPE"   "10P LOSS MUTATED" 
        TCGA-DD-A11D         TCGA-DD-A1E9         TCGA-DD-A1EA 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-DD-A1EB         TCGA-DD-A1EC         TCGA-DD-A1ED 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-DD-A1EE         TCGA-DD-A1EF         TCGA-DD-A1EG 
"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-A1EK         TCGA-DD-A1EL         TCGA-DD-A39V 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-DD-A39X         TCGA-DD-A39Y         TCGA-DD-A39Z 
"10P LOSS WILD-TYPE"   "10P LOSS MUTATED" "10P LOSS WILD-TYPE" 
        TCGA-DD-A3A0         TCGA-DD-A3A1         TCGA-DD-A3A2 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-DD-A3A3         TCGA-DD-A3A4         TCGA-DD-A3A5 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-DD-A3A6         TCGA-DD-A3A7         TCGA-DD-A3A8 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-DD-A3A9         TCGA-DD-A4NA         TCGA-DD-A4NB 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-DD-A4ND         TCGA-DD-A4NF         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 MUTATED" "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-DD-A4NR 
"10P LOSS WILD-TYPE"   "10P LOSS MUTATED" "10P LOSS WILD-TYPE" 
        TCGA-DD-A4NS         TCGA-DD-A4NV         TCGA-DD-A73A 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-DD-A73B         TCGA-DD-A73C         TCGA-DD-A73D 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-DD-A73E         TCGA-DD-A73F         TCGA-DD-A73G 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-ED-A459         TCGA-ED-A4XI         TCGA-ED-A5KG 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-ED-A627         TCGA-ED-A66X         TCGA-ED-A66Y 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-ED-A7PX         TCGA-ED-A7PY         TCGA-ED-A7PZ 
  "10P LOSS MUTATED" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-ED-A7XP         TCGA-ED-A82E         TCGA-EP-A12J 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-EP-A26S         TCGA-EP-A2KA         TCGA-EP-A2KB 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-EP-A2KC         TCGA-EP-A3JL         TCGA-EP-A3RK 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-ES-A2HS         TCGA-ES-A2HT         TCGA-FV-A23B 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-FV-A2QR         TCGA-FV-A3I0         TCGA-FV-A3I1 
"10P LOSS WILD-TYPE"   "10P LOSS MUTATED" "10P LOSS WILD-TYPE" 
        TCGA-FV-A3R2         TCGA-FV-A3R3         TCGA-FV-A495 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-FV-A496         TCGA-FV-A4ZP         TCGA-FV-A4ZQ 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-G3-A25S         TCGA-G3-A25T         TCGA-G3-A25U 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-G3-A25V         TCGA-G3-A25W         TCGA-G3-A25X 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE"   "10P LOSS MUTATED" 
        TCGA-G3-A25Y         TCGA-G3-A25Z         TCGA-G3-A3CG 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-G3-A3CH         TCGA-G3-A3CI         TCGA-G3-A3CJ 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-G3-A3CK         TCGA-G3-A5SI         TCGA-G3-A5SJ 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-G3-A5SL         TCGA-G3-A5SM         TCGA-G3-A6UC 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-GJ-A6C0         TCGA-K7-A6G5         TCGA-LG-A6GG 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-MI-A75C         TCGA-MI-A75E         TCGA-MI-A75G 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-MI-A75I         TCGA-NI-A4U2         TCGA-O8-A75V 
"10P LOSS WILD-TYPE"   "10P LOSS MUTATED" "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         3        6         0          6          0
  10P LOSS WILD-TYPE      55       30         2         24          4
                    vv
clus                 STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  10P LOSS MUTATED            0        0         1         0
  10P LOSS WILD-TYPE          5        1         0         2
D59V3, multiclass
                    vv
clus                 T1 T2 T3 T4
  10P LOSS MUTATED    4  6  7  0
  10P LOSS WILD-TYPE 57 34 33  8
D59V4, multiclass
    clus
vv   10P LOSS MUTATED 10P LOSS WILD-TYPE
  T1                4                 57
  T2                6                 34
  T3                7                 33
  T4                0                  8
D59V5, binary
                    cls
clus                  0  1
  10P LOSS MUTATED    8  1
  10P LOSS WILD-TYPE 89  2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED      8    1
  10P LOSS WILD-TYPE   89    2
   clus
vv  10P LOSS MUTATED 10P LOSS WILD-TYPE
  0                8                 89
  1                1                  2
                    vv
clus                  M0  M1  MX
  10P LOSS MUTATED    13   0   4
  10P LOSS WILD-TYPE 102   3  27
D59V6, multiclass
    clus
vv   10P LOSS MUTATED 10P LOSS WILD-TYPE
  M0               13                102
  M1                0                  3
  MX                4                 27
D59V7, binary
                    cls
clus                  0  1
  10P LOSS MUTATED    3 14
  10P LOSS WILD-TYPE 55 77
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED      3   14
  10P LOSS WILD-TYPE   55   77
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  FEMALE                3                 55
  MALE                 14                 77
                    vv
clus                  R0  R1  R2  RX
  10P LOSS MUTATED    14   2   0   1
  10P LOSS WILD-TYPE 108   9   1   9
D59V8, multiclass
    clus
vv   10P LOSS MUTATED 10P LOSS WILD-TYPE
  R0               14                108
  R1                2                  9
  R2                0                  1
  RX                1                  9

Clustering(60) Variable = 10Q LOSS MUTATION ANALYSIS
D60V1, survival
                    sevent
clus2                 0  1
  10Q LOSS MUTATED   16 12
  10Q LOSS WILD-TYPE 68 51
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                28                119 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                12                 51 
$`10Q LOSS MUTATED`
TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10W TCGA-BC-A112 TCGA-BC-A217 
       27.91        37.32        10.13         2.99         5.03        13.84 
TCGA-BC-A5W4 TCGA-CC-5260 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MC 
        9.50         2.86         3.32         0.10         0.07         0.13 
TCGA-DD-A114 TCGA-DD-A11A TCGA-DD-A11C TCGA-DD-A1EG TCGA-DD-A1EL TCGA-DD-A39Y 
       37.78         2.60        21.76        45.11        13.64         5.62 
TCGA-DD-A4NI TCGA-DD-A4NQ TCGA-ED-A459 TCGA-ED-A7PX TCGA-FV-A3I0 TCGA-FV-A496 
       18.44        12.26        13.41         0.20         0.20         0.33 
TCGA-G3-A25U TCGA-G3-A25X TCGA-G3-A5SJ TCGA-NI-A4U2 
       53.79        58.49        11.97        58.88 

$`10Q LOSS WILD-TYPE`
TCGA-BC-4072 TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10X TCGA-BC-A10Y 
       48.99        46.78        27.52        27.52        25.32        23.34 
TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A216 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A69H 
        1.12        69.57        44.42         0.26        22.36         3.95 
TCGA-BC-A69I TCGA-CC-5258 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A3MB 
        0.53         0.07         0.39         3.39         4.24         0.10 
TCGA-DD-A113 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11B 
       79.73        83.57        53.33       113.00         7.33         0.46 
TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED 
       51.29        90.71        79.40        66.31        19.79        75.65 
TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK 
        6.71        12.95        49.15         6.02        29.16        18.35 
TCGA-DD-A39V TCGA-DD-A39X TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 
       21.14        55.69        19.76        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-A4NB TCGA-DD-A4ND TCGA-DD-A4NF TCGA-DD-A4NH 
       30.61        33.14        12.85        73.38        14.07        14.24 
TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP 
       15.06        39.78        56.25        29.56        61.45        93.67 
TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C 
        0.30        80.75        66.35        10.98         9.30         7.56 
TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G TCGA-ED-A4XI TCGA-ED-A5KG 
       10.98         1.45        27.72       100.96        12.69        15.85 
TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XP 
       13.91        13.35         0.23         0.20         0.20         0.20 
TCGA-ED-A82E TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC 
        0.20        18.74        19.99        11.74        10.98         0.62 
TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QR 
        9.96        11.93        22.85        14.40        32.45        19.10 
TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A4ZP TCGA-FV-A4ZQ 
        8.12         6.38         0.13         0.03        60.36         0.39 
TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25Y TCGA-G3-A25Z 
        1.22        51.06        28.27        30.74        14.86        21.53 
TCGA-G3-A3CG TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI 
       22.13        25.64         5.92        19.53        19.23        14.70 
TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A6UC TCGA-GJ-A6C0 TCGA-K7-A6G5 TCGA-LG-A6GG 
        7.99         4.37         7.76         1.02         4.01         0.49 
TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75I TCGA-O8-A75V 
        9.57         5.10        14.24         8.71         4.44 

  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
              0.07               0.03 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
             58.88             113.00 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
             11.05              14.86 
[1] "0.1 - 58.9 (11.1)"  "0.0 - 113.0 (14.9)"
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED"   "10Q LOSS MUTATED" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-BC-A5W4 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" 
        TCGA-BC-A69H         TCGA-BC-A69I         TCGA-CC-5258 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-CC-5260         TCGA-CC-5261         TCGA-CC-5262 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-CC-5263         TCGA-CC-A1HT         TCGA-CC-A3M9 
"10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED"   "10Q LOSS MUTATED" 
        TCGA-CC-A3MA         TCGA-CC-A3MB         TCGA-CC-A3MC 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" 
        TCGA-DD-A113         TCGA-DD-A114         TCGA-DD-A115 
"10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-DD-A116         TCGA-DD-A118         TCGA-DD-A119 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-DD-A11A         TCGA-DD-A11B         TCGA-DD-A11C 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" 
        TCGA-DD-A11D         TCGA-DD-A1E9         TCGA-DD-A1EA 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-DD-A1EB         TCGA-DD-A1EC         TCGA-DD-A1ED 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-DD-A1EE         TCGA-DD-A1EF         TCGA-DD-A1EG 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" 
        TCGA-DD-A1EH         TCGA-DD-A1EI         TCGA-DD-A1EJ 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-DD-A1EK         TCGA-DD-A1EL         TCGA-DD-A39V 
"10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-DD-A39X         TCGA-DD-A39Y         TCGA-DD-A39Z 
"10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-DD-A3A0         TCGA-DD-A3A1         TCGA-DD-A3A2 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-DD-A3A3         TCGA-DD-A3A4         TCGA-DD-A3A5 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-DD-A3A6         TCGA-DD-A3A7         TCGA-DD-A3A8 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-DD-A3A9         TCGA-DD-A4NA         TCGA-DD-A4NB 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-DD-A4ND         TCGA-DD-A4NF         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 MUTATED" "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-DD-A4NR 
"10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-DD-A4NS         TCGA-DD-A4NV         TCGA-DD-A73A 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-DD-A73B         TCGA-DD-A73C         TCGA-DD-A73D 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-DD-A73E         TCGA-DD-A73F         TCGA-DD-A73G 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-ED-A459         TCGA-ED-A4XI         TCGA-ED-A5KG 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-ED-A627         TCGA-ED-A66X         TCGA-ED-A66Y 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-ED-A7PX         TCGA-ED-A7PY         TCGA-ED-A7PZ 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-ED-A7XP         TCGA-ED-A82E         TCGA-EP-A12J 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EP-A26S         TCGA-EP-A2KA         TCGA-EP-A2KB 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EP-A2KC         TCGA-EP-A3JL         TCGA-EP-A3RK 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-ES-A2HS         TCGA-ES-A2HT         TCGA-FV-A23B 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-FV-A2QR         TCGA-FV-A3I0         TCGA-FV-A3I1 
"10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-FV-A3R2         TCGA-FV-A3R3         TCGA-FV-A495 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-FV-A496         TCGA-FV-A4ZP         TCGA-FV-A4ZQ 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-G3-A25S         TCGA-G3-A25T         TCGA-G3-A25U 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" 
        TCGA-G3-A25V         TCGA-G3-A25W         TCGA-G3-A25X 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" 
        TCGA-G3-A25Y         TCGA-G3-A25Z         TCGA-G3-A3CG 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-G3-A3CH         TCGA-G3-A3CI         TCGA-G3-A3CJ 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-G3-A3CK         TCGA-G3-A5SI         TCGA-G3-A5SJ 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" 
        TCGA-G3-A5SL         TCGA-G3-A5SM         TCGA-G3-A6UC 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-GJ-A6C0         TCGA-K7-A6G5         TCGA-LG-A6GG 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-MI-A75C         TCGA-MI-A75E         TCGA-MI-A75G 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-MI-A75I         TCGA-NI-A4U2         TCGA-O8-A75V 
"10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED"   "10Q LOSS MUTATED" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-BC-A5W4 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" 
        TCGA-BC-A69H         TCGA-BC-A69I         TCGA-CC-5258 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-CC-5260         TCGA-CC-5261         TCGA-CC-5262 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-CC-5263         TCGA-CC-A1HT         TCGA-CC-A3M9 
"10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED"   "10Q LOSS MUTATED" 
        TCGA-CC-A3MA         TCGA-CC-A3MB         TCGA-CC-A3MC 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" 
        TCGA-DD-A113         TCGA-DD-A114         TCGA-DD-A115 
"10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-DD-A116         TCGA-DD-A118         TCGA-DD-A119 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-DD-A11A         TCGA-DD-A11B         TCGA-DD-A11C 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" 
        TCGA-DD-A11D         TCGA-DD-A1E9         TCGA-DD-A1EA 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-DD-A1EB         TCGA-DD-A1EC         TCGA-DD-A1ED 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-DD-A1EE         TCGA-DD-A1EF         TCGA-DD-A1EG 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" 
        TCGA-DD-A1EH         TCGA-DD-A1EI         TCGA-DD-A1EJ 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-DD-A1EK         TCGA-DD-A1EL         TCGA-DD-A39V 
"10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-DD-A39X         TCGA-DD-A39Y         TCGA-DD-A39Z 
"10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-DD-A3A0         TCGA-DD-A3A1         TCGA-DD-A3A2 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-DD-A3A3         TCGA-DD-A3A4         TCGA-DD-A3A5 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-DD-A3A6         TCGA-DD-A3A7         TCGA-DD-A3A8 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-DD-A3A9         TCGA-DD-A4NA         TCGA-DD-A4NB 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-DD-A4ND         TCGA-DD-A4NF         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 MUTATED" "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-DD-A4NR 
"10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-DD-A4NS         TCGA-DD-A4NV         TCGA-DD-A73A 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-DD-A73B         TCGA-DD-A73C         TCGA-DD-A73D 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-DD-A73E         TCGA-DD-A73F         TCGA-DD-A73G 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-ED-A459         TCGA-ED-A4XI         TCGA-ED-A5KG 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-ED-A627         TCGA-ED-A66X         TCGA-ED-A66Y 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-ED-A7PX         TCGA-ED-A7PY         TCGA-ED-A7PZ 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-ED-A7XP         TCGA-ED-A82E         TCGA-EP-A12J 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EP-A26S         TCGA-EP-A2KA         TCGA-EP-A2KB 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EP-A2KC         TCGA-EP-A3JL         TCGA-EP-A3RK 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-ES-A2HS         TCGA-ES-A2HT         TCGA-FV-A23B 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-FV-A2QR         TCGA-FV-A3I0         TCGA-FV-A3I1 
"10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-FV-A3R2         TCGA-FV-A3R3         TCGA-FV-A495 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-FV-A496         TCGA-FV-A4ZP         TCGA-FV-A4ZQ 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-G3-A25S         TCGA-G3-A25T         TCGA-G3-A25U 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" 
        TCGA-G3-A25V         TCGA-G3-A25W         TCGA-G3-A25X 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" 
        TCGA-G3-A25Y         TCGA-G3-A25Z         TCGA-G3-A3CG 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-G3-A3CH         TCGA-G3-A3CI         TCGA-G3-A3CJ 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-G3-A3CK         TCGA-G3-A5SI         TCGA-G3-A5SJ 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" 
        TCGA-G3-A5SL         TCGA-G3-A5SM         TCGA-G3-A6UC 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-GJ-A6C0         TCGA-K7-A6G5         TCGA-LG-A6GG 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-MI-A75C         TCGA-MI-A75E         TCGA-MI-A75G 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-MI-A75I         TCGA-NI-A4U2         TCGA-O8-A75V 
"10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED"   "10Q LOSS MUTATED" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-BC-A5W4 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" 
        TCGA-BC-A69H         TCGA-BC-A69I         TCGA-CC-5258 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-CC-5260         TCGA-CC-5261         TCGA-CC-5262 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-CC-5263         TCGA-CC-A1HT         TCGA-CC-A3M9 
"10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED"   "10Q LOSS MUTATED" 
        TCGA-CC-A3MA         TCGA-CC-A3MB         TCGA-CC-A3MC 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" 
        TCGA-DD-A113         TCGA-DD-A114         TCGA-DD-A115 
"10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-DD-A116         TCGA-DD-A118         TCGA-DD-A119 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-DD-A11A         TCGA-DD-A11B         TCGA-DD-A11C 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" 
        TCGA-DD-A11D         TCGA-DD-A1E9         TCGA-DD-A1EA 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-DD-A1EB         TCGA-DD-A1EC         TCGA-DD-A1ED 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-DD-A1EE         TCGA-DD-A1EF         TCGA-DD-A1EG 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" 
        TCGA-DD-A1EH         TCGA-DD-A1EI         TCGA-DD-A1EJ 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-DD-A1EK         TCGA-DD-A1EL         TCGA-DD-A39V 
"10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-DD-A39X         TCGA-DD-A39Y         TCGA-DD-A39Z 
"10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-DD-A3A0         TCGA-DD-A3A1         TCGA-DD-A3A2 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-DD-A3A3         TCGA-DD-A3A4         TCGA-DD-A3A5 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-DD-A3A6         TCGA-DD-A3A7         TCGA-DD-A3A8 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-DD-A3A9         TCGA-DD-A4NA         TCGA-DD-A4NB 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-DD-A4ND         TCGA-DD-A4NF         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 MUTATED" "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-DD-A4NR 
"10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-DD-A4NS         TCGA-DD-A4NV         TCGA-DD-A73A 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-DD-A73B         TCGA-DD-A73C         TCGA-DD-A73D 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-DD-A73E         TCGA-DD-A73F         TCGA-DD-A73G 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-ED-A459         TCGA-ED-A4XI         TCGA-ED-A5KG 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-ED-A627         TCGA-ED-A66X         TCGA-ED-A66Y 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-ED-A7PX         TCGA-ED-A7PY         TCGA-ED-A7PZ 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-ED-A7XP         TCGA-ED-A82E         TCGA-EP-A12J 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EP-A26S         TCGA-EP-A2KA         TCGA-EP-A2KB 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EP-A2KC         TCGA-EP-A3JL         TCGA-EP-A3RK 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-ES-A2HS         TCGA-ES-A2HT         TCGA-FV-A23B 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-FV-A2QR         TCGA-FV-A3I0         TCGA-FV-A3I1 
"10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-FV-A3R2         TCGA-FV-A3R3         TCGA-FV-A495 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-FV-A496         TCGA-FV-A4ZP         TCGA-FV-A4ZQ 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-G3-A25S         TCGA-G3-A25T         TCGA-G3-A25U 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" 
        TCGA-G3-A25V         TCGA-G3-A25W         TCGA-G3-A25X 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" 
        TCGA-G3-A25Y         TCGA-G3-A25Z         TCGA-G3-A3CG 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-G3-A3CH         TCGA-G3-A3CI         TCGA-G3-A3CJ 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-G3-A3CK         TCGA-G3-A5SI         TCGA-G3-A5SJ 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" 
        TCGA-G3-A5SL         TCGA-G3-A5SM         TCGA-G3-A6UC 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-GJ-A6C0         TCGA-K7-A6G5         TCGA-LG-A6GG 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-MI-A75C         TCGA-MI-A75E         TCGA-MI-A75G 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-MI-A75I         TCGA-NI-A4U2         TCGA-O8-A75V 
"10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
[1] "hr=" "1.6"
D60V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  10Q LOSS MUTATED         7        9         0          8          0
  10Q LOSS WILD-TYPE      51       27         2         22          4
                    vv
clus                 STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  10Q LOSS MUTATED            1        0         1         0
  10Q LOSS WILD-TYPE          4        1         0         2
D60V3, multiclass
                    vv
clus                 T1 T2 T3 T4
  10Q LOSS MUTATED    8 10 10  2
  10Q LOSS WILD-TYPE 53 30 30  6
D60V4, multiclass
    clus
vv   10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  T1                8                 53
  T2               10                 30
  T3               10                 30
  T4                2                  6
D60V5, binary
                    cls
clus                  0  1
  10Q LOSS MUTATED   15  1
  10Q LOSS WILD-TYPE 82  2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED     15    1
  10Q LOSS WILD-TYPE   82    2
   clus
vv  10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  0               15                 82
  1                1                  2
                    vv
clus                 M0 M1 MX
  10Q LOSS MUTATED   23  0  7
  10Q LOSS WILD-TYPE 92  3 24
D60V6, multiclass
    clus
vv   10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  M0               23                 92
  M1                0                  3
  MX                7                 24
D60V7, binary
                    cls
clus                  0  1
  10Q LOSS MUTATED    8 22
  10Q LOSS WILD-TYPE 50 69
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED      8   22
  10Q LOSS WILD-TYPE   50   69
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  FEMALE                8                 50
  MALE                 22                 69
                    vv
clus                  R0  R1  R2  RX
  10Q LOSS MUTATED    22   4   0   3
  10Q LOSS WILD-TYPE 100   7   1   7
D60V8, multiclass
    clus
vv   10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  R0               22                100
  R1                4                  7
  R2                0                  1
  RX                3                  7

Clustering(61) Variable = 11P LOSS MUTATION ANALYSIS
D61V1, survival
                    sevent
clus2                 0  1
  11P LOSS MUTATED   12 10
  11P LOSS WILD-TYPE 72 53
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                22                125 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                10                 53 
$`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        13.84         0.07         0.13 
TCGA-DD-A113 TCGA-DD-A115 TCGA-DD-A1E9 TCGA-DD-A1EF TCGA-DD-A1EJ TCGA-DD-A39X 
       79.73        83.57        90.71        12.95        29.16        55.69 
TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NI TCGA-ED-A7PZ TCGA-EP-A2KC TCGA-FV-A496 
       12.85        73.38        18.44         0.20         0.62         0.33 
TCGA-FV-A4ZP TCGA-G3-A25S TCGA-G3-A5SJ TCGA-MI-A75G 
       60.36         1.22        11.97        14.24 

$`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-BC-A69H TCGA-BC-A69I TCGA-CC-5258 TCGA-CC-5260 
       22.36         9.50         3.95         0.53         0.07         2.86 
TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MB 
        0.39         3.39         4.24         3.32         0.10         0.10 
TCGA-DD-A114 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B 
       37.78        53.33       113.00         7.33         2.60         0.46 
TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED 
       21.76        51.29        79.40        66.31        19.79        75.65 
TCGA-DD-A1EE TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EK TCGA-DD-A1EL 
        6.71        45.11        49.15         6.02        18.35        13.64 
TCGA-DD-A39V TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 
       21.14         5.62        19.76        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-A4NF TCGA-DD-A4NH TCGA-DD-A4NJ TCGA-DD-A4NK 
       30.61        33.14        14.07        14.24        15.06        39.78 
TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR 
       56.25        29.56        61.45        93.67        12.26         0.30 
TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D 
       80.75        66.35        10.98         9.30         7.56        10.98 
TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG 
        1.45        27.72       100.96        13.41        12.69        15.85 
TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7XP 
       13.91        13.35         0.23         0.20         0.20         0.20 
TCGA-ED-A82E TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A3JL 
        0.20        18.74        19.99        11.74        10.98         9.96 
TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-A3I0 
       11.93        22.85        14.40        32.45        19.10         0.20 
TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A4ZQ TCGA-G3-A25T 
        8.12         6.38         0.13         0.03         0.39        51.06 
TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A25Z 
       53.79        28.27        30.74        58.49        14.86        21.53 
TCGA-G3-A3CG TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI 
       22.13        25.64         5.92        19.53        19.23        14.70 
TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A6UC TCGA-GJ-A6C0 TCGA-K7-A6G5 TCGA-LG-A6GG 
        7.99         4.37         7.76         1.02         4.01         0.49 
TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75I TCGA-NI-A4U2 TCGA-O8-A75V 
        9.57         5.10         8.71        58.88         4.44 

  11P LOSS MUTATED 11P LOSS WILD-TYPE 
              0.07               0.03 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
             90.71             113.00 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
             14.04              14.07 
[1] "0.1 - 90.7 (14.0)"  "0.0 - 113.0 (14.1)"
        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-BC-A69H         TCGA-BC-A69I         TCGA-CC-5258 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-CC-5260         TCGA-CC-5261         TCGA-CC-5262 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-CC-5263         TCGA-CC-A1HT         TCGA-CC-A3M9 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-CC-A3MA         TCGA-CC-A3MB         TCGA-CC-A3MC 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE"   "11P LOSS MUTATED" 
        TCGA-DD-A113         TCGA-DD-A114         TCGA-DD-A115 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE"   "11P LOSS MUTATED" 
        TCGA-DD-A116         TCGA-DD-A118         TCGA-DD-A119 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-DD-A11A         TCGA-DD-A11B         TCGA-DD-A11C 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-DD-A11D         TCGA-DD-A1E9         TCGA-DD-A1EA 
"11P LOSS WILD-TYPE"   "11P LOSS MUTATED" "11P LOSS WILD-TYPE" 
        TCGA-DD-A1EB         TCGA-DD-A1EC         TCGA-DD-A1ED 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-DD-A1EE         TCGA-DD-A1EF         TCGA-DD-A1EG 
"11P LOSS WILD-TYPE"   "11P LOSS MUTATED" "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-A1EK         TCGA-DD-A1EL         TCGA-DD-A39V 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-DD-A39X         TCGA-DD-A39Y         TCGA-DD-A39Z 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-DD-A3A0         TCGA-DD-A3A1         TCGA-DD-A3A2 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-DD-A3A3         TCGA-DD-A3A4         TCGA-DD-A3A5 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-DD-A3A6         TCGA-DD-A3A7         TCGA-DD-A3A8 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-DD-A3A9         TCGA-DD-A4NA         TCGA-DD-A4NB 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE"   "11P LOSS MUTATED" 
        TCGA-DD-A4ND         TCGA-DD-A4NF         TCGA-DD-A4NH 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-DD-A4NI         TCGA-DD-A4NJ         TCGA-DD-A4NK 
  "11P LOSS MUTATED" "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-DD-A4NR 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-DD-A4NS         TCGA-DD-A4NV         TCGA-DD-A73A 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-DD-A73B         TCGA-DD-A73C         TCGA-DD-A73D 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-DD-A73E         TCGA-DD-A73F         TCGA-DD-A73G 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-ED-A459         TCGA-ED-A4XI         TCGA-ED-A5KG 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-ED-A627         TCGA-ED-A66X         TCGA-ED-A66Y 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-ED-A7PX         TCGA-ED-A7PY         TCGA-ED-A7PZ 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE"   "11P LOSS MUTATED" 
        TCGA-ED-A7XP         TCGA-ED-A82E         TCGA-EP-A12J 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-EP-A26S         TCGA-EP-A2KA         TCGA-EP-A2KB 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-EP-A2KC         TCGA-EP-A3JL         TCGA-EP-A3RK 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-ES-A2HS         TCGA-ES-A2HT         TCGA-FV-A23B 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-FV-A2QR         TCGA-FV-A3I0         TCGA-FV-A3I1 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-FV-A3R2         TCGA-FV-A3R3         TCGA-FV-A495 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-FV-A496         TCGA-FV-A4ZP         TCGA-FV-A4ZQ 
  "11P LOSS MUTATED"   "11P LOSS MUTATED" "11P LOSS WILD-TYPE" 
        TCGA-G3-A25S         TCGA-G3-A25T         TCGA-G3-A25U 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-G3-A25V         TCGA-G3-A25W         TCGA-G3-A25X 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-G3-A25Y         TCGA-G3-A25Z         TCGA-G3-A3CG 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-G3-A3CH         TCGA-G3-A3CI         TCGA-G3-A3CJ 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-G3-A3CK         TCGA-G3-A5SI         TCGA-G3-A5SJ 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE"   "11P LOSS MUTATED" 
        TCGA-G3-A5SL         TCGA-G3-A5SM         TCGA-G3-A6UC 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-GJ-A6C0         TCGA-K7-A6G5         TCGA-LG-A6GG 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-MI-A75C         TCGA-MI-A75E         TCGA-MI-A75G 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE"   "11P LOSS MUTATED" 
        TCGA-MI-A75I         TCGA-NI-A4U2         TCGA-O8-A75V 
"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-BC-A69H         TCGA-BC-A69I         TCGA-CC-5258 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-CC-5260         TCGA-CC-5261         TCGA-CC-5262 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-CC-5263         TCGA-CC-A1HT         TCGA-CC-A3M9 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-CC-A3MA         TCGA-CC-A3MB         TCGA-CC-A3MC 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE"   "11P LOSS MUTATED" 
        TCGA-DD-A113         TCGA-DD-A114         TCGA-DD-A115 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE"   "11P LOSS MUTATED" 
        TCGA-DD-A116         TCGA-DD-A118         TCGA-DD-A119 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-DD-A11A         TCGA-DD-A11B         TCGA-DD-A11C 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-DD-A11D         TCGA-DD-A1E9         TCGA-DD-A1EA 
"11P LOSS WILD-TYPE"   "11P LOSS MUTATED" "11P LOSS WILD-TYPE" 
        TCGA-DD-A1EB         TCGA-DD-A1EC         TCGA-DD-A1ED 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-DD-A1EE         TCGA-DD-A1EF         TCGA-DD-A1EG 
"11P LOSS WILD-TYPE"   "11P LOSS MUTATED" "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-A1EK         TCGA-DD-A1EL         TCGA-DD-A39V 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-DD-A39X         TCGA-DD-A39Y         TCGA-DD-A39Z 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-DD-A3A0         TCGA-DD-A3A1         TCGA-DD-A3A2 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-DD-A3A3         TCGA-DD-A3A4         TCGA-DD-A3A5 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-DD-A3A6         TCGA-DD-A3A7         TCGA-DD-A3A8 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-DD-A3A9         TCGA-DD-A4NA         TCGA-DD-A4NB 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE"   "11P LOSS MUTATED" 
        TCGA-DD-A4ND         TCGA-DD-A4NF         TCGA-DD-A4NH 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-DD-A4NI         TCGA-DD-A4NJ         TCGA-DD-A4NK 
  "11P LOSS MUTATED" "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-DD-A4NR 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-DD-A4NS         TCGA-DD-A4NV         TCGA-DD-A73A 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-DD-A73B         TCGA-DD-A73C         TCGA-DD-A73D 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-DD-A73E         TCGA-DD-A73F         TCGA-DD-A73G 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-ED-A459         TCGA-ED-A4XI         TCGA-ED-A5KG 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-ED-A627         TCGA-ED-A66X         TCGA-ED-A66Y 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-ED-A7PX         TCGA-ED-A7PY         TCGA-ED-A7PZ 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE"   "11P LOSS MUTATED" 
        TCGA-ED-A7XP         TCGA-ED-A82E         TCGA-EP-A12J 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-EP-A26S         TCGA-EP-A2KA         TCGA-EP-A2KB 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-EP-A2KC         TCGA-EP-A3JL         TCGA-EP-A3RK 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-ES-A2HS         TCGA-ES-A2HT         TCGA-FV-A23B 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-FV-A2QR         TCGA-FV-A3I0         TCGA-FV-A3I1 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-FV-A3R2         TCGA-FV-A3R3         TCGA-FV-A495 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-FV-A496         TCGA-FV-A4ZP         TCGA-FV-A4ZQ 
  "11P LOSS MUTATED"   "11P LOSS MUTATED" "11P LOSS WILD-TYPE" 
        TCGA-G3-A25S         TCGA-G3-A25T         TCGA-G3-A25U 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-G3-A25V         TCGA-G3-A25W         TCGA-G3-A25X 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-G3-A25Y         TCGA-G3-A25Z         TCGA-G3-A3CG 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-G3-A3CH         TCGA-G3-A3CI         TCGA-G3-A3CJ 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-G3-A3CK         TCGA-G3-A5SI         TCGA-G3-A5SJ 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE"   "11P LOSS MUTATED" 
        TCGA-G3-A5SL         TCGA-G3-A5SM         TCGA-G3-A6UC 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-GJ-A6C0         TCGA-K7-A6G5         TCGA-LG-A6GG 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-MI-A75C         TCGA-MI-A75E         TCGA-MI-A75G 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE"   "11P LOSS MUTATED" 
        TCGA-MI-A75I         TCGA-NI-A4U2         TCGA-O8-A75V 
"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-BC-A69H         TCGA-BC-A69I         TCGA-CC-5258 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-CC-5260         TCGA-CC-5261         TCGA-CC-5262 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-CC-5263         TCGA-CC-A1HT         TCGA-CC-A3M9 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-CC-A3MA         TCGA-CC-A3MB         TCGA-CC-A3MC 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE"   "11P LOSS MUTATED" 
        TCGA-DD-A113         TCGA-DD-A114         TCGA-DD-A115 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE"   "11P LOSS MUTATED" 
        TCGA-DD-A116         TCGA-DD-A118         TCGA-DD-A119 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-DD-A11A         TCGA-DD-A11B         TCGA-DD-A11C 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-DD-A11D         TCGA-DD-A1E9         TCGA-DD-A1EA 
"11P LOSS WILD-TYPE"   "11P LOSS MUTATED" "11P LOSS WILD-TYPE" 
        TCGA-DD-A1EB         TCGA-DD-A1EC         TCGA-DD-A1ED 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-DD-A1EE         TCGA-DD-A1EF         TCGA-DD-A1EG 
"11P LOSS WILD-TYPE"   "11P LOSS MUTATED" "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-A1EK         TCGA-DD-A1EL         TCGA-DD-A39V 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-DD-A39X         TCGA-DD-A39Y         TCGA-DD-A39Z 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-DD-A3A0         TCGA-DD-A3A1         TCGA-DD-A3A2 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-DD-A3A3         TCGA-DD-A3A4         TCGA-DD-A3A5 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-DD-A3A6         TCGA-DD-A3A7         TCGA-DD-A3A8 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-DD-A3A9         TCGA-DD-A4NA         TCGA-DD-A4NB 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE"   "11P LOSS MUTATED" 
        TCGA-DD-A4ND         TCGA-DD-A4NF         TCGA-DD-A4NH 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-DD-A4NI         TCGA-DD-A4NJ         TCGA-DD-A4NK 
  "11P LOSS MUTATED" "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-DD-A4NR 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-DD-A4NS         TCGA-DD-A4NV         TCGA-DD-A73A 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-DD-A73B         TCGA-DD-A73C         TCGA-DD-A73D 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-DD-A73E         TCGA-DD-A73F         TCGA-DD-A73G 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-ED-A459         TCGA-ED-A4XI         TCGA-ED-A5KG 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-ED-A627         TCGA-ED-A66X         TCGA-ED-A66Y 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-ED-A7PX         TCGA-ED-A7PY         TCGA-ED-A7PZ 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE"   "11P LOSS MUTATED" 
        TCGA-ED-A7XP         TCGA-ED-A82E         TCGA-EP-A12J 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-EP-A26S         TCGA-EP-A2KA         TCGA-EP-A2KB 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-EP-A2KC         TCGA-EP-A3JL         TCGA-EP-A3RK 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-ES-A2HS         TCGA-ES-A2HT         TCGA-FV-A23B 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-FV-A2QR         TCGA-FV-A3I0         TCGA-FV-A3I1 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-FV-A3R2         TCGA-FV-A3R3         TCGA-FV-A495 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-FV-A496         TCGA-FV-A4ZP         TCGA-FV-A4ZQ 
  "11P LOSS MUTATED"   "11P LOSS MUTATED" "11P LOSS WILD-TYPE" 
        TCGA-G3-A25S         TCGA-G3-A25T         TCGA-G3-A25U 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-G3-A25V         TCGA-G3-A25W         TCGA-G3-A25X 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-G3-A25Y         TCGA-G3-A25Z         TCGA-G3-A3CG 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-G3-A3CH         TCGA-G3-A3CI         TCGA-G3-A3CJ 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-G3-A3CK         TCGA-G3-A5SI         TCGA-G3-A5SJ 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE"   "11P LOSS MUTATED" 
        TCGA-G3-A5SL         TCGA-G3-A5SM         TCGA-G3-A6UC 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-GJ-A6C0         TCGA-K7-A6G5         TCGA-LG-A6GG 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-MI-A75C         TCGA-MI-A75E         TCGA-MI-A75G 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE"   "11P LOSS MUTATED" 
        TCGA-MI-A75I         TCGA-NI-A4U2         TCGA-O8-A75V 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
[1] "hr=" "1.1"
D61V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  11P LOSS MUTATED         9        5         0          5          0
  11P LOSS WILD-TYPE      49       31         2         25          4
                    vv
clus                 STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  11P LOSS MUTATED            1        0         1         0
  11P LOSS WILD-TYPE          4        1         0         2
D61V3, multiclass
                    vv
clus                 T1 T2 T3 T4
  11P LOSS MUTATED   11  6  7  0
  11P LOSS WILD-TYPE 50 34 33  8
D61V4, multiclass
    clus
vv   11P LOSS MUTATED 11P LOSS WILD-TYPE
  T1               11                 50
  T2                6                 34
  T3                7                 33
  T4                0                  8
D61V5, binary
                    cls
clus                  0  1
  11P LOSS MUTATED   11  2
  11P LOSS WILD-TYPE 86  1
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED     11    2
  11P LOSS WILD-TYPE   86    1
   clus
vv  11P LOSS MUTATED 11P LOSS WILD-TYPE
  0               11                 86
  1                2                  1
                    vv
clus                 M0 M1 MX
  11P LOSS MUTATED   19  0  5
  11P LOSS WILD-TYPE 96  3 26
D61V6, multiclass
    clus
vv   11P LOSS MUTATED 11P LOSS WILD-TYPE
  M0               19                 96
  M1                0                  3
  MX                5                 26
D61V7, binary
                    cls
clus                  0  1
  11P LOSS MUTATED    8 16
  11P LOSS WILD-TYPE 50 75
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED      8   16
  11P LOSS WILD-TYPE   50   75
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  FEMALE                8                 50
  MALE                 16                 75
                    vv
clus                  R0  R1  R2  RX
  11P LOSS MUTATED    20   3   0   1
  11P LOSS WILD-TYPE 102   8   1   9
D61V8, multiclass
    clus
vv   11P LOSS MUTATED 11P LOSS WILD-TYPE
  R0               20                102
  R1                3                  8
  R2                0                  1
  RX                1                  9

Clustering(62) Variable = 11Q LOSS MUTATION ANALYSIS
D62V1, survival
                    sevent
clus2                 0  1
  11Q LOSS MUTATED   13 12
  11Q LOSS WILD-TYPE 71 51
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                25                122 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                12                 51 
$`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        13.84         4.24 
TCGA-CC-A3MC TCGA-DD-A113 TCGA-DD-A115 TCGA-DD-A11A TCGA-DD-A1E9 TCGA-DD-A1EF 
        0.13        79.73        83.57         2.60        90.71        12.95 
TCGA-DD-A1EJ TCGA-DD-A39X TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NI TCGA-DD-A73B 
       29.16        55.69        12.85        73.38        18.44         9.30 
TCGA-ED-A7PZ TCGA-EP-A2KC TCGA-FV-A496 TCGA-FV-A4ZP TCGA-G3-A25S TCGA-G3-A5SJ 
        0.20         0.62         0.33        60.36         1.22        11.97 
TCGA-MI-A75G 
       14.24 

$`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        22.36 
TCGA-BC-A5W4 TCGA-BC-A69H TCGA-BC-A69I TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5261 
        9.50         3.95         0.53         0.07         2.86         0.39 
TCGA-CC-5262 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-DD-A114 
        3.39         3.32         0.10         0.07         0.10        37.78 
TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D 
       53.33       113.00         7.33         0.46        21.76        51.29 
TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EG 
       79.40        66.31        19.79        75.65         6.71        45.11 
TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39Y 
       49.15         6.02        18.35        13.64        21.14         5.62 
TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 
       19.76        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        30.61        33.14 
TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN 
       14.07        14.24        15.06        39.78        56.25        29.56 
TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV 
       61.45        93.67        12.26         0.30        80.75        66.35 
TCGA-DD-A73A TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G 
       10.98         7.56        10.98         1.45        27.72       100.96 
TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y 
       13.41        12.69        15.85        13.91        13.35         0.23 
TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7XP TCGA-ED-A82E TCGA-EP-A12J TCGA-EP-A26S 
        0.20         0.20         0.20         0.20        18.74        19.99 
TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT 
       11.74        10.98         9.96        11.93        22.85        14.40 
TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 
       32.45        19.10         0.20         8.12         6.38         0.13 
TCGA-FV-A495 TCGA-FV-A4ZQ TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W 
        0.03         0.39        51.06        53.79        28.27        30.74 
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         5.92 
TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A6UC 
       19.53        19.23        14.70         7.99         4.37         7.76 
TCGA-GJ-A6C0 TCGA-K7-A6G5 TCGA-LG-A6GG TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75I 
        1.02         4.01         0.49         9.57         5.10         8.71 
TCGA-NI-A4U2 TCGA-O8-A75V 
       58.88         4.44 

  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
              0.13               0.03 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
             90.71             113.00 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
            13.840             14.155 
[1] "0.1 - 90.7 (13.8)"  "0.0 - 113.0 (14.2)"
        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-BC-A69H         TCGA-BC-A69I         TCGA-CC-5258 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-CC-5260         TCGA-CC-5261         TCGA-CC-5262 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-CC-5263         TCGA-CC-A1HT         TCGA-CC-A3M9 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-CC-A3MA         TCGA-CC-A3MB         TCGA-CC-A3MC 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" 
        TCGA-DD-A113         TCGA-DD-A114         TCGA-DD-A115 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" 
        TCGA-DD-A116         TCGA-DD-A118         TCGA-DD-A119 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-DD-A11A         TCGA-DD-A11B         TCGA-DD-A11C 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-DD-A11D         TCGA-DD-A1E9         TCGA-DD-A1EA 
"11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" 
        TCGA-DD-A1EB         TCGA-DD-A1EC         TCGA-DD-A1ED 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-DD-A1EE         TCGA-DD-A1EF         TCGA-DD-A1EG 
"11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" "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-A1EK         TCGA-DD-A1EL         TCGA-DD-A39V 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-DD-A39X         TCGA-DD-A39Y         TCGA-DD-A39Z 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-DD-A3A0         TCGA-DD-A3A1         TCGA-DD-A3A2 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-DD-A3A3         TCGA-DD-A3A4         TCGA-DD-A3A5 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-DD-A3A6         TCGA-DD-A3A7         TCGA-DD-A3A8 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-DD-A3A9         TCGA-DD-A4NA         TCGA-DD-A4NB 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" 
        TCGA-DD-A4ND         TCGA-DD-A4NF         TCGA-DD-A4NH 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-DD-A4NI         TCGA-DD-A4NJ         TCGA-DD-A4NK 
  "11Q LOSS MUTATED" "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-DD-A4NR 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-DD-A4NS         TCGA-DD-A4NV         TCGA-DD-A73A 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-DD-A73B         TCGA-DD-A73C         TCGA-DD-A73D 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-DD-A73E         TCGA-DD-A73F         TCGA-DD-A73G 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-ED-A459         TCGA-ED-A4XI         TCGA-ED-A5KG 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-ED-A627         TCGA-ED-A66X         TCGA-ED-A66Y 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-ED-A7PX         TCGA-ED-A7PY         TCGA-ED-A7PZ 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" 
        TCGA-ED-A7XP         TCGA-ED-A82E         TCGA-EP-A12J 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-EP-A26S         TCGA-EP-A2KA         TCGA-EP-A2KB 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-EP-A2KC         TCGA-EP-A3JL         TCGA-EP-A3RK 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-ES-A2HS         TCGA-ES-A2HT         TCGA-FV-A23B 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-FV-A2QR         TCGA-FV-A3I0         TCGA-FV-A3I1 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-FV-A3R2         TCGA-FV-A3R3         TCGA-FV-A495 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-FV-A496         TCGA-FV-A4ZP         TCGA-FV-A4ZQ 
  "11Q LOSS MUTATED"   "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" 
        TCGA-G3-A25S         TCGA-G3-A25T         TCGA-G3-A25U 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-G3-A25V         TCGA-G3-A25W         TCGA-G3-A25X 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-G3-A25Y         TCGA-G3-A25Z         TCGA-G3-A3CG 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-G3-A3CH         TCGA-G3-A3CI         TCGA-G3-A3CJ 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-G3-A3CK         TCGA-G3-A5SI         TCGA-G3-A5SJ 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" 
        TCGA-G3-A5SL         TCGA-G3-A5SM         TCGA-G3-A6UC 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-GJ-A6C0         TCGA-K7-A6G5         TCGA-LG-A6GG 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-MI-A75C         TCGA-MI-A75E         TCGA-MI-A75G 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" 
        TCGA-MI-A75I         TCGA-NI-A4U2         TCGA-O8-A75V 
"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-BC-A69H         TCGA-BC-A69I         TCGA-CC-5258 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-CC-5260         TCGA-CC-5261         TCGA-CC-5262 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-CC-5263         TCGA-CC-A1HT         TCGA-CC-A3M9 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-CC-A3MA         TCGA-CC-A3MB         TCGA-CC-A3MC 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" 
        TCGA-DD-A113         TCGA-DD-A114         TCGA-DD-A115 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" 
        TCGA-DD-A116         TCGA-DD-A118         TCGA-DD-A119 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-DD-A11A         TCGA-DD-A11B         TCGA-DD-A11C 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-DD-A11D         TCGA-DD-A1E9         TCGA-DD-A1EA 
"11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" 
        TCGA-DD-A1EB         TCGA-DD-A1EC         TCGA-DD-A1ED 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-DD-A1EE         TCGA-DD-A1EF         TCGA-DD-A1EG 
"11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" "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-A1EK         TCGA-DD-A1EL         TCGA-DD-A39V 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-DD-A39X         TCGA-DD-A39Y         TCGA-DD-A39Z 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-DD-A3A0         TCGA-DD-A3A1         TCGA-DD-A3A2 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-DD-A3A3         TCGA-DD-A3A4         TCGA-DD-A3A5 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-DD-A3A6         TCGA-DD-A3A7         TCGA-DD-A3A8 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-DD-A3A9         TCGA-DD-A4NA         TCGA-DD-A4NB 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" 
        TCGA-DD-A4ND         TCGA-DD-A4NF         TCGA-DD-A4NH 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-DD-A4NI         TCGA-DD-A4NJ         TCGA-DD-A4NK 
  "11Q LOSS MUTATED" "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-DD-A4NR 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-DD-A4NS         TCGA-DD-A4NV         TCGA-DD-A73A 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-DD-A73B         TCGA-DD-A73C         TCGA-DD-A73D 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-DD-A73E         TCGA-DD-A73F         TCGA-DD-A73G 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-ED-A459         TCGA-ED-A4XI         TCGA-ED-A5KG 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-ED-A627         TCGA-ED-A66X         TCGA-ED-A66Y 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-ED-A7PX         TCGA-ED-A7PY         TCGA-ED-A7PZ 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" 
        TCGA-ED-A7XP         TCGA-ED-A82E         TCGA-EP-A12J 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-EP-A26S         TCGA-EP-A2KA         TCGA-EP-A2KB 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-EP-A2KC         TCGA-EP-A3JL         TCGA-EP-A3RK 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-ES-A2HS         TCGA-ES-A2HT         TCGA-FV-A23B 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-FV-A2QR         TCGA-FV-A3I0         TCGA-FV-A3I1 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-FV-A3R2         TCGA-FV-A3R3         TCGA-FV-A495 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-FV-A496         TCGA-FV-A4ZP         TCGA-FV-A4ZQ 
  "11Q LOSS MUTATED"   "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" 
        TCGA-G3-A25S         TCGA-G3-A25T         TCGA-G3-A25U 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-G3-A25V         TCGA-G3-A25W         TCGA-G3-A25X 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-G3-A25Y         TCGA-G3-A25Z         TCGA-G3-A3CG 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-G3-A3CH         TCGA-G3-A3CI         TCGA-G3-A3CJ 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-G3-A3CK         TCGA-G3-A5SI         TCGA-G3-A5SJ 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" 
        TCGA-G3-A5SL         TCGA-G3-A5SM         TCGA-G3-A6UC 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-GJ-A6C0         TCGA-K7-A6G5         TCGA-LG-A6GG 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-MI-A75C         TCGA-MI-A75E         TCGA-MI-A75G 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" 
        TCGA-MI-A75I         TCGA-NI-A4U2         TCGA-O8-A75V 
"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-BC-A69H         TCGA-BC-A69I         TCGA-CC-5258 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-CC-5260         TCGA-CC-5261         TCGA-CC-5262 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-CC-5263         TCGA-CC-A1HT         TCGA-CC-A3M9 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-CC-A3MA         TCGA-CC-A3MB         TCGA-CC-A3MC 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" 
        TCGA-DD-A113         TCGA-DD-A114         TCGA-DD-A115 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" 
        TCGA-DD-A116         TCGA-DD-A118         TCGA-DD-A119 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-DD-A11A         TCGA-DD-A11B         TCGA-DD-A11C 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-DD-A11D         TCGA-DD-A1E9         TCGA-DD-A1EA 
"11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" 
        TCGA-DD-A1EB         TCGA-DD-A1EC         TCGA-DD-A1ED 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-DD-A1EE         TCGA-DD-A1EF         TCGA-DD-A1EG 
"11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" "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-A1EK         TCGA-DD-A1EL         TCGA-DD-A39V 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-DD-A39X         TCGA-DD-A39Y         TCGA-DD-A39Z 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-DD-A3A0         TCGA-DD-A3A1         TCGA-DD-A3A2 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-DD-A3A3         TCGA-DD-A3A4         TCGA-DD-A3A5 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-DD-A3A6         TCGA-DD-A3A7         TCGA-DD-A3A8 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-DD-A3A9         TCGA-DD-A4NA         TCGA-DD-A4NB 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" 
        TCGA-DD-A4ND         TCGA-DD-A4NF         TCGA-DD-A4NH 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-DD-A4NI         TCGA-DD-A4NJ         TCGA-DD-A4NK 
  "11Q LOSS MUTATED" "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-DD-A4NR 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-DD-A4NS         TCGA-DD-A4NV         TCGA-DD-A73A 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-DD-A73B         TCGA-DD-A73C         TCGA-DD-A73D 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-DD-A73E         TCGA-DD-A73F         TCGA-DD-A73G 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-ED-A459         TCGA-ED-A4XI         TCGA-ED-A5KG 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-ED-A627         TCGA-ED-A66X         TCGA-ED-A66Y 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-ED-A7PX         TCGA-ED-A7PY         TCGA-ED-A7PZ 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" 
        TCGA-ED-A7XP         TCGA-ED-A82E         TCGA-EP-A12J 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-EP-A26S         TCGA-EP-A2KA         TCGA-EP-A2KB 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-EP-A2KC         TCGA-EP-A3JL         TCGA-EP-A3RK 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-ES-A2HS         TCGA-ES-A2HT         TCGA-FV-A23B 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-FV-A2QR         TCGA-FV-A3I0         TCGA-FV-A3I1 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-FV-A3R2         TCGA-FV-A3R3         TCGA-FV-A495 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-FV-A496         TCGA-FV-A4ZP         TCGA-FV-A4ZQ 
  "11Q LOSS MUTATED"   "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" 
        TCGA-G3-A25S         TCGA-G3-A25T         TCGA-G3-A25U 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-G3-A25V         TCGA-G3-A25W         TCGA-G3-A25X 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-G3-A25Y         TCGA-G3-A25Z         TCGA-G3-A3CG 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-G3-A3CH         TCGA-G3-A3CI         TCGA-G3-A3CJ 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-G3-A3CK         TCGA-G3-A5SI         TCGA-G3-A5SJ 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" 
        TCGA-G3-A5SL         TCGA-G3-A5SM         TCGA-G3-A6UC 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-GJ-A6C0         TCGA-K7-A6G5         TCGA-LG-A6GG 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-MI-A75C         TCGA-MI-A75E         TCGA-MI-A75G 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" 
        TCGA-MI-A75I         TCGA-NI-A4U2         TCGA-O8-A75V 
"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        11        5         0          6          0
  11Q LOSS WILD-TYPE      47       31         2         24          4
                    vv
clus                 STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  11Q LOSS MUTATED            1        0         1         0
  11Q LOSS WILD-TYPE          4        1         0         2
D62V3, multiclass
                    vv
clus                 T1 T2 T3 T4
  11Q LOSS MUTATED   13  6  8  0
  11Q LOSS WILD-TYPE 48 34 32  8
D62V4, multiclass
    clus
vv   11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  T1               13                 48
  T2                6                 34
  T3                8                 32
  T4                0                  8
D62V5, binary
                    cls
clus                  0  1
  11Q LOSS MUTATED   14  2
  11Q LOSS WILD-TYPE 83  1
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED     14    2
  11Q LOSS WILD-TYPE   83    1
   clus
vv  11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  0               14                 83
  1                2                  1
                    vv
clus                 M0 M1 MX
  11Q LOSS MUTATED   21  0  6
  11Q LOSS WILD-TYPE 94  3 25
D62V6, multiclass
    clus
vv   11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  M0               21                 94
  M1                0                  3
  MX                6                 25
D62V7, binary
                    cls
clus                  0  1
  11Q LOSS MUTATED    9 18
  11Q LOSS WILD-TYPE 49 73
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED      9   18
  11Q LOSS WILD-TYPE   49   73
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  FEMALE                9                 49
  MALE                 18                 73
                    vv
clus                  R0  R1  R2  RX
  11Q LOSS MUTATED    21   4   0   2
  11Q LOSS WILD-TYPE 101   7   1   8
D62V8, multiclass
    clus
vv   11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  R0               21                101
  R1                4                  7
  R2                0                  1
  RX                2                  8

Clustering(63) Variable = 12P LOSS MUTATION ANALYSIS
D63V1, survival
                    sevent
clus2                 0  1
  12P LOSS MUTATED   15 12
  12P LOSS WILD-TYPE 69 51
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                27                120 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                12                 51 
$`12P LOSS MUTATED`
TCGA-BC-A217 TCGA-BC-A5W4 TCGA-CC-A1HT TCGA-CC-A3MC TCGA-DD-A119 TCGA-DD-A1EG 
       13.84         9.50         3.32         0.13         7.33        45.11 
TCGA-DD-A1EH TCGA-DD-A1EJ TCGA-DD-A1EL TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A3A1 
       49.15        29.16        13.64        55.69         5.62         7.66 
TCGA-DD-A4NA TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NO TCGA-DD-A73F 
       33.14        14.24        18.44        15.06        61.45        27.72 
TCGA-ED-A7XP TCGA-EP-A2KC TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A496 TCGA-G3-A25S 
        0.20         0.62         8.12         6.38         0.33         1.22 
TCGA-G3-A25Z TCGA-MI-A75G TCGA-MI-A75I 
       21.53        14.24         8.71 

$`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-BC-A69H TCGA-BC-A69I 
        5.03        44.42         0.26        22.36         3.95         0.53 
TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A3M9 
        0.07         2.86         0.39         3.39         4.24         0.10 
TCGA-CC-A3MA TCGA-CC-A3MB TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 
        0.07         0.10        79.73        37.78        83.57        53.33 
TCGA-DD-A118 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 
      113.00         2.60         0.46        21.76        51.29        90.71 
TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EF 
       79.40        66.31        19.79        75.65         6.71        12.95 
TCGA-DD-A1EI TCGA-DD-A1EK TCGA-DD-A39V TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A2 
        6.02        18.35        21.14        19.76        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-A4NB TCGA-DD-A4ND TCGA-DD-A4NF TCGA-DD-A4NK TCGA-DD-A4NL 
       30.61        12.85        73.38        14.07        39.78        56.25 
TCGA-DD-A4NN TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV 
       29.56        93.67        12.26         0.30        80.75        66.35 
TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73G 
       10.98         9.30         7.56        10.98         1.45       100.96 
TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y 
       13.41        12.69        15.85        13.91        13.35         0.23 
TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A82E TCGA-EP-A12J TCGA-EP-A26S 
        0.20         0.20         0.20         0.20        18.74        19.99 
TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT 
       11.74        10.98         9.96        11.93        22.85        14.40 
TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A4ZP 
       32.45        19.10         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        51.06        53.79        28.27        30.74        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         5.92        19.53        19.23 
TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A6UC TCGA-GJ-A6C0 
       14.70        11.97         7.99         4.37         7.76         1.02 
TCGA-K7-A6G5 TCGA-LG-A6GG TCGA-MI-A75C TCGA-MI-A75E TCGA-NI-A4U2 TCGA-O8-A75V 
        4.01         0.49         9.57         5.10        58.88         4.44 

  12P LOSS MUTATED 12P LOSS WILD-TYPE 
              0.13               0.03 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
             61.45             113.00 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
             13.64              14.55 
[1] "0.1 - 61.5 (13.6)"  "0.0 - 113.0 (14.6)"
        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-BC-A69H         TCGA-BC-A69I         TCGA-CC-5258 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-CC-5260         TCGA-CC-5261         TCGA-CC-5262 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-CC-5263         TCGA-CC-A1HT         TCGA-CC-A3M9 
"12P LOSS WILD-TYPE"   "12P LOSS MUTATED" "12P LOSS WILD-TYPE" 
        TCGA-CC-A3MA         TCGA-CC-A3MB         TCGA-CC-A3MC 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE"   "12P LOSS MUTATED" 
        TCGA-DD-A113         TCGA-DD-A114         TCGA-DD-A115 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DD-A116         TCGA-DD-A118         TCGA-DD-A119 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE"   "12P LOSS MUTATED" 
        TCGA-DD-A11A         TCGA-DD-A11B         TCGA-DD-A11C 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DD-A11D         TCGA-DD-A1E9         TCGA-DD-A1EA 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DD-A1EB         TCGA-DD-A1EC         TCGA-DD-A1ED 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DD-A1EE         TCGA-DD-A1EF         TCGA-DD-A1EG 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE"   "12P LOSS MUTATED" 
        TCGA-DD-A1EH         TCGA-DD-A1EI         TCGA-DD-A1EJ 
  "12P LOSS MUTATED" "12P LOSS WILD-TYPE"   "12P LOSS MUTATED" 
        TCGA-DD-A1EK         TCGA-DD-A1EL         TCGA-DD-A39V 
"12P LOSS WILD-TYPE"   "12P LOSS MUTATED" "12P LOSS WILD-TYPE" 
        TCGA-DD-A39X         TCGA-DD-A39Y         TCGA-DD-A39Z 
  "12P LOSS MUTATED"   "12P LOSS MUTATED" "12P LOSS WILD-TYPE" 
        TCGA-DD-A3A0         TCGA-DD-A3A1         TCGA-DD-A3A2 
"12P LOSS WILD-TYPE"   "12P LOSS MUTATED" "12P LOSS WILD-TYPE" 
        TCGA-DD-A3A3         TCGA-DD-A3A4         TCGA-DD-A3A5 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DD-A3A6         TCGA-DD-A3A7         TCGA-DD-A3A8 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DD-A3A9         TCGA-DD-A4NA         TCGA-DD-A4NB 
"12P LOSS WILD-TYPE"   "12P LOSS MUTATED" "12P LOSS WILD-TYPE" 
        TCGA-DD-A4ND         TCGA-DD-A4NF         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 MUTATED"   "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-DD-A4NR 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DD-A4NS         TCGA-DD-A4NV         TCGA-DD-A73A 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DD-A73B         TCGA-DD-A73C         TCGA-DD-A73D 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DD-A73E         TCGA-DD-A73F         TCGA-DD-A73G 
"12P LOSS WILD-TYPE"   "12P LOSS MUTATED" "12P LOSS WILD-TYPE" 
        TCGA-ED-A459         TCGA-ED-A4XI         TCGA-ED-A5KG 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-ED-A627         TCGA-ED-A66X         TCGA-ED-A66Y 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-ED-A7PX         TCGA-ED-A7PY         TCGA-ED-A7PZ 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-ED-A7XP         TCGA-ED-A82E         TCGA-EP-A12J 
  "12P LOSS MUTATED" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EP-A26S         TCGA-EP-A2KA         TCGA-EP-A2KB 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EP-A2KC         TCGA-EP-A3JL         TCGA-EP-A3RK 
  "12P LOSS MUTATED" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-ES-A2HS         TCGA-ES-A2HT         TCGA-FV-A23B 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-FV-A2QR         TCGA-FV-A3I0         TCGA-FV-A3I1 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE"   "12P LOSS MUTATED" 
        TCGA-FV-A3R2         TCGA-FV-A3R3         TCGA-FV-A495 
  "12P LOSS MUTATED" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-FV-A496         TCGA-FV-A4ZP         TCGA-FV-A4ZQ 
  "12P LOSS MUTATED" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-G3-A25S         TCGA-G3-A25T         TCGA-G3-A25U 
  "12P LOSS MUTATED" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-G3-A25V         TCGA-G3-A25W         TCGA-G3-A25X 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-G3-A25Y         TCGA-G3-A25Z         TCGA-G3-A3CG 
"12P LOSS WILD-TYPE"   "12P LOSS MUTATED" "12P LOSS WILD-TYPE" 
        TCGA-G3-A3CH         TCGA-G3-A3CI         TCGA-G3-A3CJ 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-G3-A3CK         TCGA-G3-A5SI         TCGA-G3-A5SJ 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-G3-A5SL         TCGA-G3-A5SM         TCGA-G3-A6UC 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-GJ-A6C0         TCGA-K7-A6G5         TCGA-LG-A6GG 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-MI-A75C         TCGA-MI-A75E         TCGA-MI-A75G 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE"   "12P LOSS MUTATED" 
        TCGA-MI-A75I         TCGA-NI-A4U2         TCGA-O8-A75V 
  "12P LOSS MUTATED" "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-BC-A69H         TCGA-BC-A69I         TCGA-CC-5258 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-CC-5260         TCGA-CC-5261         TCGA-CC-5262 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-CC-5263         TCGA-CC-A1HT         TCGA-CC-A3M9 
"12P LOSS WILD-TYPE"   "12P LOSS MUTATED" "12P LOSS WILD-TYPE" 
        TCGA-CC-A3MA         TCGA-CC-A3MB         TCGA-CC-A3MC 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE"   "12P LOSS MUTATED" 
        TCGA-DD-A113         TCGA-DD-A114         TCGA-DD-A115 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DD-A116         TCGA-DD-A118         TCGA-DD-A119 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE"   "12P LOSS MUTATED" 
        TCGA-DD-A11A         TCGA-DD-A11B         TCGA-DD-A11C 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DD-A11D         TCGA-DD-A1E9         TCGA-DD-A1EA 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DD-A1EB         TCGA-DD-A1EC         TCGA-DD-A1ED 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DD-A1EE         TCGA-DD-A1EF         TCGA-DD-A1EG 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE"   "12P LOSS MUTATED" 
        TCGA-DD-A1EH         TCGA-DD-A1EI         TCGA-DD-A1EJ 
  "12P LOSS MUTATED" "12P LOSS WILD-TYPE"   "12P LOSS MUTATED" 
        TCGA-DD-A1EK         TCGA-DD-A1EL         TCGA-DD-A39V 
"12P LOSS WILD-TYPE"   "12P LOSS MUTATED" "12P LOSS WILD-TYPE" 
        TCGA-DD-A39X         TCGA-DD-A39Y         TCGA-DD-A39Z 
  "12P LOSS MUTATED"   "12P LOSS MUTATED" "12P LOSS WILD-TYPE" 
        TCGA-DD-A3A0         TCGA-DD-A3A1         TCGA-DD-A3A2 
"12P LOSS WILD-TYPE"   "12P LOSS MUTATED" "12P LOSS WILD-TYPE" 
        TCGA-DD-A3A3         TCGA-DD-A3A4         TCGA-DD-A3A5 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DD-A3A6         TCGA-DD-A3A7         TCGA-DD-A3A8 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DD-A3A9         TCGA-DD-A4NA         TCGA-DD-A4NB 
"12P LOSS WILD-TYPE"   "12P LOSS MUTATED" "12P LOSS WILD-TYPE" 
        TCGA-DD-A4ND         TCGA-DD-A4NF         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 MUTATED"   "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-DD-A4NR 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DD-A4NS         TCGA-DD-A4NV         TCGA-DD-A73A 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DD-A73B         TCGA-DD-A73C         TCGA-DD-A73D 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DD-A73E         TCGA-DD-A73F         TCGA-DD-A73G 
"12P LOSS WILD-TYPE"   "12P LOSS MUTATED" "12P LOSS WILD-TYPE" 
        TCGA-ED-A459         TCGA-ED-A4XI         TCGA-ED-A5KG 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-ED-A627         TCGA-ED-A66X         TCGA-ED-A66Y 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-ED-A7PX         TCGA-ED-A7PY         TCGA-ED-A7PZ 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-ED-A7XP         TCGA-ED-A82E         TCGA-EP-A12J 
  "12P LOSS MUTATED" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EP-A26S         TCGA-EP-A2KA         TCGA-EP-A2KB 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EP-A2KC         TCGA-EP-A3JL         TCGA-EP-A3RK 
  "12P LOSS MUTATED" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-ES-A2HS         TCGA-ES-A2HT         TCGA-FV-A23B 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-FV-A2QR         TCGA-FV-A3I0         TCGA-FV-A3I1 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE"   "12P LOSS MUTATED" 
        TCGA-FV-A3R2         TCGA-FV-A3R3         TCGA-FV-A495 
  "12P LOSS MUTATED" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-FV-A496         TCGA-FV-A4ZP         TCGA-FV-A4ZQ 
  "12P LOSS MUTATED" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-G3-A25S         TCGA-G3-A25T         TCGA-G3-A25U 
  "12P LOSS MUTATED" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-G3-A25V         TCGA-G3-A25W         TCGA-G3-A25X 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-G3-A25Y         TCGA-G3-A25Z         TCGA-G3-A3CG 
"12P LOSS WILD-TYPE"   "12P LOSS MUTATED" "12P LOSS WILD-TYPE" 
        TCGA-G3-A3CH         TCGA-G3-A3CI         TCGA-G3-A3CJ 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-G3-A3CK         TCGA-G3-A5SI         TCGA-G3-A5SJ 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-G3-A5SL         TCGA-G3-A5SM         TCGA-G3-A6UC 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-GJ-A6C0         TCGA-K7-A6G5         TCGA-LG-A6GG 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-MI-A75C         TCGA-MI-A75E         TCGA-MI-A75G 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE"   "12P LOSS MUTATED" 
        TCGA-MI-A75I         TCGA-NI-A4U2         TCGA-O8-A75V 
  "12P LOSS MUTATED" "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-BC-A69H         TCGA-BC-A69I         TCGA-CC-5258 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-CC-5260         TCGA-CC-5261         TCGA-CC-5262 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-CC-5263         TCGA-CC-A1HT         TCGA-CC-A3M9 
"12P LOSS WILD-TYPE"   "12P LOSS MUTATED" "12P LOSS WILD-TYPE" 
        TCGA-CC-A3MA         TCGA-CC-A3MB         TCGA-CC-A3MC 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE"   "12P LOSS MUTATED" 
        TCGA-DD-A113         TCGA-DD-A114         TCGA-DD-A115 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DD-A116         TCGA-DD-A118         TCGA-DD-A119 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE"   "12P LOSS MUTATED" 
        TCGA-DD-A11A         TCGA-DD-A11B         TCGA-DD-A11C 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DD-A11D         TCGA-DD-A1E9         TCGA-DD-A1EA 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DD-A1EB         TCGA-DD-A1EC         TCGA-DD-A1ED 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DD-A1EE         TCGA-DD-A1EF         TCGA-DD-A1EG 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE"   "12P LOSS MUTATED" 
        TCGA-DD-A1EH         TCGA-DD-A1EI         TCGA-DD-A1EJ 
  "12P LOSS MUTATED" "12P LOSS WILD-TYPE"   "12P LOSS MUTATED" 
        TCGA-DD-A1EK         TCGA-DD-A1EL         TCGA-DD-A39V 
"12P LOSS WILD-TYPE"   "12P LOSS MUTATED" "12P LOSS WILD-TYPE" 
        TCGA-DD-A39X         TCGA-DD-A39Y         TCGA-DD-A39Z 
  "12P LOSS MUTATED"   "12P LOSS MUTATED" "12P LOSS WILD-TYPE" 
        TCGA-DD-A3A0         TCGA-DD-A3A1         TCGA-DD-A3A2 
"12P LOSS WILD-TYPE"   "12P LOSS MUTATED" "12P LOSS WILD-TYPE" 
        TCGA-DD-A3A3         TCGA-DD-A3A4         TCGA-DD-A3A5 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DD-A3A6         TCGA-DD-A3A7         TCGA-DD-A3A8 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DD-A3A9         TCGA-DD-A4NA         TCGA-DD-A4NB 
"12P LOSS WILD-TYPE"   "12P LOSS MUTATED" "12P LOSS WILD-TYPE" 
        TCGA-DD-A4ND         TCGA-DD-A4NF         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 MUTATED"   "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-DD-A4NR 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DD-A4NS         TCGA-DD-A4NV         TCGA-DD-A73A 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DD-A73B         TCGA-DD-A73C         TCGA-DD-A73D 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DD-A73E         TCGA-DD-A73F         TCGA-DD-A73G 
"12P LOSS WILD-TYPE"   "12P LOSS MUTATED" "12P LOSS WILD-TYPE" 
        TCGA-ED-A459         TCGA-ED-A4XI         TCGA-ED-A5KG 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-ED-A627         TCGA-ED-A66X         TCGA-ED-A66Y 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-ED-A7PX         TCGA-ED-A7PY         TCGA-ED-A7PZ 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-ED-A7XP         TCGA-ED-A82E         TCGA-EP-A12J 
  "12P LOSS MUTATED" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EP-A26S         TCGA-EP-A2KA         TCGA-EP-A2KB 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EP-A2KC         TCGA-EP-A3JL         TCGA-EP-A3RK 
  "12P LOSS MUTATED" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-ES-A2HS         TCGA-ES-A2HT         TCGA-FV-A23B 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-FV-A2QR         TCGA-FV-A3I0         TCGA-FV-A3I1 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE"   "12P LOSS MUTATED" 
        TCGA-FV-A3R2         TCGA-FV-A3R3         TCGA-FV-A495 
  "12P LOSS MUTATED" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-FV-A496         TCGA-FV-A4ZP         TCGA-FV-A4ZQ 
  "12P LOSS MUTATED" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-G3-A25S         TCGA-G3-A25T         TCGA-G3-A25U 
  "12P LOSS MUTATED" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-G3-A25V         TCGA-G3-A25W         TCGA-G3-A25X 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-G3-A25Y         TCGA-G3-A25Z         TCGA-G3-A3CG 
"12P LOSS WILD-TYPE"   "12P LOSS MUTATED" "12P LOSS WILD-TYPE" 
        TCGA-G3-A3CH         TCGA-G3-A3CI         TCGA-G3-A3CJ 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-G3-A3CK         TCGA-G3-A5SI         TCGA-G3-A5SJ 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-G3-A5SL         TCGA-G3-A5SM         TCGA-G3-A6UC 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-GJ-A6C0         TCGA-K7-A6G5         TCGA-LG-A6GG 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-MI-A75C         TCGA-MI-A75E         TCGA-MI-A75G 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE"   "12P LOSS MUTATED" 
        TCGA-MI-A75I         TCGA-NI-A4U2         TCGA-O8-A75V 
  "12P LOSS MUTATED" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
[1] "hr=" "1.5"
D63V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  12P LOSS MUTATED        10        7         1          4          1
  12P LOSS WILD-TYPE      48       29         1         26          3
                    vv
clus                 STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  12P LOSS MUTATED            2        1         0         0
  12P LOSS WILD-TYPE          3        0         1         2
D63V3, multiclass
                    vv
clus                 T1 T2 T3 T4
  12P LOSS MUTATED   11  9  7  0
  12P LOSS WILD-TYPE 50 31 33  8
D63V4, multiclass
    clus
vv   12P LOSS MUTATED 12P LOSS WILD-TYPE
  T1               11                 50
  T2                9                 31
  T3                7                 33
  T4                0                  8
D63V5, binary
                    cls
clus                  0  1
  12P LOSS MUTATED   16  2
  12P LOSS WILD-TYPE 81  1
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED     16    2
  12P LOSS WILD-TYPE   81    1
   clus
vv  12P LOSS MUTATED 12P LOSS WILD-TYPE
  0               16                 81
  1                2                  1
                    vv
clus                 M0 M1 MX
  12P LOSS MUTATED   22  1  4
  12P LOSS WILD-TYPE 93  2 27
D63V6, multiclass
    clus
vv   12P LOSS MUTATED 12P LOSS WILD-TYPE
  M0               22                 93
  M1                1                  2
  MX                4                 27
D63V7, binary
                    cls
clus                  0  1
  12P LOSS MUTATED   10 17
  12P LOSS WILD-TYPE 48 74
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED     10   17
  12P LOSS WILD-TYPE   48   74
        clus
vv       12P LOSS MUTATED 12P LOSS WILD-TYPE
  FEMALE               10                 48
  MALE                 17                 74
                    vv
clus                 R0 R1 R2 RX
  12P LOSS MUTATED   23  2  1  0
  12P LOSS WILD-TYPE 99  9  0 10
D63V8, multiclass
    clus
vv   12P LOSS MUTATED 12P LOSS WILD-TYPE
  R0               23                 99
  R1                2                  9
  R2                1                  0
  RX                0                 10

Clustering(64) Variable = 12Q LOSS MUTATION ANALYSIS
D64V1, survival
                    sevent
clus2                 0  1
  12Q LOSS MUTATED    8  8
  12Q LOSS WILD-TYPE 76 55
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                16                131 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                 8                 55 
$`12Q LOSS MUTATED`
TCGA-BC-A217 TCGA-CC-A1HT TCGA-CC-A3MC TCGA-DD-A119 TCGA-DD-A1EG TCGA-DD-A1EH 
       13.84         3.32         0.13         7.33        45.11        49.15 
TCGA-DD-A1EL TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A4NI TCGA-DD-A4NO TCGA-EP-A2KC 
       13.64        55.69         5.62        18.44        61.45         0.62 
TCGA-FV-A3I1 TCGA-FV-A496 TCGA-G3-A25Z TCGA-MI-A75G 
        8.12         0.33        21.53        14.24 

$`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-BC-A69H 
        5.03        44.42         0.26        22.36         9.50         3.95 
TCGA-BC-A69I TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 
        0.53         0.07         2.86         0.39         3.39         4.24 
TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 
        0.10         0.07         0.10        79.73        37.78        83.57 
TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D 
       53.33       113.00         2.60         0.46        21.76        51.29 
TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE 
       90.71        79.40        66.31        19.79        75.65         6.71 
TCGA-DD-A1EF TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A39V TCGA-DD-A39Z 
       12.95         6.02        29.16        18.35        21.14        19.76 
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-A4NB 
      107.11        13.78         0.36        30.61        33.14        12.85 
TCGA-DD-A4ND TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL 
       73.38        14.07        14.24        15.06        39.78        56.25 
TCGA-DD-A4NN TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV 
       29.56        93.67        12.26         0.30        80.75        66.35 
TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F 
       10.98         9.30         7.56        10.98         1.45        27.72 
TCGA-DD-A73G TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X 
      100.96        13.41        12.69        15.85        13.91        13.35 
TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XP TCGA-ED-A82E 
        0.23         0.20         0.20         0.20         0.20         0.20 
TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A3JL TCGA-EP-A3RK 
       18.74        19.99        11.74        10.98         9.96        11.93 
TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3R2 
       22.85        14.40        32.45        19.10         0.20         6.38 
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        51.06 
TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A3CG 
       53.79        28.27        30.74        58.49        14.86        22.13 
TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ 
       25.64         5.92        19.53        19.23        14.70        11.97 
TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A6UC TCGA-GJ-A6C0 TCGA-K7-A6G5 TCGA-LG-A6GG 
        7.99         4.37         7.76         1.02         4.01         0.49 
TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75I TCGA-NI-A4U2 TCGA-O8-A75V 
        9.57         5.10         8.71        58.88         4.44 

  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
              0.13               0.03 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
             61.45             113.00 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
             13.74              14.24 
[1] "0.1 - 61.5 (13.7)"  "0.0 - 113.0 (14.2)"
        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-BC-A69H         TCGA-BC-A69I         TCGA-CC-5258 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-CC-5260         TCGA-CC-5261         TCGA-CC-5262 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-CC-5263         TCGA-CC-A1HT         TCGA-CC-A3M9 
"12Q LOSS WILD-TYPE"   "12Q LOSS MUTATED" "12Q LOSS WILD-TYPE" 
        TCGA-CC-A3MA         TCGA-CC-A3MB         TCGA-CC-A3MC 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE"   "12Q LOSS MUTATED" 
        TCGA-DD-A113         TCGA-DD-A114         TCGA-DD-A115 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DD-A116         TCGA-DD-A118         TCGA-DD-A119 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE"   "12Q LOSS MUTATED" 
        TCGA-DD-A11A         TCGA-DD-A11B         TCGA-DD-A11C 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DD-A11D         TCGA-DD-A1E9         TCGA-DD-A1EA 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DD-A1EB         TCGA-DD-A1EC         TCGA-DD-A1ED 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DD-A1EE         TCGA-DD-A1EF         TCGA-DD-A1EG 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE"   "12Q LOSS MUTATED" 
        TCGA-DD-A1EH         TCGA-DD-A1EI         TCGA-DD-A1EJ 
  "12Q LOSS MUTATED" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DD-A1EK         TCGA-DD-A1EL         TCGA-DD-A39V 
"12Q LOSS WILD-TYPE"   "12Q LOSS MUTATED" "12Q LOSS WILD-TYPE" 
        TCGA-DD-A39X         TCGA-DD-A39Y         TCGA-DD-A39Z 
  "12Q LOSS MUTATED"   "12Q LOSS MUTATED" "12Q LOSS WILD-TYPE" 
        TCGA-DD-A3A0         TCGA-DD-A3A1         TCGA-DD-A3A2 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DD-A3A3         TCGA-DD-A3A4         TCGA-DD-A3A5 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DD-A3A6         TCGA-DD-A3A7         TCGA-DD-A3A8 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DD-A3A9         TCGA-DD-A4NA         TCGA-DD-A4NB 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DD-A4ND         TCGA-DD-A4NF         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 MUTATED" "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-DD-A4NR 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DD-A4NS         TCGA-DD-A4NV         TCGA-DD-A73A 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DD-A73B         TCGA-DD-A73C         TCGA-DD-A73D 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DD-A73E         TCGA-DD-A73F         TCGA-DD-A73G 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-ED-A459         TCGA-ED-A4XI         TCGA-ED-A5KG 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-ED-A627         TCGA-ED-A66X         TCGA-ED-A66Y 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-ED-A7PX         TCGA-ED-A7PY         TCGA-ED-A7PZ 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-ED-A7XP         TCGA-ED-A82E         TCGA-EP-A12J 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-EP-A26S         TCGA-EP-A2KA         TCGA-EP-A2KB 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-EP-A2KC         TCGA-EP-A3JL         TCGA-EP-A3RK 
  "12Q LOSS MUTATED" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-ES-A2HS         TCGA-ES-A2HT         TCGA-FV-A23B 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-FV-A2QR         TCGA-FV-A3I0         TCGA-FV-A3I1 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE"   "12Q LOSS MUTATED" 
        TCGA-FV-A3R2         TCGA-FV-A3R3         TCGA-FV-A495 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-FV-A496         TCGA-FV-A4ZP         TCGA-FV-A4ZQ 
  "12Q LOSS MUTATED" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-G3-A25S         TCGA-G3-A25T         TCGA-G3-A25U 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-G3-A25V         TCGA-G3-A25W         TCGA-G3-A25X 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-G3-A25Y         TCGA-G3-A25Z         TCGA-G3-A3CG 
"12Q LOSS WILD-TYPE"   "12Q LOSS MUTATED" "12Q LOSS WILD-TYPE" 
        TCGA-G3-A3CH         TCGA-G3-A3CI         TCGA-G3-A3CJ 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-G3-A3CK         TCGA-G3-A5SI         TCGA-G3-A5SJ 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-G3-A5SL         TCGA-G3-A5SM         TCGA-G3-A6UC 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-GJ-A6C0         TCGA-K7-A6G5         TCGA-LG-A6GG 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-MI-A75C         TCGA-MI-A75E         TCGA-MI-A75G 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE"   "12Q LOSS MUTATED" 
        TCGA-MI-A75I         TCGA-NI-A4U2         TCGA-O8-A75V 
"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-BC-A69H         TCGA-BC-A69I         TCGA-CC-5258 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-CC-5260         TCGA-CC-5261         TCGA-CC-5262 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-CC-5263         TCGA-CC-A1HT         TCGA-CC-A3M9 
"12Q LOSS WILD-TYPE"   "12Q LOSS MUTATED" "12Q LOSS WILD-TYPE" 
        TCGA-CC-A3MA         TCGA-CC-A3MB         TCGA-CC-A3MC 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE"   "12Q LOSS MUTATED" 
        TCGA-DD-A113         TCGA-DD-A114         TCGA-DD-A115 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DD-A116         TCGA-DD-A118         TCGA-DD-A119 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE"   "12Q LOSS MUTATED" 
        TCGA-DD-A11A         TCGA-DD-A11B         TCGA-DD-A11C 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DD-A11D         TCGA-DD-A1E9         TCGA-DD-A1EA 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DD-A1EB         TCGA-DD-A1EC         TCGA-DD-A1ED 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DD-A1EE         TCGA-DD-A1EF         TCGA-DD-A1EG 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE"   "12Q LOSS MUTATED" 
        TCGA-DD-A1EH         TCGA-DD-A1EI         TCGA-DD-A1EJ 
  "12Q LOSS MUTATED" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DD-A1EK         TCGA-DD-A1EL         TCGA-DD-A39V 
"12Q LOSS WILD-TYPE"   "12Q LOSS MUTATED" "12Q LOSS WILD-TYPE" 
        TCGA-DD-A39X         TCGA-DD-A39Y         TCGA-DD-A39Z 
  "12Q LOSS MUTATED"   "12Q LOSS MUTATED" "12Q LOSS WILD-TYPE" 
        TCGA-DD-A3A0         TCGA-DD-A3A1         TCGA-DD-A3A2 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DD-A3A3         TCGA-DD-A3A4         TCGA-DD-A3A5 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DD-A3A6         TCGA-DD-A3A7         TCGA-DD-A3A8 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DD-A3A9         TCGA-DD-A4NA         TCGA-DD-A4NB 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DD-A4ND         TCGA-DD-A4NF         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 MUTATED" "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-DD-A4NR 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DD-A4NS         TCGA-DD-A4NV         TCGA-DD-A73A 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DD-A73B         TCGA-DD-A73C         TCGA-DD-A73D 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DD-A73E         TCGA-DD-A73F         TCGA-DD-A73G 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-ED-A459         TCGA-ED-A4XI         TCGA-ED-A5KG 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-ED-A627         TCGA-ED-A66X         TCGA-ED-A66Y 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-ED-A7PX         TCGA-ED-A7PY         TCGA-ED-A7PZ 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-ED-A7XP         TCGA-ED-A82E         TCGA-EP-A12J 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-EP-A26S         TCGA-EP-A2KA         TCGA-EP-A2KB 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-EP-A2KC         TCGA-EP-A3JL         TCGA-EP-A3RK 
  "12Q LOSS MUTATED" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-ES-A2HS         TCGA-ES-A2HT         TCGA-FV-A23B 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-FV-A2QR         TCGA-FV-A3I0         TCGA-FV-A3I1 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE"   "12Q LOSS MUTATED" 
        TCGA-FV-A3R2         TCGA-FV-A3R3         TCGA-FV-A495 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-FV-A496         TCGA-FV-A4ZP         TCGA-FV-A4ZQ 
  "12Q LOSS MUTATED" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-G3-A25S         TCGA-G3-A25T         TCGA-G3-A25U 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-G3-A25V         TCGA-G3-A25W         TCGA-G3-A25X 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-G3-A25Y         TCGA-G3-A25Z         TCGA-G3-A3CG 
"12Q LOSS WILD-TYPE"   "12Q LOSS MUTATED" "12Q LOSS WILD-TYPE" 
        TCGA-G3-A3CH         TCGA-G3-A3CI         TCGA-G3-A3CJ 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-G3-A3CK         TCGA-G3-A5SI         TCGA-G3-A5SJ 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-G3-A5SL         TCGA-G3-A5SM         TCGA-G3-A6UC 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-GJ-A6C0         TCGA-K7-A6G5         TCGA-LG-A6GG 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-MI-A75C         TCGA-MI-A75E         TCGA-MI-A75G 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE"   "12Q LOSS MUTATED" 
        TCGA-MI-A75I         TCGA-NI-A4U2         TCGA-O8-A75V 
"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-BC-A69H         TCGA-BC-A69I         TCGA-CC-5258 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-CC-5260         TCGA-CC-5261         TCGA-CC-5262 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-CC-5263         TCGA-CC-A1HT         TCGA-CC-A3M9 
"12Q LOSS WILD-TYPE"   "12Q LOSS MUTATED" "12Q LOSS WILD-TYPE" 
        TCGA-CC-A3MA         TCGA-CC-A3MB         TCGA-CC-A3MC 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE"   "12Q LOSS MUTATED" 
        TCGA-DD-A113         TCGA-DD-A114         TCGA-DD-A115 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DD-A116         TCGA-DD-A118         TCGA-DD-A119 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE"   "12Q LOSS MUTATED" 
        TCGA-DD-A11A         TCGA-DD-A11B         TCGA-DD-A11C 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DD-A11D         TCGA-DD-A1E9         TCGA-DD-A1EA 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DD-A1EB         TCGA-DD-A1EC         TCGA-DD-A1ED 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DD-A1EE         TCGA-DD-A1EF         TCGA-DD-A1EG 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE"   "12Q LOSS MUTATED" 
        TCGA-DD-A1EH         TCGA-DD-A1EI         TCGA-DD-A1EJ 
  "12Q LOSS MUTATED" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DD-A1EK         TCGA-DD-A1EL         TCGA-DD-A39V 
"12Q LOSS WILD-TYPE"   "12Q LOSS MUTATED" "12Q LOSS WILD-TYPE" 
        TCGA-DD-A39X         TCGA-DD-A39Y         TCGA-DD-A39Z 
  "12Q LOSS MUTATED"   "12Q LOSS MUTATED" "12Q LOSS WILD-TYPE" 
        TCGA-DD-A3A0         TCGA-DD-A3A1         TCGA-DD-A3A2 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DD-A3A3         TCGA-DD-A3A4         TCGA-DD-A3A5 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DD-A3A6         TCGA-DD-A3A7         TCGA-DD-A3A8 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DD-A3A9         TCGA-DD-A4NA         TCGA-DD-A4NB 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DD-A4ND         TCGA-DD-A4NF         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 MUTATED" "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-DD-A4NR 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DD-A4NS         TCGA-DD-A4NV         TCGA-DD-A73A 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DD-A73B         TCGA-DD-A73C         TCGA-DD-A73D 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DD-A73E         TCGA-DD-A73F         TCGA-DD-A73G 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-ED-A459         TCGA-ED-A4XI         TCGA-ED-A5KG 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-ED-A627         TCGA-ED-A66X         TCGA-ED-A66Y 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-ED-A7PX         TCGA-ED-A7PY         TCGA-ED-A7PZ 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-ED-A7XP         TCGA-ED-A82E         TCGA-EP-A12J 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-EP-A26S         TCGA-EP-A2KA         TCGA-EP-A2KB 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-EP-A2KC         TCGA-EP-A3JL         TCGA-EP-A3RK 
  "12Q LOSS MUTATED" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-ES-A2HS         TCGA-ES-A2HT         TCGA-FV-A23B 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-FV-A2QR         TCGA-FV-A3I0         TCGA-FV-A3I1 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE"   "12Q LOSS MUTATED" 
        TCGA-FV-A3R2         TCGA-FV-A3R3         TCGA-FV-A495 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-FV-A496         TCGA-FV-A4ZP         TCGA-FV-A4ZQ 
  "12Q LOSS MUTATED" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-G3-A25S         TCGA-G3-A25T         TCGA-G3-A25U 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-G3-A25V         TCGA-G3-A25W         TCGA-G3-A25X 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-G3-A25Y         TCGA-G3-A25Z         TCGA-G3-A3CG 
"12Q LOSS WILD-TYPE"   "12Q LOSS MUTATED" "12Q LOSS WILD-TYPE" 
        TCGA-G3-A3CH         TCGA-G3-A3CI         TCGA-G3-A3CJ 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-G3-A3CK         TCGA-G3-A5SI         TCGA-G3-A5SJ 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-G3-A5SL         TCGA-G3-A5SM         TCGA-G3-A6UC 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-GJ-A6C0         TCGA-K7-A6G5         TCGA-LG-A6GG 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-MI-A75C         TCGA-MI-A75E         TCGA-MI-A75G 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE"   "12Q LOSS MUTATED" 
        TCGA-MI-A75I         TCGA-NI-A4U2         TCGA-O8-A75V 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
[1] "hr=" "1.5"
D64V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  12Q LOSS MUTATED         7        5         1          2          0
  12Q LOSS WILD-TYPE      51       31         1         28          4
                    vv
clus                 STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  12Q LOSS MUTATED            0        1         0         0
  12Q LOSS WILD-TYPE          5        0         1         2
D64V3, multiclass
                    vv
clus                 T1 T2 T3 T4
  12Q LOSS MUTATED    7  5  4  0
  12Q LOSS WILD-TYPE 54 35 36  8
D64V4, multiclass
    clus
vv   12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  T1                7                 54
  T2                5                 35
  T3                4                 36
  T4                0                  8
D64V5, binary
                    cls
clus                  0  1
  12Q LOSS MUTATED   10  0
  12Q LOSS WILD-TYPE 87  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED     10    0
  12Q LOSS WILD-TYPE   87    3
   clus
vv  12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  0               10                 87
  1                0                  3
                    vv
clus                  M0  M1  MX
  12Q LOSS MUTATED    13   1   2
  12Q LOSS WILD-TYPE 102   2  29
D64V6, multiclass
    clus
vv   12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  M0               13                102
  M1                1                  2
  MX                2                 29
D64V7, binary
                    cls
clus                  0  1
  12Q LOSS MUTATED    4 12
  12Q LOSS WILD-TYPE 54 79
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED      4   12
  12Q LOSS WILD-TYPE   54   79
        clus
vv       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  FEMALE                4                 54
  MALE                 12                 79
                    vv
clus                  R0  R1  R2  RX
  12Q LOSS MUTATED    14   0   1   0
  12Q LOSS WILD-TYPE 108  11   0  10
D64V8, multiclass
    clus
vv   12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  R0               14                108
  R1                0                 11
  R2                1                  0
  RX                0                 10

Clustering(65) Variable = 13Q LOSS MUTATION ANALYSIS
D65V1, survival
                    sevent
clus2                 0  1
  13Q LOSS MUTATED   30 21
  13Q LOSS WILD-TYPE 54 42
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                51                 96 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                21                 42 
$`13Q LOSS MUTATED`
TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A10W TCGA-BC-A112 TCGA-BC-A217 
       37.32        10.13        27.52         2.99         5.03        13.84 
TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69H TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5261 
       22.36         9.50         3.95         0.07         2.86         0.39 
TCGA-CC-5262 TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-DD-A113 TCGA-DD-A115 TCGA-DD-A116 
        3.39         0.10         0.07        79.73        83.57        53.33 
TCGA-DD-A118 TCGA-DD-A11A TCGA-DD-A11C TCGA-DD-A1EF TCGA-DD-A1EI TCGA-DD-A1EK 
      113.00         2.60        21.76        12.95         6.02        18.35 
TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A3A0 TCGA-DD-A3A5 TCGA-DD-A3A9 TCGA-DD-A4NA 
       55.69         5.62        25.81       102.74        30.61        33.14 
TCGA-DD-A4NH TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NQ TCGA-DD-A73F TCGA-DD-A73G 
       14.24        29.56        61.45        12.26        27.72       100.96 
TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A7PX TCGA-ED-A7PZ TCGA-ED-A7XP TCGA-EP-A3RK 
       13.41        12.69         0.20         0.20         0.20        11.93 
TCGA-FV-A3I0 TCGA-FV-A3R2 TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25X TCGA-G3-A3CH 
        0.20         6.38         1.22        51.06        58.49        25.64 
TCGA-G3-A5SM TCGA-MI-A75G TCGA-MI-A75I 
        4.37        14.24         8.71 

$`13Q LOSS WILD-TYPE`
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10S TCGA-BC-A10U TCGA-BC-A10X TCGA-BC-A10Y 
       48.99        27.91        46.78        27.52        25.32        23.34 
TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A216 TCGA-BC-A3KF TCGA-BC-A69I TCGA-CC-5263 
        1.12        69.57        44.42         0.26         0.53         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        37.78         7.33         0.46 
TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED 
       51.29        90.71        79.40        66.31        19.79        75.65 
TCGA-DD-A1EE TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EJ TCGA-DD-A1EL TCGA-DD-A39V 
        6.71        45.11        49.15        29.16        13.64        21.14 
TCGA-DD-A39Z TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A6 
       19.76         7.66        70.06        17.59        20.12       107.11 
TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NF TCGA-DD-A4NI 
       13.78         0.36        12.85        73.38        14.07        18.44 
TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NP TCGA-DD-A4NR TCGA-DD-A4NS 
       15.06        39.78        56.25        93.67         0.30        80.75 
TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E 
       66.35        10.98         9.30         7.56        10.98         1.45 
TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PY TCGA-ED-A82E 
       15.85        13.91        13.35         0.23         0.20         0.20 
TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL 
       18.74        19.99        11.74        10.98         0.62         9.96 
TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-A3I1 TCGA-FV-A3R3 
       22.85        14.40        32.45        19.10         8.12         0.13 
TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25U TCGA-G3-A25V 
        0.03         0.33        60.36         0.39        53.79        28.27 
TCGA-G3-A25W TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CI TCGA-G3-A3CJ 
       30.74        14.86        21.53        22.13         5.92        19.53 
TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SL TCGA-G3-A6UC TCGA-GJ-A6C0 
       19.23        14.70        11.97         7.99         7.76         1.02 
TCGA-K7-A6G5 TCGA-LG-A6GG TCGA-MI-A75C TCGA-MI-A75E TCGA-NI-A4U2 TCGA-O8-A75V 
        4.01         0.49         9.57         5.10        58.88         4.44 

  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
              0.07               0.03 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
            113.00             107.11 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
             12.95              14.78 
[1] "0.1 - 113.0 (12.9)" "0.0 - 107.1 (14.8)"
        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 MUTATED" "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-BC-A69H         TCGA-BC-A69I         TCGA-CC-5258 
  "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" 
        TCGA-CC-5260         TCGA-CC-5261         TCGA-CC-5262 
  "13Q LOSS MUTATED"   "13Q LOSS MUTATED"   "13Q LOSS MUTATED" 
        TCGA-CC-5263         TCGA-CC-A1HT         TCGA-CC-A3M9 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" 
        TCGA-CC-A3MA         TCGA-CC-A3MB         TCGA-CC-A3MC 
  "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-DD-A113         TCGA-DD-A114         TCGA-DD-A115 
  "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" 
        TCGA-DD-A116         TCGA-DD-A118         TCGA-DD-A119 
  "13Q LOSS MUTATED"   "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" 
        TCGA-DD-A11A         TCGA-DD-A11B         TCGA-DD-A11C 
  "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" 
        TCGA-DD-A11D         TCGA-DD-A1E9         TCGA-DD-A1EA 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-DD-A1EB         TCGA-DD-A1EC         TCGA-DD-A1ED 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-DD-A1EE         TCGA-DD-A1EF         TCGA-DD-A1EG 
"13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" 
        TCGA-DD-A1EH         TCGA-DD-A1EI         TCGA-DD-A1EJ 
"13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" 
        TCGA-DD-A1EK         TCGA-DD-A1EL         TCGA-DD-A39V 
  "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-DD-A39X         TCGA-DD-A39Y         TCGA-DD-A39Z 
  "13Q LOSS MUTATED"   "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" 
        TCGA-DD-A3A0         TCGA-DD-A3A1         TCGA-DD-A3A2 
  "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-DD-A3A3         TCGA-DD-A3A4         TCGA-DD-A3A5 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" 
        TCGA-DD-A3A6         TCGA-DD-A3A7         TCGA-DD-A3A8 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-DD-A3A9         TCGA-DD-A4NA         TCGA-DD-A4NB 
  "13Q LOSS MUTATED"   "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" 
        TCGA-DD-A4ND         TCGA-DD-A4NF         TCGA-DD-A4NH 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE"   "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-DD-A4NR 
"13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" 
        TCGA-DD-A4NS         TCGA-DD-A4NV         TCGA-DD-A73A 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-DD-A73B         TCGA-DD-A73C         TCGA-DD-A73D 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-DD-A73E         TCGA-DD-A73F         TCGA-DD-A73G 
"13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED"   "13Q LOSS MUTATED" 
        TCGA-ED-A459         TCGA-ED-A4XI         TCGA-ED-A5KG 
  "13Q LOSS MUTATED"   "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" 
        TCGA-ED-A627         TCGA-ED-A66X         TCGA-ED-A66Y 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-ED-A7PX         TCGA-ED-A7PY         TCGA-ED-A7PZ 
  "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" 
        TCGA-ED-A7XP         TCGA-ED-A82E         TCGA-EP-A12J 
  "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EP-A26S         TCGA-EP-A2KA         TCGA-EP-A2KB 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EP-A2KC         TCGA-EP-A3JL         TCGA-EP-A3RK 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" 
        TCGA-ES-A2HS         TCGA-ES-A2HT         TCGA-FV-A23B 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-FV-A2QR         TCGA-FV-A3I0         TCGA-FV-A3I1 
"13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" 
        TCGA-FV-A3R2         TCGA-FV-A3R3         TCGA-FV-A495 
  "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-FV-A496         TCGA-FV-A4ZP         TCGA-FV-A4ZQ 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-G3-A25S         TCGA-G3-A25T         TCGA-G3-A25U 
  "13Q LOSS MUTATED"   "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" 
        TCGA-G3-A25V         TCGA-G3-A25W         TCGA-G3-A25X 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" 
        TCGA-G3-A25Y         TCGA-G3-A25Z         TCGA-G3-A3CG 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-G3-A3CH         TCGA-G3-A3CI         TCGA-G3-A3CJ 
  "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-G3-A3CK         TCGA-G3-A5SI         TCGA-G3-A5SJ 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-G3-A5SL         TCGA-G3-A5SM         TCGA-G3-A6UC 
"13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" 
        TCGA-GJ-A6C0         TCGA-K7-A6G5         TCGA-LG-A6GG 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-MI-A75C         TCGA-MI-A75E         TCGA-MI-A75G 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" 
        TCGA-MI-A75I         TCGA-NI-A4U2         TCGA-O8-A75V 
  "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
  "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" "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-BC-A69H         TCGA-BC-A69I         TCGA-CC-5258 
  "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" 
        TCGA-CC-5260         TCGA-CC-5261         TCGA-CC-5262 
  "13Q LOSS MUTATED"   "13Q LOSS MUTATED"   "13Q LOSS MUTATED" 
        TCGA-CC-5263         TCGA-CC-A1HT         TCGA-CC-A3M9 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" 
        TCGA-CC-A3MA         TCGA-CC-A3MB         TCGA-CC-A3MC 
  "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-DD-A113         TCGA-DD-A114         TCGA-DD-A115 
  "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" 
        TCGA-DD-A116         TCGA-DD-A118         TCGA-DD-A119 
  "13Q LOSS MUTATED"   "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" 
        TCGA-DD-A11A         TCGA-DD-A11B         TCGA-DD-A11C 
  "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" 
        TCGA-DD-A11D         TCGA-DD-A1E9         TCGA-DD-A1EA 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-DD-A1EB         TCGA-DD-A1EC         TCGA-DD-A1ED 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-DD-A1EE         TCGA-DD-A1EF         TCGA-DD-A1EG 
"13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" 
        TCGA-DD-A1EH         TCGA-DD-A1EI         TCGA-DD-A1EJ 
"13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" 
        TCGA-DD-A1EK         TCGA-DD-A1EL         TCGA-DD-A39V 
  "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-DD-A39X         TCGA-DD-A39Y         TCGA-DD-A39Z 
  "13Q LOSS MUTATED"   "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" 
        TCGA-DD-A3A0         TCGA-DD-A3A1         TCGA-DD-A3A2 
  "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-DD-A3A3         TCGA-DD-A3A4         TCGA-DD-A3A5 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" 
        TCGA-DD-A3A6         TCGA-DD-A3A7         TCGA-DD-A3A8 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-DD-A3A9         TCGA-DD-A4NA         TCGA-DD-A4NB 
  "13Q LOSS MUTATED"   "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" 
        TCGA-DD-A4ND         TCGA-DD-A4NF         TCGA-DD-A4NH 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE"   "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-DD-A4NR 
"13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" 
        TCGA-DD-A4NS         TCGA-DD-A4NV         TCGA-DD-A73A 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-DD-A73B         TCGA-DD-A73C         TCGA-DD-A73D 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-DD-A73E         TCGA-DD-A73F         TCGA-DD-A73G 
"13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED"   "13Q LOSS MUTATED" 
        TCGA-ED-A459         TCGA-ED-A4XI         TCGA-ED-A5KG 
  "13Q LOSS MUTATED"   "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" 
        TCGA-ED-A627         TCGA-ED-A66X         TCGA-ED-A66Y 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-ED-A7PX         TCGA-ED-A7PY         TCGA-ED-A7PZ 
  "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" 
        TCGA-ED-A7XP         TCGA-ED-A82E         TCGA-EP-A12J 
  "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EP-A26S         TCGA-EP-A2KA         TCGA-EP-A2KB 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EP-A2KC         TCGA-EP-A3JL         TCGA-EP-A3RK 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" 
        TCGA-ES-A2HS         TCGA-ES-A2HT         TCGA-FV-A23B 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-FV-A2QR         TCGA-FV-A3I0         TCGA-FV-A3I1 
"13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" 
        TCGA-FV-A3R2         TCGA-FV-A3R3         TCGA-FV-A495 
  "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-FV-A496         TCGA-FV-A4ZP         TCGA-FV-A4ZQ 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-G3-A25S         TCGA-G3-A25T         TCGA-G3-A25U 
  "13Q LOSS MUTATED"   "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" 
        TCGA-G3-A25V         TCGA-G3-A25W         TCGA-G3-A25X 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" 
        TCGA-G3-A25Y         TCGA-G3-A25Z         TCGA-G3-A3CG 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-G3-A3CH         TCGA-G3-A3CI         TCGA-G3-A3CJ 
  "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-G3-A3CK         TCGA-G3-A5SI         TCGA-G3-A5SJ 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-G3-A5SL         TCGA-G3-A5SM         TCGA-G3-A6UC 
"13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" 
        TCGA-GJ-A6C0         TCGA-K7-A6G5         TCGA-LG-A6GG 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-MI-A75C         TCGA-MI-A75E         TCGA-MI-A75G 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" 
        TCGA-MI-A75I         TCGA-NI-A4U2         TCGA-O8-A75V 
  "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
  "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" "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-BC-A69H         TCGA-BC-A69I         TCGA-CC-5258 
  "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" 
        TCGA-CC-5260         TCGA-CC-5261         TCGA-CC-5262 
  "13Q LOSS MUTATED"   "13Q LOSS MUTATED"   "13Q LOSS MUTATED" 
        TCGA-CC-5263         TCGA-CC-A1HT         TCGA-CC-A3M9 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" 
        TCGA-CC-A3MA         TCGA-CC-A3MB         TCGA-CC-A3MC 
  "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-DD-A113         TCGA-DD-A114         TCGA-DD-A115 
  "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" 
        TCGA-DD-A116         TCGA-DD-A118         TCGA-DD-A119 
  "13Q LOSS MUTATED"   "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" 
        TCGA-DD-A11A         TCGA-DD-A11B         TCGA-DD-A11C 
  "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" 
        TCGA-DD-A11D         TCGA-DD-A1E9         TCGA-DD-A1EA 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-DD-A1EB         TCGA-DD-A1EC         TCGA-DD-A1ED 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-DD-A1EE         TCGA-DD-A1EF         TCGA-DD-A1EG 
"13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" 
        TCGA-DD-A1EH         TCGA-DD-A1EI         TCGA-DD-A1EJ 
"13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" 
        TCGA-DD-A1EK         TCGA-DD-A1EL         TCGA-DD-A39V 
  "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-DD-A39X         TCGA-DD-A39Y         TCGA-DD-A39Z 
  "13Q LOSS MUTATED"   "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" 
        TCGA-DD-A3A0         TCGA-DD-A3A1         TCGA-DD-A3A2 
  "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-DD-A3A3         TCGA-DD-A3A4         TCGA-DD-A3A5 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" 
        TCGA-DD-A3A6         TCGA-DD-A3A7         TCGA-DD-A3A8 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-DD-A3A9         TCGA-DD-A4NA         TCGA-DD-A4NB 
  "13Q LOSS MUTATED"   "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" 
        TCGA-DD-A4ND         TCGA-DD-A4NF         TCGA-DD-A4NH 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE"   "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-DD-A4NR 
"13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" 
        TCGA-DD-A4NS         TCGA-DD-A4NV         TCGA-DD-A73A 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-DD-A73B         TCGA-DD-A73C         TCGA-DD-A73D 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-DD-A73E         TCGA-DD-A73F         TCGA-DD-A73G 
"13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED"   "13Q LOSS MUTATED" 
        TCGA-ED-A459         TCGA-ED-A4XI         TCGA-ED-A5KG 
  "13Q LOSS MUTATED"   "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" 
        TCGA-ED-A627         TCGA-ED-A66X         TCGA-ED-A66Y 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-ED-A7PX         TCGA-ED-A7PY         TCGA-ED-A7PZ 
  "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" 
        TCGA-ED-A7XP         TCGA-ED-A82E         TCGA-EP-A12J 
  "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EP-A26S         TCGA-EP-A2KA         TCGA-EP-A2KB 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EP-A2KC         TCGA-EP-A3JL         TCGA-EP-A3RK 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" 
        TCGA-ES-A2HS         TCGA-ES-A2HT         TCGA-FV-A23B 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-FV-A2QR         TCGA-FV-A3I0         TCGA-FV-A3I1 
"13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" 
        TCGA-FV-A3R2         TCGA-FV-A3R3         TCGA-FV-A495 
  "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-FV-A496         TCGA-FV-A4ZP         TCGA-FV-A4ZQ 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-G3-A25S         TCGA-G3-A25T         TCGA-G3-A25U 
  "13Q LOSS MUTATED"   "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" 
        TCGA-G3-A25V         TCGA-G3-A25W         TCGA-G3-A25X 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" 
        TCGA-G3-A25Y         TCGA-G3-A25Z         TCGA-G3-A3CG 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-G3-A3CH         TCGA-G3-A3CI         TCGA-G3-A3CJ 
  "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-G3-A3CK         TCGA-G3-A5SI         TCGA-G3-A5SJ 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-G3-A5SL         TCGA-G3-A5SM         TCGA-G3-A6UC 
"13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" 
        TCGA-GJ-A6C0         TCGA-K7-A6G5         TCGA-LG-A6GG 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-MI-A75C         TCGA-MI-A75E         TCGA-MI-A75G 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" 
        TCGA-MI-A75I         TCGA-NI-A4U2         TCGA-O8-A75V 
  "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
[1] "hr=" "1.1"
D65V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  13Q LOSS MUTATED        13       17         1          9          1
  13Q LOSS WILD-TYPE      45       19         1         21          3
                    vv
clus                 STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  13Q LOSS MUTATED            3        0         0         2
  13Q LOSS WILD-TYPE          2        1         1         0
D65V3, multiclass
                    vv
clus                 T1 T2 T3 T4
  13Q LOSS MUTATED   13 20 13  6
  13Q LOSS WILD-TYPE 48 20 27  2
D65V4, multiclass
    clus
vv   13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  T1               13                 48
  T2               20                 20
  T3               13                 27
  T4                6                  2
D65V5, binary
                    cls
clus                  0  1
  13Q LOSS MUTATED   33  1
  13Q LOSS WILD-TYPE 64  2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED     33    1
  13Q LOSS WILD-TYPE   64    2
   clus
vv  13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  0               33                 64
  1                1                  2
                    vv
clus                 M0 M1 MX
  13Q LOSS MUTATED   42  2  8
  13Q LOSS WILD-TYPE 73  1 23
D65V6, multiclass
    clus
vv   13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  M0               42                 73
  M1                2                  1
  MX                8                 23
D65V7, binary
                    cls
clus                  0  1
  13Q LOSS MUTATED   21 31
  13Q LOSS WILD-TYPE 37 60
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED     21   31
  13Q LOSS WILD-TYPE   37   60
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  FEMALE               21                 37
  MALE                 31                 60
                    vv
clus                 R0 R1 R2 RX
  13Q LOSS MUTATED   40  5  0  5
  13Q LOSS WILD-TYPE 82  6  1  5
D65V8, multiclass
    clus
vv   13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  R0               40                 82
  R1                5                  6
  R2                0                  1
  RX                5                  5

Clustering(66) Variable = 14Q LOSS MUTATION ANALYSIS
D66V1, survival
                    sevent
clus2                 0  1
  14Q LOSS MUTATED   24 20
  14Q LOSS WILD-TYPE 60 43
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                44                103 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                20                 43 
$`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        13.84         0.26 
TCGA-BC-A3KG TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-A1HT TCGA-CC-A3MA 
       22.36         0.07         2.86         0.39         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       113.00         2.60 
TCGA-DD-A11C TCGA-DD-A1E9 TCGA-DD-A1EG TCGA-DD-A1EJ TCGA-DD-A1EL TCGA-DD-A39X 
       21.76        90.71        45.11        29.16        13.64        55.69 
TCGA-DD-A39Y TCGA-DD-A3A1 TCGA-DD-A3A7 TCGA-DD-A3A9 TCGA-DD-A4NB TCGA-DD-A4NH 
        5.62         7.66        13.78        30.61        12.85        14.24 
TCGA-DD-A4NI TCGA-DD-A4NO TCGA-DD-A4NQ TCGA-ED-A459 TCGA-ED-A7PX TCGA-ED-A7PZ 
       18.44        61.45        12.26        13.41         0.20         0.20 
TCGA-ED-A82E TCGA-EP-A2KB TCGA-EP-A3RK TCGA-FV-A4ZP TCGA-G3-A25S TCGA-G3-A25X 
        0.20        10.98        11.93        60.36         1.22        58.49 
TCGA-G3-A3CH TCGA-G3-A5SM 
       25.64         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-BC-A69H 
       23.34         1.12        69.57        44.42         9.50         3.95 
TCGA-BC-A69I TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A3M9 TCGA-DD-A114 TCGA-DD-A116 
        0.53         3.39         4.24         0.10        37.78        53.33 
TCGA-DD-A119 TCGA-DD-A11B TCGA-DD-A11D TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC 
        7.33         0.46        51.29        79.40        66.31        19.79 
TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EK 
       75.65         6.71        12.95        49.15         6.02        18.35 
TCGA-DD-A39V TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 
       21.14        19.76        25.81        70.06        17.59        20.12 
TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A8 TCGA-DD-A4NA TCGA-DD-A4ND TCGA-DD-A4NF 
      102.74       107.11         0.36        33.14        73.38        14.07 
TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NP TCGA-DD-A4NR 
       15.06        39.78        56.25        29.56        93.67         0.30 
TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D 
       80.75        66.35        10.98         9.30         7.56        10.98 
TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 
        1.45        27.72       100.96        12.69        15.85        13.91 
TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PY TCGA-ED-A7XP TCGA-EP-A12J TCGA-EP-A26S 
       13.35         0.23         0.20         0.20        18.74        19.99 
TCGA-EP-A2KA TCGA-EP-A2KC TCGA-EP-A3JL TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A23B 
       11.74         0.62         9.96        22.85        14.40        32.45 
TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 
       19.10         0.20         8.12         6.38         0.13         0.03 
TCGA-FV-A496 TCGA-FV-A4ZQ TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W 
        0.33         0.39        51.06        53.79        28.27        30.74 
TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK 
       14.86        21.53        22.13         5.92        19.53        19.23 
TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SL TCGA-G3-A6UC TCGA-GJ-A6C0 TCGA-K7-A6G5 
       14.70        11.97         7.99         7.76         1.02         4.01 
TCGA-LG-A6GG TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75I TCGA-NI-A4U2 
        0.49         9.57         5.10        14.24         8.71        58.88 
TCGA-O8-A75V 
        4.44 

  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
              0.07               0.03 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
            113.00             107.11 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
             13.13              14.86 
[1] "0.1 - 113.0 (13.1)" "0.0 - 107.1 (14.9)"
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-BC-A5W4 
  "14Q LOSS MUTATED"   "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" 
        TCGA-BC-A69H         TCGA-BC-A69I         TCGA-CC-5258 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-CC-5260         TCGA-CC-5261         TCGA-CC-5262 
  "14Q LOSS MUTATED"   "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" 
        TCGA-CC-5263         TCGA-CC-A1HT         TCGA-CC-A3M9 
"14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" 
        TCGA-CC-A3MA         TCGA-CC-A3MB         TCGA-CC-A3MC 
  "14Q LOSS MUTATED"   "14Q LOSS MUTATED"   "14Q LOSS MUTATED" 
        TCGA-DD-A113         TCGA-DD-A114         TCGA-DD-A115 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-DD-A116         TCGA-DD-A118         TCGA-DD-A119 
"14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" 
        TCGA-DD-A11A         TCGA-DD-A11B         TCGA-DD-A11C 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-DD-A11D         TCGA-DD-A1E9         TCGA-DD-A1EA 
"14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" 
        TCGA-DD-A1EB         TCGA-DD-A1EC         TCGA-DD-A1ED 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-DD-A1EE         TCGA-DD-A1EF         TCGA-DD-A1EG 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-DD-A1EH         TCGA-DD-A1EI         TCGA-DD-A1EJ 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-DD-A1EK         TCGA-DD-A1EL         TCGA-DD-A39V 
"14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" 
        TCGA-DD-A39X         TCGA-DD-A39Y         TCGA-DD-A39Z 
  "14Q LOSS MUTATED"   "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" 
        TCGA-DD-A3A0         TCGA-DD-A3A1         TCGA-DD-A3A2 
"14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" 
        TCGA-DD-A3A3         TCGA-DD-A3A4         TCGA-DD-A3A5 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-DD-A3A6         TCGA-DD-A3A7         TCGA-DD-A3A8 
"14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" 
        TCGA-DD-A3A9         TCGA-DD-A4NA         TCGA-DD-A4NB 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-DD-A4ND         TCGA-DD-A4NF         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 MUTATED" "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-DD-A4NR 
"14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" 
        TCGA-DD-A4NS         TCGA-DD-A4NV         TCGA-DD-A73A 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-DD-A73B         TCGA-DD-A73C         TCGA-DD-A73D 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-DD-A73E         TCGA-DD-A73F         TCGA-DD-A73G 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-ED-A459         TCGA-ED-A4XI         TCGA-ED-A5KG 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-ED-A627         TCGA-ED-A66X         TCGA-ED-A66Y 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-ED-A7PX         TCGA-ED-A7PY         TCGA-ED-A7PZ 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-ED-A7XP         TCGA-ED-A82E         TCGA-EP-A12J 
"14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" 
        TCGA-EP-A26S         TCGA-EP-A2KA         TCGA-EP-A2KB 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-EP-A2KC         TCGA-EP-A3JL         TCGA-EP-A3RK 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-ES-A2HS         TCGA-ES-A2HT         TCGA-FV-A23B 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-FV-A2QR         TCGA-FV-A3I0         TCGA-FV-A3I1 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-FV-A3R2         TCGA-FV-A3R3         TCGA-FV-A495 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-FV-A496         TCGA-FV-A4ZP         TCGA-FV-A4ZQ 
"14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" 
        TCGA-G3-A25S         TCGA-G3-A25T         TCGA-G3-A25U 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-G3-A25V         TCGA-G3-A25W         TCGA-G3-A25X 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-G3-A25Y         TCGA-G3-A25Z         TCGA-G3-A3CG 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-G3-A3CH         TCGA-G3-A3CI         TCGA-G3-A3CJ 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-G3-A3CK         TCGA-G3-A5SI         TCGA-G3-A5SJ 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-G3-A5SL         TCGA-G3-A5SM         TCGA-G3-A6UC 
"14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" 
        TCGA-GJ-A6C0         TCGA-K7-A6G5         TCGA-LG-A6GG 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-MI-A75C         TCGA-MI-A75E         TCGA-MI-A75G 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-MI-A75I         TCGA-NI-A4U2         TCGA-O8-A75V 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-BC-A5W4 
  "14Q LOSS MUTATED"   "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" 
        TCGA-BC-A69H         TCGA-BC-A69I         TCGA-CC-5258 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-CC-5260         TCGA-CC-5261         TCGA-CC-5262 
  "14Q LOSS MUTATED"   "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" 
        TCGA-CC-5263         TCGA-CC-A1HT         TCGA-CC-A3M9 
"14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" 
        TCGA-CC-A3MA         TCGA-CC-A3MB         TCGA-CC-A3MC 
  "14Q LOSS MUTATED"   "14Q LOSS MUTATED"   "14Q LOSS MUTATED" 
        TCGA-DD-A113         TCGA-DD-A114         TCGA-DD-A115 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-DD-A116         TCGA-DD-A118         TCGA-DD-A119 
"14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" 
        TCGA-DD-A11A         TCGA-DD-A11B         TCGA-DD-A11C 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-DD-A11D         TCGA-DD-A1E9         TCGA-DD-A1EA 
"14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" 
        TCGA-DD-A1EB         TCGA-DD-A1EC         TCGA-DD-A1ED 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-DD-A1EE         TCGA-DD-A1EF         TCGA-DD-A1EG 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-DD-A1EH         TCGA-DD-A1EI         TCGA-DD-A1EJ 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-DD-A1EK         TCGA-DD-A1EL         TCGA-DD-A39V 
"14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" 
        TCGA-DD-A39X         TCGA-DD-A39Y         TCGA-DD-A39Z 
  "14Q LOSS MUTATED"   "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" 
        TCGA-DD-A3A0         TCGA-DD-A3A1         TCGA-DD-A3A2 
"14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" 
        TCGA-DD-A3A3         TCGA-DD-A3A4         TCGA-DD-A3A5 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-DD-A3A6         TCGA-DD-A3A7         TCGA-DD-A3A8 
"14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" 
        TCGA-DD-A3A9         TCGA-DD-A4NA         TCGA-DD-A4NB 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-DD-A4ND         TCGA-DD-A4NF         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 MUTATED" "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-DD-A4NR 
"14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" 
        TCGA-DD-A4NS         TCGA-DD-A4NV         TCGA-DD-A73A 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-DD-A73B         TCGA-DD-A73C         TCGA-DD-A73D 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-DD-A73E         TCGA-DD-A73F         TCGA-DD-A73G 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-ED-A459         TCGA-ED-A4XI         TCGA-ED-A5KG 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-ED-A627         TCGA-ED-A66X         TCGA-ED-A66Y 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-ED-A7PX         TCGA-ED-A7PY         TCGA-ED-A7PZ 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-ED-A7XP         TCGA-ED-A82E         TCGA-EP-A12J 
"14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" 
        TCGA-EP-A26S         TCGA-EP-A2KA         TCGA-EP-A2KB 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-EP-A2KC         TCGA-EP-A3JL         TCGA-EP-A3RK 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-ES-A2HS         TCGA-ES-A2HT         TCGA-FV-A23B 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-FV-A2QR         TCGA-FV-A3I0         TCGA-FV-A3I1 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-FV-A3R2         TCGA-FV-A3R3         TCGA-FV-A495 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-FV-A496         TCGA-FV-A4ZP         TCGA-FV-A4ZQ 
"14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" 
        TCGA-G3-A25S         TCGA-G3-A25T         TCGA-G3-A25U 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-G3-A25V         TCGA-G3-A25W         TCGA-G3-A25X 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-G3-A25Y         TCGA-G3-A25Z         TCGA-G3-A3CG 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-G3-A3CH         TCGA-G3-A3CI         TCGA-G3-A3CJ 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-G3-A3CK         TCGA-G3-A5SI         TCGA-G3-A5SJ 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-G3-A5SL         TCGA-G3-A5SM         TCGA-G3-A6UC 
"14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" 
        TCGA-GJ-A6C0         TCGA-K7-A6G5         TCGA-LG-A6GG 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-MI-A75C         TCGA-MI-A75E         TCGA-MI-A75G 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-MI-A75I         TCGA-NI-A4U2         TCGA-O8-A75V 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-BC-A5W4 
  "14Q LOSS MUTATED"   "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" 
        TCGA-BC-A69H         TCGA-BC-A69I         TCGA-CC-5258 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-CC-5260         TCGA-CC-5261         TCGA-CC-5262 
  "14Q LOSS MUTATED"   "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" 
        TCGA-CC-5263         TCGA-CC-A1HT         TCGA-CC-A3M9 
"14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" 
        TCGA-CC-A3MA         TCGA-CC-A3MB         TCGA-CC-A3MC 
  "14Q LOSS MUTATED"   "14Q LOSS MUTATED"   "14Q LOSS MUTATED" 
        TCGA-DD-A113         TCGA-DD-A114         TCGA-DD-A115 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-DD-A116         TCGA-DD-A118         TCGA-DD-A119 
"14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" 
        TCGA-DD-A11A         TCGA-DD-A11B         TCGA-DD-A11C 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-DD-A11D         TCGA-DD-A1E9         TCGA-DD-A1EA 
"14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" 
        TCGA-DD-A1EB         TCGA-DD-A1EC         TCGA-DD-A1ED 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-DD-A1EE         TCGA-DD-A1EF         TCGA-DD-A1EG 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-DD-A1EH         TCGA-DD-A1EI         TCGA-DD-A1EJ 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-DD-A1EK         TCGA-DD-A1EL         TCGA-DD-A39V 
"14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" 
        TCGA-DD-A39X         TCGA-DD-A39Y         TCGA-DD-A39Z 
  "14Q LOSS MUTATED"   "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" 
        TCGA-DD-A3A0         TCGA-DD-A3A1         TCGA-DD-A3A2 
"14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" 
        TCGA-DD-A3A3         TCGA-DD-A3A4         TCGA-DD-A3A5 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-DD-A3A6         TCGA-DD-A3A7         TCGA-DD-A3A8 
"14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" 
        TCGA-DD-A3A9         TCGA-DD-A4NA         TCGA-DD-A4NB 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-DD-A4ND         TCGA-DD-A4NF         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 MUTATED" "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-DD-A4NR 
"14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" 
        TCGA-DD-A4NS         TCGA-DD-A4NV         TCGA-DD-A73A 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-DD-A73B         TCGA-DD-A73C         TCGA-DD-A73D 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-DD-A73E         TCGA-DD-A73F         TCGA-DD-A73G 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-ED-A459         TCGA-ED-A4XI         TCGA-ED-A5KG 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-ED-A627         TCGA-ED-A66X         TCGA-ED-A66Y 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-ED-A7PX         TCGA-ED-A7PY         TCGA-ED-A7PZ 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-ED-A7XP         TCGA-ED-A82E         TCGA-EP-A12J 
"14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" 
        TCGA-EP-A26S         TCGA-EP-A2KA         TCGA-EP-A2KB 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-EP-A2KC         TCGA-EP-A3JL         TCGA-EP-A3RK 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-ES-A2HS         TCGA-ES-A2HT         TCGA-FV-A23B 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-FV-A2QR         TCGA-FV-A3I0         TCGA-FV-A3I1 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-FV-A3R2         TCGA-FV-A3R3         TCGA-FV-A495 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-FV-A496         TCGA-FV-A4ZP         TCGA-FV-A4ZQ 
"14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" 
        TCGA-G3-A25S         TCGA-G3-A25T         TCGA-G3-A25U 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-G3-A25V         TCGA-G3-A25W         TCGA-G3-A25X 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-G3-A25Y         TCGA-G3-A25Z         TCGA-G3-A3CG 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-G3-A3CH         TCGA-G3-A3CI         TCGA-G3-A3CJ 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-G3-A3CK         TCGA-G3-A5SI         TCGA-G3-A5SJ 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-G3-A5SL         TCGA-G3-A5SM         TCGA-G3-A6UC 
"14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" 
        TCGA-GJ-A6C0         TCGA-K7-A6G5         TCGA-LG-A6GG 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-MI-A75C         TCGA-MI-A75E         TCGA-MI-A75G 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-MI-A75I         TCGA-NI-A4U2         TCGA-O8-A75V 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
[1] "hr=" "1.1"
D66V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  14Q LOSS MUTATED        11       14         0         11          2
  14Q LOSS WILD-TYPE      47       22         2         19          2
                    vv
clus                 STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  14Q LOSS MUTATED            2        0         0         1
  14Q LOSS WILD-TYPE          3        1         1         1
D66V3, multiclass
                    vv
clus                 T1 T2 T3 T4
  14Q LOSS MUTATED   12 15 15  3
  14Q LOSS WILD-TYPE 49 25 25  5
D66V4, multiclass
    clus
vv   14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  T1               12                 49
  T2               15                 25
  T3               15                 25
  T4                3                  5
D66V5, binary
                    cls
clus                  0  1
  14Q LOSS MUTATED   29  1
  14Q LOSS WILD-TYPE 68  2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED     29    1
  14Q LOSS WILD-TYPE   68    2
   clus
vv  14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  0               29                 68
  1                1                  2
                    vv
clus                 M0 M1 MX
  14Q LOSS MUTATED   38  1  6
  14Q LOSS WILD-TYPE 77  2 25
D66V6, multiclass
    clus
vv   14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  M0               38                 77
  M1                1                  2
  MX                6                 25
D66V7, binary
                    cls
clus                  0  1
  14Q LOSS MUTATED   15 30
  14Q LOSS WILD-TYPE 43 61
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED     15   30
  14Q LOSS WILD-TYPE   43   61
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  FEMALE               15                 43
  MALE                 30                 61
                    vv
clus                 R0 R1 R2 RX
  14Q LOSS MUTATED   34  4  0  5
  14Q LOSS WILD-TYPE 88  7  1  5
D66V8, multiclass
    clus
vv   14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  R0               34                 88
  R1                4                  7
  R2                0                  1
  RX                5                  5

Clustering(67) Variable = 15Q LOSS MUTATION ANALYSIS
D67V1, survival
                    sevent
clus2                 0  1
  15Q LOSS MUTATED   17 11
  15Q LOSS WILD-TYPE 67 52
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                28                119 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                11                 52 
$`15Q LOSS MUTATED`
TCGA-BC-A112 TCGA-BC-A5W4 TCGA-BC-A69H TCGA-CC-5258 TCGA-CC-A3MA TCGA-DD-A113 
        5.03         9.50         3.95         0.07         0.07        79.73 
TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A11A TCGA-DD-A1E9 TCGA-DD-A1EI TCGA-DD-A1EJ 
       37.78        83.57         2.60        90.71         6.02        29.16 
TCGA-DD-A1EL TCGA-DD-A39Y TCGA-DD-A3A5 TCGA-DD-A4NA TCGA-DD-A4NQ TCGA-DD-A73B 
       13.64         5.62       102.74        33.14        12.26         9.30 
TCGA-ED-A459 TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PZ TCGA-ED-A82E TCGA-EP-A2KB 
       13.41         0.23         0.20         0.20         0.20        10.98 
TCGA-FV-A496 TCGA-FV-A4ZP TCGA-G3-A25Z TCGA-G3-A5SM 
        0.33        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-BC-A69I TCGA-CC-5260 
       44.42        13.84         0.26        22.36         0.53         2.86 
TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MB 
        0.39         3.39         4.24         3.32         0.10         0.10 
TCGA-CC-A3MC TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11B TCGA-DD-A11C 
        0.13        53.33       113.00         7.33         0.46        21.76 
TCGA-DD-A11D TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE 
       51.29        79.40        66.31        19.79        75.65         6.71 
TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EK TCGA-DD-A39V TCGA-DD-A39X 
       12.95        45.11        49.15        18.35        21.14        55.69 
TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 
       19.76        25.81         7.66        70.06        17.59        20.12 
TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A3A9 TCGA-DD-A4NB TCGA-DD-A4ND 
      107.11        13.78         0.36        30.61        12.85        73.38 
TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL 
       14.07        14.24        18.44        15.06        39.78        56.25 
TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV 
       29.56        61.45        93.67         0.30        80.75        66.35 
TCGA-DD-A73A TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G 
       10.98         7.56        10.98         1.45        27.72       100.96 
TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A7PY TCGA-ED-A7XP 
       12.69        15.85        13.91        13.35         0.20         0.20 
TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK 
       18.74        19.99        11.74         0.62         9.96        11.93 
TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3I1 
       22.85        14.40        32.45        19.10         0.20         8.12 
TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T 
        6.38         0.13         0.03         0.39         1.22        51.06 
TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A3CG 
       53.79        28.27        30.74        58.49        14.86        22.13 
TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ 
       25.64         5.92        19.53        19.23        14.70        11.97 
TCGA-G3-A5SL TCGA-G3-A6UC TCGA-GJ-A6C0 TCGA-K7-A6G5 TCGA-LG-A6GG TCGA-MI-A75C 
        7.99         7.76         1.02         4.01         0.49         9.57 
TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75I TCGA-NI-A4U2 TCGA-O8-A75V 
        5.10        14.24         8.71        58.88         4.44 

  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
              0.07               0.03 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
            102.74             113.00 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
              9.40              14.86 
[1] "0.1 - 102.7 (9.4)"  "0.0 - 113.0 (14.9)"
        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-BC-A69H         TCGA-BC-A69I         TCGA-CC-5258 
  "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" 
        TCGA-CC-5260         TCGA-CC-5261         TCGA-CC-5262 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-CC-5263         TCGA-CC-A1HT         TCGA-CC-A3M9 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-CC-A3MA         TCGA-CC-A3MB         TCGA-CC-A3MC 
  "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-DD-A113         TCGA-DD-A114         TCGA-DD-A115 
  "15Q LOSS MUTATED"   "15Q LOSS MUTATED"   "15Q LOSS MUTATED" 
        TCGA-DD-A116         TCGA-DD-A118         TCGA-DD-A119 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-DD-A11A         TCGA-DD-A11B         TCGA-DD-A11C 
  "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-DD-A11D         TCGA-DD-A1E9         TCGA-DD-A1EA 
"15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" 
        TCGA-DD-A1EB         TCGA-DD-A1EC         TCGA-DD-A1ED 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-DD-A1EE         TCGA-DD-A1EF         TCGA-DD-A1EG 
"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-A1EK         TCGA-DD-A1EL         TCGA-DD-A39V 
"15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" 
        TCGA-DD-A39X         TCGA-DD-A39Y         TCGA-DD-A39Z 
"15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" 
        TCGA-DD-A3A0         TCGA-DD-A3A1         TCGA-DD-A3A2 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-DD-A3A3         TCGA-DD-A3A4         TCGA-DD-A3A5 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" 
        TCGA-DD-A3A6         TCGA-DD-A3A7         TCGA-DD-A3A8 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-DD-A3A9         TCGA-DD-A4NA         TCGA-DD-A4NB 
"15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" 
        TCGA-DD-A4ND         TCGA-DD-A4NF         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-DD-A4NR 
"15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" 
        TCGA-DD-A4NS         TCGA-DD-A4NV         TCGA-DD-A73A 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-DD-A73B         TCGA-DD-A73C         TCGA-DD-A73D 
  "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-DD-A73E         TCGA-DD-A73F         TCGA-DD-A73G 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-ED-A459         TCGA-ED-A4XI         TCGA-ED-A5KG 
  "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-ED-A627         TCGA-ED-A66X         TCGA-ED-A66Y 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" 
        TCGA-ED-A7PX         TCGA-ED-A7PY         TCGA-ED-A7PZ 
  "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" 
        TCGA-ED-A7XP         TCGA-ED-A82E         TCGA-EP-A12J 
"15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" 
        TCGA-EP-A26S         TCGA-EP-A2KA         TCGA-EP-A2KB 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" 
        TCGA-EP-A2KC         TCGA-EP-A3JL         TCGA-EP-A3RK 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-ES-A2HS         TCGA-ES-A2HT         TCGA-FV-A23B 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-FV-A2QR         TCGA-FV-A3I0         TCGA-FV-A3I1 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-FV-A3R2         TCGA-FV-A3R3         TCGA-FV-A495 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-FV-A496         TCGA-FV-A4ZP         TCGA-FV-A4ZQ 
  "15Q LOSS MUTATED"   "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" 
        TCGA-G3-A25S         TCGA-G3-A25T         TCGA-G3-A25U 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-G3-A25V         TCGA-G3-A25W         TCGA-G3-A25X 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-G3-A25Y         TCGA-G3-A25Z         TCGA-G3-A3CG 
"15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" 
        TCGA-G3-A3CH         TCGA-G3-A3CI         TCGA-G3-A3CJ 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-G3-A3CK         TCGA-G3-A5SI         TCGA-G3-A5SJ 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-G3-A5SL         TCGA-G3-A5SM         TCGA-G3-A6UC 
"15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" 
        TCGA-GJ-A6C0         TCGA-K7-A6G5         TCGA-LG-A6GG 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-MI-A75C         TCGA-MI-A75E         TCGA-MI-A75G 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-MI-A75I         TCGA-NI-A4U2         TCGA-O8-A75V 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
  "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-BC-A5W4 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" 
        TCGA-BC-A69H         TCGA-BC-A69I         TCGA-CC-5258 
  "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" 
        TCGA-CC-5260         TCGA-CC-5261         TCGA-CC-5262 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-CC-5263         TCGA-CC-A1HT         TCGA-CC-A3M9 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-CC-A3MA         TCGA-CC-A3MB         TCGA-CC-A3MC 
  "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-DD-A113         TCGA-DD-A114         TCGA-DD-A115 
  "15Q LOSS MUTATED"   "15Q LOSS MUTATED"   "15Q LOSS MUTATED" 
        TCGA-DD-A116         TCGA-DD-A118         TCGA-DD-A119 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-DD-A11A         TCGA-DD-A11B         TCGA-DD-A11C 
  "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-DD-A11D         TCGA-DD-A1E9         TCGA-DD-A1EA 
"15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" 
        TCGA-DD-A1EB         TCGA-DD-A1EC         TCGA-DD-A1ED 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-DD-A1EE         TCGA-DD-A1EF         TCGA-DD-A1EG 
"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-A1EK         TCGA-DD-A1EL         TCGA-DD-A39V 
"15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" 
        TCGA-DD-A39X         TCGA-DD-A39Y         TCGA-DD-A39Z 
"15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" 
        TCGA-DD-A3A0         TCGA-DD-A3A1         TCGA-DD-A3A2 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-DD-A3A3         TCGA-DD-A3A4         TCGA-DD-A3A5 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" 
        TCGA-DD-A3A6         TCGA-DD-A3A7         TCGA-DD-A3A8 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-DD-A3A9         TCGA-DD-A4NA         TCGA-DD-A4NB 
"15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" 
        TCGA-DD-A4ND         TCGA-DD-A4NF         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-DD-A4NR 
"15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" 
        TCGA-DD-A4NS         TCGA-DD-A4NV         TCGA-DD-A73A 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-DD-A73B         TCGA-DD-A73C         TCGA-DD-A73D 
  "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-DD-A73E         TCGA-DD-A73F         TCGA-DD-A73G 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-ED-A459         TCGA-ED-A4XI         TCGA-ED-A5KG 
  "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-ED-A627         TCGA-ED-A66X         TCGA-ED-A66Y 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" 
        TCGA-ED-A7PX         TCGA-ED-A7PY         TCGA-ED-A7PZ 
  "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" 
        TCGA-ED-A7XP         TCGA-ED-A82E         TCGA-EP-A12J 
"15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" 
        TCGA-EP-A26S         TCGA-EP-A2KA         TCGA-EP-A2KB 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" 
        TCGA-EP-A2KC         TCGA-EP-A3JL         TCGA-EP-A3RK 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-ES-A2HS         TCGA-ES-A2HT         TCGA-FV-A23B 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-FV-A2QR         TCGA-FV-A3I0         TCGA-FV-A3I1 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-FV-A3R2         TCGA-FV-A3R3         TCGA-FV-A495 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-FV-A496         TCGA-FV-A4ZP         TCGA-FV-A4ZQ 
  "15Q LOSS MUTATED"   "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" 
        TCGA-G3-A25S         TCGA-G3-A25T         TCGA-G3-A25U 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-G3-A25V         TCGA-G3-A25W         TCGA-G3-A25X 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-G3-A25Y         TCGA-G3-A25Z         TCGA-G3-A3CG 
"15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" 
        TCGA-G3-A3CH         TCGA-G3-A3CI         TCGA-G3-A3CJ 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-G3-A3CK         TCGA-G3-A5SI         TCGA-G3-A5SJ 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-G3-A5SL         TCGA-G3-A5SM         TCGA-G3-A6UC 
"15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" 
        TCGA-GJ-A6C0         TCGA-K7-A6G5         TCGA-LG-A6GG 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-MI-A75C         TCGA-MI-A75E         TCGA-MI-A75G 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-MI-A75I         TCGA-NI-A4U2         TCGA-O8-A75V 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
  "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-BC-A5W4 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" 
        TCGA-BC-A69H         TCGA-BC-A69I         TCGA-CC-5258 
  "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" 
        TCGA-CC-5260         TCGA-CC-5261         TCGA-CC-5262 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-CC-5263         TCGA-CC-A1HT         TCGA-CC-A3M9 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-CC-A3MA         TCGA-CC-A3MB         TCGA-CC-A3MC 
  "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-DD-A113         TCGA-DD-A114         TCGA-DD-A115 
  "15Q LOSS MUTATED"   "15Q LOSS MUTATED"   "15Q LOSS MUTATED" 
        TCGA-DD-A116         TCGA-DD-A118         TCGA-DD-A119 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-DD-A11A         TCGA-DD-A11B         TCGA-DD-A11C 
  "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-DD-A11D         TCGA-DD-A1E9         TCGA-DD-A1EA 
"15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" 
        TCGA-DD-A1EB         TCGA-DD-A1EC         TCGA-DD-A1ED 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-DD-A1EE         TCGA-DD-A1EF         TCGA-DD-A1EG 
"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-A1EK         TCGA-DD-A1EL         TCGA-DD-A39V 
"15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" 
        TCGA-DD-A39X         TCGA-DD-A39Y         TCGA-DD-A39Z 
"15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" 
        TCGA-DD-A3A0         TCGA-DD-A3A1         TCGA-DD-A3A2 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-DD-A3A3         TCGA-DD-A3A4         TCGA-DD-A3A5 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" 
        TCGA-DD-A3A6         TCGA-DD-A3A7         TCGA-DD-A3A8 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-DD-A3A9         TCGA-DD-A4NA         TCGA-DD-A4NB 
"15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" 
        TCGA-DD-A4ND         TCGA-DD-A4NF         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-DD-A4NR 
"15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" 
        TCGA-DD-A4NS         TCGA-DD-A4NV         TCGA-DD-A73A 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-DD-A73B         TCGA-DD-A73C         TCGA-DD-A73D 
  "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-DD-A73E         TCGA-DD-A73F         TCGA-DD-A73G 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-ED-A459         TCGA-ED-A4XI         TCGA-ED-A5KG 
  "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-ED-A627         TCGA-ED-A66X         TCGA-ED-A66Y 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" 
        TCGA-ED-A7PX         TCGA-ED-A7PY         TCGA-ED-A7PZ 
  "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" 
        TCGA-ED-A7XP         TCGA-ED-A82E         TCGA-EP-A12J 
"15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" 
        TCGA-EP-A26S         TCGA-EP-A2KA         TCGA-EP-A2KB 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" 
        TCGA-EP-A2KC         TCGA-EP-A3JL         TCGA-EP-A3RK 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-ES-A2HS         TCGA-ES-A2HT         TCGA-FV-A23B 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-FV-A2QR         TCGA-FV-A3I0         TCGA-FV-A3I1 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-FV-A3R2         TCGA-FV-A3R3         TCGA-FV-A495 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-FV-A496         TCGA-FV-A4ZP         TCGA-FV-A4ZQ 
  "15Q LOSS MUTATED"   "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" 
        TCGA-G3-A25S         TCGA-G3-A25T         TCGA-G3-A25U 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-G3-A25V         TCGA-G3-A25W         TCGA-G3-A25X 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-G3-A25Y         TCGA-G3-A25Z         TCGA-G3-A3CG 
"15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" 
        TCGA-G3-A3CH         TCGA-G3-A3CI         TCGA-G3-A3CJ 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-G3-A3CK         TCGA-G3-A5SI         TCGA-G3-A5SJ 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-G3-A5SL         TCGA-G3-A5SM         TCGA-G3-A6UC 
"15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" 
        TCGA-GJ-A6C0         TCGA-K7-A6G5         TCGA-LG-A6GG 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-MI-A75C         TCGA-MI-A75E         TCGA-MI-A75G 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-MI-A75I         TCGA-NI-A4U2         TCGA-O8-A75V 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
[1] "hr=" "1"  
D67V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  15Q LOSS MUTATED         8       10         1          7          0
  15Q LOSS WILD-TYPE      50       26         1         23          4
                    vv
clus                 STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  15Q LOSS MUTATED            2        0         0         0
  15Q LOSS WILD-TYPE          3        1         1         2
D67V3, multiclass
                    vv
clus                 T1 T2 T3 T4
  15Q LOSS MUTATED    9 11  9  0
  15Q LOSS WILD-TYPE 52 29 31  8
D67V4, multiclass
    clus
vv   15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  T1                9                 52
  T2               11                 29
  T3                9                 31
  T4                0                  8
D67V5, binary
                    cls
clus                  0  1
  15Q LOSS MUTATED   16  2
  15Q LOSS WILD-TYPE 81  1
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED     16    2
  15Q LOSS WILD-TYPE   81    1
   clus
vv  15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  0               16                 81
  1                2                  1
                    vv
clus                 M0 M1 MX
  15Q LOSS MUTATED   27  0  2
  15Q LOSS WILD-TYPE 88  3 29
D67V6, multiclass
    clus
vv   15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  M0               27                 88
  M1                0                  3
  MX                2                 29
D67V7, binary
                    cls
clus                  0  1
  15Q LOSS MUTATED   10 19
  15Q LOSS WILD-TYPE 48 72
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED     10   19
  15Q LOSS WILD-TYPE   48   72
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  FEMALE               10                 48
  MALE                 19                 72
                    vv
clus                 R0 R1 R2 RX
  15Q LOSS MUTATED   25  2  0  2
  15Q LOSS WILD-TYPE 97  9  1  8
D67V8, multiclass
    clus
vv   15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  R0               25                 97
  R1                2                  9
  R2                0                  1
  RX                2                  8

Clustering(68) Variable = 16P LOSS MUTATION ANALYSIS
D68V1, survival
                    sevent
clus2                 0  1
  16P LOSS MUTATED   21 19
  16P LOSS WILD-TYPE 63 44
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                40                107 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                19                 44 
$`16P LOSS MUTATED`
TCGA-BC-A217 TCGA-BC-A5W4 TCGA-BC-A69H TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5261 
       13.84         9.50         3.95         0.07         2.86         0.39 
TCGA-CC-5262 TCGA-CC-A3M9 TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A114 TCGA-DD-A11B 
        3.39         0.10         0.10         0.13        37.78         0.46 
TCGA-DD-A1EF TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A39Y TCGA-DD-A39Z 
       12.95        49.15         6.02        29.16         5.62        19.76 
TCGA-DD-A3A8 TCGA-DD-A3A9 TCGA-DD-A4ND TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NN 
        0.36        30.61        73.38        14.24        18.44        29.56 
TCGA-DD-A4NO TCGA-DD-A4NQ TCGA-DD-A73B TCGA-ED-A5KG TCGA-ED-A66X TCGA-ED-A66Y 
       61.45        12.26         9.30        15.85        13.35         0.23 
TCGA-ED-A7PY TCGA-EP-A2KB TCGA-ES-A2HS TCGA-FV-A23B TCGA-FV-A3I0 TCGA-FV-A3R2 
        0.20        10.98        22.85        32.45         0.20         6.38 
TCGA-G3-A25X TCGA-G3-A25Y TCGA-MI-A75G TCGA-MI-A75I 
       58.49        14.86        14.24         8.71 

$`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-BC-A69I TCGA-CC-5263 
        5.03        44.42         0.26        22.36         0.53         4.24 
TCGA-CC-A1HT TCGA-CC-A3MA TCGA-DD-A113 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 
        3.32         0.07        79.73        83.57        53.33       113.00 
TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA 
        7.33         2.60        21.76        51.29        90.71        79.40 
TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EG TCGA-DD-A1EK 
       66.31        19.79        75.65         6.71        45.11        18.35 
TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39X TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 
       13.64        21.14        55.69        25.81         7.66        70.06 
TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A4NA 
       17.59        20.12       102.74       107.11        13.78        33.14 
TCGA-DD-A4NB TCGA-DD-A4NF TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NP 
       12.85        14.07        15.06        39.78        56.25        93.67 
TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73C TCGA-DD-A73D 
        0.30        80.75        66.35        10.98         7.56        10.98 
TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A627 
        1.45        27.72       100.96        13.41        12.69        13.91 
TCGA-ED-A7PX TCGA-ED-A7PZ TCGA-ED-A7XP TCGA-ED-A82E TCGA-EP-A12J TCGA-EP-A26S 
        0.20         0.20         0.20         0.20        18.74        19.99 
TCGA-EP-A2KA TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A2QR 
       11.74         0.62         9.96        11.93        14.40        19.10 
TCGA-FV-A3I1 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZP TCGA-FV-A4ZQ 
        8.12         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-A25Z 
        1.22        51.06        53.79        28.27        30.74        21.53 
TCGA-G3-A3CG TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI 
       22.13        25.64         5.92        19.53        19.23        14.70 
TCGA-G3-A5SJ TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A6UC TCGA-GJ-A6C0 TCGA-K7-A6G5 
       11.97         7.99         4.37         7.76         1.02         4.01 
TCGA-LG-A6GG TCGA-MI-A75C TCGA-MI-A75E TCGA-NI-A4U2 TCGA-O8-A75V 
        0.49         9.57         5.10        58.88         4.44 

  16P LOSS MUTATED 16P LOSS WILD-TYPE 
              0.07               0.03 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
             73.38             113.00 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
             11.62              17.59 
[1] "0.1 - 73.4 (11.6)"  "0.0 - 113.0 (17.6)"
        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-BC-A69H         TCGA-BC-A69I         TCGA-CC-5258 
  "16P LOSS MUTATED" "16P LOSS WILD-TYPE"   "16P LOSS MUTATED" 
        TCGA-CC-5260         TCGA-CC-5261         TCGA-CC-5262 
  "16P LOSS MUTATED"   "16P LOSS MUTATED"   "16P LOSS MUTATED" 
        TCGA-CC-5263         TCGA-CC-A1HT         TCGA-CC-A3M9 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE"   "16P LOSS MUTATED" 
        TCGA-CC-A3MA         TCGA-CC-A3MB         TCGA-CC-A3MC 
"16P LOSS WILD-TYPE"   "16P LOSS MUTATED"   "16P LOSS MUTATED" 
        TCGA-DD-A113         TCGA-DD-A114         TCGA-DD-A115 
"16P LOSS WILD-TYPE"   "16P LOSS MUTATED" "16P LOSS WILD-TYPE" 
        TCGA-DD-A116         TCGA-DD-A118         TCGA-DD-A119 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DD-A11A         TCGA-DD-A11B         TCGA-DD-A11C 
"16P LOSS WILD-TYPE"   "16P LOSS MUTATED" "16P LOSS WILD-TYPE" 
        TCGA-DD-A11D         TCGA-DD-A1E9         TCGA-DD-A1EA 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DD-A1EB         TCGA-DD-A1EC         TCGA-DD-A1ED 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DD-A1EE         TCGA-DD-A1EF         TCGA-DD-A1EG 
"16P LOSS WILD-TYPE"   "16P LOSS MUTATED" "16P LOSS WILD-TYPE" 
        TCGA-DD-A1EH         TCGA-DD-A1EI         TCGA-DD-A1EJ 
  "16P LOSS MUTATED"   "16P LOSS MUTATED"   "16P LOSS MUTATED" 
        TCGA-DD-A1EK         TCGA-DD-A1EL         TCGA-DD-A39V 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DD-A39X         TCGA-DD-A39Y         TCGA-DD-A39Z 
"16P LOSS WILD-TYPE"   "16P LOSS MUTATED"   "16P LOSS MUTATED" 
        TCGA-DD-A3A0         TCGA-DD-A3A1         TCGA-DD-A3A2 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DD-A3A3         TCGA-DD-A3A4         TCGA-DD-A3A5 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DD-A3A6         TCGA-DD-A3A7         TCGA-DD-A3A8 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE"   "16P LOSS MUTATED" 
        TCGA-DD-A3A9         TCGA-DD-A4NA         TCGA-DD-A4NB 
  "16P LOSS MUTATED" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DD-A4ND         TCGA-DD-A4NF         TCGA-DD-A4NH 
  "16P LOSS MUTATED" "16P LOSS WILD-TYPE"   "16P LOSS MUTATED" 
        TCGA-DD-A4NI         TCGA-DD-A4NJ         TCGA-DD-A4NK 
  "16P LOSS MUTATED" "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-DD-A4NR 
"16P LOSS WILD-TYPE"   "16P LOSS MUTATED" "16P LOSS WILD-TYPE" 
        TCGA-DD-A4NS         TCGA-DD-A4NV         TCGA-DD-A73A 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DD-A73B         TCGA-DD-A73C         TCGA-DD-A73D 
  "16P LOSS MUTATED" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DD-A73E         TCGA-DD-A73F         TCGA-DD-A73G 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-ED-A459         TCGA-ED-A4XI         TCGA-ED-A5KG 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE"   "16P LOSS MUTATED" 
        TCGA-ED-A627         TCGA-ED-A66X         TCGA-ED-A66Y 
"16P LOSS WILD-TYPE"   "16P LOSS MUTATED"   "16P LOSS MUTATED" 
        TCGA-ED-A7PX         TCGA-ED-A7PY         TCGA-ED-A7PZ 
"16P LOSS WILD-TYPE"   "16P LOSS MUTATED" "16P LOSS WILD-TYPE" 
        TCGA-ED-A7XP         TCGA-ED-A82E         TCGA-EP-A12J 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EP-A26S         TCGA-EP-A2KA         TCGA-EP-A2KB 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE"   "16P LOSS MUTATED" 
        TCGA-EP-A2KC         TCGA-EP-A3JL         TCGA-EP-A3RK 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-ES-A2HS         TCGA-ES-A2HT         TCGA-FV-A23B 
  "16P LOSS MUTATED" "16P LOSS WILD-TYPE"   "16P LOSS MUTATED" 
        TCGA-FV-A2QR         TCGA-FV-A3I0         TCGA-FV-A3I1 
"16P LOSS WILD-TYPE"   "16P LOSS MUTATED" "16P LOSS WILD-TYPE" 
        TCGA-FV-A3R2         TCGA-FV-A3R3         TCGA-FV-A495 
  "16P LOSS MUTATED" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-FV-A496         TCGA-FV-A4ZP         TCGA-FV-A4ZQ 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-G3-A25S         TCGA-G3-A25T         TCGA-G3-A25U 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-G3-A25V         TCGA-G3-A25W         TCGA-G3-A25X 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE"   "16P LOSS MUTATED" 
        TCGA-G3-A25Y         TCGA-G3-A25Z         TCGA-G3-A3CG 
  "16P LOSS MUTATED" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-G3-A3CH         TCGA-G3-A3CI         TCGA-G3-A3CJ 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-G3-A3CK         TCGA-G3-A5SI         TCGA-G3-A5SJ 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-G3-A5SL         TCGA-G3-A5SM         TCGA-G3-A6UC 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-GJ-A6C0         TCGA-K7-A6G5         TCGA-LG-A6GG 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-MI-A75C         TCGA-MI-A75E         TCGA-MI-A75G 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE"   "16P LOSS MUTATED" 
        TCGA-MI-A75I         TCGA-NI-A4U2         TCGA-O8-A75V 
  "16P LOSS MUTATED" "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-BC-A69H         TCGA-BC-A69I         TCGA-CC-5258 
  "16P LOSS MUTATED" "16P LOSS WILD-TYPE"   "16P LOSS MUTATED" 
        TCGA-CC-5260         TCGA-CC-5261         TCGA-CC-5262 
  "16P LOSS MUTATED"   "16P LOSS MUTATED"   "16P LOSS MUTATED" 
        TCGA-CC-5263         TCGA-CC-A1HT         TCGA-CC-A3M9 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE"   "16P LOSS MUTATED" 
        TCGA-CC-A3MA         TCGA-CC-A3MB         TCGA-CC-A3MC 
"16P LOSS WILD-TYPE"   "16P LOSS MUTATED"   "16P LOSS MUTATED" 
        TCGA-DD-A113         TCGA-DD-A114         TCGA-DD-A115 
"16P LOSS WILD-TYPE"   "16P LOSS MUTATED" "16P LOSS WILD-TYPE" 
        TCGA-DD-A116         TCGA-DD-A118         TCGA-DD-A119 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DD-A11A         TCGA-DD-A11B         TCGA-DD-A11C 
"16P LOSS WILD-TYPE"   "16P LOSS MUTATED" "16P LOSS WILD-TYPE" 
        TCGA-DD-A11D         TCGA-DD-A1E9         TCGA-DD-A1EA 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DD-A1EB         TCGA-DD-A1EC         TCGA-DD-A1ED 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DD-A1EE         TCGA-DD-A1EF         TCGA-DD-A1EG 
"16P LOSS WILD-TYPE"   "16P LOSS MUTATED" "16P LOSS WILD-TYPE" 
        TCGA-DD-A1EH         TCGA-DD-A1EI         TCGA-DD-A1EJ 
  "16P LOSS MUTATED"   "16P LOSS MUTATED"   "16P LOSS MUTATED" 
        TCGA-DD-A1EK         TCGA-DD-A1EL         TCGA-DD-A39V 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DD-A39X         TCGA-DD-A39Y         TCGA-DD-A39Z 
"16P LOSS WILD-TYPE"   "16P LOSS MUTATED"   "16P LOSS MUTATED" 
        TCGA-DD-A3A0         TCGA-DD-A3A1         TCGA-DD-A3A2 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DD-A3A3         TCGA-DD-A3A4         TCGA-DD-A3A5 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DD-A3A6         TCGA-DD-A3A7         TCGA-DD-A3A8 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE"   "16P LOSS MUTATED" 
        TCGA-DD-A3A9         TCGA-DD-A4NA         TCGA-DD-A4NB 
  "16P LOSS MUTATED" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DD-A4ND         TCGA-DD-A4NF         TCGA-DD-A4NH 
  "16P LOSS MUTATED" "16P LOSS WILD-TYPE"   "16P LOSS MUTATED" 
        TCGA-DD-A4NI         TCGA-DD-A4NJ         TCGA-DD-A4NK 
  "16P LOSS MUTATED" "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-DD-A4NR 
"16P LOSS WILD-TYPE"   "16P LOSS MUTATED" "16P LOSS WILD-TYPE" 
        TCGA-DD-A4NS         TCGA-DD-A4NV         TCGA-DD-A73A 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DD-A73B         TCGA-DD-A73C         TCGA-DD-A73D 
  "16P LOSS MUTATED" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DD-A73E         TCGA-DD-A73F         TCGA-DD-A73G 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-ED-A459         TCGA-ED-A4XI         TCGA-ED-A5KG 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE"   "16P LOSS MUTATED" 
        TCGA-ED-A627         TCGA-ED-A66X         TCGA-ED-A66Y 
"16P LOSS WILD-TYPE"   "16P LOSS MUTATED"   "16P LOSS MUTATED" 
        TCGA-ED-A7PX         TCGA-ED-A7PY         TCGA-ED-A7PZ 
"16P LOSS WILD-TYPE"   "16P LOSS MUTATED" "16P LOSS WILD-TYPE" 
        TCGA-ED-A7XP         TCGA-ED-A82E         TCGA-EP-A12J 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EP-A26S         TCGA-EP-A2KA         TCGA-EP-A2KB 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE"   "16P LOSS MUTATED" 
        TCGA-EP-A2KC         TCGA-EP-A3JL         TCGA-EP-A3RK 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-ES-A2HS         TCGA-ES-A2HT         TCGA-FV-A23B 
  "16P LOSS MUTATED" "16P LOSS WILD-TYPE"   "16P LOSS MUTATED" 
        TCGA-FV-A2QR         TCGA-FV-A3I0         TCGA-FV-A3I1 
"16P LOSS WILD-TYPE"   "16P LOSS MUTATED" "16P LOSS WILD-TYPE" 
        TCGA-FV-A3R2         TCGA-FV-A3R3         TCGA-FV-A495 
  "16P LOSS MUTATED" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-FV-A496         TCGA-FV-A4ZP         TCGA-FV-A4ZQ 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-G3-A25S         TCGA-G3-A25T         TCGA-G3-A25U 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-G3-A25V         TCGA-G3-A25W         TCGA-G3-A25X 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE"   "16P LOSS MUTATED" 
        TCGA-G3-A25Y         TCGA-G3-A25Z         TCGA-G3-A3CG 
  "16P LOSS MUTATED" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-G3-A3CH         TCGA-G3-A3CI         TCGA-G3-A3CJ 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-G3-A3CK         TCGA-G3-A5SI         TCGA-G3-A5SJ 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-G3-A5SL         TCGA-G3-A5SM         TCGA-G3-A6UC 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-GJ-A6C0         TCGA-K7-A6G5         TCGA-LG-A6GG 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-MI-A75C         TCGA-MI-A75E         TCGA-MI-A75G 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE"   "16P LOSS MUTATED" 
        TCGA-MI-A75I         TCGA-NI-A4U2         TCGA-O8-A75V 
  "16P LOSS MUTATED" "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-BC-A69H         TCGA-BC-A69I         TCGA-CC-5258 
  "16P LOSS MUTATED" "16P LOSS WILD-TYPE"   "16P LOSS MUTATED" 
        TCGA-CC-5260         TCGA-CC-5261         TCGA-CC-5262 
  "16P LOSS MUTATED"   "16P LOSS MUTATED"   "16P LOSS MUTATED" 
        TCGA-CC-5263         TCGA-CC-A1HT         TCGA-CC-A3M9 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE"   "16P LOSS MUTATED" 
        TCGA-CC-A3MA         TCGA-CC-A3MB         TCGA-CC-A3MC 
"16P LOSS WILD-TYPE"   "16P LOSS MUTATED"   "16P LOSS MUTATED" 
        TCGA-DD-A113         TCGA-DD-A114         TCGA-DD-A115 
"16P LOSS WILD-TYPE"   "16P LOSS MUTATED" "16P LOSS WILD-TYPE" 
        TCGA-DD-A116         TCGA-DD-A118         TCGA-DD-A119 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DD-A11A         TCGA-DD-A11B         TCGA-DD-A11C 
"16P LOSS WILD-TYPE"   "16P LOSS MUTATED" "16P LOSS WILD-TYPE" 
        TCGA-DD-A11D         TCGA-DD-A1E9         TCGA-DD-A1EA 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DD-A1EB         TCGA-DD-A1EC         TCGA-DD-A1ED 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DD-A1EE         TCGA-DD-A1EF         TCGA-DD-A1EG 
"16P LOSS WILD-TYPE"   "16P LOSS MUTATED" "16P LOSS WILD-TYPE" 
        TCGA-DD-A1EH         TCGA-DD-A1EI         TCGA-DD-A1EJ 
  "16P LOSS MUTATED"   "16P LOSS MUTATED"   "16P LOSS MUTATED" 
        TCGA-DD-A1EK         TCGA-DD-A1EL         TCGA-DD-A39V 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DD-A39X         TCGA-DD-A39Y         TCGA-DD-A39Z 
"16P LOSS WILD-TYPE"   "16P LOSS MUTATED"   "16P LOSS MUTATED" 
        TCGA-DD-A3A0         TCGA-DD-A3A1         TCGA-DD-A3A2 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DD-A3A3         TCGA-DD-A3A4         TCGA-DD-A3A5 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DD-A3A6         TCGA-DD-A3A7         TCGA-DD-A3A8 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE"   "16P LOSS MUTATED" 
        TCGA-DD-A3A9         TCGA-DD-A4NA         TCGA-DD-A4NB 
  "16P LOSS MUTATED" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DD-A4ND         TCGA-DD-A4NF         TCGA-DD-A4NH 
  "16P LOSS MUTATED" "16P LOSS WILD-TYPE"   "16P LOSS MUTATED" 
        TCGA-DD-A4NI         TCGA-DD-A4NJ         TCGA-DD-A4NK 
  "16P LOSS MUTATED" "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-DD-A4NR 
"16P LOSS WILD-TYPE"   "16P LOSS MUTATED" "16P LOSS WILD-TYPE" 
        TCGA-DD-A4NS         TCGA-DD-A4NV         TCGA-DD-A73A 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DD-A73B         TCGA-DD-A73C         TCGA-DD-A73D 
  "16P LOSS MUTATED" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DD-A73E         TCGA-DD-A73F         TCGA-DD-A73G 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-ED-A459         TCGA-ED-A4XI         TCGA-ED-A5KG 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE"   "16P LOSS MUTATED" 
        TCGA-ED-A627         TCGA-ED-A66X         TCGA-ED-A66Y 
"16P LOSS WILD-TYPE"   "16P LOSS MUTATED"   "16P LOSS MUTATED" 
        TCGA-ED-A7PX         TCGA-ED-A7PY         TCGA-ED-A7PZ 
"16P LOSS WILD-TYPE"   "16P LOSS MUTATED" "16P LOSS WILD-TYPE" 
        TCGA-ED-A7XP         TCGA-ED-A82E         TCGA-EP-A12J 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EP-A26S         TCGA-EP-A2KA         TCGA-EP-A2KB 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE"   "16P LOSS MUTATED" 
        TCGA-EP-A2KC         TCGA-EP-A3JL         TCGA-EP-A3RK 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-ES-A2HS         TCGA-ES-A2HT         TCGA-FV-A23B 
  "16P LOSS MUTATED" "16P LOSS WILD-TYPE"   "16P LOSS MUTATED" 
        TCGA-FV-A2QR         TCGA-FV-A3I0         TCGA-FV-A3I1 
"16P LOSS WILD-TYPE"   "16P LOSS MUTATED" "16P LOSS WILD-TYPE" 
        TCGA-FV-A3R2         TCGA-FV-A3R3         TCGA-FV-A495 
  "16P LOSS MUTATED" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-FV-A496         TCGA-FV-A4ZP         TCGA-FV-A4ZQ 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-G3-A25S         TCGA-G3-A25T         TCGA-G3-A25U 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-G3-A25V         TCGA-G3-A25W         TCGA-G3-A25X 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE"   "16P LOSS MUTATED" 
        TCGA-G3-A25Y         TCGA-G3-A25Z         TCGA-G3-A3CG 
  "16P LOSS MUTATED" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-G3-A3CH         TCGA-G3-A3CI         TCGA-G3-A3CJ 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-G3-A3CK         TCGA-G3-A5SI         TCGA-G3-A5SJ 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-G3-A5SL         TCGA-G3-A5SM         TCGA-G3-A6UC 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-GJ-A6C0         TCGA-K7-A6G5         TCGA-LG-A6GG 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-MI-A75C         TCGA-MI-A75E         TCGA-MI-A75G 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE"   "16P LOSS MUTATED" 
        TCGA-MI-A75I         TCGA-NI-A4U2         TCGA-O8-A75V 
  "16P LOSS MUTATED" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
[1] "hr=" "2"  
D68V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  16P LOSS MUTATED        12       15         1          7          1
  16P LOSS WILD-TYPE      46       21         1         23          3
                    vv
clus                 STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  16P LOSS MUTATED            3        0         1         1
  16P LOSS WILD-TYPE          2        1         0         1
D68V3, multiclass
                    vv
clus                 T1 T2 T3 T4
  16P LOSS MUTATED   14 16  9  3
  16P LOSS WILD-TYPE 47 24 31  5
D68V4, multiclass
    clus
vv   16P LOSS MUTATED 16P LOSS WILD-TYPE
  T1               14                 47
  T2               16                 24
  T3                9                 31
  T4                3                  5
D68V5, binary
                    cls
clus                  0  1
  16P LOSS MUTATED   27  2
  16P LOSS WILD-TYPE 70  1
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED     27    2
  16P LOSS WILD-TYPE   70    1
   clus
vv  16P LOSS MUTATED 16P LOSS WILD-TYPE
  0               27                 70
  1                2                  1
                    vv
clus                 M0 M1 MX
  16P LOSS MUTATED   36  1  5
  16P LOSS WILD-TYPE 79  2 26
D68V6, multiclass
    clus
vv   16P LOSS MUTATED 16P LOSS WILD-TYPE
  M0               36                 79
  M1                1                  2
  MX                5                 26
D68V7, binary
                    cls
clus                  0  1
  16P LOSS MUTATED   17 25
  16P LOSS WILD-TYPE 41 66
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED     17   25
  16P LOSS WILD-TYPE   41   66
        clus
vv       16P LOSS MUTATED 16P LOSS WILD-TYPE
  FEMALE               17                 41
  MALE                 25                 66
                    vv
clus                 R0 R1 R2 RX
  16P LOSS MUTATED   35  1  0  5
  16P LOSS WILD-TYPE 87 10  1  5
D68V8, multiclass
    clus
vv   16P LOSS MUTATED 16P LOSS WILD-TYPE
  R0               35                 87
  R1                1                 10
  R2                0                  1
  RX                5                  5

Clustering(69) Variable = 16Q LOSS MUTATION ANALYSIS
D69V1, survival
                    sevent
clus2                 0  1
  16Q LOSS MUTATED   28 23
  16Q LOSS WILD-TYPE 56 40
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                51                 96 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                23                 40 
$`16Q LOSS MUTATED`
TCGA-BC-A10S TCGA-BC-A10W TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KG TCGA-BC-A69H 
       46.78         2.99        44.42        13.84        22.36         3.95 
TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5263 TCGA-CC-A3MB TCGA-CC-A3MC 
        0.07         2.86         0.39         4.24         0.10         0.13 
TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A116 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A1EF 
       79.73        37.78        53.33         2.60         0.46        12.95 
TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A8 
       49.15         6.02        29.16         5.62        19.76         0.36 
TCGA-DD-A3A9 TCGA-DD-A4ND TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NN TCGA-DD-A4NO 
       30.61        73.38        14.24        18.44        29.56        61.45 
TCGA-DD-A4NQ TCGA-DD-A73B TCGA-ED-A459 TCGA-ED-A5KG TCGA-ED-A66X TCGA-ED-A66Y 
       12.26         9.30        13.41        15.85        13.35         0.23 
TCGA-ED-A7PY TCGA-EP-A2KB TCGA-ES-A2HS TCGA-FV-A23B TCGA-FV-A3I0 TCGA-FV-A3R2 
        0.20        10.98        22.85        32.45         0.20         6.38 
TCGA-G3-A25S TCGA-G3-A25U TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A3CH TCGA-G3-A5SI 
        1.22        53.79        58.49        14.86        25.64        14.70 
TCGA-MI-A75G TCGA-MI-A75I TCGA-O8-A75V 
       14.24         8.71         4.44 

$`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-BC-A69I TCGA-CC-5262 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA 
        9.50         0.53         3.39         3.32         0.10         0.07 
TCGA-DD-A115 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 
       83.57       113.00         7.33        21.76        51.29        90.71 
TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EG 
       79.40        66.31        19.79        75.65         6.71        45.11 
TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39X TCGA-DD-A3A0 TCGA-DD-A3A1 
       18.35        13.64        21.14        55.69        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-A4NA TCGA-DD-A4NB TCGA-DD-A4NF TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL 
       33.14        12.85        14.07        15.06        39.78        56.25 
TCGA-DD-A4NP TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73C 
       93.67         0.30        80.75        66.35        10.98         7.56 
TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G TCGA-ED-A4XI TCGA-ED-A627 
       10.98         1.45        27.72       100.96        12.69        13.91 
TCGA-ED-A7PX TCGA-ED-A7PZ TCGA-ED-A7XP TCGA-ED-A82E TCGA-EP-A12J TCGA-EP-A26S 
        0.20         0.20         0.20         0.20        18.74        19.99 
TCGA-EP-A2KA TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A2QR 
       11.74         0.62         9.96        11.93        14.40        19.10 
TCGA-FV-A3I1 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZP TCGA-FV-A4ZQ 
        8.12         0.13         0.03         0.33        60.36         0.39 
TCGA-G3-A25T TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CI 
       51.06        28.27        30.74        21.53        22.13         5.92 
TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SJ TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A6UC 
       19.53        19.23        11.97         7.99         4.37         7.76 
TCGA-GJ-A6C0 TCGA-K7-A6G5 TCGA-LG-A6GG TCGA-MI-A75C TCGA-MI-A75E TCGA-NI-A4U2 
        1.02         4.01         0.49         9.57         5.10        58.88 

  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
              0.07               0.03 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
             79.73             113.00 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
             13.41              14.73 
[1] "0.1 - 79.7 (13.4)"  "0.0 - 113.0 (14.7)"
        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-BC-A69H         TCGA-BC-A69I         TCGA-CC-5258 
  "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" 
        TCGA-CC-5260         TCGA-CC-5261         TCGA-CC-5262 
  "16Q LOSS MUTATED"   "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" 
        TCGA-CC-5263         TCGA-CC-A1HT         TCGA-CC-A3M9 
  "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CC-A3MA         TCGA-CC-A3MB         TCGA-CC-A3MC 
"16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED"   "16Q LOSS MUTATED" 
        TCGA-DD-A113         TCGA-DD-A114         TCGA-DD-A115 
  "16Q LOSS MUTATED"   "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" 
        TCGA-DD-A116         TCGA-DD-A118         TCGA-DD-A119 
  "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DD-A11A         TCGA-DD-A11B         TCGA-DD-A11C 
  "16Q LOSS MUTATED"   "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" 
        TCGA-DD-A11D         TCGA-DD-A1E9         TCGA-DD-A1EA 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DD-A1EB         TCGA-DD-A1EC         TCGA-DD-A1ED 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DD-A1EE         TCGA-DD-A1EF         TCGA-DD-A1EG 
"16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" 
        TCGA-DD-A1EH         TCGA-DD-A1EI         TCGA-DD-A1EJ 
  "16Q LOSS MUTATED"   "16Q LOSS MUTATED"   "16Q LOSS MUTATED" 
        TCGA-DD-A1EK         TCGA-DD-A1EL         TCGA-DD-A39V 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DD-A39X         TCGA-DD-A39Y         TCGA-DD-A39Z 
"16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED"   "16Q LOSS MUTATED" 
        TCGA-DD-A3A0         TCGA-DD-A3A1         TCGA-DD-A3A2 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DD-A3A3         TCGA-DD-A3A4         TCGA-DD-A3A5 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DD-A3A6         TCGA-DD-A3A7         TCGA-DD-A3A8 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" 
        TCGA-DD-A3A9         TCGA-DD-A4NA         TCGA-DD-A4NB 
  "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DD-A4ND         TCGA-DD-A4NF         TCGA-DD-A4NH 
  "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" 
        TCGA-DD-A4NI         TCGA-DD-A4NJ         TCGA-DD-A4NK 
  "16Q LOSS MUTATED" "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-DD-A4NR 
"16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" 
        TCGA-DD-A4NS         TCGA-DD-A4NV         TCGA-DD-A73A 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DD-A73B         TCGA-DD-A73C         TCGA-DD-A73D 
  "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DD-A73E         TCGA-DD-A73F         TCGA-DD-A73G 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-ED-A459         TCGA-ED-A4XI         TCGA-ED-A5KG 
  "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" 
        TCGA-ED-A627         TCGA-ED-A66X         TCGA-ED-A66Y 
"16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED"   "16Q LOSS MUTATED" 
        TCGA-ED-A7PX         TCGA-ED-A7PY         TCGA-ED-A7PZ 
"16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" 
        TCGA-ED-A7XP         TCGA-ED-A82E         TCGA-EP-A12J 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EP-A26S         TCGA-EP-A2KA         TCGA-EP-A2KB 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" 
        TCGA-EP-A2KC         TCGA-EP-A3JL         TCGA-EP-A3RK 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-ES-A2HS         TCGA-ES-A2HT         TCGA-FV-A23B 
  "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" 
        TCGA-FV-A2QR         TCGA-FV-A3I0         TCGA-FV-A3I1 
"16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" 
        TCGA-FV-A3R2         TCGA-FV-A3R3         TCGA-FV-A495 
  "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-FV-A496         TCGA-FV-A4ZP         TCGA-FV-A4ZQ 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-G3-A25S         TCGA-G3-A25T         TCGA-G3-A25U 
  "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" 
        TCGA-G3-A25V         TCGA-G3-A25W         TCGA-G3-A25X 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" 
        TCGA-G3-A25Y         TCGA-G3-A25Z         TCGA-G3-A3CG 
  "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-G3-A3CH         TCGA-G3-A3CI         TCGA-G3-A3CJ 
  "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-G3-A3CK         TCGA-G3-A5SI         TCGA-G3-A5SJ 
"16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" 
        TCGA-G3-A5SL         TCGA-G3-A5SM         TCGA-G3-A6UC 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-GJ-A6C0         TCGA-K7-A6G5         TCGA-LG-A6GG 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-MI-A75C         TCGA-MI-A75E         TCGA-MI-A75G 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" 
        TCGA-MI-A75I         TCGA-NI-A4U2         TCGA-O8-A75V 
  "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" 
        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-BC-A69H         TCGA-BC-A69I         TCGA-CC-5258 
  "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" 
        TCGA-CC-5260         TCGA-CC-5261         TCGA-CC-5262 
  "16Q LOSS MUTATED"   "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" 
        TCGA-CC-5263         TCGA-CC-A1HT         TCGA-CC-A3M9 
  "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CC-A3MA         TCGA-CC-A3MB         TCGA-CC-A3MC 
"16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED"   "16Q LOSS MUTATED" 
        TCGA-DD-A113         TCGA-DD-A114         TCGA-DD-A115 
  "16Q LOSS MUTATED"   "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" 
        TCGA-DD-A116         TCGA-DD-A118         TCGA-DD-A119 
  "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DD-A11A         TCGA-DD-A11B         TCGA-DD-A11C 
  "16Q LOSS MUTATED"   "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" 
        TCGA-DD-A11D         TCGA-DD-A1E9         TCGA-DD-A1EA 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DD-A1EB         TCGA-DD-A1EC         TCGA-DD-A1ED 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DD-A1EE         TCGA-DD-A1EF         TCGA-DD-A1EG 
"16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" 
        TCGA-DD-A1EH         TCGA-DD-A1EI         TCGA-DD-A1EJ 
  "16Q LOSS MUTATED"   "16Q LOSS MUTATED"   "16Q LOSS MUTATED" 
        TCGA-DD-A1EK         TCGA-DD-A1EL         TCGA-DD-A39V 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DD-A39X         TCGA-DD-A39Y         TCGA-DD-A39Z 
"16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED"   "16Q LOSS MUTATED" 
        TCGA-DD-A3A0         TCGA-DD-A3A1         TCGA-DD-A3A2 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DD-A3A3         TCGA-DD-A3A4         TCGA-DD-A3A5 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DD-A3A6         TCGA-DD-A3A7         TCGA-DD-A3A8 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" 
        TCGA-DD-A3A9         TCGA-DD-A4NA         TCGA-DD-A4NB 
  "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DD-A4ND         TCGA-DD-A4NF         TCGA-DD-A4NH 
  "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" 
        TCGA-DD-A4NI         TCGA-DD-A4NJ         TCGA-DD-A4NK 
  "16Q LOSS MUTATED" "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-DD-A4NR 
"16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" 
        TCGA-DD-A4NS         TCGA-DD-A4NV         TCGA-DD-A73A 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DD-A73B         TCGA-DD-A73C         TCGA-DD-A73D 
  "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DD-A73E         TCGA-DD-A73F         TCGA-DD-A73G 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-ED-A459         TCGA-ED-A4XI         TCGA-ED-A5KG 
  "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" 
        TCGA-ED-A627         TCGA-ED-A66X         TCGA-ED-A66Y 
"16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED"   "16Q LOSS MUTATED" 
        TCGA-ED-A7PX         TCGA-ED-A7PY         TCGA-ED-A7PZ 
"16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" 
        TCGA-ED-A7XP         TCGA-ED-A82E         TCGA-EP-A12J 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EP-A26S         TCGA-EP-A2KA         TCGA-EP-A2KB 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" 
        TCGA-EP-A2KC         TCGA-EP-A3JL         TCGA-EP-A3RK 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-ES-A2HS         TCGA-ES-A2HT         TCGA-FV-A23B 
  "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" 
        TCGA-FV-A2QR         TCGA-FV-A3I0         TCGA-FV-A3I1 
"16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" 
        TCGA-FV-A3R2         TCGA-FV-A3R3         TCGA-FV-A495 
  "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-FV-A496         TCGA-FV-A4ZP         TCGA-FV-A4ZQ 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-G3-A25S         TCGA-G3-A25T         TCGA-G3-A25U 
  "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" 
        TCGA-G3-A25V         TCGA-G3-A25W         TCGA-G3-A25X 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" 
        TCGA-G3-A25Y         TCGA-G3-A25Z         TCGA-G3-A3CG 
  "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-G3-A3CH         TCGA-G3-A3CI         TCGA-G3-A3CJ 
  "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-G3-A3CK         TCGA-G3-A5SI         TCGA-G3-A5SJ 
"16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" 
        TCGA-G3-A5SL         TCGA-G3-A5SM         TCGA-G3-A6UC 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-GJ-A6C0         TCGA-K7-A6G5         TCGA-LG-A6GG 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-MI-A75C         TCGA-MI-A75E         TCGA-MI-A75G 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" 
        TCGA-MI-A75I         TCGA-NI-A4U2         TCGA-O8-A75V 
  "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" 
        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-BC-A69H         TCGA-BC-A69I         TCGA-CC-5258 
  "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" 
        TCGA-CC-5260         TCGA-CC-5261         TCGA-CC-5262 
  "16Q LOSS MUTATED"   "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" 
        TCGA-CC-5263         TCGA-CC-A1HT         TCGA-CC-A3M9 
  "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CC-A3MA         TCGA-CC-A3MB         TCGA-CC-A3MC 
"16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED"   "16Q LOSS MUTATED" 
        TCGA-DD-A113         TCGA-DD-A114         TCGA-DD-A115 
  "16Q LOSS MUTATED"   "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" 
        TCGA-DD-A116         TCGA-DD-A118         TCGA-DD-A119 
  "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DD-A11A         TCGA-DD-A11B         TCGA-DD-A11C 
  "16Q LOSS MUTATED"   "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" 
        TCGA-DD-A11D         TCGA-DD-A1E9         TCGA-DD-A1EA 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DD-A1EB         TCGA-DD-A1EC         TCGA-DD-A1ED 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DD-A1EE         TCGA-DD-A1EF         TCGA-DD-A1EG 
"16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" 
        TCGA-DD-A1EH         TCGA-DD-A1EI         TCGA-DD-A1EJ 
  "16Q LOSS MUTATED"   "16Q LOSS MUTATED"   "16Q LOSS MUTATED" 
        TCGA-DD-A1EK         TCGA-DD-A1EL         TCGA-DD-A39V 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DD-A39X         TCGA-DD-A39Y         TCGA-DD-A39Z 
"16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED"   "16Q LOSS MUTATED" 
        TCGA-DD-A3A0         TCGA-DD-A3A1         TCGA-DD-A3A2 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DD-A3A3         TCGA-DD-A3A4         TCGA-DD-A3A5 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DD-A3A6         TCGA-DD-A3A7         TCGA-DD-A3A8 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" 
        TCGA-DD-A3A9         TCGA-DD-A4NA         TCGA-DD-A4NB 
  "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DD-A4ND         TCGA-DD-A4NF         TCGA-DD-A4NH 
  "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" 
        TCGA-DD-A4NI         TCGA-DD-A4NJ         TCGA-DD-A4NK 
  "16Q LOSS MUTATED" "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-DD-A4NR 
"16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" 
        TCGA-DD-A4NS         TCGA-DD-A4NV         TCGA-DD-A73A 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DD-A73B         TCGA-DD-A73C         TCGA-DD-A73D 
  "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DD-A73E         TCGA-DD-A73F         TCGA-DD-A73G 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-ED-A459         TCGA-ED-A4XI         TCGA-ED-A5KG 
  "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" 
        TCGA-ED-A627         TCGA-ED-A66X         TCGA-ED-A66Y 
"16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED"   "16Q LOSS MUTATED" 
        TCGA-ED-A7PX         TCGA-ED-A7PY         TCGA-ED-A7PZ 
"16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" 
        TCGA-ED-A7XP         TCGA-ED-A82E         TCGA-EP-A12J 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EP-A26S         TCGA-EP-A2KA         TCGA-EP-A2KB 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" 
        TCGA-EP-A2KC         TCGA-EP-A3JL         TCGA-EP-A3RK 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-ES-A2HS         TCGA-ES-A2HT         TCGA-FV-A23B 
  "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" 
        TCGA-FV-A2QR         TCGA-FV-A3I0         TCGA-FV-A3I1 
"16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" 
        TCGA-FV-A3R2         TCGA-FV-A3R3         TCGA-FV-A495 
  "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-FV-A496         TCGA-FV-A4ZP         TCGA-FV-A4ZQ 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-G3-A25S         TCGA-G3-A25T         TCGA-G3-A25U 
  "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" 
        TCGA-G3-A25V         TCGA-G3-A25W         TCGA-G3-A25X 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" 
        TCGA-G3-A25Y         TCGA-G3-A25Z         TCGA-G3-A3CG 
  "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-G3-A3CH         TCGA-G3-A3CI         TCGA-G3-A3CJ 
  "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-G3-A3CK         TCGA-G3-A5SI         TCGA-G3-A5SJ 
"16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" 
        TCGA-G3-A5SL         TCGA-G3-A5SM         TCGA-G3-A6UC 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-GJ-A6C0         TCGA-K7-A6G5         TCGA-LG-A6GG 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-MI-A75C         TCGA-MI-A75E         TCGA-MI-A75G 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" 
        TCGA-MI-A75I         TCGA-NI-A4U2         TCGA-O8-A75V 
  "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" 
[1] "hr=" "1.5"
D69V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  16Q LOSS MUTATED        16       19         1          9          1
  16Q LOSS WILD-TYPE      42       17         1         21          3
                    vv
clus                 STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  16Q LOSS MUTATED            2        0         1         1
  16Q LOSS WILD-TYPE          3        1         0         1
D69V3, multiclass
                    vv
clus                 T1 T2 T3 T4
  16Q LOSS MUTATED   18 20 12  3
  16Q LOSS WILD-TYPE 43 20 28  5
D69V4, multiclass
    clus
vv   16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  T1               18                 43
  T2               20                 20
  T3               12                 28
  T4                3                  5
D69V5, binary
                    cls
clus                  0  1
  16Q LOSS MUTATED   35  2
  16Q LOSS WILD-TYPE 62  1
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED     35    2
  16Q LOSS WILD-TYPE   62    1
   clus
vv  16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  0               35                 62
  1                2                  1
                    vv
clus                 M0 M1 MX
  16Q LOSS MUTATED   44  1  8
  16Q LOSS WILD-TYPE 71  2 23
D69V6, multiclass
    clus
vv   16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  M0               44                 71
  M1                1                  2
  MX                8                 23
D69V7, binary
                    cls
clus                  0  1
  16Q LOSS MUTATED   21 32
  16Q LOSS WILD-TYPE 37 59
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED     21   32
  16Q LOSS WILD-TYPE   37   59
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  FEMALE               21                 37
  MALE                 32                 59
                    vv
clus                 R0 R1 R2 RX
  16Q LOSS MUTATED   44  3  0  6
  16Q LOSS WILD-TYPE 78  8  1  4
D69V8, multiclass
    clus
vv   16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  R0               44                 78
  R1                3                  8
  R2                0                  1
  RX                6                  4

Clustering(70) Variable = 17P LOSS MUTATION ANALYSIS
D70V1, survival
                    sevent
clus2                 0  1
  17P LOSS MUTATED   39 34
  17P LOSS WILD-TYPE 45 29
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                73                 74 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                34                 29 
$`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        13.84         0.26        22.36         9.50 
TCGA-BC-A69H TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 
        3.95         0.07         2.86         0.39         3.39         4.24 
TCGA-CC-A1HT TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 
        3.32         0.10         0.13        83.57        53.33       113.00 
TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1EA TCGA-DD-A1EB 
        7.33         2.60        21.76        51.29        79.40        66.31 
TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A1EL 
       45.11        49.15         6.02        29.16        18.35        13.64 
TCGA-DD-A39Y TCGA-DD-A3A0 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A4NA 
        5.62        25.81        17.59        20.12       102.74        33.14 
TCGA-DD-A4NB TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NQ TCGA-DD-A73B 
       12.85        14.24        18.44        15.06        12.26         9.30 
TCGA-DD-A73E TCGA-ED-A459 TCGA-ED-A7PX TCGA-ED-A7PZ TCGA-ED-A82E TCGA-EP-A2KC 
        1.45        13.41         0.20         0.20         0.20         0.62 
TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A495 TCGA-G3-A25S TCGA-G3-A25U 
       32.45        19.10         0.20         0.03         1.22        53.79 
TCGA-G3-A25V TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CH TCGA-G3-A5SL TCGA-G3-A5SM 
       28.27        14.86        21.53        25.64         7.99         4.37 
TCGA-GJ-A6C0 TCGA-LG-A6GG TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75I TCGA-NI-A4U2 
        1.02         0.49         5.10        14.24         8.71        58.88 
TCGA-O8-A75V 
        4.44 

$`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-BC-A69I TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A11B 
        0.53         0.10         0.07        79.73        37.78         0.46 
TCGA-DD-A1E9 TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A39V 
       90.71        19.79        75.65         6.71        12.95        21.14 
TCGA-DD-A39X TCGA-DD-A39Z TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A6 TCGA-DD-A3A7 
       55.69        19.76         7.66        70.06       107.11        13.78 
TCGA-DD-A3A8 TCGA-DD-A3A9 TCGA-DD-A4ND TCGA-DD-A4NF TCGA-DD-A4NK TCGA-DD-A4NL 
        0.36        30.61        73.38        14.07        39.78        56.25 
TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV 
       29.56        61.45        93.67         0.30        80.75        66.35 
TCGA-DD-A73A TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73F TCGA-DD-A73G TCGA-ED-A4XI 
       10.98         7.56        10.98        27.72       100.96        12.69 
TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PY TCGA-ED-A7XP 
       15.85        13.91        13.35         0.23         0.20         0.20 
TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A3JL TCGA-EP-A3RK 
       18.74        19.99        11.74        10.98         9.96        11.93 
TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A496 
       22.85        14.40         8.12         6.38         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        51.06        30.74        58.49        22.13 
TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A6UC 
        5.92        19.53        19.23        14.70        11.97         7.76 
TCGA-K7-A6G5 TCGA-MI-A75C 
        4.01         9.57 

  17P LOSS MUTATED 17P LOSS WILD-TYPE 
              0.03               0.07 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
            113.00             107.11 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
            13.410             15.275 
[1] "0.0 - 113.0 (13.4)" "0.1 - 107.1 (15.3)"
        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-BC-A69H         TCGA-BC-A69I         TCGA-CC-5258 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-CC-5260         TCGA-CC-5261         TCGA-CC-5262 
  "17P LOSS MUTATED"   "17P LOSS MUTATED"   "17P LOSS MUTATED" 
        TCGA-CC-5263         TCGA-CC-A1HT         TCGA-CC-A3M9 
  "17P LOSS MUTATED"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-CC-A3MA         TCGA-CC-A3MB         TCGA-CC-A3MC 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED"   "17P LOSS MUTATED" 
        TCGA-DD-A113         TCGA-DD-A114         TCGA-DD-A115 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-DD-A116         TCGA-DD-A118         TCGA-DD-A119 
  "17P LOSS MUTATED"   "17P LOSS MUTATED"   "17P LOSS MUTATED" 
        TCGA-DD-A11A         TCGA-DD-A11B         TCGA-DD-A11C 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-DD-A11D         TCGA-DD-A1E9         TCGA-DD-A1EA 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-DD-A1EB         TCGA-DD-A1EC         TCGA-DD-A1ED 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-DD-A1EE         TCGA-DD-A1EF         TCGA-DD-A1EG 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-DD-A1EH         TCGA-DD-A1EI         TCGA-DD-A1EJ 
  "17P LOSS MUTATED"   "17P LOSS MUTATED"   "17P LOSS MUTATED" 
        TCGA-DD-A1EK         TCGA-DD-A1EL         TCGA-DD-A39V 
  "17P LOSS MUTATED"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-DD-A39X         TCGA-DD-A39Y         TCGA-DD-A39Z 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-DD-A3A0         TCGA-DD-A3A1         TCGA-DD-A3A2 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-DD-A3A3         TCGA-DD-A3A4         TCGA-DD-A3A5 
  "17P LOSS MUTATED"   "17P LOSS MUTATED"   "17P LOSS MUTATED" 
        TCGA-DD-A3A6         TCGA-DD-A3A7         TCGA-DD-A3A8 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-DD-A3A9         TCGA-DD-A4NA         TCGA-DD-A4NB 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED"   "17P LOSS MUTATED" 
        TCGA-DD-A4ND         TCGA-DD-A4NF         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 MUTATED"   "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-DD-A4NR 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-DD-A4NS         TCGA-DD-A4NV         TCGA-DD-A73A 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-DD-A73B         TCGA-DD-A73C         TCGA-DD-A73D 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-DD-A73E         TCGA-DD-A73F         TCGA-DD-A73G 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-ED-A459         TCGA-ED-A4XI         TCGA-ED-A5KG 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-ED-A627         TCGA-ED-A66X         TCGA-ED-A66Y 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-ED-A7PX         TCGA-ED-A7PY         TCGA-ED-A7PZ 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-ED-A7XP         TCGA-ED-A82E         TCGA-EP-A12J 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-EP-A26S         TCGA-EP-A2KA         TCGA-EP-A2KB 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-EP-A2KC         TCGA-EP-A3JL         TCGA-EP-A3RK 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-ES-A2HS         TCGA-ES-A2HT         TCGA-FV-A23B 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-FV-A2QR         TCGA-FV-A3I0         TCGA-FV-A3I1 
  "17P LOSS MUTATED"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-FV-A3R2         TCGA-FV-A3R3         TCGA-FV-A495 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-FV-A496         TCGA-FV-A4ZP         TCGA-FV-A4ZQ 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-G3-A25S         TCGA-G3-A25T         TCGA-G3-A25U 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-G3-A25V         TCGA-G3-A25W         TCGA-G3-A25X 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-G3-A25Y         TCGA-G3-A25Z         TCGA-G3-A3CG 
  "17P LOSS MUTATED"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-G3-A3CH         TCGA-G3-A3CI         TCGA-G3-A3CJ 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-G3-A3CK         TCGA-G3-A5SI         TCGA-G3-A5SJ 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-G3-A5SL         TCGA-G3-A5SM         TCGA-G3-A6UC 
  "17P LOSS MUTATED"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-GJ-A6C0         TCGA-K7-A6G5         TCGA-LG-A6GG 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-MI-A75C         TCGA-MI-A75E         TCGA-MI-A75G 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED"   "17P LOSS MUTATED" 
        TCGA-MI-A75I         TCGA-NI-A4U2         TCGA-O8-A75V 
  "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-BC-A69H         TCGA-BC-A69I         TCGA-CC-5258 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-CC-5260         TCGA-CC-5261         TCGA-CC-5262 
  "17P LOSS MUTATED"   "17P LOSS MUTATED"   "17P LOSS MUTATED" 
        TCGA-CC-5263         TCGA-CC-A1HT         TCGA-CC-A3M9 
  "17P LOSS MUTATED"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-CC-A3MA         TCGA-CC-A3MB         TCGA-CC-A3MC 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED"   "17P LOSS MUTATED" 
        TCGA-DD-A113         TCGA-DD-A114         TCGA-DD-A115 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-DD-A116         TCGA-DD-A118         TCGA-DD-A119 
  "17P LOSS MUTATED"   "17P LOSS MUTATED"   "17P LOSS MUTATED" 
        TCGA-DD-A11A         TCGA-DD-A11B         TCGA-DD-A11C 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-DD-A11D         TCGA-DD-A1E9         TCGA-DD-A1EA 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-DD-A1EB         TCGA-DD-A1EC         TCGA-DD-A1ED 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-DD-A1EE         TCGA-DD-A1EF         TCGA-DD-A1EG 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-DD-A1EH         TCGA-DD-A1EI         TCGA-DD-A1EJ 
  "17P LOSS MUTATED"   "17P LOSS MUTATED"   "17P LOSS MUTATED" 
        TCGA-DD-A1EK         TCGA-DD-A1EL         TCGA-DD-A39V 
  "17P LOSS MUTATED"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-DD-A39X         TCGA-DD-A39Y         TCGA-DD-A39Z 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-DD-A3A0         TCGA-DD-A3A1         TCGA-DD-A3A2 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-DD-A3A3         TCGA-DD-A3A4         TCGA-DD-A3A5 
  "17P LOSS MUTATED"   "17P LOSS MUTATED"   "17P LOSS MUTATED" 
        TCGA-DD-A3A6         TCGA-DD-A3A7         TCGA-DD-A3A8 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-DD-A3A9         TCGA-DD-A4NA         TCGA-DD-A4NB 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED"   "17P LOSS MUTATED" 
        TCGA-DD-A4ND         TCGA-DD-A4NF         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 MUTATED"   "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-DD-A4NR 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-DD-A4NS         TCGA-DD-A4NV         TCGA-DD-A73A 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-DD-A73B         TCGA-DD-A73C         TCGA-DD-A73D 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-DD-A73E         TCGA-DD-A73F         TCGA-DD-A73G 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-ED-A459         TCGA-ED-A4XI         TCGA-ED-A5KG 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-ED-A627         TCGA-ED-A66X         TCGA-ED-A66Y 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-ED-A7PX         TCGA-ED-A7PY         TCGA-ED-A7PZ 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-ED-A7XP         TCGA-ED-A82E         TCGA-EP-A12J 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-EP-A26S         TCGA-EP-A2KA         TCGA-EP-A2KB 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-EP-A2KC         TCGA-EP-A3JL         TCGA-EP-A3RK 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-ES-A2HS         TCGA-ES-A2HT         TCGA-FV-A23B 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-FV-A2QR         TCGA-FV-A3I0         TCGA-FV-A3I1 
  "17P LOSS MUTATED"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-FV-A3R2         TCGA-FV-A3R3         TCGA-FV-A495 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-FV-A496         TCGA-FV-A4ZP         TCGA-FV-A4ZQ 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-G3-A25S         TCGA-G3-A25T         TCGA-G3-A25U 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-G3-A25V         TCGA-G3-A25W         TCGA-G3-A25X 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-G3-A25Y         TCGA-G3-A25Z         TCGA-G3-A3CG 
  "17P LOSS MUTATED"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-G3-A3CH         TCGA-G3-A3CI         TCGA-G3-A3CJ 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-G3-A3CK         TCGA-G3-A5SI         TCGA-G3-A5SJ 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-G3-A5SL         TCGA-G3-A5SM         TCGA-G3-A6UC 
  "17P LOSS MUTATED"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-GJ-A6C0         TCGA-K7-A6G5         TCGA-LG-A6GG 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-MI-A75C         TCGA-MI-A75E         TCGA-MI-A75G 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED"   "17P LOSS MUTATED" 
        TCGA-MI-A75I         TCGA-NI-A4U2         TCGA-O8-A75V 
  "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-BC-A69H         TCGA-BC-A69I         TCGA-CC-5258 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-CC-5260         TCGA-CC-5261         TCGA-CC-5262 
  "17P LOSS MUTATED"   "17P LOSS MUTATED"   "17P LOSS MUTATED" 
        TCGA-CC-5263         TCGA-CC-A1HT         TCGA-CC-A3M9 
  "17P LOSS MUTATED"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-CC-A3MA         TCGA-CC-A3MB         TCGA-CC-A3MC 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED"   "17P LOSS MUTATED" 
        TCGA-DD-A113         TCGA-DD-A114         TCGA-DD-A115 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-DD-A116         TCGA-DD-A118         TCGA-DD-A119 
  "17P LOSS MUTATED"   "17P LOSS MUTATED"   "17P LOSS MUTATED" 
        TCGA-DD-A11A         TCGA-DD-A11B         TCGA-DD-A11C 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-DD-A11D         TCGA-DD-A1E9         TCGA-DD-A1EA 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-DD-A1EB         TCGA-DD-A1EC         TCGA-DD-A1ED 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-DD-A1EE         TCGA-DD-A1EF         TCGA-DD-A1EG 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-DD-A1EH         TCGA-DD-A1EI         TCGA-DD-A1EJ 
  "17P LOSS MUTATED"   "17P LOSS MUTATED"   "17P LOSS MUTATED" 
        TCGA-DD-A1EK         TCGA-DD-A1EL         TCGA-DD-A39V 
  "17P LOSS MUTATED"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-DD-A39X         TCGA-DD-A39Y         TCGA-DD-A39Z 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-DD-A3A0         TCGA-DD-A3A1         TCGA-DD-A3A2 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-DD-A3A3         TCGA-DD-A3A4         TCGA-DD-A3A5 
  "17P LOSS MUTATED"   "17P LOSS MUTATED"   "17P LOSS MUTATED" 
        TCGA-DD-A3A6         TCGA-DD-A3A7         TCGA-DD-A3A8 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-DD-A3A9         TCGA-DD-A4NA         TCGA-DD-A4NB 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED"   "17P LOSS MUTATED" 
        TCGA-DD-A4ND         TCGA-DD-A4NF         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 MUTATED"   "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-DD-A4NR 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-DD-A4NS         TCGA-DD-A4NV         TCGA-DD-A73A 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-DD-A73B         TCGA-DD-A73C         TCGA-DD-A73D 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-DD-A73E         TCGA-DD-A73F         TCGA-DD-A73G 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-ED-A459         TCGA-ED-A4XI         TCGA-ED-A5KG 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-ED-A627         TCGA-ED-A66X         TCGA-ED-A66Y 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-ED-A7PX         TCGA-ED-A7PY         TCGA-ED-A7PZ 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-ED-A7XP         TCGA-ED-A82E         TCGA-EP-A12J 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-EP-A26S         TCGA-EP-A2KA         TCGA-EP-A2KB 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-EP-A2KC         TCGA-EP-A3JL         TCGA-EP-A3RK 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-ES-A2HS         TCGA-ES-A2HT         TCGA-FV-A23B 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-FV-A2QR         TCGA-FV-A3I0         TCGA-FV-A3I1 
  "17P LOSS MUTATED"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-FV-A3R2         TCGA-FV-A3R3         TCGA-FV-A495 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-FV-A496         TCGA-FV-A4ZP         TCGA-FV-A4ZQ 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-G3-A25S         TCGA-G3-A25T         TCGA-G3-A25U 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-G3-A25V         TCGA-G3-A25W         TCGA-G3-A25X 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-G3-A25Y         TCGA-G3-A25Z         TCGA-G3-A3CG 
  "17P LOSS MUTATED"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-G3-A3CH         TCGA-G3-A3CI         TCGA-G3-A3CJ 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-G3-A3CK         TCGA-G3-A5SI         TCGA-G3-A5SJ 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-G3-A5SL         TCGA-G3-A5SM         TCGA-G3-A6UC 
  "17P LOSS MUTATED"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-GJ-A6C0         TCGA-K7-A6G5         TCGA-LG-A6GG 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-MI-A75C         TCGA-MI-A75E         TCGA-MI-A75G 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED"   "17P LOSS MUTATED" 
        TCGA-MI-A75I         TCGA-NI-A4U2         TCGA-O8-A75V 
  "17P LOSS MUTATED"   "17P LOSS MUTATED"   "17P LOSS MUTATED" 
[1] "hr=" "1.5"
D70V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  17P LOSS MUTATED        22       21         2         15          1
  17P LOSS WILD-TYPE      36       15         0         15          3
                    vv
clus                 STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  17P LOSS MUTATED            5        1         1         1
  17P LOSS WILD-TYPE          0        0         0         1
D70V3, multiclass
                    vv
clus                 T1 T2 T3 T4
  17P LOSS MUTATED   25 24 21  5
  17P LOSS WILD-TYPE 36 16 19  3
D70V4, multiclass
    clus
vv   17P LOSS MUTATED 17P LOSS WILD-TYPE
  T1               25                 36
  T2               24                 16
  T3               21                 19
  T4                5                  3
D70V5, binary
                    cls
clus                  0  1
  17P LOSS MUTATED   48  3
  17P LOSS WILD-TYPE 49  0
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED     48    3
  17P LOSS WILD-TYPE   49    0
   clus
vv  17P LOSS MUTATED 17P LOSS WILD-TYPE
  0               48                 49
  1                3                  0
                    vv
clus                 M0 M1 MX
  17P LOSS MUTATED   60  2 13
  17P LOSS WILD-TYPE 55  1 18
D70V6, multiclass
    clus
vv   17P LOSS MUTATED 17P LOSS WILD-TYPE
  M0               60                 55
  M1                2                  1
  MX               13                 18
D70V7, binary
                    cls
clus                  0  1
  17P LOSS MUTATED   27 48
  17P LOSS WILD-TYPE 31 43
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED     27   48
  17P LOSS WILD-TYPE   31   43
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  FEMALE               27                 31
  MALE                 48                 43
                    vv
clus                 R0 R1 R2 RX
  17P LOSS MUTATED   58  6  1  8
  17P LOSS WILD-TYPE 64  5  0  2
D70V8, multiclass
    clus
vv   17P LOSS MUTATED 17P LOSS WILD-TYPE
  R0               58                 64
  R1                6                  5
  R2                1                  0
  RX                8                  2

Clustering(71) Variable = 17Q LOSS MUTATION ANALYSIS
D71V1, survival
                    sevent
clus2                 0  1
  17Q LOSS MUTATED   13  5
  17Q LOSS WILD-TYPE 71 58
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                18                129 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                 5                 58 
$`17Q LOSS MUTATED`
TCGA-BC-A10R TCGA-BC-A5W4 TCGA-DD-A116 TCGA-DD-A1EB TCGA-DD-A1EG TCGA-DD-A1EJ 
       10.13         9.50        53.33        66.31        45.11        29.16 
TCGA-DD-A3A0 TCGA-DD-A4NB TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-ED-A7PX 
       25.81        12.85        14.24        18.44        15.06         0.20 
TCGA-ED-A7PZ TCGA-ED-A82E TCGA-FV-A3I0 TCGA-G3-A5SL TCGA-G3-A5SM TCGA-MI-A75G 
        0.20         0.20         0.20         7.99         4.37        14.24 

$`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-BC-A69H TCGA-BC-A69I 
       44.42        13.84         0.26        22.36         3.95         0.53 
TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A1HT 
        0.07         2.86         0.39         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        37.78 
TCGA-DD-A115 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C 
       83.57       113.00         7.33         2.60         0.46        21.76 
TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE 
       51.29        90.71        79.40        19.79        75.65         6.71 
TCGA-DD-A1EF TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V 
       12.95        49.15         6.02        18.35        13.64        21.14 
TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 
       55.69         5.62        19.76         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        30.61 
TCGA-DD-A4NA TCGA-DD-A4ND TCGA-DD-A4NF TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN 
       33.14        73.38        14.07        39.78        56.25        29.56 
TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV 
       61.45        93.67        12.26         0.30        80.75        66.35 
TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F 
       10.98         9.30         7.56        10.98         1.45        27.72 
TCGA-DD-A73G TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X 
      100.96        13.41        12.69        15.85        13.91        13.35 
TCGA-ED-A66Y TCGA-ED-A7PY TCGA-ED-A7XP TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA 
        0.23         0.20         0.20        18.74        19.99        11.74 
TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT 
       10.98         0.62         9.96        11.93        22.85        14.40 
TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 
       32.45        19.10         8.12         6.38         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        51.06        53.79 
TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG 
       28.27        30.74        58.49        14.86        21.53        22.13 
TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ 
       25.64         5.92        19.53        19.23        14.70        11.97 
TCGA-G3-A6UC TCGA-GJ-A6C0 TCGA-K7-A6G5 TCGA-LG-A6GG TCGA-MI-A75C TCGA-MI-A75E 
        7.76         1.02         4.01         0.49         9.57         5.10 
TCGA-MI-A75I TCGA-NI-A4U2 TCGA-O8-A75V 
        8.71        58.88         4.44 

  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
              0.20               0.03 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
             66.31             113.00 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
            13.545             14.070 
[1] "0.2 - 66.3 (13.5)"  "0.0 - 113.0 (14.1)"
        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-BC-A69H         TCGA-BC-A69I         TCGA-CC-5258 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-CC-5260         TCGA-CC-5261         TCGA-CC-5262 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-CC-5263         TCGA-CC-A1HT         TCGA-CC-A3M9 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-CC-A3MA         TCGA-CC-A3MB         TCGA-CC-A3MC 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DD-A113         TCGA-DD-A114         TCGA-DD-A115 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DD-A116         TCGA-DD-A118         TCGA-DD-A119 
  "17Q LOSS MUTATED" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DD-A11A         TCGA-DD-A11B         TCGA-DD-A11C 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DD-A11D         TCGA-DD-A1E9         TCGA-DD-A1EA 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DD-A1EB         TCGA-DD-A1EC         TCGA-DD-A1ED 
  "17Q LOSS MUTATED" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DD-A1EE         TCGA-DD-A1EF         TCGA-DD-A1EG 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE"   "17Q LOSS MUTATED" 
        TCGA-DD-A1EH         TCGA-DD-A1EI         TCGA-DD-A1EJ 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE"   "17Q LOSS MUTATED" 
        TCGA-DD-A1EK         TCGA-DD-A1EL         TCGA-DD-A39V 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DD-A39X         TCGA-DD-A39Y         TCGA-DD-A39Z 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DD-A3A0         TCGA-DD-A3A1         TCGA-DD-A3A2 
  "17Q LOSS MUTATED" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DD-A3A3         TCGA-DD-A3A4         TCGA-DD-A3A5 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DD-A3A6         TCGA-DD-A3A7         TCGA-DD-A3A8 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DD-A3A9         TCGA-DD-A4NA         TCGA-DD-A4NB 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE"   "17Q LOSS MUTATED" 
        TCGA-DD-A4ND         TCGA-DD-A4NF         TCGA-DD-A4NH 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE"   "17Q LOSS MUTATED" 
        TCGA-DD-A4NI         TCGA-DD-A4NJ         TCGA-DD-A4NK 
  "17Q LOSS MUTATED"   "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-DD-A4NR 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DD-A4NS         TCGA-DD-A4NV         TCGA-DD-A73A 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DD-A73B         TCGA-DD-A73C         TCGA-DD-A73D 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DD-A73E         TCGA-DD-A73F         TCGA-DD-A73G 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-ED-A459         TCGA-ED-A4XI         TCGA-ED-A5KG 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-ED-A627         TCGA-ED-A66X         TCGA-ED-A66Y 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-ED-A7PX         TCGA-ED-A7PY         TCGA-ED-A7PZ 
  "17Q LOSS MUTATED" "17Q LOSS WILD-TYPE"   "17Q LOSS MUTATED" 
        TCGA-ED-A7XP         TCGA-ED-A82E         TCGA-EP-A12J 
"17Q LOSS WILD-TYPE"   "17Q LOSS MUTATED" "17Q LOSS WILD-TYPE" 
        TCGA-EP-A26S         TCGA-EP-A2KA         TCGA-EP-A2KB 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EP-A2KC         TCGA-EP-A3JL         TCGA-EP-A3RK 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-ES-A2HS         TCGA-ES-A2HT         TCGA-FV-A23B 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-FV-A2QR         TCGA-FV-A3I0         TCGA-FV-A3I1 
"17Q LOSS WILD-TYPE"   "17Q LOSS MUTATED" "17Q LOSS WILD-TYPE" 
        TCGA-FV-A3R2         TCGA-FV-A3R3         TCGA-FV-A495 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-FV-A496         TCGA-FV-A4ZP         TCGA-FV-A4ZQ 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-G3-A25S         TCGA-G3-A25T         TCGA-G3-A25U 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-G3-A25V         TCGA-G3-A25W         TCGA-G3-A25X 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-G3-A25Y         TCGA-G3-A25Z         TCGA-G3-A3CG 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-G3-A3CH         TCGA-G3-A3CI         TCGA-G3-A3CJ 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-G3-A3CK         TCGA-G3-A5SI         TCGA-G3-A5SJ 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-G3-A5SL         TCGA-G3-A5SM         TCGA-G3-A6UC 
  "17Q LOSS MUTATED"   "17Q LOSS MUTATED" "17Q LOSS WILD-TYPE" 
        TCGA-GJ-A6C0         TCGA-K7-A6G5         TCGA-LG-A6GG 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-MI-A75C         TCGA-MI-A75E         TCGA-MI-A75G 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE"   "17Q LOSS MUTATED" 
        TCGA-MI-A75I         TCGA-NI-A4U2         TCGA-O8-A75V 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
  "17Q LOSS MUTATED" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-BC-A5W4 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE"   "17Q LOSS MUTATED" 
        TCGA-BC-A69H         TCGA-BC-A69I         TCGA-CC-5258 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-CC-5260         TCGA-CC-5261         TCGA-CC-5262 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-CC-5263         TCGA-CC-A1HT         TCGA-CC-A3M9 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-CC-A3MA         TCGA-CC-A3MB         TCGA-CC-A3MC 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DD-A113         TCGA-DD-A114         TCGA-DD-A115 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DD-A116         TCGA-DD-A118         TCGA-DD-A119 
  "17Q LOSS MUTATED" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DD-A11A         TCGA-DD-A11B         TCGA-DD-A11C 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DD-A11D         TCGA-DD-A1E9         TCGA-DD-A1EA 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DD-A1EB         TCGA-DD-A1EC         TCGA-DD-A1ED 
  "17Q LOSS MUTATED" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DD-A1EE         TCGA-DD-A1EF         TCGA-DD-A1EG 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE"   "17Q LOSS MUTATED" 
        TCGA-DD-A1EH         TCGA-DD-A1EI         TCGA-DD-A1EJ 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE"   "17Q LOSS MUTATED" 
        TCGA-DD-A1EK         TCGA-DD-A1EL         TCGA-DD-A39V 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DD-A39X         TCGA-DD-A39Y         TCGA-DD-A39Z 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DD-A3A0         TCGA-DD-A3A1         TCGA-DD-A3A2 
  "17Q LOSS MUTATED" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DD-A3A3         TCGA-DD-A3A4         TCGA-DD-A3A5 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DD-A3A6         TCGA-DD-A3A7         TCGA-DD-A3A8 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DD-A3A9         TCGA-DD-A4NA         TCGA-DD-A4NB 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE"   "17Q LOSS MUTATED" 
        TCGA-DD-A4ND         TCGA-DD-A4NF         TCGA-DD-A4NH 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE"   "17Q LOSS MUTATED" 
        TCGA-DD-A4NI         TCGA-DD-A4NJ         TCGA-DD-A4NK 
  "17Q LOSS MUTATED"   "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-DD-A4NR 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DD-A4NS         TCGA-DD-A4NV         TCGA-DD-A73A 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DD-A73B         TCGA-DD-A73C         TCGA-DD-A73D 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DD-A73E         TCGA-DD-A73F         TCGA-DD-A73G 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-ED-A459         TCGA-ED-A4XI         TCGA-ED-A5KG 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-ED-A627         TCGA-ED-A66X         TCGA-ED-A66Y 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-ED-A7PX         TCGA-ED-A7PY         TCGA-ED-A7PZ 
  "17Q LOSS MUTATED" "17Q LOSS WILD-TYPE"   "17Q LOSS MUTATED" 
        TCGA-ED-A7XP         TCGA-ED-A82E         TCGA-EP-A12J 
"17Q LOSS WILD-TYPE"   "17Q LOSS MUTATED" "17Q LOSS WILD-TYPE" 
        TCGA-EP-A26S         TCGA-EP-A2KA         TCGA-EP-A2KB 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EP-A2KC         TCGA-EP-A3JL         TCGA-EP-A3RK 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-ES-A2HS         TCGA-ES-A2HT         TCGA-FV-A23B 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-FV-A2QR         TCGA-FV-A3I0         TCGA-FV-A3I1 
"17Q LOSS WILD-TYPE"   "17Q LOSS MUTATED" "17Q LOSS WILD-TYPE" 
        TCGA-FV-A3R2         TCGA-FV-A3R3         TCGA-FV-A495 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-FV-A496         TCGA-FV-A4ZP         TCGA-FV-A4ZQ 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-G3-A25S         TCGA-G3-A25T         TCGA-G3-A25U 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-G3-A25V         TCGA-G3-A25W         TCGA-G3-A25X 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-G3-A25Y         TCGA-G3-A25Z         TCGA-G3-A3CG 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-G3-A3CH         TCGA-G3-A3CI         TCGA-G3-A3CJ 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-G3-A3CK         TCGA-G3-A5SI         TCGA-G3-A5SJ 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-G3-A5SL         TCGA-G3-A5SM         TCGA-G3-A6UC 
  "17Q LOSS MUTATED"   "17Q LOSS MUTATED" "17Q LOSS WILD-TYPE" 
        TCGA-GJ-A6C0         TCGA-K7-A6G5         TCGA-LG-A6GG 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-MI-A75C         TCGA-MI-A75E         TCGA-MI-A75G 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE"   "17Q LOSS MUTATED" 
        TCGA-MI-A75I         TCGA-NI-A4U2         TCGA-O8-A75V 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
  "17Q LOSS MUTATED" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-BC-A5W4 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE"   "17Q LOSS MUTATED" 
        TCGA-BC-A69H         TCGA-BC-A69I         TCGA-CC-5258 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-CC-5260         TCGA-CC-5261         TCGA-CC-5262 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-CC-5263         TCGA-CC-A1HT         TCGA-CC-A3M9 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-CC-A3MA         TCGA-CC-A3MB         TCGA-CC-A3MC 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DD-A113         TCGA-DD-A114         TCGA-DD-A115 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DD-A116         TCGA-DD-A118         TCGA-DD-A119 
  "17Q LOSS MUTATED" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DD-A11A         TCGA-DD-A11B         TCGA-DD-A11C 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DD-A11D         TCGA-DD-A1E9         TCGA-DD-A1EA 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DD-A1EB         TCGA-DD-A1EC         TCGA-DD-A1ED 
  "17Q LOSS MUTATED" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DD-A1EE         TCGA-DD-A1EF         TCGA-DD-A1EG 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE"   "17Q LOSS MUTATED" 
        TCGA-DD-A1EH         TCGA-DD-A1EI         TCGA-DD-A1EJ 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE"   "17Q LOSS MUTATED" 
        TCGA-DD-A1EK         TCGA-DD-A1EL         TCGA-DD-A39V 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DD-A39X         TCGA-DD-A39Y         TCGA-DD-A39Z 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DD-A3A0         TCGA-DD-A3A1         TCGA-DD-A3A2 
  "17Q LOSS MUTATED" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DD-A3A3         TCGA-DD-A3A4         TCGA-DD-A3A5 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DD-A3A6         TCGA-DD-A3A7         TCGA-DD-A3A8 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DD-A3A9         TCGA-DD-A4NA         TCGA-DD-A4NB 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE"   "17Q LOSS MUTATED" 
        TCGA-DD-A4ND         TCGA-DD-A4NF         TCGA-DD-A4NH 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE"   "17Q LOSS MUTATED" 
        TCGA-DD-A4NI         TCGA-DD-A4NJ         TCGA-DD-A4NK 
  "17Q LOSS MUTATED"   "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-DD-A4NR 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DD-A4NS         TCGA-DD-A4NV         TCGA-DD-A73A 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DD-A73B         TCGA-DD-A73C         TCGA-DD-A73D 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DD-A73E         TCGA-DD-A73F         TCGA-DD-A73G 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-ED-A459         TCGA-ED-A4XI         TCGA-ED-A5KG 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-ED-A627         TCGA-ED-A66X         TCGA-ED-A66Y 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-ED-A7PX         TCGA-ED-A7PY         TCGA-ED-A7PZ 
  "17Q LOSS MUTATED" "17Q LOSS WILD-TYPE"   "17Q LOSS MUTATED" 
        TCGA-ED-A7XP         TCGA-ED-A82E         TCGA-EP-A12J 
"17Q LOSS WILD-TYPE"   "17Q LOSS MUTATED" "17Q LOSS WILD-TYPE" 
        TCGA-EP-A26S         TCGA-EP-A2KA         TCGA-EP-A2KB 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EP-A2KC         TCGA-EP-A3JL         TCGA-EP-A3RK 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-ES-A2HS         TCGA-ES-A2HT         TCGA-FV-A23B 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-FV-A2QR         TCGA-FV-A3I0         TCGA-FV-A3I1 
"17Q LOSS WILD-TYPE"   "17Q LOSS MUTATED" "17Q LOSS WILD-TYPE" 
        TCGA-FV-A3R2         TCGA-FV-A3R3         TCGA-FV-A495 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-FV-A496         TCGA-FV-A4ZP         TCGA-FV-A4ZQ 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-G3-A25S         TCGA-G3-A25T         TCGA-G3-A25U 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-G3-A25V         TCGA-G3-A25W         TCGA-G3-A25X 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-G3-A25Y         TCGA-G3-A25Z         TCGA-G3-A3CG 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-G3-A3CH         TCGA-G3-A3CI         TCGA-G3-A3CJ 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-G3-A3CK         TCGA-G3-A5SI         TCGA-G3-A5SJ 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-G3-A5SL         TCGA-G3-A5SM         TCGA-G3-A6UC 
  "17Q LOSS MUTATED"   "17Q LOSS MUTATED" "17Q LOSS WILD-TYPE" 
        TCGA-GJ-A6C0         TCGA-K7-A6G5         TCGA-LG-A6GG 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-MI-A75C         TCGA-MI-A75E         TCGA-MI-A75G 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE"   "17Q LOSS MUTATED" 
        TCGA-MI-A75I         TCGA-NI-A4U2         TCGA-O8-A75V 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
[1] "hr=" "1.2"
D71V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  17Q LOSS MUTATED         4        7         0          4          1
  17Q LOSS WILD-TYPE      54       29         2         26          3
                    vv
clus                 STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  17Q LOSS MUTATED            1        0         1         0
  17Q LOSS WILD-TYPE          4        1         0         2
D71V3, multiclass
                    vv
clus                 T1 T2 T3 T4
  17Q LOSS MUTATED    6  7  6  0
  17Q LOSS WILD-TYPE 55 33 34  8
D71V4, multiclass
    clus
vv   17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  T1                6                 55
  T2                7                 33
  T3                6                 34
  T4                0                  8
D71V5, binary
                    cls
clus                  0  1
  17Q LOSS MUTATED    8  2
  17Q LOSS WILD-TYPE 89  1
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED      8    2
  17Q LOSS WILD-TYPE   89    1
   clus
vv  17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  0                8                 89
  1                2                  1
                    vv
clus                 M0 M1 MX
  17Q LOSS MUTATED   17  0  2
  17Q LOSS WILD-TYPE 98  3 29
D71V6, multiclass
    clus
vv   17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  M0               17                 98
  M1                0                  3
  MX                2                 29
D71V7, binary
                    cls
clus                  0  1
  17Q LOSS MUTATED    8 11
  17Q LOSS WILD-TYPE 50 80
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED      8   11
  17Q LOSS WILD-TYPE   50   80
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  FEMALE                8                 50
  MALE                 11                 80
                    vv
clus                  R0  R1  R2  RX
  17Q LOSS MUTATED    18   1   0   0
  17Q LOSS WILD-TYPE 104  10   1  10
D71V8, multiclass
    clus
vv   17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  R0               18                104
  R1                1                 10
  R2                0                  1
  RX                0                 10

Clustering(72) Variable = 18P LOSS MUTATION ANALYSIS
D72V1, survival
                    sevent
clus2                 0  1
  18P LOSS MUTATED   16 11
  18P LOSS WILD-TYPE 68 52
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                27                120 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                11                 52 
$`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        13.84         0.10       113.00         2.60 
TCGA-DD-A11B TCGA-DD-A1EF TCGA-DD-A1EJ TCGA-DD-A1EL TCGA-DD-A39X TCGA-DD-A39Y 
        0.46        12.95        29.16        13.64        55.69         5.62 
TCGA-DD-A3A4 TCGA-DD-A4NB TCGA-DD-A4NI TCGA-DD-A4NO TCGA-DD-A73E TCGA-DD-A73G 
       20.12        12.85        18.44        61.45         1.45       100.96 
TCGA-ED-A459 TCGA-ED-A7PX TCGA-ED-A7XP TCGA-ED-A82E TCGA-ES-A2HS TCGA-FV-A3I0 
       13.41         0.20         0.20         0.20        22.85         0.20 
TCGA-FV-A496 TCGA-G3-A25S TCGA-MI-A75G 
        0.33         1.22        14.24 

$`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-BC-A69H TCGA-BC-A69I TCGA-CC-5258 
        0.26        22.36         9.50         3.95         0.53         0.07 
TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3M9 
        2.86         0.39         3.39         4.24         3.32         0.10 
TCGA-CC-A3MA TCGA-CC-A3MC TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 
        0.07         0.13        79.73        37.78        83.57        53.33 
TCGA-DD-A119 TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB 
        7.33        21.76        51.29        90.71        79.40        66.31 
TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI 
       19.79        75.65         6.71        45.11        49.15         6.02 
TCGA-DD-A1EK TCGA-DD-A39V TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 
       18.35        21.14        19.76        25.81         7.66        70.06 
TCGA-DD-A3A3 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A3A9 
       17.59       102.74       107.11        13.78         0.36        30.61 
TCGA-DD-A4NA TCGA-DD-A4ND TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NJ TCGA-DD-A4NK 
       33.14        73.38        14.07        14.24        15.06        39.78 
TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS 
       56.25        29.56        93.67        12.26         0.30        80.75 
TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73F 
       66.35        10.98         9.30         7.56        10.98        27.72 
TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PY 
       12.69        15.85        13.91        13.35         0.23         0.20 
TCGA-ED-A7PZ TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC 
        0.20        18.74        19.99        11.74        10.98         0.62 
TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-A3I1 
        9.96        11.93        14.40        32.45        19.10         8.12 
TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25T 
        6.38         0.13         0.03        60.36         0.39        51.06 
TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A25Z 
       53.79        28.27        30.74        58.49        14.86        21.53 
TCGA-G3-A3CG TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI 
       22.13        25.64         5.92        19.53        19.23        14.70 
TCGA-G3-A5SJ TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A6UC TCGA-GJ-A6C0 TCGA-K7-A6G5 
       11.97         7.99         4.37         7.76         1.02         4.01 
TCGA-LG-A6GG TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75I TCGA-NI-A4U2 TCGA-O8-A75V 
        0.49         9.57         5.10         8.71        58.88         4.44 

  18P LOSS MUTATED 18P LOSS WILD-TYPE 
              0.10               0.03 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
            113.00             107.11 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
             12.85              14.96 
[1] "0.1 - 113.0 (12.8)" "0.0 - 107.1 (15.0)"
        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-BC-A69H         TCGA-BC-A69I         TCGA-CC-5258 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-CC-5260         TCGA-CC-5261         TCGA-CC-5262 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-CC-5263         TCGA-CC-A1HT         TCGA-CC-A3M9 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-CC-A3MA         TCGA-CC-A3MB         TCGA-CC-A3MC 
"18P LOSS WILD-TYPE"   "18P LOSS MUTATED" "18P LOSS WILD-TYPE" 
        TCGA-DD-A113         TCGA-DD-A114         TCGA-DD-A115 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-DD-A116         TCGA-DD-A118         TCGA-DD-A119 
"18P LOSS WILD-TYPE"   "18P LOSS MUTATED" "18P LOSS WILD-TYPE" 
        TCGA-DD-A11A         TCGA-DD-A11B         TCGA-DD-A11C 
  "18P LOSS MUTATED"   "18P LOSS MUTATED" "18P LOSS WILD-TYPE" 
        TCGA-DD-A11D         TCGA-DD-A1E9         TCGA-DD-A1EA 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-DD-A1EB         TCGA-DD-A1EC         TCGA-DD-A1ED 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-DD-A1EE         TCGA-DD-A1EF         TCGA-DD-A1EG 
"18P LOSS WILD-TYPE"   "18P LOSS MUTATED" "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-A1EK         TCGA-DD-A1EL         TCGA-DD-A39V 
"18P LOSS WILD-TYPE"   "18P LOSS MUTATED" "18P LOSS WILD-TYPE" 
        TCGA-DD-A39X         TCGA-DD-A39Y         TCGA-DD-A39Z 
  "18P LOSS MUTATED"   "18P LOSS MUTATED" "18P LOSS WILD-TYPE" 
        TCGA-DD-A3A0         TCGA-DD-A3A1         TCGA-DD-A3A2 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-DD-A3A3         TCGA-DD-A3A4         TCGA-DD-A3A5 
"18P LOSS WILD-TYPE"   "18P LOSS MUTATED" "18P LOSS WILD-TYPE" 
        TCGA-DD-A3A6         TCGA-DD-A3A7         TCGA-DD-A3A8 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-DD-A3A9         TCGA-DD-A4NA         TCGA-DD-A4NB 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE"   "18P LOSS MUTATED" 
        TCGA-DD-A4ND         TCGA-DD-A4NF         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 MUTATED" "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-DD-A4NR 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-DD-A4NS         TCGA-DD-A4NV         TCGA-DD-A73A 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-DD-A73B         TCGA-DD-A73C         TCGA-DD-A73D 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-DD-A73E         TCGA-DD-A73F         TCGA-DD-A73G 
  "18P LOSS MUTATED" "18P LOSS WILD-TYPE"   "18P LOSS MUTATED" 
        TCGA-ED-A459         TCGA-ED-A4XI         TCGA-ED-A5KG 
  "18P LOSS MUTATED" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-ED-A627         TCGA-ED-A66X         TCGA-ED-A66Y 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-ED-A7PX         TCGA-ED-A7PY         TCGA-ED-A7PZ 
  "18P LOSS MUTATED" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-ED-A7XP         TCGA-ED-A82E         TCGA-EP-A12J 
  "18P LOSS MUTATED"   "18P LOSS MUTATED" "18P LOSS WILD-TYPE" 
        TCGA-EP-A26S         TCGA-EP-A2KA         TCGA-EP-A2KB 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EP-A2KC         TCGA-EP-A3JL         TCGA-EP-A3RK 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-ES-A2HS         TCGA-ES-A2HT         TCGA-FV-A23B 
  "18P LOSS MUTATED" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-FV-A2QR         TCGA-FV-A3I0         TCGA-FV-A3I1 
"18P LOSS WILD-TYPE"   "18P LOSS MUTATED" "18P LOSS WILD-TYPE" 
        TCGA-FV-A3R2         TCGA-FV-A3R3         TCGA-FV-A495 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-FV-A496         TCGA-FV-A4ZP         TCGA-FV-A4ZQ 
  "18P LOSS MUTATED" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-G3-A25S         TCGA-G3-A25T         TCGA-G3-A25U 
  "18P LOSS MUTATED" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-G3-A25V         TCGA-G3-A25W         TCGA-G3-A25X 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-G3-A25Y         TCGA-G3-A25Z         TCGA-G3-A3CG 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-G3-A3CH         TCGA-G3-A3CI         TCGA-G3-A3CJ 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-G3-A3CK         TCGA-G3-A5SI         TCGA-G3-A5SJ 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-G3-A5SL         TCGA-G3-A5SM         TCGA-G3-A6UC 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-GJ-A6C0         TCGA-K7-A6G5         TCGA-LG-A6GG 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-MI-A75C         TCGA-MI-A75E         TCGA-MI-A75G 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE"   "18P LOSS MUTATED" 
        TCGA-MI-A75I         TCGA-NI-A4U2         TCGA-O8-A75V 
"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-BC-A69H         TCGA-BC-A69I         TCGA-CC-5258 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-CC-5260         TCGA-CC-5261         TCGA-CC-5262 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-CC-5263         TCGA-CC-A1HT         TCGA-CC-A3M9 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-CC-A3MA         TCGA-CC-A3MB         TCGA-CC-A3MC 
"18P LOSS WILD-TYPE"   "18P LOSS MUTATED" "18P LOSS WILD-TYPE" 
        TCGA-DD-A113         TCGA-DD-A114         TCGA-DD-A115 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-DD-A116         TCGA-DD-A118         TCGA-DD-A119 
"18P LOSS WILD-TYPE"   "18P LOSS MUTATED" "18P LOSS WILD-TYPE" 
        TCGA-DD-A11A         TCGA-DD-A11B         TCGA-DD-A11C 
  "18P LOSS MUTATED"   "18P LOSS MUTATED" "18P LOSS WILD-TYPE" 
        TCGA-DD-A11D         TCGA-DD-A1E9         TCGA-DD-A1EA 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-DD-A1EB         TCGA-DD-A1EC         TCGA-DD-A1ED 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-DD-A1EE         TCGA-DD-A1EF         TCGA-DD-A1EG 
"18P LOSS WILD-TYPE"   "18P LOSS MUTATED" "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-A1EK         TCGA-DD-A1EL         TCGA-DD-A39V 
"18P LOSS WILD-TYPE"   "18P LOSS MUTATED" "18P LOSS WILD-TYPE" 
        TCGA-DD-A39X         TCGA-DD-A39Y         TCGA-DD-A39Z 
  "18P LOSS MUTATED"   "18P LOSS MUTATED" "18P LOSS WILD-TYPE" 
        TCGA-DD-A3A0         TCGA-DD-A3A1         TCGA-DD-A3A2 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-DD-A3A3         TCGA-DD-A3A4         TCGA-DD-A3A5 
"18P LOSS WILD-TYPE"   "18P LOSS MUTATED" "18P LOSS WILD-TYPE" 
        TCGA-DD-A3A6         TCGA-DD-A3A7         TCGA-DD-A3A8 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-DD-A3A9         TCGA-DD-A4NA         TCGA-DD-A4NB 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE"   "18P LOSS MUTATED" 
        TCGA-DD-A4ND         TCGA-DD-A4NF         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 MUTATED" "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-DD-A4NR 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-DD-A4NS         TCGA-DD-A4NV         TCGA-DD-A73A 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-DD-A73B         TCGA-DD-A73C         TCGA-DD-A73D 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-DD-A73E         TCGA-DD-A73F         TCGA-DD-A73G 
  "18P LOSS MUTATED" "18P LOSS WILD-TYPE"   "18P LOSS MUTATED" 
        TCGA-ED-A459         TCGA-ED-A4XI         TCGA-ED-A5KG 
  "18P LOSS MUTATED" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-ED-A627         TCGA-ED-A66X         TCGA-ED-A66Y 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-ED-A7PX         TCGA-ED-A7PY         TCGA-ED-A7PZ 
  "18P LOSS MUTATED" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-ED-A7XP         TCGA-ED-A82E         TCGA-EP-A12J 
  "18P LOSS MUTATED"   "18P LOSS MUTATED" "18P LOSS WILD-TYPE" 
        TCGA-EP-A26S         TCGA-EP-A2KA         TCGA-EP-A2KB 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EP-A2KC         TCGA-EP-A3JL         TCGA-EP-A3RK 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-ES-A2HS         TCGA-ES-A2HT         TCGA-FV-A23B 
  "18P LOSS MUTATED" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-FV-A2QR         TCGA-FV-A3I0         TCGA-FV-A3I1 
"18P LOSS WILD-TYPE"   "18P LOSS MUTATED" "18P LOSS WILD-TYPE" 
        TCGA-FV-A3R2         TCGA-FV-A3R3         TCGA-FV-A495 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-FV-A496         TCGA-FV-A4ZP         TCGA-FV-A4ZQ 
  "18P LOSS MUTATED" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-G3-A25S         TCGA-G3-A25T         TCGA-G3-A25U 
  "18P LOSS MUTATED" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-G3-A25V         TCGA-G3-A25W         TCGA-G3-A25X 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-G3-A25Y         TCGA-G3-A25Z         TCGA-G3-A3CG 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-G3-A3CH         TCGA-G3-A3CI         TCGA-G3-A3CJ 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-G3-A3CK         TCGA-G3-A5SI         TCGA-G3-A5SJ 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-G3-A5SL         TCGA-G3-A5SM         TCGA-G3-A6UC 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-GJ-A6C0         TCGA-K7-A6G5         TCGA-LG-A6GG 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-MI-A75C         TCGA-MI-A75E         TCGA-MI-A75G 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE"   "18P LOSS MUTATED" 
        TCGA-MI-A75I         TCGA-NI-A4U2         TCGA-O8-A75V 
"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-BC-A69H         TCGA-BC-A69I         TCGA-CC-5258 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-CC-5260         TCGA-CC-5261         TCGA-CC-5262 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-CC-5263         TCGA-CC-A1HT         TCGA-CC-A3M9 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-CC-A3MA         TCGA-CC-A3MB         TCGA-CC-A3MC 
"18P LOSS WILD-TYPE"   "18P LOSS MUTATED" "18P LOSS WILD-TYPE" 
        TCGA-DD-A113         TCGA-DD-A114         TCGA-DD-A115 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-DD-A116         TCGA-DD-A118         TCGA-DD-A119 
"18P LOSS WILD-TYPE"   "18P LOSS MUTATED" "18P LOSS WILD-TYPE" 
        TCGA-DD-A11A         TCGA-DD-A11B         TCGA-DD-A11C 
  "18P LOSS MUTATED"   "18P LOSS MUTATED" "18P LOSS WILD-TYPE" 
        TCGA-DD-A11D         TCGA-DD-A1E9         TCGA-DD-A1EA 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-DD-A1EB         TCGA-DD-A1EC         TCGA-DD-A1ED 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-DD-A1EE         TCGA-DD-A1EF         TCGA-DD-A1EG 
"18P LOSS WILD-TYPE"   "18P LOSS MUTATED" "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-A1EK         TCGA-DD-A1EL         TCGA-DD-A39V 
"18P LOSS WILD-TYPE"   "18P LOSS MUTATED" "18P LOSS WILD-TYPE" 
        TCGA-DD-A39X         TCGA-DD-A39Y         TCGA-DD-A39Z 
  "18P LOSS MUTATED"   "18P LOSS MUTATED" "18P LOSS WILD-TYPE" 
        TCGA-DD-A3A0         TCGA-DD-A3A1         TCGA-DD-A3A2 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-DD-A3A3         TCGA-DD-A3A4         TCGA-DD-A3A5 
"18P LOSS WILD-TYPE"   "18P LOSS MUTATED" "18P LOSS WILD-TYPE" 
        TCGA-DD-A3A6         TCGA-DD-A3A7         TCGA-DD-A3A8 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-DD-A3A9         TCGA-DD-A4NA         TCGA-DD-A4NB 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE"   "18P LOSS MUTATED" 
        TCGA-DD-A4ND         TCGA-DD-A4NF         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 MUTATED" "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-DD-A4NR 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-DD-A4NS         TCGA-DD-A4NV         TCGA-DD-A73A 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-DD-A73B         TCGA-DD-A73C         TCGA-DD-A73D 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-DD-A73E         TCGA-DD-A73F         TCGA-DD-A73G 
  "18P LOSS MUTATED" "18P LOSS WILD-TYPE"   "18P LOSS MUTATED" 
        TCGA-ED-A459         TCGA-ED-A4XI         TCGA-ED-A5KG 
  "18P LOSS MUTATED" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-ED-A627         TCGA-ED-A66X         TCGA-ED-A66Y 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-ED-A7PX         TCGA-ED-A7PY         TCGA-ED-A7PZ 
  "18P LOSS MUTATED" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-ED-A7XP         TCGA-ED-A82E         TCGA-EP-A12J 
  "18P LOSS MUTATED"   "18P LOSS MUTATED" "18P LOSS WILD-TYPE" 
        TCGA-EP-A26S         TCGA-EP-A2KA         TCGA-EP-A2KB 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EP-A2KC         TCGA-EP-A3JL         TCGA-EP-A3RK 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-ES-A2HS         TCGA-ES-A2HT         TCGA-FV-A23B 
  "18P LOSS MUTATED" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-FV-A2QR         TCGA-FV-A3I0         TCGA-FV-A3I1 
"18P LOSS WILD-TYPE"   "18P LOSS MUTATED" "18P LOSS WILD-TYPE" 
        TCGA-FV-A3R2         TCGA-FV-A3R3         TCGA-FV-A495 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-FV-A496         TCGA-FV-A4ZP         TCGA-FV-A4ZQ 
  "18P LOSS MUTATED" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-G3-A25S         TCGA-G3-A25T         TCGA-G3-A25U 
  "18P LOSS MUTATED" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-G3-A25V         TCGA-G3-A25W         TCGA-G3-A25X 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-G3-A25Y         TCGA-G3-A25Z         TCGA-G3-A3CG 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-G3-A3CH         TCGA-G3-A3CI         TCGA-G3-A3CJ 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-G3-A3CK         TCGA-G3-A5SI         TCGA-G3-A5SJ 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-G3-A5SL         TCGA-G3-A5SM         TCGA-G3-A6UC 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-GJ-A6C0         TCGA-K7-A6G5         TCGA-LG-A6GG 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-MI-A75C         TCGA-MI-A75E         TCGA-MI-A75G 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE"   "18P LOSS MUTATED" 
        TCGA-MI-A75I         TCGA-NI-A4U2         TCGA-O8-A75V 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
[1] "hr=" "1.2"
D72V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  18P LOSS MUTATED        12        9         0          3          0
  18P LOSS WILD-TYPE      46       27         2         27          4
                    vv
clus                 STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  18P LOSS MUTATED            1        0         0         0
  18P LOSS WILD-TYPE          4        1         1         2
D72V3, multiclass
                    vv
clus                 T1 T2 T3 T4
  18P LOSS MUTATED   13  9  5  0
  18P LOSS WILD-TYPE 48 31 35  8
D72V4, multiclass
    clus
vv   18P LOSS MUTATED 18P LOSS WILD-TYPE
  T1               13                 48
  T2                9                 31
  T3                5                 35
  T4                0                  8
D72V5, binary
                    cls
clus                  0  1
  18P LOSS MUTATED   16  1
  18P LOSS WILD-TYPE 81  2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED     16    1
  18P LOSS WILD-TYPE   81    2
   clus
vv  18P LOSS MUTATED 18P LOSS WILD-TYPE
  0               16                 81
  1                1                  2
                    vv
clus                 M0 M1 MX
  18P LOSS MUTATED   24  0  3
  18P LOSS WILD-TYPE 91  3 28
D72V6, multiclass
    clus
vv   18P LOSS MUTATED 18P LOSS WILD-TYPE
  M0               24                 91
  M1                0                  3
  MX                3                 28
D72V7, binary
                    cls
clus                  0  1
  18P LOSS MUTATED   12 15
  18P LOSS WILD-TYPE 46 76
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED     12   15
  18P LOSS WILD-TYPE   46   76
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  FEMALE               12                 46
  MALE                 15                 76
                    vv
clus                 R0 R1 R2 RX
  18P LOSS MUTATED   25  1  0  1
  18P LOSS WILD-TYPE 97 10  1  9
D72V8, multiclass
    clus
vv   18P LOSS MUTATED 18P LOSS WILD-TYPE
  R0               25                 97
  R1                1                 10
  R2                0                  1
  RX                1                  9

Clustering(73) Variable = 18Q LOSS MUTATION ANALYSIS
D73V1, survival
                    sevent
clus2                 0  1
  18Q LOSS MUTATED   18 12
  18Q LOSS WILD-TYPE 66 51
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                30                117 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                12                 51 
$`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        13.84         0.10       113.00 
TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A1EF TCGA-DD-A1EJ TCGA-DD-A1EL TCGA-DD-A39X 
        2.60         0.46        12.95        29.16        13.64        55.69 
TCGA-DD-A39Y TCGA-DD-A3A9 TCGA-DD-A4NB TCGA-DD-A4NI TCGA-DD-A4NO TCGA-DD-A73B 
        5.62        30.61        12.85        18.44        61.45         9.30 
TCGA-DD-A73E TCGA-DD-A73G TCGA-ED-A459 TCGA-ED-A66X TCGA-ED-A7PX TCGA-ED-A7XP 
        1.45       100.96        13.41        13.35         0.20         0.20 
TCGA-ED-A82E TCGA-ES-A2HS TCGA-FV-A3I0 TCGA-FV-A496 TCGA-G3-A25S TCGA-MI-A75G 
        0.20        22.85         0.20         0.33         1.22        14.24 

$`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-BC-A69H TCGA-BC-A69I TCGA-CC-5258 TCGA-CC-5260 
       22.36         9.50         3.95         0.53         0.07         2.86 
TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA 
        0.39         3.39         4.24         3.32         0.10         0.07 
TCGA-CC-A3MC TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A119 
        0.13        79.73        37.78        83.57        53.33         7.33 
TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC 
       21.76        51.29        90.71        79.40        66.31        19.79 
TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EK 
       75.65         6.71        45.11        49.15         6.02        18.35 
TCGA-DD-A39V TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 
       21.14        19.76        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-A4NF TCGA-DD-A4NH TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL 
       73.38        14.07        14.24        15.06        39.78        56.25 
TCGA-DD-A4NN TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV 
       29.56        93.67        12.26         0.30        80.75        66.35 
TCGA-DD-A73A TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73F TCGA-ED-A4XI TCGA-ED-A5KG 
       10.98         7.56        10.98        27.72        12.69        15.85 
TCGA-ED-A627 TCGA-ED-A66Y TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-EP-A12J TCGA-EP-A26S 
       13.91         0.23         0.20         0.20        18.74        19.99 
TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HT 
       11.74        10.98         0.62         9.96        11.93        14.40 
TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 
       32.45        19.10         8.12         6.38         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        51.06        53.79        28.27        30.74 
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         5.92 
TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SL TCGA-G3-A5SM 
       19.53        19.23        14.70        11.97         7.99         4.37 
TCGA-G3-A6UC TCGA-GJ-A6C0 TCGA-K7-A6G5 TCGA-LG-A6GG TCGA-MI-A75C TCGA-MI-A75E 
        7.76         1.02         4.01         0.49         9.57         5.10 
TCGA-MI-A75I TCGA-NI-A4U2 TCGA-O8-A75V 
        8.71        58.88         4.44 

  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
              0.10               0.03 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
            113.00             107.11 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
             12.90              15.06 
[1] "0.1 - 113.0 (12.9)" "0.0 - 107.1 (15.1)"
        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-BC-A69H         TCGA-BC-A69I         TCGA-CC-5258 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-CC-5260         TCGA-CC-5261         TCGA-CC-5262 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-CC-5263         TCGA-CC-A1HT         TCGA-CC-A3M9 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-CC-A3MA         TCGA-CC-A3MB         TCGA-CC-A3MC 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" 
        TCGA-DD-A113         TCGA-DD-A114         TCGA-DD-A115 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-DD-A116         TCGA-DD-A118         TCGA-DD-A119 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" 
        TCGA-DD-A11A         TCGA-DD-A11B         TCGA-DD-A11C 
  "18Q LOSS MUTATED"   "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" 
        TCGA-DD-A11D         TCGA-DD-A1E9         TCGA-DD-A1EA 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-DD-A1EB         TCGA-DD-A1EC         TCGA-DD-A1ED 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-DD-A1EE         TCGA-DD-A1EF         TCGA-DD-A1EG 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" "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-A1EK         TCGA-DD-A1EL         TCGA-DD-A39V 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" 
        TCGA-DD-A39X         TCGA-DD-A39Y         TCGA-DD-A39Z 
  "18Q LOSS MUTATED"   "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" 
        TCGA-DD-A3A0         TCGA-DD-A3A1         TCGA-DD-A3A2 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-DD-A3A3         TCGA-DD-A3A4         TCGA-DD-A3A5 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-DD-A3A6         TCGA-DD-A3A7         TCGA-DD-A3A8 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-DD-A3A9         TCGA-DD-A4NA         TCGA-DD-A4NB 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" 
        TCGA-DD-A4ND         TCGA-DD-A4NF         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 MUTATED" "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-DD-A4NR 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-DD-A4NS         TCGA-DD-A4NV         TCGA-DD-A73A 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-DD-A73B         TCGA-DD-A73C         TCGA-DD-A73D 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-DD-A73E         TCGA-DD-A73F         TCGA-DD-A73G 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" 
        TCGA-ED-A459         TCGA-ED-A4XI         TCGA-ED-A5KG 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-ED-A627         TCGA-ED-A66X         TCGA-ED-A66Y 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" 
        TCGA-ED-A7PX         TCGA-ED-A7PY         TCGA-ED-A7PZ 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-ED-A7XP         TCGA-ED-A82E         TCGA-EP-A12J 
  "18Q LOSS MUTATED"   "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" 
        TCGA-EP-A26S         TCGA-EP-A2KA         TCGA-EP-A2KB 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EP-A2KC         TCGA-EP-A3JL         TCGA-EP-A3RK 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-ES-A2HS         TCGA-ES-A2HT         TCGA-FV-A23B 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-FV-A2QR         TCGA-FV-A3I0         TCGA-FV-A3I1 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" 
        TCGA-FV-A3R2         TCGA-FV-A3R3         TCGA-FV-A495 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-FV-A496         TCGA-FV-A4ZP         TCGA-FV-A4ZQ 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-G3-A25S         TCGA-G3-A25T         TCGA-G3-A25U 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-G3-A25V         TCGA-G3-A25W         TCGA-G3-A25X 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-G3-A25Y         TCGA-G3-A25Z         TCGA-G3-A3CG 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-G3-A3CH         TCGA-G3-A3CI         TCGA-G3-A3CJ 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-G3-A3CK         TCGA-G3-A5SI         TCGA-G3-A5SJ 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-G3-A5SL         TCGA-G3-A5SM         TCGA-G3-A6UC 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-GJ-A6C0         TCGA-K7-A6G5         TCGA-LG-A6GG 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-MI-A75C         TCGA-MI-A75E         TCGA-MI-A75G 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" 
        TCGA-MI-A75I         TCGA-NI-A4U2         TCGA-O8-A75V 
"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-BC-A69H         TCGA-BC-A69I         TCGA-CC-5258 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-CC-5260         TCGA-CC-5261         TCGA-CC-5262 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-CC-5263         TCGA-CC-A1HT         TCGA-CC-A3M9 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-CC-A3MA         TCGA-CC-A3MB         TCGA-CC-A3MC 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" 
        TCGA-DD-A113         TCGA-DD-A114         TCGA-DD-A115 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-DD-A116         TCGA-DD-A118         TCGA-DD-A119 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" 
        TCGA-DD-A11A         TCGA-DD-A11B         TCGA-DD-A11C 
  "18Q LOSS MUTATED"   "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" 
        TCGA-DD-A11D         TCGA-DD-A1E9         TCGA-DD-A1EA 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-DD-A1EB         TCGA-DD-A1EC         TCGA-DD-A1ED 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-DD-A1EE         TCGA-DD-A1EF         TCGA-DD-A1EG 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" "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-A1EK         TCGA-DD-A1EL         TCGA-DD-A39V 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" 
        TCGA-DD-A39X         TCGA-DD-A39Y         TCGA-DD-A39Z 
  "18Q LOSS MUTATED"   "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" 
        TCGA-DD-A3A0         TCGA-DD-A3A1         TCGA-DD-A3A2 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-DD-A3A3         TCGA-DD-A3A4         TCGA-DD-A3A5 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-DD-A3A6         TCGA-DD-A3A7         TCGA-DD-A3A8 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-DD-A3A9         TCGA-DD-A4NA         TCGA-DD-A4NB 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" 
        TCGA-DD-A4ND         TCGA-DD-A4NF         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 MUTATED" "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-DD-A4NR 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-DD-A4NS         TCGA-DD-A4NV         TCGA-DD-A73A 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-DD-A73B         TCGA-DD-A73C         TCGA-DD-A73D 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-DD-A73E         TCGA-DD-A73F         TCGA-DD-A73G 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" 
        TCGA-ED-A459         TCGA-ED-A4XI         TCGA-ED-A5KG 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-ED-A627         TCGA-ED-A66X         TCGA-ED-A66Y 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" 
        TCGA-ED-A7PX         TCGA-ED-A7PY         TCGA-ED-A7PZ 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-ED-A7XP         TCGA-ED-A82E         TCGA-EP-A12J 
  "18Q LOSS MUTATED"   "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" 
        TCGA-EP-A26S         TCGA-EP-A2KA         TCGA-EP-A2KB 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EP-A2KC         TCGA-EP-A3JL         TCGA-EP-A3RK 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-ES-A2HS         TCGA-ES-A2HT         TCGA-FV-A23B 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-FV-A2QR         TCGA-FV-A3I0         TCGA-FV-A3I1 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" 
        TCGA-FV-A3R2         TCGA-FV-A3R3         TCGA-FV-A495 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-FV-A496         TCGA-FV-A4ZP         TCGA-FV-A4ZQ 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-G3-A25S         TCGA-G3-A25T         TCGA-G3-A25U 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-G3-A25V         TCGA-G3-A25W         TCGA-G3-A25X 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-G3-A25Y         TCGA-G3-A25Z         TCGA-G3-A3CG 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-G3-A3CH         TCGA-G3-A3CI         TCGA-G3-A3CJ 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-G3-A3CK         TCGA-G3-A5SI         TCGA-G3-A5SJ 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-G3-A5SL         TCGA-G3-A5SM         TCGA-G3-A6UC 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-GJ-A6C0         TCGA-K7-A6G5         TCGA-LG-A6GG 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-MI-A75C         TCGA-MI-A75E         TCGA-MI-A75G 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" 
        TCGA-MI-A75I         TCGA-NI-A4U2         TCGA-O8-A75V 
"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-BC-A69H         TCGA-BC-A69I         TCGA-CC-5258 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-CC-5260         TCGA-CC-5261         TCGA-CC-5262 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-CC-5263         TCGA-CC-A1HT         TCGA-CC-A3M9 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-CC-A3MA         TCGA-CC-A3MB         TCGA-CC-A3MC 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" 
        TCGA-DD-A113         TCGA-DD-A114         TCGA-DD-A115 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-DD-A116         TCGA-DD-A118         TCGA-DD-A119 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" 
        TCGA-DD-A11A         TCGA-DD-A11B         TCGA-DD-A11C 
  "18Q LOSS MUTATED"   "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" 
        TCGA-DD-A11D         TCGA-DD-A1E9         TCGA-DD-A1EA 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-DD-A1EB         TCGA-DD-A1EC         TCGA-DD-A1ED 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-DD-A1EE         TCGA-DD-A1EF         TCGA-DD-A1EG 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" "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-A1EK         TCGA-DD-A1EL         TCGA-DD-A39V 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" 
        TCGA-DD-A39X         TCGA-DD-A39Y         TCGA-DD-A39Z 
  "18Q LOSS MUTATED"   "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" 
        TCGA-DD-A3A0         TCGA-DD-A3A1         TCGA-DD-A3A2 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-DD-A3A3         TCGA-DD-A3A4         TCGA-DD-A3A5 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-DD-A3A6         TCGA-DD-A3A7         TCGA-DD-A3A8 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-DD-A3A9         TCGA-DD-A4NA         TCGA-DD-A4NB 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" 
        TCGA-DD-A4ND         TCGA-DD-A4NF         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 MUTATED" "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-DD-A4NR 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-DD-A4NS         TCGA-DD-A4NV         TCGA-DD-A73A 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-DD-A73B         TCGA-DD-A73C         TCGA-DD-A73D 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-DD-A73E         TCGA-DD-A73F         TCGA-DD-A73G 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" 
        TCGA-ED-A459         TCGA-ED-A4XI         TCGA-ED-A5KG 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-ED-A627         TCGA-ED-A66X         TCGA-ED-A66Y 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" 
        TCGA-ED-A7PX         TCGA-ED-A7PY         TCGA-ED-A7PZ 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-ED-A7XP         TCGA-ED-A82E         TCGA-EP-A12J 
  "18Q LOSS MUTATED"   "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" 
        TCGA-EP-A26S         TCGA-EP-A2KA         TCGA-EP-A2KB 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EP-A2KC         TCGA-EP-A3JL         TCGA-EP-A3RK 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-ES-A2HS         TCGA-ES-A2HT         TCGA-FV-A23B 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-FV-A2QR         TCGA-FV-A3I0         TCGA-FV-A3I1 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" 
        TCGA-FV-A3R2         TCGA-FV-A3R3         TCGA-FV-A495 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-FV-A496         TCGA-FV-A4ZP         TCGA-FV-A4ZQ 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-G3-A25S         TCGA-G3-A25T         TCGA-G3-A25U 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-G3-A25V         TCGA-G3-A25W         TCGA-G3-A25X 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-G3-A25Y         TCGA-G3-A25Z         TCGA-G3-A3CG 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-G3-A3CH         TCGA-G3-A3CI         TCGA-G3-A3CJ 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-G3-A3CK         TCGA-G3-A5SI         TCGA-G3-A5SJ 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-G3-A5SL         TCGA-G3-A5SM         TCGA-G3-A6UC 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-GJ-A6C0         TCGA-K7-A6G5         TCGA-LG-A6GG 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-MI-A75C         TCGA-MI-A75E         TCGA-MI-A75G 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" 
        TCGA-MI-A75I         TCGA-NI-A4U2         TCGA-O8-A75V 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
[1] "hr=" "1.1"
D73V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  18Q LOSS MUTATED        13        9         0          4          0
  18Q LOSS WILD-TYPE      45       27         2         26          4
                    vv
clus                 STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  18Q LOSS MUTATED            1        0         0         1
  18Q LOSS WILD-TYPE          4        1         1         1
D73V3, multiclass
                    vv
clus                 T1 T2 T3 T4
  18Q LOSS MUTATED   14  9  6  1
  18Q LOSS WILD-TYPE 47 31 34  7
D73V4, multiclass
    clus
vv   18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  T1               14                 47
  T2                9                 31
  T3                6                 34
  T4                1                  7
D73V5, binary
                    cls
clus                  0  1
  18Q LOSS MUTATED   18  1
  18Q LOSS WILD-TYPE 79  2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED     18    1
  18Q LOSS WILD-TYPE   79    2
   clus
vv  18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  0               18                 79
  1                1                  2
                    vv
clus                 M0 M1 MX
  18Q LOSS MUTATED   26  1  3
  18Q LOSS WILD-TYPE 89  2 28
D73V6, multiclass
    clus
vv   18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  M0               26                 89
  M1                1                  2
  MX                3                 28
D73V7, binary
                    cls
clus                  0  1
  18Q LOSS MUTATED   15 15
  18Q LOSS WILD-TYPE 43 76
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED     15   15
  18Q LOSS WILD-TYPE   43   76
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  FEMALE               15                 43
  MALE                 15                 76
                    vv
clus                 R0 R1 R2 RX
  18Q LOSS MUTATED   28  1  0  1
  18Q LOSS WILD-TYPE 94 10  1  9
D73V8, multiclass
    clus
vv   18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  R0               28                 94
  R1                1                 10
  R2                0                  1
  RX                1                  9

Clustering(74) Variable = 19P LOSS MUTATION ANALYSIS
D74V1, survival
                    sevent
clus2                 0  1
  19P LOSS MUTATED    8  8
  19P LOSS WILD-TYPE 76 55
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                16                131 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                 8                 55 
$`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-A1EG TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A39Y TCGA-DD-A4NJ 
        2.60        45.11         6.02        29.16         5.62        15.06 
TCGA-FV-A496 TCGA-FV-A4ZP TCGA-G3-A25S TCGA-G3-A3CH 
        0.33        60.36         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-BC-A69H TCGA-BC-A69I TCGA-CC-5260 
       13.84        22.36         9.50         3.95         0.53         2.86 
TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC 
        0.39         3.39         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        37.78        83.57        53.33       113.00         7.33 
TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB 
        0.46        21.76        51.29        90.71        79.40        66.31 
TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EH TCGA-DD-A1EK 
       19.79        75.65         6.71        12.95        49.15        18.35 
TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39X TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 
       13.64        21.14        55.69        19.76        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-A4NB TCGA-DD-A4ND TCGA-DD-A4NF 
        0.36        30.61        33.14        12.85        73.38        14.07 
TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO 
       14.24        18.44        39.78        56.25        29.56        61.45 
TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A 
       93.67        12.26         0.30        80.75        66.35        10.98 
TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G 
        9.30         7.56        10.98         1.45        27.72       100.96 
TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y 
       13.41        12.69        15.85        13.91        13.35         0.23 
TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XP TCGA-ED-A82E TCGA-EP-A12J 
        0.20         0.20         0.20         0.20         0.20        18.74 
TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK 
       19.99        11.74        10.98         0.62         9.96        11.93 
TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3I1 
       22.85        14.40        32.45        19.10         0.20         8.12 
TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A4ZQ TCGA-G3-A25T TCGA-G3-A25U 
        6.38         0.13         0.03         0.39        51.06        53.79 
TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG 
       28.27        30.74        58.49        14.86        21.53        22.13 
TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SL 
        5.92        19.53        19.23        14.70        11.97         7.99 
TCGA-G3-A5SM TCGA-G3-A6UC TCGA-GJ-A6C0 TCGA-K7-A6G5 TCGA-LG-A6GG TCGA-MI-A75C 
        4.37         7.76         1.02         4.01         0.49         9.57 
TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75I TCGA-NI-A4U2 TCGA-O8-A75V 
        5.10        14.24         8.71        58.88         4.44 

  19P LOSS MUTATED 19P LOSS WILD-TYPE 
              0.07               0.03 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
             60.36             113.00 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
             4.635             14.400 
[1] "0.1 - 60.4 (4.6)"   "0.0 - 113.0 (14.4)"
        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-BC-A69H         TCGA-BC-A69I         TCGA-CC-5258 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE"   "19P LOSS MUTATED" 
        TCGA-CC-5260         TCGA-CC-5261         TCGA-CC-5262 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-CC-5263         TCGA-CC-A1HT         TCGA-CC-A3M9 
  "19P LOSS MUTATED"   "19P LOSS MUTATED" "19P LOSS WILD-TYPE" 
        TCGA-CC-A3MA         TCGA-CC-A3MB         TCGA-CC-A3MC 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DD-A113         TCGA-DD-A114         TCGA-DD-A115 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DD-A116         TCGA-DD-A118         TCGA-DD-A119 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DD-A11A         TCGA-DD-A11B         TCGA-DD-A11C 
  "19P LOSS MUTATED" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DD-A11D         TCGA-DD-A1E9         TCGA-DD-A1EA 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DD-A1EB         TCGA-DD-A1EC         TCGA-DD-A1ED 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DD-A1EE         TCGA-DD-A1EF         TCGA-DD-A1EG 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE"   "19P LOSS MUTATED" 
        TCGA-DD-A1EH         TCGA-DD-A1EI         TCGA-DD-A1EJ 
"19P LOSS WILD-TYPE"   "19P LOSS MUTATED"   "19P LOSS MUTATED" 
        TCGA-DD-A1EK         TCGA-DD-A1EL         TCGA-DD-A39V 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DD-A39X         TCGA-DD-A39Y         TCGA-DD-A39Z 
"19P LOSS WILD-TYPE"   "19P LOSS MUTATED" "19P LOSS WILD-TYPE" 
        TCGA-DD-A3A0         TCGA-DD-A3A1         TCGA-DD-A3A2 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DD-A3A3         TCGA-DD-A3A4         TCGA-DD-A3A5 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DD-A3A6         TCGA-DD-A3A7         TCGA-DD-A3A8 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DD-A3A9         TCGA-DD-A4NA         TCGA-DD-A4NB 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DD-A4ND         TCGA-DD-A4NF         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-DD-A4NR 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DD-A4NS         TCGA-DD-A4NV         TCGA-DD-A73A 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DD-A73B         TCGA-DD-A73C         TCGA-DD-A73D 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DD-A73E         TCGA-DD-A73F         TCGA-DD-A73G 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-ED-A459         TCGA-ED-A4XI         TCGA-ED-A5KG 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-ED-A627         TCGA-ED-A66X         TCGA-ED-A66Y 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-ED-A7PX         TCGA-ED-A7PY         TCGA-ED-A7PZ 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-ED-A7XP         TCGA-ED-A82E         TCGA-EP-A12J 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EP-A26S         TCGA-EP-A2KA         TCGA-EP-A2KB 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EP-A2KC         TCGA-EP-A3JL         TCGA-EP-A3RK 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-ES-A2HS         TCGA-ES-A2HT         TCGA-FV-A23B 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-FV-A2QR         TCGA-FV-A3I0         TCGA-FV-A3I1 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-FV-A3R2         TCGA-FV-A3R3         TCGA-FV-A495 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-FV-A496         TCGA-FV-A4ZP         TCGA-FV-A4ZQ 
  "19P LOSS MUTATED"   "19P LOSS MUTATED" "19P LOSS WILD-TYPE" 
        TCGA-G3-A25S         TCGA-G3-A25T         TCGA-G3-A25U 
  "19P LOSS MUTATED" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-G3-A25V         TCGA-G3-A25W         TCGA-G3-A25X 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-G3-A25Y         TCGA-G3-A25Z         TCGA-G3-A3CG 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-G3-A3CH         TCGA-G3-A3CI         TCGA-G3-A3CJ 
  "19P LOSS MUTATED" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-G3-A3CK         TCGA-G3-A5SI         TCGA-G3-A5SJ 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-G3-A5SL         TCGA-G3-A5SM         TCGA-G3-A6UC 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-GJ-A6C0         TCGA-K7-A6G5         TCGA-LG-A6GG 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-MI-A75C         TCGA-MI-A75E         TCGA-MI-A75G 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-MI-A75I         TCGA-NI-A4U2         TCGA-O8-A75V 
"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-BC-A69H         TCGA-BC-A69I         TCGA-CC-5258 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE"   "19P LOSS MUTATED" 
        TCGA-CC-5260         TCGA-CC-5261         TCGA-CC-5262 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-CC-5263         TCGA-CC-A1HT         TCGA-CC-A3M9 
  "19P LOSS MUTATED"   "19P LOSS MUTATED" "19P LOSS WILD-TYPE" 
        TCGA-CC-A3MA         TCGA-CC-A3MB         TCGA-CC-A3MC 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DD-A113         TCGA-DD-A114         TCGA-DD-A115 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DD-A116         TCGA-DD-A118         TCGA-DD-A119 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DD-A11A         TCGA-DD-A11B         TCGA-DD-A11C 
  "19P LOSS MUTATED" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DD-A11D         TCGA-DD-A1E9         TCGA-DD-A1EA 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DD-A1EB         TCGA-DD-A1EC         TCGA-DD-A1ED 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DD-A1EE         TCGA-DD-A1EF         TCGA-DD-A1EG 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE"   "19P LOSS MUTATED" 
        TCGA-DD-A1EH         TCGA-DD-A1EI         TCGA-DD-A1EJ 
"19P LOSS WILD-TYPE"   "19P LOSS MUTATED"   "19P LOSS MUTATED" 
        TCGA-DD-A1EK         TCGA-DD-A1EL         TCGA-DD-A39V 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DD-A39X         TCGA-DD-A39Y         TCGA-DD-A39Z 
"19P LOSS WILD-TYPE"   "19P LOSS MUTATED" "19P LOSS WILD-TYPE" 
        TCGA-DD-A3A0         TCGA-DD-A3A1         TCGA-DD-A3A2 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DD-A3A3         TCGA-DD-A3A4         TCGA-DD-A3A5 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DD-A3A6         TCGA-DD-A3A7         TCGA-DD-A3A8 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DD-A3A9         TCGA-DD-A4NA         TCGA-DD-A4NB 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DD-A4ND         TCGA-DD-A4NF         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-DD-A4NR 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DD-A4NS         TCGA-DD-A4NV         TCGA-DD-A73A 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DD-A73B         TCGA-DD-A73C         TCGA-DD-A73D 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DD-A73E         TCGA-DD-A73F         TCGA-DD-A73G 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-ED-A459         TCGA-ED-A4XI         TCGA-ED-A5KG 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-ED-A627         TCGA-ED-A66X         TCGA-ED-A66Y 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-ED-A7PX         TCGA-ED-A7PY         TCGA-ED-A7PZ 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-ED-A7XP         TCGA-ED-A82E         TCGA-EP-A12J 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EP-A26S         TCGA-EP-A2KA         TCGA-EP-A2KB 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EP-A2KC         TCGA-EP-A3JL         TCGA-EP-A3RK 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-ES-A2HS         TCGA-ES-A2HT         TCGA-FV-A23B 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-FV-A2QR         TCGA-FV-A3I0         TCGA-FV-A3I1 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-FV-A3R2         TCGA-FV-A3R3         TCGA-FV-A495 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-FV-A496         TCGA-FV-A4ZP         TCGA-FV-A4ZQ 
  "19P LOSS MUTATED"   "19P LOSS MUTATED" "19P LOSS WILD-TYPE" 
        TCGA-G3-A25S         TCGA-G3-A25T         TCGA-G3-A25U 
  "19P LOSS MUTATED" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-G3-A25V         TCGA-G3-A25W         TCGA-G3-A25X 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-G3-A25Y         TCGA-G3-A25Z         TCGA-G3-A3CG 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-G3-A3CH         TCGA-G3-A3CI         TCGA-G3-A3CJ 
  "19P LOSS MUTATED" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-G3-A3CK         TCGA-G3-A5SI         TCGA-G3-A5SJ 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-G3-A5SL         TCGA-G3-A5SM         TCGA-G3-A6UC 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-GJ-A6C0         TCGA-K7-A6G5         TCGA-LG-A6GG 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-MI-A75C         TCGA-MI-A75E         TCGA-MI-A75G 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-MI-A75I         TCGA-NI-A4U2         TCGA-O8-A75V 
"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-BC-A69H         TCGA-BC-A69I         TCGA-CC-5258 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE"   "19P LOSS MUTATED" 
        TCGA-CC-5260         TCGA-CC-5261         TCGA-CC-5262 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-CC-5263         TCGA-CC-A1HT         TCGA-CC-A3M9 
  "19P LOSS MUTATED"   "19P LOSS MUTATED" "19P LOSS WILD-TYPE" 
        TCGA-CC-A3MA         TCGA-CC-A3MB         TCGA-CC-A3MC 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DD-A113         TCGA-DD-A114         TCGA-DD-A115 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DD-A116         TCGA-DD-A118         TCGA-DD-A119 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DD-A11A         TCGA-DD-A11B         TCGA-DD-A11C 
  "19P LOSS MUTATED" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DD-A11D         TCGA-DD-A1E9         TCGA-DD-A1EA 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DD-A1EB         TCGA-DD-A1EC         TCGA-DD-A1ED 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DD-A1EE         TCGA-DD-A1EF         TCGA-DD-A1EG 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE"   "19P LOSS MUTATED" 
        TCGA-DD-A1EH         TCGA-DD-A1EI         TCGA-DD-A1EJ 
"19P LOSS WILD-TYPE"   "19P LOSS MUTATED"   "19P LOSS MUTATED" 
        TCGA-DD-A1EK         TCGA-DD-A1EL         TCGA-DD-A39V 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DD-A39X         TCGA-DD-A39Y         TCGA-DD-A39Z 
"19P LOSS WILD-TYPE"   "19P LOSS MUTATED" "19P LOSS WILD-TYPE" 
        TCGA-DD-A3A0         TCGA-DD-A3A1         TCGA-DD-A3A2 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DD-A3A3         TCGA-DD-A3A4         TCGA-DD-A3A5 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DD-A3A6         TCGA-DD-A3A7         TCGA-DD-A3A8 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DD-A3A9         TCGA-DD-A4NA         TCGA-DD-A4NB 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DD-A4ND         TCGA-DD-A4NF         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-DD-A4NR 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DD-A4NS         TCGA-DD-A4NV         TCGA-DD-A73A 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DD-A73B         TCGA-DD-A73C         TCGA-DD-A73D 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DD-A73E         TCGA-DD-A73F         TCGA-DD-A73G 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-ED-A459         TCGA-ED-A4XI         TCGA-ED-A5KG 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-ED-A627         TCGA-ED-A66X         TCGA-ED-A66Y 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-ED-A7PX         TCGA-ED-A7PY         TCGA-ED-A7PZ 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-ED-A7XP         TCGA-ED-A82E         TCGA-EP-A12J 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EP-A26S         TCGA-EP-A2KA         TCGA-EP-A2KB 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EP-A2KC         TCGA-EP-A3JL         TCGA-EP-A3RK 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-ES-A2HS         TCGA-ES-A2HT         TCGA-FV-A23B 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-FV-A2QR         TCGA-FV-A3I0         TCGA-FV-A3I1 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-FV-A3R2         TCGA-FV-A3R3         TCGA-FV-A495 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-FV-A496         TCGA-FV-A4ZP         TCGA-FV-A4ZQ 
  "19P LOSS MUTATED"   "19P LOSS MUTATED" "19P LOSS WILD-TYPE" 
        TCGA-G3-A25S         TCGA-G3-A25T         TCGA-G3-A25U 
  "19P LOSS MUTATED" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-G3-A25V         TCGA-G3-A25W         TCGA-G3-A25X 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-G3-A25Y         TCGA-G3-A25Z         TCGA-G3-A3CG 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-G3-A3CH         TCGA-G3-A3CI         TCGA-G3-A3CJ 
  "19P LOSS MUTATED" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-G3-A3CK         TCGA-G3-A5SI         TCGA-G3-A5SJ 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-G3-A5SL         TCGA-G3-A5SM         TCGA-G3-A6UC 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-GJ-A6C0         TCGA-K7-A6G5         TCGA-LG-A6GG 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-MI-A75C         TCGA-MI-A75E         TCGA-MI-A75G 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-MI-A75I         TCGA-NI-A4U2         TCGA-O8-A75V 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
[1] "hr=" "2.3"
D74V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  19P LOSS MUTATED         7        2         0          4          0
  19P LOSS WILD-TYPE      51       34         2         26          4
                    vv
clus                 STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  19P LOSS MUTATED            1        0         0         0
  19P LOSS WILD-TYPE          4        1         1         2
D74V3, multiclass
                    vv
clus                 T1 T2 T3 T4
  19P LOSS MUTATED    8  2  5  1
  19P LOSS WILD-TYPE 53 38 35  7
D74V4, multiclass
    clus
vv   19P LOSS MUTATED 19P LOSS WILD-TYPE
  T1                8                 53
  T2                2                 38
  T3                5                 35
  T4                1                  7
D74V5, binary
                    cls
clus                  0  1
  19P LOSS MUTATED    9  1
  19P LOSS WILD-TYPE 88  2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED      9    1
  19P LOSS WILD-TYPE   88    2
   clus
vv  19P LOSS MUTATED 19P LOSS WILD-TYPE
  0                9                 88
  1                1                  2
                    vv
clus                  M0  M1  MX
  19P LOSS MUTATED    14   0   2
  19P LOSS WILD-TYPE 101   3  29
D74V6, multiclass
    clus
vv   19P LOSS MUTATED 19P LOSS WILD-TYPE
  M0               14                101
  M1                0                  3
  MX                2                 29
D74V7, binary
                    cls
clus                  0  1
  19P LOSS MUTATED    4 12
  19P LOSS WILD-TYPE 54 79
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED      4   12
  19P LOSS WILD-TYPE   54   79
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  FEMALE                4                 54
  MALE                 12                 79
                    vv
clus                  R0  R1  R2  RX
  19P LOSS MUTATED    10   3   0   2
  19P LOSS WILD-TYPE 112   8   1   8
D74V8, multiclass
    clus
vv   19P LOSS MUTATED 19P LOSS WILD-TYPE
  R0               10                112
  R1                3                  8
  R2                0                  1
  RX                2                  8

Clustering(75) Variable = 19Q LOSS MUTATION ANALYSIS
D75V1, survival
                    sevent
clus2                 0  1
  19Q LOSS MUTATED    6  5
  19Q LOSS WILD-TYPE 78 58
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                11                136 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                 5                 58 
$`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-A39Y TCGA-DD-A4NJ TCGA-FV-A4ZP 
        6.02        29.16         5.62        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-BC-A69H TCGA-BC-A69I 
       44.42        13.84        22.36         9.50         3.95         0.53 
TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB 
        2.86         0.39         3.39         0.10         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        37.78        83.57        53.33       113.00 
TCGA-DD-A119 TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA 
        7.33         0.46        21.76        51.29        90.71        79.40 
TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EG 
       66.31        19.79        75.65         6.71        12.95        45.11 
TCGA-DD-A1EH TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39X TCGA-DD-A39Z 
       49.15        18.35        13.64        21.14        55.69        19.76 
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-A4NB 
      107.11        13.78         0.36        30.61        33.14        12.85 
TCGA-DD-A4ND TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NK TCGA-DD-A4NL 
       73.38        14.07        14.24        18.44        39.78        56.25 
TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS 
       29.56        61.45        93.67        12.26         0.30        80.75 
TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E 
       66.35        10.98         9.30         7.56        10.98         1.45 
TCGA-DD-A73F TCGA-DD-A73G TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 
       27.72       100.96        13.41        12.69        15.85        13.91 
TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XP 
       13.35         0.23         0.20         0.20         0.20         0.20 
TCGA-ED-A82E TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC 
        0.20        18.74        19.99        11.74        10.98         0.62 
TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QR 
        9.96        11.93        22.85        14.40        32.45        19.10 
TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 
        0.20         8.12         6.38         0.13         0.03         0.33 
TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W 
        0.39         1.22        51.06        53.79        28.27        30.74 
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         5.92 
TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SL TCGA-G3-A5SM 
       19.53        19.23        14.70        11.97         7.99         4.37 
TCGA-G3-A6UC TCGA-GJ-A6C0 TCGA-K7-A6G5 TCGA-LG-A6GG TCGA-MI-A75C TCGA-MI-A75E 
        7.76         1.02         4.01         0.49         9.57         5.10 
TCGA-MI-A75G TCGA-MI-A75I TCGA-NI-A4U2 TCGA-O8-A75V 
       14.24         8.71        58.88         4.44 

  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
              0.07               0.03 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
             60.36             113.00 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
              5.03              14.32 
[1] "0.1 - 60.4 (5.0)"   "0.0 - 113.0 (14.3)"
        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-BC-A69H         TCGA-BC-A69I         TCGA-CC-5258 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE"   "19Q LOSS MUTATED" 
        TCGA-CC-5260         TCGA-CC-5261         TCGA-CC-5262 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-CC-5263         TCGA-CC-A1HT         TCGA-CC-A3M9 
  "19Q LOSS MUTATED"   "19Q LOSS MUTATED" "19Q LOSS WILD-TYPE" 
        TCGA-CC-A3MA         TCGA-CC-A3MB         TCGA-CC-A3MC 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DD-A113         TCGA-DD-A114         TCGA-DD-A115 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DD-A116         TCGA-DD-A118         TCGA-DD-A119 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DD-A11A         TCGA-DD-A11B         TCGA-DD-A11C 
  "19Q LOSS MUTATED" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DD-A11D         TCGA-DD-A1E9         TCGA-DD-A1EA 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DD-A1EB         TCGA-DD-A1EC         TCGA-DD-A1ED 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DD-A1EE         TCGA-DD-A1EF         TCGA-DD-A1EG 
"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-A1EK         TCGA-DD-A1EL         TCGA-DD-A39V 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DD-A39X         TCGA-DD-A39Y         TCGA-DD-A39Z 
"19Q LOSS WILD-TYPE"   "19Q LOSS MUTATED" "19Q LOSS WILD-TYPE" 
        TCGA-DD-A3A0         TCGA-DD-A3A1         TCGA-DD-A3A2 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DD-A3A3         TCGA-DD-A3A4         TCGA-DD-A3A5 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DD-A3A6         TCGA-DD-A3A7         TCGA-DD-A3A8 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DD-A3A9         TCGA-DD-A4NA         TCGA-DD-A4NB 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DD-A4ND         TCGA-DD-A4NF         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-DD-A4NR 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DD-A4NS         TCGA-DD-A4NV         TCGA-DD-A73A 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DD-A73B         TCGA-DD-A73C         TCGA-DD-A73D 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DD-A73E         TCGA-DD-A73F         TCGA-DD-A73G 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-ED-A459         TCGA-ED-A4XI         TCGA-ED-A5KG 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-ED-A627         TCGA-ED-A66X         TCGA-ED-A66Y 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-ED-A7PX         TCGA-ED-A7PY         TCGA-ED-A7PZ 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-ED-A7XP         TCGA-ED-A82E         TCGA-EP-A12J 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-EP-A26S         TCGA-EP-A2KA         TCGA-EP-A2KB 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-EP-A2KC         TCGA-EP-A3JL         TCGA-EP-A3RK 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-ES-A2HS         TCGA-ES-A2HT         TCGA-FV-A23B 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-FV-A2QR         TCGA-FV-A3I0         TCGA-FV-A3I1 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-FV-A3R2         TCGA-FV-A3R3         TCGA-FV-A495 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-FV-A496         TCGA-FV-A4ZP         TCGA-FV-A4ZQ 
"19Q LOSS WILD-TYPE"   "19Q LOSS MUTATED" "19Q LOSS WILD-TYPE" 
        TCGA-G3-A25S         TCGA-G3-A25T         TCGA-G3-A25U 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-G3-A25V         TCGA-G3-A25W         TCGA-G3-A25X 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-G3-A25Y         TCGA-G3-A25Z         TCGA-G3-A3CG 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-G3-A3CH         TCGA-G3-A3CI         TCGA-G3-A3CJ 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-G3-A3CK         TCGA-G3-A5SI         TCGA-G3-A5SJ 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-G3-A5SL         TCGA-G3-A5SM         TCGA-G3-A6UC 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-GJ-A6C0         TCGA-K7-A6G5         TCGA-LG-A6GG 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-MI-A75C         TCGA-MI-A75E         TCGA-MI-A75G 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-MI-A75I         TCGA-NI-A4U2         TCGA-O8-A75V 
"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-BC-A69H         TCGA-BC-A69I         TCGA-CC-5258 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE"   "19Q LOSS MUTATED" 
        TCGA-CC-5260         TCGA-CC-5261         TCGA-CC-5262 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-CC-5263         TCGA-CC-A1HT         TCGA-CC-A3M9 
  "19Q LOSS MUTATED"   "19Q LOSS MUTATED" "19Q LOSS WILD-TYPE" 
        TCGA-CC-A3MA         TCGA-CC-A3MB         TCGA-CC-A3MC 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DD-A113         TCGA-DD-A114         TCGA-DD-A115 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DD-A116         TCGA-DD-A118         TCGA-DD-A119 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DD-A11A         TCGA-DD-A11B         TCGA-DD-A11C 
  "19Q LOSS MUTATED" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DD-A11D         TCGA-DD-A1E9         TCGA-DD-A1EA 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DD-A1EB         TCGA-DD-A1EC         TCGA-DD-A1ED 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DD-A1EE         TCGA-DD-A1EF         TCGA-DD-A1EG 
"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-A1EK         TCGA-DD-A1EL         TCGA-DD-A39V 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DD-A39X         TCGA-DD-A39Y         TCGA-DD-A39Z 
"19Q LOSS WILD-TYPE"   "19Q LOSS MUTATED" "19Q LOSS WILD-TYPE" 
        TCGA-DD-A3A0         TCGA-DD-A3A1         TCGA-DD-A3A2 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DD-A3A3         TCGA-DD-A3A4         TCGA-DD-A3A5 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DD-A3A6         TCGA-DD-A3A7         TCGA-DD-A3A8 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DD-A3A9         TCGA-DD-A4NA         TCGA-DD-A4NB 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DD-A4ND         TCGA-DD-A4NF         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-DD-A4NR 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DD-A4NS         TCGA-DD-A4NV         TCGA-DD-A73A 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DD-A73B         TCGA-DD-A73C         TCGA-DD-A73D 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DD-A73E         TCGA-DD-A73F         TCGA-DD-A73G 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-ED-A459         TCGA-ED-A4XI         TCGA-ED-A5KG 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-ED-A627         TCGA-ED-A66X         TCGA-ED-A66Y 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-ED-A7PX         TCGA-ED-A7PY         TCGA-ED-A7PZ 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-ED-A7XP         TCGA-ED-A82E         TCGA-EP-A12J 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-EP-A26S         TCGA-EP-A2KA         TCGA-EP-A2KB 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-EP-A2KC         TCGA-EP-A3JL         TCGA-EP-A3RK 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-ES-A2HS         TCGA-ES-A2HT         TCGA-FV-A23B 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-FV-A2QR         TCGA-FV-A3I0         TCGA-FV-A3I1 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-FV-A3R2         TCGA-FV-A3R3         TCGA-FV-A495 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-FV-A496         TCGA-FV-A4ZP         TCGA-FV-A4ZQ 
"19Q LOSS WILD-TYPE"   "19Q LOSS MUTATED" "19Q LOSS WILD-TYPE" 
        TCGA-G3-A25S         TCGA-G3-A25T         TCGA-G3-A25U 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-G3-A25V         TCGA-G3-A25W         TCGA-G3-A25X 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-G3-A25Y         TCGA-G3-A25Z         TCGA-G3-A3CG 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-G3-A3CH         TCGA-G3-A3CI         TCGA-G3-A3CJ 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-G3-A3CK         TCGA-G3-A5SI         TCGA-G3-A5SJ 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-G3-A5SL         TCGA-G3-A5SM         TCGA-G3-A6UC 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-GJ-A6C0         TCGA-K7-A6G5         TCGA-LG-A6GG 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-MI-A75C         TCGA-MI-A75E         TCGA-MI-A75G 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-MI-A75I         TCGA-NI-A4U2         TCGA-O8-A75V 
"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-BC-A69H         TCGA-BC-A69I         TCGA-CC-5258 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE"   "19Q LOSS MUTATED" 
        TCGA-CC-5260         TCGA-CC-5261         TCGA-CC-5262 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-CC-5263         TCGA-CC-A1HT         TCGA-CC-A3M9 
  "19Q LOSS MUTATED"   "19Q LOSS MUTATED" "19Q LOSS WILD-TYPE" 
        TCGA-CC-A3MA         TCGA-CC-A3MB         TCGA-CC-A3MC 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DD-A113         TCGA-DD-A114         TCGA-DD-A115 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DD-A116         TCGA-DD-A118         TCGA-DD-A119 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DD-A11A         TCGA-DD-A11B         TCGA-DD-A11C 
  "19Q LOSS MUTATED" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DD-A11D         TCGA-DD-A1E9         TCGA-DD-A1EA 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DD-A1EB         TCGA-DD-A1EC         TCGA-DD-A1ED 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DD-A1EE         TCGA-DD-A1EF         TCGA-DD-A1EG 
"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-A1EK         TCGA-DD-A1EL         TCGA-DD-A39V 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DD-A39X         TCGA-DD-A39Y         TCGA-DD-A39Z 
"19Q LOSS WILD-TYPE"   "19Q LOSS MUTATED" "19Q LOSS WILD-TYPE" 
        TCGA-DD-A3A0         TCGA-DD-A3A1         TCGA-DD-A3A2 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DD-A3A3         TCGA-DD-A3A4         TCGA-DD-A3A5 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DD-A3A6         TCGA-DD-A3A7         TCGA-DD-A3A8 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DD-A3A9         TCGA-DD-A4NA         TCGA-DD-A4NB 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DD-A4ND         TCGA-DD-A4NF         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-DD-A4NR 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DD-A4NS         TCGA-DD-A4NV         TCGA-DD-A73A 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DD-A73B         TCGA-DD-A73C         TCGA-DD-A73D 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DD-A73E         TCGA-DD-A73F         TCGA-DD-A73G 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-ED-A459         TCGA-ED-A4XI         TCGA-ED-A5KG 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-ED-A627         TCGA-ED-A66X         TCGA-ED-A66Y 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-ED-A7PX         TCGA-ED-A7PY         TCGA-ED-A7PZ 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-ED-A7XP         TCGA-ED-A82E         TCGA-EP-A12J 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-EP-A26S         TCGA-EP-A2KA         TCGA-EP-A2KB 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-EP-A2KC         TCGA-EP-A3JL         TCGA-EP-A3RK 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-ES-A2HS         TCGA-ES-A2HT         TCGA-FV-A23B 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-FV-A2QR         TCGA-FV-A3I0         TCGA-FV-A3I1 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-FV-A3R2         TCGA-FV-A3R3         TCGA-FV-A495 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-FV-A496         TCGA-FV-A4ZP         TCGA-FV-A4ZQ 
"19Q LOSS WILD-TYPE"   "19Q LOSS MUTATED" "19Q LOSS WILD-TYPE" 
        TCGA-G3-A25S         TCGA-G3-A25T         TCGA-G3-A25U 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-G3-A25V         TCGA-G3-A25W         TCGA-G3-A25X 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-G3-A25Y         TCGA-G3-A25Z         TCGA-G3-A3CG 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-G3-A3CH         TCGA-G3-A3CI         TCGA-G3-A3CJ 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-G3-A3CK         TCGA-G3-A5SI         TCGA-G3-A5SJ 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-G3-A5SL         TCGA-G3-A5SM         TCGA-G3-A6UC 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-GJ-A6C0         TCGA-K7-A6G5         TCGA-LG-A6GG 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-MI-A75C         TCGA-MI-A75E         TCGA-MI-A75G 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-MI-A75I         TCGA-NI-A4U2         TCGA-O8-A75V 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
[1] "hr=" "2.1"
D75V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  19Q LOSS MUTATED         4        2         0          3          0
  19Q LOSS WILD-TYPE      54       34         2         27          4
                    vv
clus                 STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  19Q LOSS MUTATED            1        0         0         0
  19Q LOSS WILD-TYPE          4        1         1         2
D75V3, multiclass
                    vv
clus                 T1 T2 T3 T4
  19Q LOSS MUTATED    5  2  4  0
  19Q LOSS WILD-TYPE 56 38 36  8
D75V4, multiclass
    clus
vv   19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  T1                5                 56
  T2                2                 38
  T3                4                 36
  T4                0                  8
D75V5, binary
                    cls
clus                  0  1
  19Q LOSS MUTATED    6  1
  19Q LOSS WILD-TYPE 91  2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED      6    1
  19Q LOSS WILD-TYPE   91    2
   clus
vv  19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  0                6                 91
  1                1                  2
                    vv
clus                  M0  M1  MX
  19Q LOSS MUTATED    10   0   1
  19Q LOSS WILD-TYPE 105   3  30
D75V6, multiclass
    clus
vv   19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  M0               10                105
  M1                0                  3
  MX                1                 30
D75V7, binary
                    cls
clus                  0  1
  19Q LOSS MUTATED    3  8
  19Q LOSS WILD-TYPE 55 83
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED      3    8
  19Q LOSS WILD-TYPE   55   83
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  FEMALE                3                 55
  MALE                  8                 83
                    vv
clus                  R0  R1  R2  RX
  19Q LOSS MUTATED     7   1   0   2
  19Q LOSS WILD-TYPE 115  10   1   8
D75V8, multiclass
    clus
vv   19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  R0                7                115
  R1                1                 10
  R2                0                  1
  RX                2                  8

Clustering(76) Variable = 20P LOSS MUTATION ANALYSIS
D76V1, survival
                    sevent
clus2                 0  1
  20P LOSS MUTATED    3  5
  20P LOSS WILD-TYPE 81 58
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                 8                139 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                 5                 58 
$`20P LOSS MUTATED`
TCGA-BC-A10Z TCGA-CC-A3MC TCGA-DD-A113 TCGA-DD-A1EK TCGA-DD-A39Y TCGA-DD-A3A3 
        1.12         0.13        79.73        18.35         5.62        17.59 
TCGA-DD-A4NO TCGA-DD-A4NQ 
       61.45        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-BC-A69H 
       44.42        13.84         0.26        22.36         9.50         3.95 
TCGA-BC-A69I TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 
        0.53         0.07         2.86         0.39         3.39         4.24 
TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-DD-A114 TCGA-DD-A115 
        3.32         0.10         0.07         0.10        37.78        83.57 
TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C 
       53.33       113.00         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 
       51.29        90.71        79.40        66.31        19.79        75.65 
TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ 
        6.71        12.95        45.11        49.15         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        55.69        19.76        25.81         7.66 
TCGA-DD-A3A2 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A8 
       70.06        20.12       102.74       107.11        13.78         0.36 
TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NF TCGA-DD-A4NH 
       30.61        33.14        12.85        73.38        14.07        14.24 
TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NP 
       18.44        15.06        39.78        56.25        29.56        93.67 
TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C 
        0.30        80.75        66.35        10.98         9.30         7.56 
TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G TCGA-ED-A459 TCGA-ED-A4XI 
       10.98         1.45        27.72       100.96        13.41        12.69 
TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY 
       15.85        13.91        13.35         0.23         0.20         0.20 
TCGA-ED-A7PZ TCGA-ED-A7XP TCGA-ED-A82E TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA 
        0.20         0.20         0.20        18.74        19.99        11.74 
TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT 
       10.98         0.62         9.96        11.93        22.85        14.40 
TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 
       32.45        19.10         0.20         8.12         6.38         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        51.06 
TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A25Z 
       53.79        28.27        30.74        58.49        14.86        21.53 
TCGA-G3-A3CG TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI 
       22.13        25.64         5.92        19.53        19.23        14.70 
TCGA-G3-A5SJ TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A6UC TCGA-GJ-A6C0 TCGA-K7-A6G5 
       11.97         7.99         4.37         7.76         1.02         4.01 
TCGA-LG-A6GG TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75I TCGA-NI-A4U2 
        0.49         9.57         5.10        14.24         8.71        58.88 
TCGA-O8-A75V 
        4.44 

  20P LOSS MUTATED 20P LOSS WILD-TYPE 
              0.13               0.03 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
             79.73             113.00 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
            14.925             14.070 
[1] "0.1 - 79.7 (14.9)"  "0.0 - 113.0 (14.1)"
        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-BC-A69H         TCGA-BC-A69I         TCGA-CC-5258 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CC-5260         TCGA-CC-5261         TCGA-CC-5262 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CC-5263         TCGA-CC-A1HT         TCGA-CC-A3M9 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CC-A3MA         TCGA-CC-A3MB         TCGA-CC-A3MC 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE"   "20P LOSS MUTATED" 
        TCGA-DD-A113         TCGA-DD-A114         TCGA-DD-A115 
  "20P LOSS MUTATED" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DD-A116         TCGA-DD-A118         TCGA-DD-A119 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DD-A11A         TCGA-DD-A11B         TCGA-DD-A11C 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DD-A11D         TCGA-DD-A1E9         TCGA-DD-A1EA 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DD-A1EB         TCGA-DD-A1EC         TCGA-DD-A1ED 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DD-A1EE         TCGA-DD-A1EF         TCGA-DD-A1EG 
"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-A1EK         TCGA-DD-A1EL         TCGA-DD-A39V 
  "20P LOSS MUTATED" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DD-A39X         TCGA-DD-A39Y         TCGA-DD-A39Z 
"20P LOSS WILD-TYPE"   "20P LOSS MUTATED" "20P LOSS WILD-TYPE" 
        TCGA-DD-A3A0         TCGA-DD-A3A1         TCGA-DD-A3A2 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DD-A3A3         TCGA-DD-A3A4         TCGA-DD-A3A5 
  "20P LOSS MUTATED" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DD-A3A6         TCGA-DD-A3A7         TCGA-DD-A3A8 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DD-A3A9         TCGA-DD-A4NA         TCGA-DD-A4NB 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DD-A4ND         TCGA-DD-A4NF         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-DD-A4NR 
"20P LOSS WILD-TYPE"   "20P LOSS MUTATED" "20P LOSS WILD-TYPE" 
        TCGA-DD-A4NS         TCGA-DD-A4NV         TCGA-DD-A73A 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DD-A73B         TCGA-DD-A73C         TCGA-DD-A73D 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DD-A73E         TCGA-DD-A73F         TCGA-DD-A73G 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-ED-A459         TCGA-ED-A4XI         TCGA-ED-A5KG 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-ED-A627         TCGA-ED-A66X         TCGA-ED-A66Y 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-ED-A7PX         TCGA-ED-A7PY         TCGA-ED-A7PZ 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-ED-A7XP         TCGA-ED-A82E         TCGA-EP-A12J 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EP-A26S         TCGA-EP-A2KA         TCGA-EP-A2KB 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EP-A2KC         TCGA-EP-A3JL         TCGA-EP-A3RK 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-ES-A2HS         TCGA-ES-A2HT         TCGA-FV-A23B 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-FV-A2QR         TCGA-FV-A3I0         TCGA-FV-A3I1 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-FV-A3R2         TCGA-FV-A3R3         TCGA-FV-A495 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-FV-A496         TCGA-FV-A4ZP         TCGA-FV-A4ZQ 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-G3-A25S         TCGA-G3-A25T         TCGA-G3-A25U 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-G3-A25V         TCGA-G3-A25W         TCGA-G3-A25X 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-G3-A25Y         TCGA-G3-A25Z         TCGA-G3-A3CG 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-G3-A3CH         TCGA-G3-A3CI         TCGA-G3-A3CJ 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-G3-A3CK         TCGA-G3-A5SI         TCGA-G3-A5SJ 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-G3-A5SL         TCGA-G3-A5SM         TCGA-G3-A6UC 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-GJ-A6C0         TCGA-K7-A6G5         TCGA-LG-A6GG 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-MI-A75C         TCGA-MI-A75E         TCGA-MI-A75G 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-MI-A75I         TCGA-NI-A4U2         TCGA-O8-A75V 
"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-BC-A69H         TCGA-BC-A69I         TCGA-CC-5258 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CC-5260         TCGA-CC-5261         TCGA-CC-5262 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CC-5263         TCGA-CC-A1HT         TCGA-CC-A3M9 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CC-A3MA         TCGA-CC-A3MB         TCGA-CC-A3MC 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE"   "20P LOSS MUTATED" 
        TCGA-DD-A113         TCGA-DD-A114         TCGA-DD-A115 
  "20P LOSS MUTATED" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DD-A116         TCGA-DD-A118         TCGA-DD-A119 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DD-A11A         TCGA-DD-A11B         TCGA-DD-A11C 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DD-A11D         TCGA-DD-A1E9         TCGA-DD-A1EA 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DD-A1EB         TCGA-DD-A1EC         TCGA-DD-A1ED 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DD-A1EE         TCGA-DD-A1EF         TCGA-DD-A1EG 
"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-A1EK         TCGA-DD-A1EL         TCGA-DD-A39V 
  "20P LOSS MUTATED" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DD-A39X         TCGA-DD-A39Y         TCGA-DD-A39Z 
"20P LOSS WILD-TYPE"   "20P LOSS MUTATED" "20P LOSS WILD-TYPE" 
        TCGA-DD-A3A0         TCGA-DD-A3A1         TCGA-DD-A3A2 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DD-A3A3         TCGA-DD-A3A4         TCGA-DD-A3A5 
  "20P LOSS MUTATED" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DD-A3A6         TCGA-DD-A3A7         TCGA-DD-A3A8 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DD-A3A9         TCGA-DD-A4NA         TCGA-DD-A4NB 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DD-A4ND         TCGA-DD-A4NF         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-DD-A4NR 
"20P LOSS WILD-TYPE"   "20P LOSS MUTATED" "20P LOSS WILD-TYPE" 
        TCGA-DD-A4NS         TCGA-DD-A4NV         TCGA-DD-A73A 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DD-A73B         TCGA-DD-A73C         TCGA-DD-A73D 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DD-A73E         TCGA-DD-A73F         TCGA-DD-A73G 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-ED-A459         TCGA-ED-A4XI         TCGA-ED-A5KG 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-ED-A627         TCGA-ED-A66X         TCGA-ED-A66Y 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-ED-A7PX         TCGA-ED-A7PY         TCGA-ED-A7PZ 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-ED-A7XP         TCGA-ED-A82E         TCGA-EP-A12J 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EP-A26S         TCGA-EP-A2KA         TCGA-EP-A2KB 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EP-A2KC         TCGA-EP-A3JL         TCGA-EP-A3RK 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-ES-A2HS         TCGA-ES-A2HT         TCGA-FV-A23B 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-FV-A2QR         TCGA-FV-A3I0         TCGA-FV-A3I1 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-FV-A3R2         TCGA-FV-A3R3         TCGA-FV-A495 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-FV-A496         TCGA-FV-A4ZP         TCGA-FV-A4ZQ 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-G3-A25S         TCGA-G3-A25T         TCGA-G3-A25U 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-G3-A25V         TCGA-G3-A25W         TCGA-G3-A25X 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-G3-A25Y         TCGA-G3-A25Z         TCGA-G3-A3CG 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-G3-A3CH         TCGA-G3-A3CI         TCGA-G3-A3CJ 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-G3-A3CK         TCGA-G3-A5SI         TCGA-G3-A5SJ 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-G3-A5SL         TCGA-G3-A5SM         TCGA-G3-A6UC 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-GJ-A6C0         TCGA-K7-A6G5         TCGA-LG-A6GG 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-MI-A75C         TCGA-MI-A75E         TCGA-MI-A75G 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-MI-A75I         TCGA-NI-A4U2         TCGA-O8-A75V 
"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-BC-A69H         TCGA-BC-A69I         TCGA-CC-5258 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CC-5260         TCGA-CC-5261         TCGA-CC-5262 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CC-5263         TCGA-CC-A1HT         TCGA-CC-A3M9 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CC-A3MA         TCGA-CC-A3MB         TCGA-CC-A3MC 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE"   "20P LOSS MUTATED" 
        TCGA-DD-A113         TCGA-DD-A114         TCGA-DD-A115 
  "20P LOSS MUTATED" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DD-A116         TCGA-DD-A118         TCGA-DD-A119 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DD-A11A         TCGA-DD-A11B         TCGA-DD-A11C 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DD-A11D         TCGA-DD-A1E9         TCGA-DD-A1EA 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DD-A1EB         TCGA-DD-A1EC         TCGA-DD-A1ED 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DD-A1EE         TCGA-DD-A1EF         TCGA-DD-A1EG 
"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-A1EK         TCGA-DD-A1EL         TCGA-DD-A39V 
  "20P LOSS MUTATED" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DD-A39X         TCGA-DD-A39Y         TCGA-DD-A39Z 
"20P LOSS WILD-TYPE"   "20P LOSS MUTATED" "20P LOSS WILD-TYPE" 
        TCGA-DD-A3A0         TCGA-DD-A3A1         TCGA-DD-A3A2 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DD-A3A3         TCGA-DD-A3A4         TCGA-DD-A3A5 
  "20P LOSS MUTATED" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DD-A3A6         TCGA-DD-A3A7         TCGA-DD-A3A8 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DD-A3A9         TCGA-DD-A4NA         TCGA-DD-A4NB 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DD-A4ND         TCGA-DD-A4NF         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-DD-A4NR 
"20P LOSS WILD-TYPE"   "20P LOSS MUTATED" "20P LOSS WILD-TYPE" 
        TCGA-DD-A4NS         TCGA-DD-A4NV         TCGA-DD-A73A 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DD-A73B         TCGA-DD-A73C         TCGA-DD-A73D 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DD-A73E         TCGA-DD-A73F         TCGA-DD-A73G 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-ED-A459         TCGA-ED-A4XI         TCGA-ED-A5KG 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-ED-A627         TCGA-ED-A66X         TCGA-ED-A66Y 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-ED-A7PX         TCGA-ED-A7PY         TCGA-ED-A7PZ 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-ED-A7XP         TCGA-ED-A82E         TCGA-EP-A12J 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EP-A26S         TCGA-EP-A2KA         TCGA-EP-A2KB 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EP-A2KC         TCGA-EP-A3JL         TCGA-EP-A3RK 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-ES-A2HS         TCGA-ES-A2HT         TCGA-FV-A23B 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-FV-A2QR         TCGA-FV-A3I0         TCGA-FV-A3I1 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-FV-A3R2         TCGA-FV-A3R3         TCGA-FV-A495 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-FV-A496         TCGA-FV-A4ZP         TCGA-FV-A4ZQ 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-G3-A25S         TCGA-G3-A25T         TCGA-G3-A25U 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-G3-A25V         TCGA-G3-A25W         TCGA-G3-A25X 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-G3-A25Y         TCGA-G3-A25Z         TCGA-G3-A3CG 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-G3-A3CH         TCGA-G3-A3CI         TCGA-G3-A3CJ 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-G3-A3CK         TCGA-G3-A5SI         TCGA-G3-A5SJ 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-G3-A5SL         TCGA-G3-A5SM         TCGA-G3-A6UC 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-GJ-A6C0         TCGA-K7-A6G5         TCGA-LG-A6GG 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-MI-A75C         TCGA-MI-A75E         TCGA-MI-A75G 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-MI-A75I         TCGA-NI-A4U2         TCGA-O8-A75V 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
[1] "hr=" "1.6"
D76V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  20P LOSS MUTATED         4        2         0          1          0
  20P LOSS WILD-TYPE      54       34         2         29          4
                    vv
clus                 STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  20P LOSS MUTATED            0        0         0         1
  20P LOSS WILD-TYPE          5        1         1         1
D76V3, multiclass
                    vv
clus                 T1 T2 T3 T4
  20P LOSS MUTATED    4  2  1  1
  20P LOSS WILD-TYPE 57 38 39  7
D76V4, multiclass
    clus
vv   20P LOSS MUTATED 20P LOSS WILD-TYPE
  T1                4                 57
  T2                2                 38
  T3                1                 39
  T4                1                  7
D76V5, binary
                    cls
clus                  0  1
  20P LOSS MUTATED    7  0
  20P LOSS WILD-TYPE 90  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED      7    0
  20P LOSS WILD-TYPE   90    3
   clus
vv  20P LOSS MUTATED 20P LOSS WILD-TYPE
  0                7                 90
  1                0                  3
                    vv
clus                  M0  M1  MX
  20P LOSS MUTATED     6   1   1
  20P LOSS WILD-TYPE 109   2  30
D76V6, multiclass
    clus
vv   20P LOSS MUTATED 20P LOSS WILD-TYPE
  M0                6                109
  M1                1                  2
  MX                1                 30
D76V7, binary
                    cls
clus                  0  1
  20P LOSS MUTATED    3  5
  20P LOSS WILD-TYPE 55 86
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED      3    5
  20P LOSS WILD-TYPE   55   86
        clus
vv       20P LOSS MUTATED 20P LOSS WILD-TYPE
  FEMALE                3                 55
  MALE                  5                 86
                    vv
clus                  R0  R1  R2  RX
  20P LOSS MUTATED     8   0   0   0
  20P LOSS WILD-TYPE 114  11   1  10
D76V8, multiclass
    clus
vv   20P LOSS MUTATED 20P LOSS WILD-TYPE
  R0                8                114
  R1                0                 11
  R2                0                  1
  RX                0                 10

Clustering(77) Variable = 20Q LOSS MUTATION ANALYSIS
D77V1, survival
                    sevent
clus2                 0  1
  20Q LOSS MUTATED    2  2
  20Q LOSS WILD-TYPE 82 61
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 4                143 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 2                 61 
$`20Q LOSS MUTATED`
TCGA-DD-A113 TCGA-DD-A39Y TCGA-DD-A4NO TCGA-DD-A4NQ 
       79.73         5.62        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        13.84         0.26        22.36         9.50 
TCGA-BC-A69H TCGA-BC-A69I TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 
        3.95         0.53         0.07         2.86         0.39         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-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A 
       37.78        83.57        53.33       113.00         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        51.29        90.71        79.40        66.31 
TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH 
       19.79        75.65         6.71        12.95        45.11        49.15 
TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39X 
        6.02        29.16        18.35        13.64        21.14        55.69 
TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 
       19.76        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        30.61        33.14 
TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ 
       12.85        73.38        14.07        14.24        18.44        15.06 
TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NP TCGA-DD-A4NR TCGA-DD-A4NS 
       39.78        56.25        29.56        93.67         0.30        80.75 
TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E 
       66.35        10.98         9.30         7.56        10.98         1.45 
TCGA-DD-A73F TCGA-DD-A73G TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 
       27.72       100.96        13.41        12.69        15.85        13.91 
TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XP 
       13.35         0.23         0.20         0.20         0.20         0.20 
TCGA-ED-A82E TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC 
        0.20        18.74        19.99        11.74        10.98         0.62 
TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QR 
        9.96        11.93        22.85        14.40        32.45        19.10 
TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 
        0.20         8.12         6.38         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        51.06        53.79        28.27 
TCGA-G3-A25W TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CH 
       30.74        58.49        14.86        21.53        22.13        25.64 
TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SL 
        5.92        19.53        19.23        14.70        11.97         7.99 
TCGA-G3-A5SM TCGA-G3-A6UC TCGA-GJ-A6C0 TCGA-K7-A6G5 TCGA-LG-A6GG TCGA-MI-A75C 
        4.37         7.76         1.02         4.01         0.49         9.57 
TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75I TCGA-NI-A4U2 TCGA-O8-A75V 
        5.10        14.24         8.71        58.88         4.44 

  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
              5.62               0.03 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
             79.73             113.00 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
            36.855             14.070 
[1] "5.6 - 79.7 (36.9)"  "0.0 - 113.0 (14.1)"
        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-BC-A69H         TCGA-BC-A69I         TCGA-CC-5258 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-CC-5260         TCGA-CC-5261         TCGA-CC-5262 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-CC-5263         TCGA-CC-A1HT         TCGA-CC-A3M9 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-CC-A3MA         TCGA-CC-A3MB         TCGA-CC-A3MC 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-DD-A113         TCGA-DD-A114         TCGA-DD-A115 
  "20Q LOSS MUTATED" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-DD-A116         TCGA-DD-A118         TCGA-DD-A119 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-DD-A11A         TCGA-DD-A11B         TCGA-DD-A11C 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-DD-A11D         TCGA-DD-A1E9         TCGA-DD-A1EA 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-DD-A1EB         TCGA-DD-A1EC         TCGA-DD-A1ED 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-DD-A1EE         TCGA-DD-A1EF         TCGA-DD-A1EG 
"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-A1EK         TCGA-DD-A1EL         TCGA-DD-A39V 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-DD-A39X         TCGA-DD-A39Y         TCGA-DD-A39Z 
"20Q LOSS WILD-TYPE"   "20Q LOSS MUTATED" "20Q LOSS WILD-TYPE" 
        TCGA-DD-A3A0         TCGA-DD-A3A1         TCGA-DD-A3A2 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-DD-A3A3         TCGA-DD-A3A4         TCGA-DD-A3A5 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-DD-A3A6         TCGA-DD-A3A7         TCGA-DD-A3A8 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-DD-A3A9         TCGA-DD-A4NA         TCGA-DD-A4NB 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-DD-A4ND         TCGA-DD-A4NF         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-DD-A4NR 
"20Q LOSS WILD-TYPE"   "20Q LOSS MUTATED" "20Q LOSS WILD-TYPE" 
        TCGA-DD-A4NS         TCGA-DD-A4NV         TCGA-DD-A73A 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-DD-A73B         TCGA-DD-A73C         TCGA-DD-A73D 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-DD-A73E         TCGA-DD-A73F         TCGA-DD-A73G 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-ED-A459         TCGA-ED-A4XI         TCGA-ED-A5KG 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-ED-A627         TCGA-ED-A66X         TCGA-ED-A66Y 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-ED-A7PX         TCGA-ED-A7PY         TCGA-ED-A7PZ 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-ED-A7XP         TCGA-ED-A82E         TCGA-EP-A12J 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-EP-A26S         TCGA-EP-A2KA         TCGA-EP-A2KB 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-EP-A2KC         TCGA-EP-A3JL         TCGA-EP-A3RK 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-ES-A2HS         TCGA-ES-A2HT         TCGA-FV-A23B 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-FV-A2QR         TCGA-FV-A3I0         TCGA-FV-A3I1 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-FV-A3R2         TCGA-FV-A3R3         TCGA-FV-A495 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-FV-A496         TCGA-FV-A4ZP         TCGA-FV-A4ZQ 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-G3-A25S         TCGA-G3-A25T         TCGA-G3-A25U 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-G3-A25V         TCGA-G3-A25W         TCGA-G3-A25X 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-G3-A25Y         TCGA-G3-A25Z         TCGA-G3-A3CG 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-G3-A3CH         TCGA-G3-A3CI         TCGA-G3-A3CJ 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-G3-A3CK         TCGA-G3-A5SI         TCGA-G3-A5SJ 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-G3-A5SL         TCGA-G3-A5SM         TCGA-G3-A6UC 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-GJ-A6C0         TCGA-K7-A6G5         TCGA-LG-A6GG 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-MI-A75C         TCGA-MI-A75E         TCGA-MI-A75G 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-MI-A75I         TCGA-NI-A4U2         TCGA-O8-A75V 
"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-BC-A69H         TCGA-BC-A69I         TCGA-CC-5258 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-CC-5260         TCGA-CC-5261         TCGA-CC-5262 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-CC-5263         TCGA-CC-A1HT         TCGA-CC-A3M9 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-CC-A3MA         TCGA-CC-A3MB         TCGA-CC-A3MC 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-DD-A113         TCGA-DD-A114         TCGA-DD-A115 
  "20Q LOSS MUTATED" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-DD-A116         TCGA-DD-A118         TCGA-DD-A119 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-DD-A11A         TCGA-DD-A11B         TCGA-DD-A11C 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-DD-A11D         TCGA-DD-A1E9         TCGA-DD-A1EA 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-DD-A1EB         TCGA-DD-A1EC         TCGA-DD-A1ED 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-DD-A1EE         TCGA-DD-A1EF         TCGA-DD-A1EG 
"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-A1EK         TCGA-DD-A1EL         TCGA-DD-A39V 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-DD-A39X         TCGA-DD-A39Y         TCGA-DD-A39Z 
"20Q LOSS WILD-TYPE"   "20Q LOSS MUTATED" "20Q LOSS WILD-TYPE" 
        TCGA-DD-A3A0         TCGA-DD-A3A1         TCGA-DD-A3A2 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-DD-A3A3         TCGA-DD-A3A4         TCGA-DD-A3A5 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-DD-A3A6         TCGA-DD-A3A7         TCGA-DD-A3A8 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-DD-A3A9         TCGA-DD-A4NA         TCGA-DD-A4NB 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-DD-A4ND         TCGA-DD-A4NF         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-DD-A4NR 
"20Q LOSS WILD-TYPE"   "20Q LOSS MUTATED" "20Q LOSS WILD-TYPE" 
        TCGA-DD-A4NS         TCGA-DD-A4NV         TCGA-DD-A73A 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-DD-A73B         TCGA-DD-A73C         TCGA-DD-A73D 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-DD-A73E         TCGA-DD-A73F         TCGA-DD-A73G 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-ED-A459         TCGA-ED-A4XI         TCGA-ED-A5KG 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-ED-A627         TCGA-ED-A66X         TCGA-ED-A66Y 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-ED-A7PX         TCGA-ED-A7PY         TCGA-ED-A7PZ 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-ED-A7XP         TCGA-ED-A82E         TCGA-EP-A12J 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-EP-A26S         TCGA-EP-A2KA         TCGA-EP-A2KB 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-EP-A2KC         TCGA-EP-A3JL         TCGA-EP-A3RK 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-ES-A2HS         TCGA-ES-A2HT         TCGA-FV-A23B 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-FV-A2QR         TCGA-FV-A3I0         TCGA-FV-A3I1 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-FV-A3R2         TCGA-FV-A3R3         TCGA-FV-A495 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-FV-A496         TCGA-FV-A4ZP         TCGA-FV-A4ZQ 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-G3-A25S         TCGA-G3-A25T         TCGA-G3-A25U 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-G3-A25V         TCGA-G3-A25W         TCGA-G3-A25X 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-G3-A25Y         TCGA-G3-A25Z         TCGA-G3-A3CG 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-G3-A3CH         TCGA-G3-A3CI         TCGA-G3-A3CJ 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-G3-A3CK         TCGA-G3-A5SI         TCGA-G3-A5SJ 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-G3-A5SL         TCGA-G3-A5SM         TCGA-G3-A6UC 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-GJ-A6C0         TCGA-K7-A6G5         TCGA-LG-A6GG 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-MI-A75C         TCGA-MI-A75E         TCGA-MI-A75G 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-MI-A75I         TCGA-NI-A4U2         TCGA-O8-A75V 
"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-BC-A69H         TCGA-BC-A69I         TCGA-CC-5258 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-CC-5260         TCGA-CC-5261         TCGA-CC-5262 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-CC-5263         TCGA-CC-A1HT         TCGA-CC-A3M9 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-CC-A3MA         TCGA-CC-A3MB         TCGA-CC-A3MC 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-DD-A113         TCGA-DD-A114         TCGA-DD-A115 
  "20Q LOSS MUTATED" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-DD-A116         TCGA-DD-A118         TCGA-DD-A119 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-DD-A11A         TCGA-DD-A11B         TCGA-DD-A11C 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-DD-A11D         TCGA-DD-A1E9         TCGA-DD-A1EA 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-DD-A1EB         TCGA-DD-A1EC         TCGA-DD-A1ED 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-DD-A1EE         TCGA-DD-A1EF         TCGA-DD-A1EG 
"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-A1EK         TCGA-DD-A1EL         TCGA-DD-A39V 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-DD-A39X         TCGA-DD-A39Y         TCGA-DD-A39Z 
"20Q LOSS WILD-TYPE"   "20Q LOSS MUTATED" "20Q LOSS WILD-TYPE" 
        TCGA-DD-A3A0         TCGA-DD-A3A1         TCGA-DD-A3A2 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-DD-A3A3         TCGA-DD-A3A4         TCGA-DD-A3A5 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-DD-A3A6         TCGA-DD-A3A7         TCGA-DD-A3A8 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-DD-A3A9         TCGA-DD-A4NA         TCGA-DD-A4NB 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-DD-A4ND         TCGA-DD-A4NF         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-DD-A4NR 
"20Q LOSS WILD-TYPE"   "20Q LOSS MUTATED" "20Q LOSS WILD-TYPE" 
        TCGA-DD-A4NS         TCGA-DD-A4NV         TCGA-DD-A73A 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-DD-A73B         TCGA-DD-A73C         TCGA-DD-A73D 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-DD-A73E         TCGA-DD-A73F         TCGA-DD-A73G 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-ED-A459         TCGA-ED-A4XI         TCGA-ED-A5KG 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-ED-A627         TCGA-ED-A66X         TCGA-ED-A66Y 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-ED-A7PX         TCGA-ED-A7PY         TCGA-ED-A7PZ 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-ED-A7XP         TCGA-ED-A82E         TCGA-EP-A12J 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-EP-A26S         TCGA-EP-A2KA         TCGA-EP-A2KB 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-EP-A2KC         TCGA-EP-A3JL         TCGA-EP-A3RK 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-ES-A2HS         TCGA-ES-A2HT         TCGA-FV-A23B 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-FV-A2QR         TCGA-FV-A3I0         TCGA-FV-A3I1 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-FV-A3R2         TCGA-FV-A3R3         TCGA-FV-A495 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-FV-A496         TCGA-FV-A4ZP         TCGA-FV-A4ZQ 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-G3-A25S         TCGA-G3-A25T         TCGA-G3-A25U 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-G3-A25V         TCGA-G3-A25W         TCGA-G3-A25X 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-G3-A25Y         TCGA-G3-A25Z         TCGA-G3-A3CG 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-G3-A3CH         TCGA-G3-A3CI         TCGA-G3-A3CJ 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-G3-A3CK         TCGA-G3-A5SI         TCGA-G3-A5SJ 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-G3-A5SL         TCGA-G3-A5SM         TCGA-G3-A6UC 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-GJ-A6C0         TCGA-K7-A6G5         TCGA-LG-A6GG 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-MI-A75C         TCGA-MI-A75E         TCGA-MI-A75G 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-MI-A75I         TCGA-NI-A4U2         TCGA-O8-A75V 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
[1] "hr=" "1.3"
D77V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  20Q LOSS MUTATED         2        2         0          0          0
  20Q LOSS WILD-TYPE      56       34         2         30          4
                    vv
clus                 STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  20Q LOSS MUTATED            0        0         0         0
  20Q LOSS WILD-TYPE          5        1         1         2
D77V3, multiclass
                    vv
clus                 T1 T2 T3 T4
  20Q LOSS MUTATED    2  2  0  0
  20Q LOSS WILD-TYPE 59 38 40  8
D77V4, multiclass
    clus
vv   20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  T1                2                 59
  T2                2                 38
  T3                0                 40
  T4                0                  8
D77V5, binary
                    cls
clus                  0  1
  20Q LOSS MUTATED    3  0
  20Q LOSS WILD-TYPE 94  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED      3    0
  20Q LOSS WILD-TYPE   94    3
   clus
vv  20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  0                3                 94
  1                0                  3
                    vv
clus                  M0  M1  MX
  20Q LOSS MUTATED     4   0   0
  20Q LOSS WILD-TYPE 111   3  31
D77V6, multiclass
    clus
vv   20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  M0                4                111
  M1                0                  3
  MX                0                 31
D77V7, binary
                    cls
clus                  0  1
  20Q LOSS MUTATED    1  3
  20Q LOSS WILD-TYPE 57 88
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED      1    3
  20Q LOSS WILD-TYPE   57   88
        clus
vv       20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  FEMALE                1                 57
  MALE                  3                 88
                    vv
clus                  R0  R1  R2  RX
  20Q LOSS MUTATED     4   0   0   0
  20Q LOSS WILD-TYPE 118  11   1  10
D77V8, multiclass
    clus
vv   20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  R0                4                118
  R1                0                 11
  R2                0                  1
  RX                0                 10

Clustering(78) Variable = 21Q LOSS MUTATION ANALYSIS
D78V1, survival
                    sevent
clus2                 0  1
  21Q LOSS MUTATED   19 19
  21Q LOSS WILD-TYPE 65 44
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                38                109 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                19                 44 
$`21Q LOSS MUTATED`
TCGA-BC-A10U TCGA-BC-A112 TCGA-BC-A216 TCGA-BC-A69H TCGA-CC-5262 TCGA-CC-A1HT 
       27.52         5.03        44.42         3.95         3.39         3.32 
TCGA-CC-A3MB TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A1E9 TCGA-DD-A1EF TCGA-DD-A1EG 
        0.10         7.33         2.60        90.71        12.95        45.11 
TCGA-DD-A1EH TCGA-DD-A1EJ TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39Y TCGA-DD-A3A0 
       49.15        29.16        13.64        21.14         5.62        25.81 
TCGA-DD-A3A1 TCGA-DD-A3A7 TCGA-DD-A3A9 TCGA-DD-A4NB TCGA-DD-A4NI TCGA-DD-A73G 
        7.66        13.78        30.61        12.85        18.44       100.96 
TCGA-ED-A459 TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PZ TCGA-EP-A2KC TCGA-EP-A3JL 
       13.41         0.23         0.20         0.20         0.62         9.96 
TCGA-EP-A3RK TCGA-FV-A23B TCGA-FV-A496 TCGA-FV-A4ZP TCGA-G3-A25S TCGA-G3-A25Z 
       11.93        32.45         0.33        60.36         1.22        21.53 
TCGA-LG-A6GG TCGA-MI-A75E 
        0.49         5.10 

$`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        13.84 
TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69I TCGA-CC-5258 TCGA-CC-5260 
        0.26        22.36         9.50         0.53         0.07         2.86 
TCGA-CC-5261 TCGA-CC-5263 TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MC TCGA-DD-A113 
        0.39         4.24         0.10         0.07         0.13        79.73 
TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A11B TCGA-DD-A11C 
       37.78        83.57        53.33       113.00         0.46        21.76 
TCGA-DD-A11D TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE 
       51.29        79.40        66.31        19.79        75.65         6.71 
TCGA-DD-A1EI TCGA-DD-A1EK TCGA-DD-A39X TCGA-DD-A39Z TCGA-DD-A3A2 TCGA-DD-A3A3 
        6.02        18.35        55.69        19.76        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-A4NF TCGA-DD-A4NH TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN 
       14.07        14.24        15.06        39.78        56.25        29.56 
TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV 
       61.45        93.67        12.26         0.30        80.75        66.35 
TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F 
       10.98         9.30         7.56        10.98         1.45        27.72 
TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A7PY TCGA-ED-A7XP 
       12.69        15.85        13.91        13.35         0.20         0.20 
TCGA-ED-A82E TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-ES-A2HS 
        0.20        18.74        19.99        11.74        10.98        22.85 
TCGA-ES-A2HT TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 
       14.40        19.10         0.20         8.12         6.38         0.13 
TCGA-FV-A495 TCGA-FV-A4ZQ TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W 
        0.03         0.39        51.06        53.79        28.27        30.74 
TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A3CG TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ 
       58.49        14.86        22.13        25.64         5.92        19.53 
TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A6UC 
       19.23        14.70        11.97         7.99         4.37         7.76 
TCGA-GJ-A6C0 TCGA-K7-A6G5 TCGA-MI-A75C TCGA-MI-A75G TCGA-MI-A75I TCGA-NI-A4U2 
        1.02         4.01         9.57        14.24         8.71        58.88 
TCGA-O8-A75V 
        4.44 

  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
              0.10               0.03 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
            100.96             113.00 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
             12.39              14.86 
[1] "0.1 - 101.0 (12.4)" "0.0 - 113.0 (14.9)"
        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-BC-A69H         TCGA-BC-A69I         TCGA-CC-5258 
  "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-CC-5260         TCGA-CC-5261         TCGA-CC-5262 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" 
        TCGA-CC-5263         TCGA-CC-A1HT         TCGA-CC-A3M9 
"21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-CC-A3MA         TCGA-CC-A3MB         TCGA-CC-A3MC 
"21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-DD-A113         TCGA-DD-A114         TCGA-DD-A115 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-DD-A116         TCGA-DD-A118         TCGA-DD-A119 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" 
        TCGA-DD-A11A         TCGA-DD-A11B         TCGA-DD-A11C 
  "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-DD-A11D         TCGA-DD-A1E9         TCGA-DD-A1EA 
"21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-DD-A1EB         TCGA-DD-A1EC         TCGA-DD-A1ED 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-DD-A1EE         TCGA-DD-A1EF         TCGA-DD-A1EG 
"21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED"   "21Q LOSS MUTATED" 
        TCGA-DD-A1EH         TCGA-DD-A1EI         TCGA-DD-A1EJ 
  "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" 
        TCGA-DD-A1EK         TCGA-DD-A1EL         TCGA-DD-A39V 
"21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED"   "21Q LOSS MUTATED" 
        TCGA-DD-A39X         TCGA-DD-A39Y         TCGA-DD-A39Z 
"21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-DD-A3A0         TCGA-DD-A3A1         TCGA-DD-A3A2 
  "21Q LOSS MUTATED"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-DD-A3A3         TCGA-DD-A3A4         TCGA-DD-A3A5 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-DD-A3A6         TCGA-DD-A3A7         TCGA-DD-A3A8 
"21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-DD-A3A9         TCGA-DD-A4NA         TCGA-DD-A4NB 
  "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" 
        TCGA-DD-A4ND         TCGA-DD-A4NF         TCGA-DD-A4NH 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-DD-A4NI         TCGA-DD-A4NJ         TCGA-DD-A4NK 
  "21Q LOSS MUTATED" "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-DD-A4NR 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-DD-A4NS         TCGA-DD-A4NV         TCGA-DD-A73A 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-DD-A73B         TCGA-DD-A73C         TCGA-DD-A73D 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-DD-A73E         TCGA-DD-A73F         TCGA-DD-A73G 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" 
        TCGA-ED-A459         TCGA-ED-A4XI         TCGA-ED-A5KG 
  "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-ED-A627         TCGA-ED-A66X         TCGA-ED-A66Y 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" 
        TCGA-ED-A7PX         TCGA-ED-A7PY         TCGA-ED-A7PZ 
  "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" 
        TCGA-ED-A7XP         TCGA-ED-A82E         TCGA-EP-A12J 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-EP-A26S         TCGA-EP-A2KA         TCGA-EP-A2KB 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-EP-A2KC         TCGA-EP-A3JL         TCGA-EP-A3RK 
  "21Q LOSS MUTATED"   "21Q LOSS MUTATED"   "21Q LOSS MUTATED" 
        TCGA-ES-A2HS         TCGA-ES-A2HT         TCGA-FV-A23B 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" 
        TCGA-FV-A2QR         TCGA-FV-A3I0         TCGA-FV-A3I1 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-FV-A3R2         TCGA-FV-A3R3         TCGA-FV-A495 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-FV-A496         TCGA-FV-A4ZP         TCGA-FV-A4ZQ 
  "21Q LOSS MUTATED"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-G3-A25S         TCGA-G3-A25T         TCGA-G3-A25U 
  "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-G3-A25V         TCGA-G3-A25W         TCGA-G3-A25X 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-G3-A25Y         TCGA-G3-A25Z         TCGA-G3-A3CG 
"21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-G3-A3CH         TCGA-G3-A3CI         TCGA-G3-A3CJ 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-G3-A3CK         TCGA-G3-A5SI         TCGA-G3-A5SJ 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-G3-A5SL         TCGA-G3-A5SM         TCGA-G3-A6UC 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-GJ-A6C0         TCGA-K7-A6G5         TCGA-LG-A6GG 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" 
        TCGA-MI-A75C         TCGA-MI-A75E         TCGA-MI-A75G 
"21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-MI-A75I         TCGA-NI-A4U2         TCGA-O8-A75V 
"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-BC-A69H         TCGA-BC-A69I         TCGA-CC-5258 
  "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-CC-5260         TCGA-CC-5261         TCGA-CC-5262 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" 
        TCGA-CC-5263         TCGA-CC-A1HT         TCGA-CC-A3M9 
"21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-CC-A3MA         TCGA-CC-A3MB         TCGA-CC-A3MC 
"21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-DD-A113         TCGA-DD-A114         TCGA-DD-A115 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-DD-A116         TCGA-DD-A118         TCGA-DD-A119 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" 
        TCGA-DD-A11A         TCGA-DD-A11B         TCGA-DD-A11C 
  "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-DD-A11D         TCGA-DD-A1E9         TCGA-DD-A1EA 
"21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-DD-A1EB         TCGA-DD-A1EC         TCGA-DD-A1ED 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-DD-A1EE         TCGA-DD-A1EF         TCGA-DD-A1EG 
"21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED"   "21Q LOSS MUTATED" 
        TCGA-DD-A1EH         TCGA-DD-A1EI         TCGA-DD-A1EJ 
  "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" 
        TCGA-DD-A1EK         TCGA-DD-A1EL         TCGA-DD-A39V 
"21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED"   "21Q LOSS MUTATED" 
        TCGA-DD-A39X         TCGA-DD-A39Y         TCGA-DD-A39Z 
"21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-DD-A3A0         TCGA-DD-A3A1         TCGA-DD-A3A2 
  "21Q LOSS MUTATED"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-DD-A3A3         TCGA-DD-A3A4         TCGA-DD-A3A5 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-DD-A3A6         TCGA-DD-A3A7         TCGA-DD-A3A8 
"21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-DD-A3A9         TCGA-DD-A4NA         TCGA-DD-A4NB 
  "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" 
        TCGA-DD-A4ND         TCGA-DD-A4NF         TCGA-DD-A4NH 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-DD-A4NI         TCGA-DD-A4NJ         TCGA-DD-A4NK 
  "21Q LOSS MUTATED" "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-DD-A4NR 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-DD-A4NS         TCGA-DD-A4NV         TCGA-DD-A73A 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-DD-A73B         TCGA-DD-A73C         TCGA-DD-A73D 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-DD-A73E         TCGA-DD-A73F         TCGA-DD-A73G 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" 
        TCGA-ED-A459         TCGA-ED-A4XI         TCGA-ED-A5KG 
  "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-ED-A627         TCGA-ED-A66X         TCGA-ED-A66Y 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" 
        TCGA-ED-A7PX         TCGA-ED-A7PY         TCGA-ED-A7PZ 
  "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" 
        TCGA-ED-A7XP         TCGA-ED-A82E         TCGA-EP-A12J 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-EP-A26S         TCGA-EP-A2KA         TCGA-EP-A2KB 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-EP-A2KC         TCGA-EP-A3JL         TCGA-EP-A3RK 
  "21Q LOSS MUTATED"   "21Q LOSS MUTATED"   "21Q LOSS MUTATED" 
        TCGA-ES-A2HS         TCGA-ES-A2HT         TCGA-FV-A23B 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" 
        TCGA-FV-A2QR         TCGA-FV-A3I0         TCGA-FV-A3I1 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-FV-A3R2         TCGA-FV-A3R3         TCGA-FV-A495 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-FV-A496         TCGA-FV-A4ZP         TCGA-FV-A4ZQ 
  "21Q LOSS MUTATED"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-G3-A25S         TCGA-G3-A25T         TCGA-G3-A25U 
  "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-G3-A25V         TCGA-G3-A25W         TCGA-G3-A25X 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-G3-A25Y         TCGA-G3-A25Z         TCGA-G3-A3CG 
"21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-G3-A3CH         TCGA-G3-A3CI         TCGA-G3-A3CJ 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-G3-A3CK         TCGA-G3-A5SI         TCGA-G3-A5SJ 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-G3-A5SL         TCGA-G3-A5SM         TCGA-G3-A6UC 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-GJ-A6C0         TCGA-K7-A6G5         TCGA-LG-A6GG 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" 
        TCGA-MI-A75C         TCGA-MI-A75E         TCGA-MI-A75G 
"21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-MI-A75I         TCGA-NI-A4U2         TCGA-O8-A75V 
"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-BC-A69H         TCGA-BC-A69I         TCGA-CC-5258 
  "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-CC-5260         TCGA-CC-5261         TCGA-CC-5262 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" 
        TCGA-CC-5263         TCGA-CC-A1HT         TCGA-CC-A3M9 
"21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-CC-A3MA         TCGA-CC-A3MB         TCGA-CC-A3MC 
"21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-DD-A113         TCGA-DD-A114         TCGA-DD-A115 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-DD-A116         TCGA-DD-A118         TCGA-DD-A119 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" 
        TCGA-DD-A11A         TCGA-DD-A11B         TCGA-DD-A11C 
  "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-DD-A11D         TCGA-DD-A1E9         TCGA-DD-A1EA 
"21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-DD-A1EB         TCGA-DD-A1EC         TCGA-DD-A1ED 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-DD-A1EE         TCGA-DD-A1EF         TCGA-DD-A1EG 
"21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED"   "21Q LOSS MUTATED" 
        TCGA-DD-A1EH         TCGA-DD-A1EI         TCGA-DD-A1EJ 
  "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" 
        TCGA-DD-A1EK         TCGA-DD-A1EL         TCGA-DD-A39V 
"21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED"   "21Q LOSS MUTATED" 
        TCGA-DD-A39X         TCGA-DD-A39Y         TCGA-DD-A39Z 
"21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-DD-A3A0         TCGA-DD-A3A1         TCGA-DD-A3A2 
  "21Q LOSS MUTATED"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-DD-A3A3         TCGA-DD-A3A4         TCGA-DD-A3A5 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-DD-A3A6         TCGA-DD-A3A7         TCGA-DD-A3A8 
"21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-DD-A3A9         TCGA-DD-A4NA         TCGA-DD-A4NB 
  "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" 
        TCGA-DD-A4ND         TCGA-DD-A4NF         TCGA-DD-A4NH 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-DD-A4NI         TCGA-DD-A4NJ         TCGA-DD-A4NK 
  "21Q LOSS MUTATED" "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-DD-A4NR 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-DD-A4NS         TCGA-DD-A4NV         TCGA-DD-A73A 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-DD-A73B         TCGA-DD-A73C         TCGA-DD-A73D 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-DD-A73E         TCGA-DD-A73F         TCGA-DD-A73G 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" 
        TCGA-ED-A459         TCGA-ED-A4XI         TCGA-ED-A5KG 
  "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-ED-A627         TCGA-ED-A66X         TCGA-ED-A66Y 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" 
        TCGA-ED-A7PX         TCGA-ED-A7PY         TCGA-ED-A7PZ 
  "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" 
        TCGA-ED-A7XP         TCGA-ED-A82E         TCGA-EP-A12J 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-EP-A26S         TCGA-EP-A2KA         TCGA-EP-A2KB 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-EP-A2KC         TCGA-EP-A3JL         TCGA-EP-A3RK 
  "21Q LOSS MUTATED"   "21Q LOSS MUTATED"   "21Q LOSS MUTATED" 
        TCGA-ES-A2HS         TCGA-ES-A2HT         TCGA-FV-A23B 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" 
        TCGA-FV-A2QR         TCGA-FV-A3I0         TCGA-FV-A3I1 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-FV-A3R2         TCGA-FV-A3R3         TCGA-FV-A495 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-FV-A496         TCGA-FV-A4ZP         TCGA-FV-A4ZQ 
  "21Q LOSS MUTATED"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-G3-A25S         TCGA-G3-A25T         TCGA-G3-A25U 
  "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-G3-A25V         TCGA-G3-A25W         TCGA-G3-A25X 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-G3-A25Y         TCGA-G3-A25Z         TCGA-G3-A3CG 
"21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-G3-A3CH         TCGA-G3-A3CI         TCGA-G3-A3CJ 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-G3-A3CK         TCGA-G3-A5SI         TCGA-G3-A5SJ 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-G3-A5SL         TCGA-G3-A5SM         TCGA-G3-A6UC 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-GJ-A6C0         TCGA-K7-A6G5         TCGA-LG-A6GG 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" 
        TCGA-MI-A75C         TCGA-MI-A75E         TCGA-MI-A75G 
"21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-MI-A75I         TCGA-NI-A4U2         TCGA-O8-A75V 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
[1] "hr=" "1.6"
D78V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  21Q LOSS MUTATED        13        9         1          8          1
  21Q LOSS WILD-TYPE      45       27         1         22          3
                    vv
clus                 STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  21Q LOSS MUTATED            3        1         1         1
  21Q LOSS WILD-TYPE          2        0         0         1
D78V3, multiclass
                    vv
clus                 T1 T2 T3 T4
  21Q LOSS MUTATED   15 10 12  3
  21Q LOSS WILD-TYPE 46 30 28  5
D78V4, multiclass
    clus
vv   21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  T1               15                 46
  T2               10                 30
  T3               12                 28
  T4                3                  5
D78V5, binary
                    cls
clus                  0  1
  21Q LOSS MUTATED   22  2
  21Q LOSS WILD-TYPE 75  1
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED     22    2
  21Q LOSS WILD-TYPE   75    1
   clus
vv  21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  0               22                 75
  1                2                  1
                    vv
clus                 M0 M1 MX
  21Q LOSS MUTATED   32  2  6
  21Q LOSS WILD-TYPE 83  1 25
D78V6, multiclass
    clus
vv   21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  M0               32                 83
  M1                2                  1
  MX                6                 25
D78V7, binary
                    cls
clus                  0  1
  21Q LOSS MUTATED   10 30
  21Q LOSS WILD-TYPE 48 61
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED     10   30
  21Q LOSS WILD-TYPE   48   61
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  FEMALE               10                 48
  MALE                 30                 61
                    vv
clus                 R0 R1 R2 RX
  21Q LOSS MUTATED   31  3  1  1
  21Q LOSS WILD-TYPE 91  8  0  9
D78V8, multiclass
    clus
vv   21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  R0               31                 91
  R1                3                  8
  R2                1                  0
  RX                1                  9

Clustering(79) Variable = 22Q LOSS MUTATION ANALYSIS
D79V1, survival
                    sevent
clus2                 0  1
  22Q LOSS MUTATED   19 11
  22Q LOSS WILD-TYPE 65 52
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                30                117 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                11                 52 
$`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        13.84         0.26         9.50         2.86 
TCGA-CC-A1HT TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A11A TCGA-DD-A39X TCGA-DD-A39Y 
        3.32        79.73        37.78         2.60        55.69         5.62 
TCGA-DD-A3A6 TCGA-DD-A4NB TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NO TCGA-DD-A4NP 
      107.11        12.85        18.44        15.06        61.45        93.67 
TCGA-DD-A73B TCGA-ED-A459 TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7XP TCGA-EP-A2KB 
        9.30        13.41         0.23         0.20         0.20        10.98 
TCGA-FV-A4ZP TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A5SI TCGA-MI-A75G TCGA-MI-A75I 
       60.36         1.22        51.06        14.70        14.24         8.71 

$`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-BC-A69H TCGA-BC-A69I TCGA-CC-5258 TCGA-CC-5261 TCGA-CC-5262 
       22.36         3.95         0.53         0.07         0.39         3.39 
TCGA-CC-5263 TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A115 
        4.24         0.10         0.07         0.10         0.13        83.57 
TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D 
       53.33       113.00         7.33         0.46        21.76        51.29 
TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE 
       90.71        79.40        66.31        19.79        75.65         6.71 
TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK 
       12.95        45.11        49.15         6.02        29.16        18.35 
TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 
       13.64        21.14        19.76        25.81         7.66        70.06 
TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A3A9 
       17.59        20.12       102.74        13.78         0.36        30.61 
TCGA-DD-A4NA TCGA-DD-A4ND TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NK TCGA-DD-A4NL 
       33.14        73.38        14.07        14.24        39.78        56.25 
TCGA-DD-A4NN TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A 
       29.56        12.26         0.30        80.75        66.35        10.98 
TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G TCGA-ED-A4XI 
        7.56        10.98         1.45        27.72       100.96        12.69 
TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A82E 
       15.85        13.91        13.35         0.20         0.20         0.20 
TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK 
       18.74        19.99        11.74         0.62         9.96        11.93 
TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3I1 
       22.85        14.40        32.45        19.10         0.20         8.12 
TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZQ TCGA-G3-A25U 
        6.38         0.13         0.03         0.33         0.39        53.79 
TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG 
       28.27        30.74        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-A5SL 
       25.64         5.92        19.53        19.23        11.97         7.99 
TCGA-G3-A5SM TCGA-G3-A6UC TCGA-GJ-A6C0 TCGA-K7-A6G5 TCGA-LG-A6GG TCGA-MI-A75C 
        4.37         7.76         1.02         4.01         0.49         9.57 
TCGA-MI-A75E TCGA-NI-A4U2 TCGA-O8-A75V 
        5.10        58.88         4.44 

  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
              0.20               0.03 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
            107.11             113.00 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
            13.625             14.240 
[1] "0.2 - 107.1 (13.6)" "0.0 - 113.0 (14.2)"
        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-BC-A69H         TCGA-BC-A69I         TCGA-CC-5258 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-CC-5260         TCGA-CC-5261         TCGA-CC-5262 
  "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-CC-5263         TCGA-CC-A1HT         TCGA-CC-A3M9 
"22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" 
        TCGA-CC-A3MA         TCGA-CC-A3MB         TCGA-CC-A3MC 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-DD-A113         TCGA-DD-A114         TCGA-DD-A115 
  "22Q LOSS MUTATED"   "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" 
        TCGA-DD-A116         TCGA-DD-A118         TCGA-DD-A119 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-DD-A11A         TCGA-DD-A11B         TCGA-DD-A11C 
  "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-DD-A11D         TCGA-DD-A1E9         TCGA-DD-A1EA 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-DD-A1EB         TCGA-DD-A1EC         TCGA-DD-A1ED 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-DD-A1EE         TCGA-DD-A1EF         TCGA-DD-A1EG 
"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-A1EK         TCGA-DD-A1EL         TCGA-DD-A39V 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-DD-A39X         TCGA-DD-A39Y         TCGA-DD-A39Z 
  "22Q LOSS MUTATED"   "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" 
        TCGA-DD-A3A0         TCGA-DD-A3A1         TCGA-DD-A3A2 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-DD-A3A3         TCGA-DD-A3A4         TCGA-DD-A3A5 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-DD-A3A6         TCGA-DD-A3A7         TCGA-DD-A3A8 
  "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-DD-A3A9         TCGA-DD-A4NA         TCGA-DD-A4NB 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" 
        TCGA-DD-A4ND         TCGA-DD-A4NF         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 MUTATED"   "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-DD-A4NR 
  "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-DD-A4NS         TCGA-DD-A4NV         TCGA-DD-A73A 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-DD-A73B         TCGA-DD-A73C         TCGA-DD-A73D 
  "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-DD-A73E         TCGA-DD-A73F         TCGA-DD-A73G 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-ED-A459         TCGA-ED-A4XI         TCGA-ED-A5KG 
  "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-ED-A627         TCGA-ED-A66X         TCGA-ED-A66Y 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" 
        TCGA-ED-A7PX         TCGA-ED-A7PY         TCGA-ED-A7PZ 
  "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-ED-A7XP         TCGA-ED-A82E         TCGA-EP-A12J 
  "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-EP-A26S         TCGA-EP-A2KA         TCGA-EP-A2KB 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" 
        TCGA-EP-A2KC         TCGA-EP-A3JL         TCGA-EP-A3RK 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-ES-A2HS         TCGA-ES-A2HT         TCGA-FV-A23B 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-FV-A2QR         TCGA-FV-A3I0         TCGA-FV-A3I1 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-FV-A3R2         TCGA-FV-A3R3         TCGA-FV-A495 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-FV-A496         TCGA-FV-A4ZP         TCGA-FV-A4ZQ 
"22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" 
        TCGA-G3-A25S         TCGA-G3-A25T         TCGA-G3-A25U 
  "22Q LOSS MUTATED"   "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" 
        TCGA-G3-A25V         TCGA-G3-A25W         TCGA-G3-A25X 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-G3-A25Y         TCGA-G3-A25Z         TCGA-G3-A3CG 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-G3-A3CH         TCGA-G3-A3CI         TCGA-G3-A3CJ 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-G3-A3CK         TCGA-G3-A5SI         TCGA-G3-A5SJ 
"22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" 
        TCGA-G3-A5SL         TCGA-G3-A5SM         TCGA-G3-A6UC 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-GJ-A6C0         TCGA-K7-A6G5         TCGA-LG-A6GG 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-MI-A75C         TCGA-MI-A75E         TCGA-MI-A75G 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" 
        TCGA-MI-A75I         TCGA-NI-A4U2         TCGA-O8-A75V 
  "22Q LOSS MUTATED" "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-BC-A69H         TCGA-BC-A69I         TCGA-CC-5258 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-CC-5260         TCGA-CC-5261         TCGA-CC-5262 
  "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-CC-5263         TCGA-CC-A1HT         TCGA-CC-A3M9 
"22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" 
        TCGA-CC-A3MA         TCGA-CC-A3MB         TCGA-CC-A3MC 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-DD-A113         TCGA-DD-A114         TCGA-DD-A115 
  "22Q LOSS MUTATED"   "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" 
        TCGA-DD-A116         TCGA-DD-A118         TCGA-DD-A119 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-DD-A11A         TCGA-DD-A11B         TCGA-DD-A11C 
  "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-DD-A11D         TCGA-DD-A1E9         TCGA-DD-A1EA 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-DD-A1EB         TCGA-DD-A1EC         TCGA-DD-A1ED 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-DD-A1EE         TCGA-DD-A1EF         TCGA-DD-A1EG 
"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-A1EK         TCGA-DD-A1EL         TCGA-DD-A39V 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-DD-A39X         TCGA-DD-A39Y         TCGA-DD-A39Z 
  "22Q LOSS MUTATED"   "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" 
        TCGA-DD-A3A0         TCGA-DD-A3A1         TCGA-DD-A3A2 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-DD-A3A3         TCGA-DD-A3A4         TCGA-DD-A3A5 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-DD-A3A6         TCGA-DD-A3A7         TCGA-DD-A3A8 
  "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-DD-A3A9         TCGA-DD-A4NA         TCGA-DD-A4NB 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" 
        TCGA-DD-A4ND         TCGA-DD-A4NF         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 MUTATED"   "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-DD-A4NR 
  "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-DD-A4NS         TCGA-DD-A4NV         TCGA-DD-A73A 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-DD-A73B         TCGA-DD-A73C         TCGA-DD-A73D 
  "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-DD-A73E         TCGA-DD-A73F         TCGA-DD-A73G 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-ED-A459         TCGA-ED-A4XI         TCGA-ED-A5KG 
  "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-ED-A627         TCGA-ED-A66X         TCGA-ED-A66Y 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" 
        TCGA-ED-A7PX         TCGA-ED-A7PY         TCGA-ED-A7PZ 
  "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-ED-A7XP         TCGA-ED-A82E         TCGA-EP-A12J 
  "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-EP-A26S         TCGA-EP-A2KA         TCGA-EP-A2KB 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" 
        TCGA-EP-A2KC         TCGA-EP-A3JL         TCGA-EP-A3RK 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-ES-A2HS         TCGA-ES-A2HT         TCGA-FV-A23B 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-FV-A2QR         TCGA-FV-A3I0         TCGA-FV-A3I1 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-FV-A3R2         TCGA-FV-A3R3         TCGA-FV-A495 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-FV-A496         TCGA-FV-A4ZP         TCGA-FV-A4ZQ 
"22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" 
        TCGA-G3-A25S         TCGA-G3-A25T         TCGA-G3-A25U 
  "22Q LOSS MUTATED"   "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" 
        TCGA-G3-A25V         TCGA-G3-A25W         TCGA-G3-A25X 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-G3-A25Y         TCGA-G3-A25Z         TCGA-G3-A3CG 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-G3-A3CH         TCGA-G3-A3CI         TCGA-G3-A3CJ 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-G3-A3CK         TCGA-G3-A5SI         TCGA-G3-A5SJ 
"22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" 
        TCGA-G3-A5SL         TCGA-G3-A5SM         TCGA-G3-A6UC 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-GJ-A6C0         TCGA-K7-A6G5         TCGA-LG-A6GG 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-MI-A75C         TCGA-MI-A75E         TCGA-MI-A75G 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" 
        TCGA-MI-A75I         TCGA-NI-A4U2         TCGA-O8-A75V 
  "22Q LOSS MUTATED" "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-BC-A69H         TCGA-BC-A69I         TCGA-CC-5258 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-CC-5260         TCGA-CC-5261         TCGA-CC-5262 
  "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-CC-5263         TCGA-CC-A1HT         TCGA-CC-A3M9 
"22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" 
        TCGA-CC-A3MA         TCGA-CC-A3MB         TCGA-CC-A3MC 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-DD-A113         TCGA-DD-A114         TCGA-DD-A115 
  "22Q LOSS MUTATED"   "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" 
        TCGA-DD-A116         TCGA-DD-A118         TCGA-DD-A119 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-DD-A11A         TCGA-DD-A11B         TCGA-DD-A11C 
  "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-DD-A11D         TCGA-DD-A1E9         TCGA-DD-A1EA 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-DD-A1EB         TCGA-DD-A1EC         TCGA-DD-A1ED 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-DD-A1EE         TCGA-DD-A1EF         TCGA-DD-A1EG 
"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-A1EK         TCGA-DD-A1EL         TCGA-DD-A39V 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-DD-A39X         TCGA-DD-A39Y         TCGA-DD-A39Z 
  "22Q LOSS MUTATED"   "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" 
        TCGA-DD-A3A0         TCGA-DD-A3A1         TCGA-DD-A3A2 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-DD-A3A3         TCGA-DD-A3A4         TCGA-DD-A3A5 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-DD-A3A6         TCGA-DD-A3A7         TCGA-DD-A3A8 
  "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-DD-A3A9         TCGA-DD-A4NA         TCGA-DD-A4NB 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" 
        TCGA-DD-A4ND         TCGA-DD-A4NF         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 MUTATED"   "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-DD-A4NR 
  "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-DD-A4NS         TCGA-DD-A4NV         TCGA-DD-A73A 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-DD-A73B         TCGA-DD-A73C         TCGA-DD-A73D 
  "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-DD-A73E         TCGA-DD-A73F         TCGA-DD-A73G 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-ED-A459         TCGA-ED-A4XI         TCGA-ED-A5KG 
  "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-ED-A627         TCGA-ED-A66X         TCGA-ED-A66Y 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" 
        TCGA-ED-A7PX         TCGA-ED-A7PY         TCGA-ED-A7PZ 
  "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-ED-A7XP         TCGA-ED-A82E         TCGA-EP-A12J 
  "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-EP-A26S         TCGA-EP-A2KA         TCGA-EP-A2KB 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" 
        TCGA-EP-A2KC         TCGA-EP-A3JL         TCGA-EP-A3RK 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-ES-A2HS         TCGA-ES-A2HT         TCGA-FV-A23B 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-FV-A2QR         TCGA-FV-A3I0         TCGA-FV-A3I1 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-FV-A3R2         TCGA-FV-A3R3         TCGA-FV-A495 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-FV-A496         TCGA-FV-A4ZP         TCGA-FV-A4ZQ 
"22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" 
        TCGA-G3-A25S         TCGA-G3-A25T         TCGA-G3-A25U 
  "22Q LOSS MUTATED"   "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" 
        TCGA-G3-A25V         TCGA-G3-A25W         TCGA-G3-A25X 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-G3-A25Y         TCGA-G3-A25Z         TCGA-G3-A3CG 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-G3-A3CH         TCGA-G3-A3CI         TCGA-G3-A3CJ 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-G3-A3CK         TCGA-G3-A5SI         TCGA-G3-A5SJ 
"22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" 
        TCGA-G3-A5SL         TCGA-G3-A5SM         TCGA-G3-A6UC 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-GJ-A6C0         TCGA-K7-A6G5         TCGA-LG-A6GG 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-MI-A75C         TCGA-MI-A75E         TCGA-MI-A75G 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" 
        TCGA-MI-A75I         TCGA-NI-A4U2         TCGA-O8-A75V 
  "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
[1] "hr=" "1.3"
D79V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  22Q LOSS MUTATED        10       11         0          6          0
  22Q LOSS WILD-TYPE      48       25         2         24          4
                    vv
clus                 STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  22Q LOSS MUTATED            1        0         0         0
  22Q LOSS WILD-TYPE          4        1         1         2
D79V3, multiclass
                    vv
clus                 T1 T2 T3 T4
  22Q LOSS MUTATED   10 13  6  2
  22Q LOSS WILD-TYPE 51 27 34  6
D79V4, multiclass
    clus
vv   22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  T1               10                 51
  T2               13                 27
  T3                6                 34
  T4                2                  6
D79V5, binary
                    cls
clus                  0  1
  22Q LOSS MUTATED   18  0
  22Q LOSS WILD-TYPE 79  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED     18    0
  22Q LOSS WILD-TYPE   79    3
   clus
vv  22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  0               18                 79
  1                0                  3
                    vv
clus                 M0 M1 MX
  22Q LOSS MUTATED   27  0  4
  22Q LOSS WILD-TYPE 88  3 27
D79V6, multiclass
    clus
vv   22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  M0               27                 88
  M1                0                  3
  MX                4                 27
D79V7, binary
                    cls
clus                  0  1
  22Q LOSS MUTATED   14 17
  22Q LOSS WILD-TYPE 44 74
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED     14   17
  22Q LOSS WILD-TYPE   44   74
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  FEMALE               14                 44
  MALE                 17                 74
                    vv
clus                 R0 R1 R2 RX
  22Q LOSS MUTATED   23  5  0  2
  22Q LOSS WILD-TYPE 99  6  1  8
D79V8, multiclass
    clus
vv   22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  R0               23                 99
  R1                5                  6
  R2                0                  1
  RX                2                  8

Clustering(80) Variable = XQ LOSS MUTATION ANALYSIS
D80V1, survival
                   sevent
clus2                0  1
  XQ LOSS MUTATED   12  8
  XQ LOSS WILD-TYPE 72 55
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               20               127 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
                8                55 
$`XQ LOSS MUTATED`
TCGA-BC-A10R TCGA-BC-A112 TCGA-BC-A217 TCGA-BC-A5W4 TCGA-BC-A69I TCGA-CC-A3MA 
       10.13         5.03        13.84         9.50         0.53         0.07 
TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A11B TCGA-DD-A4NA TCGA-DD-A4NO 
       37.78        83.57        53.33         0.46        33.14        61.45 
TCGA-DD-A73B TCGA-ED-A459 TCGA-ED-A7PX TCGA-ED-A7PZ TCGA-FV-A2QR TCGA-FV-A3I0 
        9.30        13.41         0.20         0.20        19.10         0.20 
TCGA-G3-A6UC TCGA-MI-A75E 
        7.76         5.10 

$`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-BC-A3KG TCGA-BC-A69H TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5261 
        0.26        22.36         3.95         0.07         2.86         0.39 
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-A113 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11C TCGA-DD-A11D 
       79.73       113.00         7.33         2.60        21.76        51.29 
TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE 
       90.71        79.40        66.31        19.79        75.65         6.71 
TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK 
       12.95        45.11        49.15         6.02        29.16        18.35 
TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A0 
       13.64        21.14        55.69         5.62        19.76        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-A4NB TCGA-DD-A4ND TCGA-DD-A4NF 
       13.78         0.36        30.61        12.85        73.38        14.07 
TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN 
       14.24        18.44        15.06        39.78        56.25        29.56 
TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A 
       93.67        12.26         0.30        80.75        66.35        10.98 
TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G TCGA-ED-A4XI 
        7.56        10.98         1.45        27.72       100.96        12.69 
TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PY TCGA-ED-A7XP 
       15.85        13.91        13.35         0.23         0.20         0.20 
TCGA-ED-A82E TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC 
        0.20        18.74        19.99        11.74        10.98         0.62 
TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A3I1 
        9.96        11.93        22.85        14.40        32.45         8.12 
TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZP TCGA-FV-A4ZQ 
        6.38         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        51.06        53.79        28.27        30.74        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         5.92        19.53 
TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SL TCGA-G3-A5SM TCGA-GJ-A6C0 
       19.23        14.70        11.97         7.99         4.37         1.02 
TCGA-K7-A6G5 TCGA-LG-A6GG TCGA-MI-A75C TCGA-MI-A75G TCGA-MI-A75I TCGA-NI-A4U2 
        4.01         0.49         9.57        14.24         8.71        58.88 
TCGA-O8-A75V 
        4.44 

  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
             0.07              0.03 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
            83.57            113.00 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
              9.4              14.7 
[1] "0.1 - 83.6 (9.4)"   "0.0 - 113.0 (14.7)"
       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-BC-A69H        TCGA-BC-A69I 
"XQ LOSS WILD-TYPE"   "XQ LOSS MUTATED" "XQ LOSS WILD-TYPE"   "XQ LOSS MUTATED" 
       TCGA-CC-5258        TCGA-CC-5260        TCGA-CC-5261        TCGA-CC-5262 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-CC-5263        TCGA-CC-A1HT        TCGA-CC-A3M9        TCGA-CC-A3MA 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE"   "XQ LOSS MUTATED" 
       TCGA-CC-A3MB        TCGA-CC-A3MC        TCGA-DD-A113        TCGA-DD-A114 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE"   "XQ LOSS MUTATED" 
       TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118        TCGA-DD-A119 
  "XQ LOSS MUTATED"   "XQ LOSS MUTATED" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C        TCGA-DD-A11D 
"XQ LOSS WILD-TYPE"   "XQ LOSS MUTATED" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB        TCGA-DD-A1EC 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EF        TCGA-DD-A1EG 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DD-A1EH        TCGA-DD-A1EI        TCGA-DD-A1EJ        TCGA-DD-A1EK 
"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-A4NB        TCGA-DD-A4ND        TCGA-DD-A4NF        TCGA-DD-A4NH 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DD-A4NI        TCGA-DD-A4NJ        TCGA-DD-A4NK        TCGA-DD-A4NL 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DD-A4NN        TCGA-DD-A4NO        TCGA-DD-A4NP        TCGA-DD-A4NQ 
"XQ LOSS WILD-TYPE"   "XQ LOSS MUTATED" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DD-A4NR        TCGA-DD-A4NS        TCGA-DD-A4NV        TCGA-DD-A73A 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DD-A73B        TCGA-DD-A73C        TCGA-DD-A73D        TCGA-DD-A73E 
  "XQ LOSS MUTATED" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DD-A73F        TCGA-DD-A73G        TCGA-ED-A459        TCGA-ED-A4XI 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE"   "XQ LOSS MUTATED" "XQ LOSS WILD-TYPE" 
       TCGA-ED-A5KG        TCGA-ED-A627        TCGA-ED-A66X        TCGA-ED-A66Y 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-ED-A7PX        TCGA-ED-A7PY        TCGA-ED-A7PZ        TCGA-ED-A7XP 
  "XQ LOSS MUTATED" "XQ LOSS WILD-TYPE"   "XQ LOSS MUTATED" "XQ LOSS WILD-TYPE" 
       TCGA-ED-A82E        TCGA-EP-A12J        TCGA-EP-A26S        TCGA-EP-A2KA 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EP-A2KB        TCGA-EP-A2KC        TCGA-EP-A3JL        TCGA-EP-A3RK 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-ES-A2HS        TCGA-ES-A2HT        TCGA-FV-A23B        TCGA-FV-A2QR 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE"   "XQ LOSS MUTATED" 
       TCGA-FV-A3I0        TCGA-FV-A3I1        TCGA-FV-A3R2        TCGA-FV-A3R3 
  "XQ LOSS MUTATED" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-FV-A495        TCGA-FV-A496        TCGA-FV-A4ZP        TCGA-FV-A4ZQ 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U        TCGA-G3-A25V 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y        TCGA-G3-A25Z 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI        TCGA-G3-A3CJ 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-G3-A3CK        TCGA-G3-A5SI        TCGA-G3-A5SJ        TCGA-G3-A5SL 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-G3-A5SM        TCGA-G3-A6UC        TCGA-GJ-A6C0        TCGA-K7-A6G5 
"XQ LOSS WILD-TYPE"   "XQ LOSS MUTATED" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-LG-A6GG        TCGA-MI-A75C        TCGA-MI-A75E        TCGA-MI-A75G 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE"   "XQ LOSS MUTATED" "XQ LOSS WILD-TYPE" 
       TCGA-MI-A75I        TCGA-NI-A4U2        TCGA-O8-A75V 
"XQ LOSS WILD-TYPE" "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-BC-A69H        TCGA-BC-A69I 
"XQ LOSS WILD-TYPE"   "XQ LOSS MUTATED" "XQ LOSS WILD-TYPE"   "XQ LOSS MUTATED" 
       TCGA-CC-5258        TCGA-CC-5260        TCGA-CC-5261        TCGA-CC-5262 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-CC-5263        TCGA-CC-A1HT        TCGA-CC-A3M9        TCGA-CC-A3MA 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE"   "XQ LOSS MUTATED" 
       TCGA-CC-A3MB        TCGA-CC-A3MC        TCGA-DD-A113        TCGA-DD-A114 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE"   "XQ LOSS MUTATED" 
       TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118        TCGA-DD-A119 
  "XQ LOSS MUTATED"   "XQ LOSS MUTATED" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C        TCGA-DD-A11D 
"XQ LOSS WILD-TYPE"   "XQ LOSS MUTATED" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB        TCGA-DD-A1EC 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EF        TCGA-DD-A1EG 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DD-A1EH        TCGA-DD-A1EI        TCGA-DD-A1EJ        TCGA-DD-A1EK 
"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-A4NB        TCGA-DD-A4ND        TCGA-DD-A4NF        TCGA-DD-A4NH 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DD-A4NI        TCGA-DD-A4NJ        TCGA-DD-A4NK        TCGA-DD-A4NL 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DD-A4NN        TCGA-DD-A4NO        TCGA-DD-A4NP        TCGA-DD-A4NQ 
"XQ LOSS WILD-TYPE"   "XQ LOSS MUTATED" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DD-A4NR        TCGA-DD-A4NS        TCGA-DD-A4NV        TCGA-DD-A73A 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DD-A73B        TCGA-DD-A73C        TCGA-DD-A73D        TCGA-DD-A73E 
  "XQ LOSS MUTATED" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DD-A73F        TCGA-DD-A73G        TCGA-ED-A459        TCGA-ED-A4XI 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE"   "XQ LOSS MUTATED" "XQ LOSS WILD-TYPE" 
       TCGA-ED-A5KG        TCGA-ED-A627        TCGA-ED-A66X        TCGA-ED-A66Y 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-ED-A7PX        TCGA-ED-A7PY        TCGA-ED-A7PZ        TCGA-ED-A7XP 
  "XQ LOSS MUTATED" "XQ LOSS WILD-TYPE"   "XQ LOSS MUTATED" "XQ LOSS WILD-TYPE" 
       TCGA-ED-A82E        TCGA-EP-A12J        TCGA-EP-A26S        TCGA-EP-A2KA 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EP-A2KB        TCGA-EP-A2KC        TCGA-EP-A3JL        TCGA-EP-A3RK 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-ES-A2HS        TCGA-ES-A2HT        TCGA-FV-A23B        TCGA-FV-A2QR 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE"   "XQ LOSS MUTATED" 
       TCGA-FV-A3I0        TCGA-FV-A3I1        TCGA-FV-A3R2        TCGA-FV-A3R3 
  "XQ LOSS MUTATED" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-FV-A495        TCGA-FV-A496        TCGA-FV-A4ZP        TCGA-FV-A4ZQ 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U        TCGA-G3-A25V 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y        TCGA-G3-A25Z 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI        TCGA-G3-A3CJ 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-G3-A3CK        TCGA-G3-A5SI        TCGA-G3-A5SJ        TCGA-G3-A5SL 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-G3-A5SM        TCGA-G3-A6UC        TCGA-GJ-A6C0        TCGA-K7-A6G5 
"XQ LOSS WILD-TYPE"   "XQ LOSS MUTATED" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-LG-A6GG        TCGA-MI-A75C        TCGA-MI-A75E        TCGA-MI-A75G 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE"   "XQ LOSS MUTATED" "XQ LOSS WILD-TYPE" 
       TCGA-MI-A75I        TCGA-NI-A4U2        TCGA-O8-A75V 
"XQ LOSS WILD-TYPE" "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-BC-A69H        TCGA-BC-A69I 
"XQ LOSS WILD-TYPE"   "XQ LOSS MUTATED" "XQ LOSS WILD-TYPE"   "XQ LOSS MUTATED" 
       TCGA-CC-5258        TCGA-CC-5260        TCGA-CC-5261        TCGA-CC-5262 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-CC-5263        TCGA-CC-A1HT        TCGA-CC-A3M9        TCGA-CC-A3MA 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE"   "XQ LOSS MUTATED" 
       TCGA-CC-A3MB        TCGA-CC-A3MC        TCGA-DD-A113        TCGA-DD-A114 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE"   "XQ LOSS MUTATED" 
       TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118        TCGA-DD-A119 
  "XQ LOSS MUTATED"   "XQ LOSS MUTATED" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C        TCGA-DD-A11D 
"XQ LOSS WILD-TYPE"   "XQ LOSS MUTATED" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB        TCGA-DD-A1EC 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EF        TCGA-DD-A1EG 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DD-A1EH        TCGA-DD-A1EI        TCGA-DD-A1EJ        TCGA-DD-A1EK 
"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-A4NB        TCGA-DD-A4ND        TCGA-DD-A4NF        TCGA-DD-A4NH 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DD-A4NI        TCGA-DD-A4NJ        TCGA-DD-A4NK        TCGA-DD-A4NL 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DD-A4NN        TCGA-DD-A4NO        TCGA-DD-A4NP        TCGA-DD-A4NQ 
"XQ LOSS WILD-TYPE"   "XQ LOSS MUTATED" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DD-A4NR        TCGA-DD-A4NS        TCGA-DD-A4NV        TCGA-DD-A73A 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DD-A73B        TCGA-DD-A73C        TCGA-DD-A73D        TCGA-DD-A73E 
  "XQ LOSS MUTATED" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DD-A73F        TCGA-DD-A73G        TCGA-ED-A459        TCGA-ED-A4XI 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE"   "XQ LOSS MUTATED" "XQ LOSS WILD-TYPE" 
       TCGA-ED-A5KG        TCGA-ED-A627        TCGA-ED-A66X        TCGA-ED-A66Y 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-ED-A7PX        TCGA-ED-A7PY        TCGA-ED-A7PZ        TCGA-ED-A7XP 
  "XQ LOSS MUTATED" "XQ LOSS WILD-TYPE"   "XQ LOSS MUTATED" "XQ LOSS WILD-TYPE" 
       TCGA-ED-A82E        TCGA-EP-A12J        TCGA-EP-A26S        TCGA-EP-A2KA 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EP-A2KB        TCGA-EP-A2KC        TCGA-EP-A3JL        TCGA-EP-A3RK 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-ES-A2HS        TCGA-ES-A2HT        TCGA-FV-A23B        TCGA-FV-A2QR 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE"   "XQ LOSS MUTATED" 
       TCGA-FV-A3I0        TCGA-FV-A3I1        TCGA-FV-A3R2        TCGA-FV-A3R3 
  "XQ LOSS MUTATED" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-FV-A495        TCGA-FV-A496        TCGA-FV-A4ZP        TCGA-FV-A4ZQ 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U        TCGA-G3-A25V 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y        TCGA-G3-A25Z 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI        TCGA-G3-A3CJ 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-G3-A3CK        TCGA-G3-A5SI        TCGA-G3-A5SJ        TCGA-G3-A5SL 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-G3-A5SM        TCGA-G3-A6UC        TCGA-GJ-A6C0        TCGA-K7-A6G5 
"XQ LOSS WILD-TYPE"   "XQ LOSS MUTATED" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-LG-A6GG        TCGA-MI-A75C        TCGA-MI-A75E        TCGA-MI-A75G 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE"   "XQ LOSS MUTATED" "XQ LOSS WILD-TYPE" 
       TCGA-MI-A75I        TCGA-NI-A4U2        TCGA-O8-A75V 
"XQ LOSS WILD-TYPE" "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         5        6         0          4          1          2
  XQ LOSS WILD-TYPE      53       30         2         26          3          3
                   vv
clus                STAGE IV STAGE IVA STAGE IVB
  XQ LOSS MUTATED          0         0         0
  XQ LOSS WILD-TYPE        1         1         2
D80V3, multiclass
                   vv
clus                T1 T2 T3 T4
  XQ LOSS MUTATED    5  7  7  1
  XQ LOSS WILD-TYPE 56 33 33  7
D80V4, multiclass
    clus
vv   XQ LOSS MUTATED XQ LOSS WILD-TYPE
  T1               5                56
  T2               7                33
  T3               7                33
  T4               1                 7
D80V5, binary
                   cls
clus                 0  1
  XQ LOSS MUTATED   11  1
  XQ LOSS WILD-TYPE 86  2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED     11    1
  XQ LOSS WILD-TYPE   86    2
   clus
vv  XQ LOSS MUTATED XQ LOSS WILD-TYPE
  0              11                86
  1               1                 2
                   vv
clus                M0 M1 MX
  XQ LOSS MUTATED   18  0  2
  XQ LOSS WILD-TYPE 97  3 29
D80V6, multiclass
    clus
vv   XQ LOSS MUTATED XQ LOSS WILD-TYPE
  M0              18                97
  M1               0                 3
  MX               2                29
D80V7, binary
                   cls
clus                 0  1
  XQ LOSS MUTATED    6 14
  XQ LOSS WILD-TYPE 52 77
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED      6   14
  XQ LOSS WILD-TYPE   52   77
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  FEMALE               6                52
  MALE                14                77
                   vv
clus                 R0  R1  R2  RX
  XQ LOSS MUTATED    17   1   0   2
  XQ LOSS WILD-TYPE 105  10   1   8
D80V8, multiclass
    clus
vv   XQ LOSS MUTATED XQ LOSS WILD-TYPE
  R0              17               105
  R1               1                10
  R2               0                 1
  RX               2                 8
> q(save="no")
